@article {pmid41298861,
year = {2025},
author = {Han, H and Zhang, K and Qian, Z},
title = {Adaptability analysis and spatial correlation characteristics of water-energy-food-ecology system in the Yellow River Basin from the perspective of symbiosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42266},
pmid = {41298861},
issn = {2045-2322},
support = {2025-ZZJH-052//2025 General Project of Humanities and Social Science Research of Universities in Henan Province/ ; 2024CJJ151//2024 Philosophy and Social Sciences Planning project in Henan Province/ ; 42301357//National Natural Science Foundation of China/ ; },
abstract = {Based on the symbiosis theory, the concept of compatibility within the regional water-energy-food-ecology (WEFE) system was proposed. An indicator system for adaptability analysis was constructed from three subsystems: coordination, stability, and sustainability. Using the co-evolution model and partial autocorrelation analysis, the spatiotemporal evolutionary patterns and spatial correlation patterns of WEFE adaptability in the Yellow River Basin (YRB) from 2011 to 2022 were assessed. The results indicated that: (1) The order of subsystem weights was: stability > sustainability > coordination. (2) The absolute adaptability of the indicator was significantly higher than the relative adaptability. The adaptability degree of the three subsystems increased to varying degrees. Overall, the adaptability of the WEFE system in the middle and lower reaches of the YRB was obviously higher than in the upper reaches. (3) In terms of system coordination, the coordination and stability subsystems improved, whereas the coordination of the sustainability subsystem gradually declined. (4) The adaptability levels of the WEFE system in the YRB had a random distribution. In terms of local spatial autocorrelation, there were significant spatial disparities and path dependencies in the WEFE system adaptability across the YRB. This study enhances the understanding of the symbiotic adaptability development among water resources, food, energy and ecology in the YRB and provides important insights for regional multi-resource collaborative management.},
}

@article {pmid41298464,
year = {2025},
author = {Ricci, F and Bay, SK and Nauer, PA and Wong, WW and Ni, G and Jimenez, L and Jirapanjawat, T and Leung, PM and Bradley, JA and Eate, VM and Hall, M and Stubbusch, AKM and Fernández-Marín, B and de Los Ríos, A and Cook, PLM and Schroth, MH and Chiri, E and Greening, C},
title = {Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66734-4},
pmid = {41298464},
issn = {2041-1723},
support = {APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE230101346//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; 101115755//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PID2019-105469RB-C22//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
abstract = {An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonise both forelands and persist across soil decadal chronosequences serving as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using organic and inorganic compounds, including atmospheric trace gases and sulphur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable environment for subsequent colonisation.},
}

@article {pmid41297937,
year = {2025},
author = {Endo, K and Mutoh, A and Satoh, M and Ogawa, K and Shimatani, K and Suzuki, N},
title = {Urban veterinary accessibility and community well-being in Japan: a cross-sectional analysis using regional indicators.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0396},
pmid = {41297937},
issn = {1347-7439},
abstract = {Access to medical care is important not only for humans, but also for companion animals. However, the distribution of veterinary services and their potential benefits to human well-being remain unclear. This study examined the relationship between veterinary clinics and community well-being in urban areas of Japan. The dataset included total 191 wards in Tokyo (a metropolitan city) and 19 ordinance-designated cities. Veterinary clinical locations were obtained from a high-resolution commercial database provided by ZENRIN Marketing Solutions Co., Ltd. Community well-being scores were obtained from the Digital Agency of Japan. Multiple linear regression analysis was conducted to predict the well-being scores based on the number of veterinary or human clinics per 100,000 residents. The results of veterinary clinics showed positive satisfaction with environmental symbiosis (β=1.17), natural disasters (β=1.04), community connections (β=1.00), self-efficacy (β=1.18), health status (β=1.32), employment and income (β=0.89), recreation and entertainment (β=0.91), culture and arts (β=1.53), abundance of educational opportunities (β=1.34), and business creation (β=1.03), while the results of human clinics showed negative satisfaction with public spaces (β=-0.69). Findings suggest that residents who place a high value on pets and the care they require may be attracted to areas with high concentrations of art, entertainment, education, and business resources. Although unmeasured confounding factors were related, this study posits a new assumption that the enrichment of animal welfare services is associated with regional well-being.},
}

@article {pmid41297850,
year = {2025},
author = {Dell'Aglio, E and Ferrarini, MG and Rebollo, R},
title = {Epigenetics and non-coding RNAs in host-endosymbiont interactions: insights from Wolbachia and beyond.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101464},
doi = {10.1016/j.cois.2025.101464},
pmid = {41297850},
issn = {2214-5753},
abstract = {Symbioses are widespread in nature and are among major evolutionary forces. Insects have recurrently established intracellular symbioses with bacteria, balancing between immune responses and homeostasis. The processes involved in endosymbiosis establishment, maintenance, and control have recently been associated with epigenetic pathways and non-coding RNAs, which are known to regulate a wide range of cellular processes, including development, differentiation, immune response, and metabolism. Using the well-studied Wolbachia-Aedes aegypti model as a reference, we summarize how these mechanisms influence host gene expression, endosymbiont maintenance, and antiviral defence. Beyond Wolbachia, only a few examples have provided functional evidence of the role of epigenetics in regulating natural insect-bacteria associations. Collectively, these studies demonstrate that epigenetic factors can act as mediators of host-endosymbiont coordination; however, determining if such factors are drivers or by-products of symbiosis establishment will require further investigation.},
}

@article {pmid41297327,
year = {2025},
author = {Fuad, MTI and Dong, Y and Li, Z and Ge, M and Sharifuzzaman, SM and Liu, X and Zhang, X and Xu, Q},
title = {Seasonal gut microbiota and functional dynamics in brittle star (Ophiothrix exigua) from the Yellow Sea, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107734},
doi = {10.1016/j.marenvres.2025.107734},
pmid = {41297327},
issn = {1879-0291},
abstract = {The gut microbiota forms a complex symbiotic community that performs essential functions for the host, including metabolism, nutrient absorption, and environmental adaptation, while being shaped by both environmental and intrinsic host factors. This study represents the first comprehensive investigation of seasonal gut microbiota diversity in brittle stars, examining Ophiothrix exigua from the Yellow Sea using full-length 16S rRNA gene metabarcoding. A total of 565 amplicon sequence variants were identified from gut samples, distributed across 20 phyla, 135 genera, and 46 species. The dominant phyla included Proteobacteria, and Spirochaetota, with Salinispira identified as the core genus. Seasonal variations in microbiota diversity were evident, with Caulobacter predominating in summer, and Kistimonas and Trichococcus driving winter community shift. Corresponding seasonal changes in gut microbiota functions and functional pathways were observed. Fatty acid biosynthesis pathways were enriched in winter, while aromatic compound degradation pathways showed elevated activity in summer. Although seawater microbiota exerted relatively minor influence on gut microbial diversity, correlations with abiotic factors such as pH were observed. This study highlights the intricate relationship between gut microbiota, environmental microbiota, and abiotic factors in shaping the seasonal gut microbiota diversity of O. exigua, contributing to a better understanding of the host-microbiome ecology of invertebrates.},
}

@article {pmid41297304,
year = {2025},
author = {Ding, J and Wang, D and Ji, B and Li, A and Li, XY},
title = {Effect of Nitrosomonas europaea on Chlorella vulgaris in bio-hydrogels for startup of microalgal-bacterial granular sludge: Performance and microscopic mechanism.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {125023},
doi = {10.1016/j.watres.2025.125023},
pmid = {41297304},
issn = {1879-2448},
abstract = {Algal-bacterial granular sludge technology holds significant promise for treating municipal wastewater with carbon emission reduction. However, its practical application has been constrained by the long startup period. In this study, bio-hydrogels co-encapsulating autotrophic ammonia-oxidizing bacteria (Nitrosomonas europaea) and photomixotrophic microalgae (Chlorella vulgaris) were used in a microalgal-bacterial granules system (MBGS) for the treatment of low C/N wastewater. The operating conditions of the MBGS system included inoculation volume ratio of 1:6 (bio-hydrogel granules: wastewater), initial biomass of 0.33 g suspended solids (SS) /L, light intensity of 300 μmol/m[2]·s, and no aeration. The results showed that this strategy reduced the typical MBGS startup period to just 6 days, with biomass accumulation (1.53 g SS/L, >4 g SS/L after running 120 days) and efficient chemical oxygen demand (COD) and total nitrogen (TN) removal (effluent COD <20.00 mg/L and TN <2.50 mg/L). Transcriptomic analysis revealed that the symbiosis with Nitrosomonas significantly upregulated the expression of the PetH gene, which encodes a reductase (EC:1.18.1.2) in the photosynthetic system of Chlorella (log2 fold change=13.63), thereby enhancing the supply of NADPH required for the Calvin cycle. Concurrently, the expression of the rbcL gene, encoding the large subunit of Rubisco in Chlorella, was upregulated by 1.4-fold, which promoted photosynthetic carbon fixation. The symbiosis also suppressed heterotrophic metabolism in Chlorella, as evidenced by downregulation of 72.5 % of genes in glycolysis and the tricarboxylic acid cycle, thereby mitigating the adverse effects of encapsulating material biodegradation on the bio-hydrogel structure. In addition, cell proliferation of Chlorella was stimulated (over 13-fold upregulation of DNA replication licensing factors MCM5 and MCM6), which increased biomass and nutrient removal efficiency. Furthermore, a higher light intensity of 400 μmol/m[2]/s promoted a significant increase in extracellular polymeric substances (EPS) content (106.76 mg/g SS), improved granule stability (integrity coefficient < 20 %), and enhanced biomass production (4.68 g SS/L after 120 days of operation). These findings highlight a promising strategy for sustainable wastewater treatment.},
}

@article {pmid41297084,
year = {2025},
author = {Cameron, CC and Gebbie, W and Bowman, C and Waters, ER and Kalyuzhnaya, MG},
title = {Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126670},
doi = {10.1016/j.syapm.2025.126670},
pmid = {41297084},
issn = {1618-0984},
abstract = {Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N2O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.},
}

@article {pmid41295393,
year = {2025},
author = {Tame, A},
title = {Integrated Regulation of Immunity and Nutritional Symbiosis in Deep-Sea Mussels.},
journal = {Marine drugs},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/md23110425},
pmid = {41295393},
issn = {1660-3397},
support = {JP24K18110//the Japan Society for the Promotion of Science (JSPS) through KAKENHI/ ; },
mesh = {Animals ; *Symbiosis/immunology ; *Bivalvia/immunology/microbiology ; Gills/immunology/microbiology ; Immunity, Innate ; Phagocytosis/immunology ; Hemocytes/immunology ; Bacteria ; },
abstract = {Deep-sea mussels of the genus Bathymodiolus exhibit adaptability to nutrient-poor deep-sea environments by establishing nutritional intracellular symbiosis with chemosynthetic bacteria harbored within the gill epithelial cells. However, this poses a conflict for the innate immune system of the host, which must balance the tolerance of beneficial symbiotic bacteria with the need to eliminate exogenous microbes. This review synthesizes existing knowledge and recent findings on Bathymodiolus japonicus to outline the cellular and molecular mechanisms governing this symbiotic relationship. In the host immune system, hemocytes are responsible for systemic defense, whereas gill cells are involved in local symbiotic acceptance. Central to the establishment of symbiosis is the host's phagocytic system, which non-selectively engulfs bacteria but selectively retains symbionts. We highlight a series of cellular events in gill cells involving the engulfment, selection, retention and/or digestion of symbionts, and the regulatory mechanism of phagocytosis through mechanistic target of rapamycin complex 1, which connects bacterial nutrient supply with host immune and metabolic responses. This integrated model of symbiosis regulation, which links immunity, metabolism, and symbiosis, provides a fundamental framework for understanding how hosts establish and maintain a stable coexistence with microbes, offering a new perspective on symbiotic strategies in diverse organisms.},
}

Animals
*Symbiosis/immunology
*Bivalvia/immunology/microbiology
Gills/immunology/microbiology
Immunity, Innate
Phagocytosis/immunology
Hemocytes/immunology
Bacteria

@article {pmid41295187,
year = {2025},
author = {Luna-Fontalvo, JA and Balocchi, O and Martínez, O and Alonso, M and Ferrada, E},
title = {Symbiosis Between Epichloë Fungi and Bromus Grasses: A Review of Current Knowledge and Future Directions.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110807},
pmid = {41295187},
issn = {2309-608X},
support = {1220448//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {Epichloë is a genus of endophytic fungi that forms systemic, vertically transmitted, and asymptomatic mutualistic associations with grasses in the subfamily Pooideae. These symbioses are non-pathogenic and are of considerable importance in agronomic and livestock systems due to their roles in enhancing host fitness under biotic and abiotic stress. Several studies have reported associations between Epichloë endophytes and species of the genus Bromus, a taxonomically complex group characterized by varying ploidy levels and frequent hybridization. Among its sections, Bromopsis includes the highest number of species naturally colonized by Epichloë fungi, while sections Bromus and Ceratochloa show lower infection rates. In South America, endophytes such as E. pampeana, E. tembladerae, E. typhina, and morphotypes of Neotyphodium spp. have been documented in species including B. auleticus, B. brachyanthera, and B. setifolius, where they appear to contribute to stress resilience. Although most findings originate from Argentina, significant knowledge gaps remain regarding the diversity and distribution of these endophytes in native Bromus species across the continent. This review synthesizes the current understanding of Epichloë-Bromus interactions, emphasizing their ecological and agronomic relevance, particularly in South America. Key factors influencing the establishment of these symbioses are examined, and future research directions are proposed to advance the study of these associations.},
}

@article {pmid41295153,
year = {2025},
author = {Jiang, S and Cheng, Z and Pan, H and Liu, S and Qu, H and Gao, M and Yang, L and Zhou, J},
title = {High Fire Drives the Reorganization of Taiga Soil Fungal Communities with Ascomycota as the Dominant Phylum After Long-Term Recovery.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110772},
pmid = {41295153},
issn = {2309-608X},
support = {GZ2024066//Guidance Project of Heilongjiang Provincial Key Research and Development Plan/ ; GZCG2023-024//Forestry and Grassland Ecological Protection and Restoration Funds Project/ ; CZKYF2024-1-A008//the Financial Special Project of Heilongjiang Province/ ; },
abstract = {Forest fires are key disturbance factors in forest ecosystems, and soil fungi play an irreplaceable role in post-fire recovery. This study focused on forest areas burned in 2000 in the Daxing'anling region of China, targeting long-term recovery sites with different fire intensities. Illumina MiSeq sequencing was used to analyze the structural characteristics of fungal communities and their environmental drivers. Results showed that compared with the control check (CK), the Shannon index of the low fire group (L) increased significantly (p < 0.05), while moderate (M) and high (H) fire groups reduced fungal diversity significantly. PCoA indicated significant differences in community structure (R[2] = 0.97, p = 0.001). In highly burned areas, the relative abundance of Ascomycota reached 94.17%, and Basidiomycota lost its dominance. Spearman analysis showed that pH, available phosphorus, available potassium, soil fluorescein diacetate hydrolase, soil dehydrogenase, and soil urease were significantly positively correlated with fungal alpha diversity. RDA revealed that total nitrogen, available phosphorus, soil water content, alkaline nitrogen, active potassium, and dissolved organic carbon had extremely significant effects on soil fungal community composition (p < 0.01). Co-occurrence network analysis indicated that symbiotic relationships dominated all groups. Networks in L and M groups were more complex, while that in H group was simplified and severely damaged. This study indicated that after long-term recovery, soil fungal communities in low fire areas returned to pre-fire levels; those in moderate and high fire areas did not recover, with high fire burns causing severe damage and community structure reorganization.},
}

@article {pmid41295138,
year = {2025},
author = {Li, P and Liu, J and Zhang, S and Zhu, Y and Yin, X and Xing, L and Wei, D and Jin, L},
title = {Effects of Nitrogen and Phosphorus Levels on Arbuscular Mycorrhizal Symbiosis and Associated Bacterial Communities in Culture.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110757},
pmid = {41295138},
issn = {2309-608X},
support = {KJCX20230116; ZHS202306//Special Project for the Construction of Scientific and Technological Innovation Capacity of Beijing Academy of Agriculture and Forestry Sciences/ ; },
abstract = {Arbuscular mycorrhizal (AM) fungi establish mutualistic symbioses with plant roots, enhancing plant growth and improving soil fertility through nutrient exchange. Among these, soil nitrogen (N) and phosphorus (P) are critical for symbiosis formation, directly influencing nutrient uptake and translocation within the symbiotic system. This study aimed to examine the regulatory roles of N and P levels on AM fungal development and associated bacterial communities in culture. Sorghum was used as the host plant in pot experiments with two AM fungi, Rhizophagus irregularis and Funneliformis mosseae, under varying N and P concentrations. The analyzed parameters included mycorrhizal colonization, propagule production, plant biomass, nutrient contents (N, P, and K), and bacterial community diversity. N3P1 treatment (150 mg/L N, 30 mg/L P) yielded the highest colonization rate, spore production, and arbuscule abundance in both AM fungal symbionts. At equivalent N and P concentrations, the N, P, and K contents in inoculated plants were significantly higher than those in controls. AM fungal inoculation markedly increased the bacterial diversity in the culture (Shannon index raised by 15.2-28.7%) and enriched beneficial taxa, such as Bradyrhizobium and Pseudomonas. N and P concentrations substantially influenced AM fungal symbiosis, with optimal development observed under N3P1 conditions. By regulating AM symbiotic establishment, N and P levels reshaped microbial community composition, providing theoretical guidance for industrialized AM fungal cultivation and inoculant production.},
}

@article {pmid41294327,
year = {2025},
author = {Huang, J and Xu, S and Liu, J and Wang, Q and Han, L and Ji, M and Lei, C and Zhu, Q and Chen, H},
title = {The viral proteins of influenza A virus competitively bind to TRIM31 with MAVS to fine-tune the antiviral innate immunity.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0189325},
doi = {10.1128/jvi.01893-25},
pmid = {41294327},
issn = {1098-5514},
abstract = {UNLABELLED: The influenza A virus (IAV) continues to pose a serious threat to animals and humans, making it urgent to reveal more about IAV-host interactions. Tripartite motif protein 31 (TRIM31), an E3 ubiquitin ligase, has been identified as an agonist of the type-I interferon (IFN-I) response against RNA viruses by targeting mitochondrial antiviral signaling protein (MAVS). Here, we demonstrated that TRIM31 plays critical and novel roles in the life cycle of IAV. TRIM31 promoted the IFN-I signaling induced by IAV; however, it was surprisingly found that TRIM31 does not affect IAV replication. Instead, IAV replication was significantly promoted by TRIM31 in MAVS- or interferon receptor-deficient cells, suggesting TRIM31 may facilitate IAV replication in an interferon-independent manner. Mechanistically, TRIM31 interacted specifically with the basic polymerase 1 (PB1), acidic polymerase (PA), and hemagglutinin (HA) proteins of different subtypes of IAV. The interaction between TRIM31 and the PB1, PA, and HA proteins enhances the stability and polymerase and membrane fusion activities of these viral proteins by catalyzing the K63-linked ubiquitination. Further, the PB1, PA, and HA proteins competitively bind to TRIM31 for IAV replication, leading to the attenuation of the TRIM31-MVAS complex-mediated IFN-I signaling activation. Therefore, the antiviral and proviral effects of TRIM31 reach a balance in IAV-infected cells, resulting in no significant impact on IAV replication. Our novel findings revealed an IAV-specific mechanism that IAV exploits TRIM31 to fine-tune the antiviral innate response and maintain the homeostasis of viral replication.

IMPORTANCE: During the long-term symbiosis with the host, IAVs have evolved a series of unique mechanisms to adapt to the host and support their own replication. The MAVS-mediated IFN-I signaling pathway is crucial for host cells to defend against RNA virus invasion, with TRIM31 functioning as a specific agonist for the activation of IFN-I antiviral response. In the present study, we demonstrated that IAV exploits TRIM31 to promote the stability and activity of viral proteins and reduces the positive effect of TRIM31 on the IFN-I response, thereby preventing TRIM31 from inhibiting IAV replication. Therefore, our results revealed a novel mechanism employed by IAV to adapt to host antiviral response and expanded our understanding of virus-host interactions.},
}

@article {pmid41294280,
year = {2025},
author = {Ullah, I and Zhou, D and Khan, AR and Muhammad, M and Zhang, Q and Ma, J and Egamberdieva, D and Shurigin, V and Li, L},
title = {Unveiling the Adaptation Mechanisms of Symbiotic Microbial Communities in Glycyrrhiza glabra Under Extreme Environmental Conditions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf291},
pmid = {41294280},
issn = {1365-2672},
abstract = {Glycyrrhiza glabra is a medicinal legume species that is adapted to arid and saline environments, as well as climate stressors such as drought, salinity and extreme heat. This review highlights the latest developments in understanding the microbial communities associated with G. glabra, which enhance stress tolerance through nutrient acquisition, phytohormone modification, the production of antioxidants and osmotic regulation. This review synthesizes research on the distribution, diversity, and functionality of these microbial communities including endophytes, rhizobacteria, and arbuscular mycorrhizal fungi within the ecological context of degraded and marginal soils, which functionally enhances G. glabra as a model plant for studying plant-microbial interactions in extreme environments. We specifically highlight the microbial regulation of glycyrrhizin biosynthesis, a critical defense-related secondary metabolite with known therapeutic applications. Finally, we present an overview of new and emerging multi-omics tools that elucidate the molecular mechanisms underpinning these beneficial microbial interactions, and their potential in developing bio-inoculants for climate-resilient agriculture and providing a blueprint for harnessing native microbial partnerships to enhance plant survival, productivity, and soil restoration under climate uncertainty.},
}

@article {pmid41293613,
year = {2025},
author = {Zecca, N and Lücking, L and van Dijk, HAJ and Manzolini, G},
title = {Techno-Economic Assessment of Industrial Symbiosis Between Steel and Urea Plants: The INITIATE Process.},
journal = {Energy & fuels : an American Chemical Society journal},
volume = {39},
number = {46},
pages = {22293-22310},
pmid = {41293613},
issn = {0887-0624},
abstract = {The steelmaking and fertilizer industries accounted for approximately 10% of global anthropogenic CO2 emissions in 2024. This study examines an industrial symbiosis concept, termed INITIATE, which integrates these two sectors to enhance resource efficiency and to reduce CO2 emissions. The proposed system utilizes process gases from steel production as a feedstock for urea synthesis, using the sorption enhanced water gas shift (SEWGS) technology for simultaneous CO2 capture and production of a H2-N2 mixture. This stream is suitable for ammonia synthesis, which subsequently reacts with part of captured CO2 in a downstream urea production process. Two sizes of fertilizer production are analyzed: a small-scale configuration producing 224 turea/day and a large-scale case with a production capacity of 1500 turea/day. Simulation results indicate that the integrated symbiotic configuration of the INITIATE system enables substantial reductions in both the natural gas consumption and direct CO2 emissions. Under scenarios utilizing renewable electricity, the level of CO2 avoidance can reach up to 68%. The specific primary energy consumption per unit of CO2 avoided (SPECCA) ranges from -2.5 to 2.5 GJ/tCO2 . Negative values reflect a net reduction in primary energy demand, resulting from process integration and efficient resource utilization. From an economic perspective, the cost of CO2 avoidance is estimated at 24 €/tCO2 for the small-scale plant, increasing to 130 €/tCO2 for the large-scale configuration. Sensitivity analyses reveal that these costs are highly dependent on the prices of electricity and natural gas, with lower electricity prices and higher natural gas prices improving the economic performance of the INITIATE system compared with the base and reference cases.},
}

@article {pmid41292562,
year = {2025},
author = {Ullah, F and Zaman, F and Ishfaq, M and Ullah, H and Wang, C and Zhifang, L and Geilfus, CM},
title = {Sustainable Greenhouse Tomato Production: Benefits of Inoculation With Arbuscular Mycorrhizal Fungi Under Low Nitrogen and Phosphorus Conditions.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {6},
pages = {e70058},
pmid = {41292562},
issn = {2575-6265},
abstract = {The effects of overused chemical fertilizers, which threaten soil, plant, and human health, have always remained a topic of interest in theory and practice, emphasizing the judicious use of mineral nutrients. This study was aimed at reducing the harmful effects of excessive chemical fertilizer application and at exploring alternative approaches that can improve soil fertility without environmental and health damage. The experimental design involved a controlled greenhouse setup where tomato cultivars were inoculated with different AMF species under varying nitrogen (N) and phosphorus (P) doses. The tomato cultivars Rio Grande and Nadir were inoculated with arbuscular mycorrhizal fungi species, including Glomus claroideum, Glomus etunicatum, Glomus fasciculatum, and Glomus mosseae-within a commercial greenhouse. This study aimed to evaluate the potential effects of these fungi on tomato growth physiology, yield, and fruit quality when subjected to varying doses of N and P. Glomus mosseae significantly increased plant height by 14%, stem diameter by 22.25%, dry matter by 23.59%, yield by 38.57%, N uptake by 16.40%, P uptake by 37.5%, potassium (K) uptake by 18.55%, chlorophyll a (Chl a) content by 15.18%, and chlorophyll b (Chl b) content by 25.19% when compared to untreated controls. Additionally, Glomus mosseae improved fruit diameter by 9.98%, fruit firmness by 18.45%, juice content by 15.20%, titratable acidity (TA) by 10.42%, and ascorbic acid concentration by 16.75%. The interaction between the N and P levels of 140:42 mg L[-1] and the arbuscular mycorrhizal fungus (AMF) species Glomus mosseae resulted in the highest improvement in growth, yield, and fruit quality-related traits. Among the cultivars, Rio Grande exhibited the greatest root colonization, plant dry matter content, N, P, K uptake, plant height, Chl a, Chl b, and yield when compared to the control. In contrast, cultivar Nadir showed the highest stem diameter, fruit size, firmness, ascorbic acid, fruit juice contents, and TA. This study recommends that AMF inoculation in combination with a low N and P supply can be promising for improving tomato growth, productivity, and fruit quality on a commercial scale with minimum threats to the environment and human health. This study suggests the exploration of long-term sustainability and scalability of AMF inoculation methods in diverse agricultural settings.},
}

@article {pmid41292049,
year = {2025},
author = {Tian, Z and Zhang, K and Sheng, S and Kan, C and Han, F and Sun, X},
title = {The Role of Lactate Metabolism in Tumors: From Metabolic Byproduct to Signaling Molecule.},
journal = {American journal of clinical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1097/COC.0000000000001276},
pmid = {41292049},
issn = {1537-453X},
abstract = {Lactate, once viewed as a metabolic by-product of glycolysis, is now recognized as a central regulator in cancer biology. Accumulating evidence reveals that lactate actively participates in tumor progression by functioning as a metabolic fuel, signaling mediator, epigenetic modifier, and immune modulator. Tumor cells exhibit elevated glycolytic flux through the Warburg effect, producing large quantities of lactate through LDHA and exporting it through MCTs, which acidifies the tumor microenvironment and drives metabolic symbiosis, angiogenesis, and immune evasion. Lactate also stabilizes HIF-1α and activates the receptor GPR81, triggering signaling pathways that promote proliferation, invasion, and immune checkpoint expression. Epigenetically, lactate regulates histone acetylation and lactylation, modulating gene expression and supporting adaptive transcriptional programs. Immune suppression is reinforced through direct inhibition of effector T and NK cells and expansion of Tregs and MDSCs. Given its multifaceted role, lactate metabolism has emerged as a promising therapeutic target. Inhibitors of LDHA, MCT1/4, and GPR81 are under active development and show synergistic potential with immunotherapy and chemoradiotherapy. This review summarizes current advances in lactate biology and therapeutic strategies, highlighting the need for personalized approaches that consider tumor-specific lactate dependencies and signaling contexts.},
}

@article {pmid41291109,
year = {2025},
author = {Cohen, DD and Faigenboim, A and Elingold, I and Sher, Y and Galpaz, N and Minz, D},
title = {Dynamics in Microbial Communities Associated with the Development of Soil Fatigue in Banana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02637-7},
pmid = {41291109},
issn = {1432-184X},
abstract = {Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.},
}

@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66678-9},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}

@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}

*Geologic Sediments/virology/microbiology
Genome, Viral/genetics
China
Virome/genetics
Metagenomics
Mining
Metagenome
Phylogeny
Ecosystem
Acids
*Host Microbial Interactions

@article {pmid41290153,
year = {2025},
author = {Spilmont, N and Zardi, GI and Nicastro, KR},
title = {Intertidal mussel-symbiont associations act as CO2 sinks during daily emersion.},
journal = {Biology letters},
volume = {21},
number = {11},
pages = {20250498},
doi = {10.1098/rsbl.2025.0498},
pmid = {41290153},
issn = {1744-957X},
support = {//EMIMA experimental platform (Lille University)/ ; //FEDER/ ; //ANR/ ; },
mesh = {Animals ; *Carbon Dioxide/metabolism ; *Symbiosis ; *Mytilus edulis/microbiology/physiology/metabolism ; *Cyanobacteria/physiology ; *Carbon Sequestration ; Carbon Cycle ; },
abstract = {Human activities have disrupted the global carbon cycle, reducing carbon dioxide (CO2) uptake by tidal wetlands and submerged vegetation. This exacerbates climate challenges, including rising temperatures and ocean acidification. Coastal systems such as mangroves and seagrasses serve as key carbon sinks, promising for CO2 removal (CDR). Growing attention is being given to bivalves, whose calcification and reef-building activities shape coastal carbon dynamics. Most studies reduce bivalve impacts to a balance between individual CO2 emissions and the carbon stored in their shells and tissues, often overlooking species interactions-such as symbioses-that may modulate carbon fluxes. Here, we examined the mussel-symbiont holobiont using Mytilus edulis under emersion in a controlled chamber to quantify CO2 exchange. Mussels hosting cyanobacterial symbionts exhibited net atmospheric CO2 uptake during daily air exposure, a critical phase of the tidal cycle. To evaluate the potential significance at larger ecological scales, we combined laboratory-derived CO2 uptake data with field-based estimates of symbiont prevalence to model carbon fluxes at the mussel bed scale and compared them with values of established blue carbon systems. This research highlights the importance of species interactions in coastal carbon cycling and underscores the need to incorporate the mussel-symbiont holobiont into CDR models.},
}

Animals
*Carbon Dioxide/metabolism
*Symbiosis
*Mytilus edulis/microbiology/physiology/metabolism
*Cyanobacteria/physiology
*Carbon Sequestration
Carbon Cycle

@article {pmid41289393,
year = {2025},
author = {He, T and Zhao, Y and Wang, X and Qiu, Y and Deng, J and Zhang, K and Xu, X and Zhao, Y and Qian, K and Wang, H and Bai, T and Zhang, Y and Feng, C and Guo, L and Chen, H and Guo, L and Wang, Y and Hu, S},
title = {Precipitation increase promotes soil organic carbon formation and stability via the mycorrhizal fungal pathway.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2519072122},
doi = {10.1073/pnas.2519072122},
pmid = {41289393},
issn = {1091-6490},
support = {32371626//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20240193//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
mesh = {*Mycorrhizae/metabolism/physiology ; *Carbon/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Plant Roots/microbiology/metabolism ; *Rain ; Climate Change ; Grassland ; Biomass ; Symbiosis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with roots of most terrestrial plants, playing a crucial role in regulating soil organic carbon (SOC) dynamics. While precipitation increase (Pi) is a major facet of climate change, its impacts on root- and AMF-mediated SOC formation and stability remain largely unexplored. Here, we combined a meta-analysis across global grasslands with a multiyear precipitation manipulation experiment in a semiarid grassland on the Loess Plateau to disentangle the relative effects of roots and their associated AMF on microbial communities and SOC as influenced by Pi. We show that Pi induced tradeoffs between roots and AMF, and promoted SOC formation and stability via the mycelium- rather than the root-pathway, leading to an increase of 136% (±40) and 297% (±90) in mycelium-derived C and mineral-associated organic C (MAOC), respectively. Pi altered plant community composition, favoring subshrubs and forbs over grasses. Also, Pi reduced specific root length, but increased root diameter, tissue density, and root colonization and extraradical biomass of AMF. Furthermore, Pi-induced change in AMF shifted the soil bacterial community by favoring K-strategists, increasing bacterial necromass C and promoting MAOC accumulation. Our findings provide direct evidence that Pi enhances AMF-driven SOC sequestration by expanding the mycorrhizosphere and promoting microbiota with high C use efficiency, highlighting a key mechanism by which mycorrhizal fungi mediate SOC formation and stability under shifting precipitation regimes.},
}

*Mycorrhizae/metabolism/physiology
*Carbon/metabolism
*Soil/chemistry
*Soil Microbiology
Plant Roots/microbiology/metabolism
*Rain
Climate Change
Grassland
Biomass
Symbiosis

@article {pmid41289084,
year = {2025},
author = {Chen, H and Li, M and Zhong, Z and Seim, I and Wang, M and Lian, C and Zhuo, L and Wan, X and Wang, H and Han, G and Zhou, L and Zhang, H and Cao, L and Li, C},
title = {Function and Development of Deep-sea Mussel Bacteriocytes Revealed by SnRNA-seq and Spatial Transcriptomics.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf109},
pmid = {41289084},
issn = {2210-3244},
abstract = {The deep-sea chemosynthetic ecosystems are among one of the most unusual ecosystems on Earth, where most megafauna form close symbiotic associations with chemosynthetic microbes to obtain nutrition and shelter from the toxic environment. Despite the diverse forms of symbiotic organs in these deep-sea holobionts, the function and development of bacteriocytes, the host cells harboring symbionts, are still largely uncharacterized. Here, we have conducted the in situ decolonization assay and state-of-the-art single-nucleus and spatial transcriptomics to reveal the function and development of deep-sea mussel bacteriocytes. The bacteriocytes appear to optimize immune processes to facilitate recognition, engulfment, and elimination of endosymbionts. They also interact directly with them in carbohydrate and ammonia metabolism by exchanging metabolic intermediates via transporters such as SLC37A2 and RHBG-A. Bacteriocytes arise from three different proliferating cell types, and their successive development trajectory was delineated by multi-omics data and 3D reconstruction analyses. The molecular functions and the developmental processes of bacteriocytes were found to be guided by the same set of molluscan-conserved transcription factors and may be influenced by endosymbionts through sterol metabolism. The coordination in the functions and development of bacteriocytes and between the host and symbionts highlights the phenotypic plasticity of symbiotic cells, and underpins host-symbiont interdependence in adaptation to the deep sea.},
}

@article {pmid41288984,
year = {2025},
author = {Hernandez-Benitez, EM and Martínez-Romero, E and Aguirre-Noyola, JL and Farias-Rico, JA and Ledezma-Tejeida, D},
title = {Computational inference of Rhizobium phaseoli transcriptional regulatory network predicts Transcription Factors involved in nodulation.},
journal = {Briefings in functional genomics},
volume = {24},
number = {},
pages = {},
doi = {10.1093/bfgp/elaf020},
pmid = {41288984},
issn = {2041-2657},
support = {IA204925//Universidad Nacional Autónoma de México, Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; 2057038//Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México/ ; //Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; },
mesh = {*Transcription Factors/metabolism/genetics ; *Gene Regulatory Networks ; *Rhizobium/genetics ; *Plant Root Nodulation/genetics ; *Phaseolus/microbiology/genetics ; *Computational Biology/methods ; Bacterial Proteins/genetics/metabolism ; Symbiosis/genetics ; },
abstract = {Growth of the common bean plant Phaseolus vulgaris is tightly linked to its symbiotic relationship with diverse rhizobial species, particularly Rhizobium phaseoli, an alphaproteobacterium that forms root nodules and provides high levels of nitrogen to the plant. Molecular cross-talk is known to happen through plant-derived metabolites, but only flavonoids have been identified as nodulation signals, which act through the activation of the NodD Transcription Factor (TF). The identification of signals that mediate nodulation via TFs can aid in the rational design of biofertilizers that promote plant-bacteria symbiosis. Here, we identified 57 TFs in the R. phaseoli genome through sequence conservation from Escherichia coli, and predicted a transcriptional regulatory network comprising 16 TFs, and 1,371 target genes. We identified the regulatory interactions relevant to nodulation via transcriptome analysis, and hypothesize that PuuR is a TF involved in nodulation, potentially acting via its known binding metabolite putrescine. Sequence and structural evidence predict a model where putrescine acts as a signaling metabolite in nodulation via the TF PuuR, and the regulation of the nodI gene.},
}

*Transcription Factors/metabolism/genetics
*Gene Regulatory Networks
*Rhizobium/genetics
*Plant Root Nodulation/genetics
*Phaseolus/microbiology/genetics
*Computational Biology/methods
Bacterial Proteins/genetics/metabolism
Symbiosis/genetics

@article {pmid41288789,
year = {2025},
author = {Carrara, JE and Smith, AH and Heller, WP},
title = {Application of spent mushroom compost enhances wheat yield but reduces mycorrhizal associations and grain nutrient concentration.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {67},
pmid = {41288789},
issn = {1432-1890},
support = {8072-12000-014-000-D//USDA-ARS in-house project/ ; },
mesh = {*Triticum/growth & development/microbiology/metabolism/chemistry ; *Mycorrhizae/physiology ; *Composting ; Soil Microbiology ; *Agaricales ; Nutrients/analysis/metabolism ; Soil/chemistry ; Edible Grain/chemistry/growth & development ; },
abstract = {Developing management practices that enhance crop yield while maintaining soil health is the foremost objective of the regenerative agriculture movement. One avenue to achieving this goal is using biofertilizers and alternative soil amendments to supplement or replace agrochemicals. Here we report the results of a pairwise field trial of spring wheat (Triticum aestivum) wherein we investigated individual and combined impacts of inoculation with arbuscular mycorrhizal fungi (AMF) and a spent mushroom compost amendment (herein mushroom compost). The symbiotic relationship between AMF and plants has been demonstrated to benefit the yield and nutritional quality of many crops by enhancing access to mineral nutrients and water. Mushroom compost, consisting of the devitalized residual substrate following harvest of edible mushrooms, is a byproduct of the mushroom industry and is comprised of a variety of nutrient-rich organic material inputs. Therefore, the objective of this study was to (1) determine the effect to which AMF and mushroom compost individually impact wheat yield and nutritional quality, and (2) examine if these effects are synergistic or antagonistic when both amendments are applied together. We found that mushroom compost addition, regardless of AMF inoculation, enhanced grain yield by ~ 40%, but reduced AMF root colonization level by ~ 25-40%. Additionally, despite yield increases, mushroom compost addition reduced grain phosphorus (P), potassium (K), and magnesium (Mg) concentrations by ~ 10% and boron concentration by ~ 45%. In fact, grain P, K, and Mg concentrations were all correlated with mycorrhizal colonization level. These results suggest that while spent mushroom compost additions enhanced grain yield, this may have led to a mineral nutrient 'dilution effect' exacerbated by negative impacts on AMF colonization and community composition.},
}

*Triticum/growth & development/microbiology/metabolism/chemistry
*Mycorrhizae/physiology
*Composting
Soil Microbiology
*Agaricales
Nutrients/analysis/metabolism
Soil/chemistry
Edible Grain/chemistry/growth & development

@article {pmid41288749,
year = {2025},
author = {Ndabankulu, KP and Zama, N and Suinyuy, TN and Magadlela, A},
title = {Soil Microbe Interaction and Extracellular Enzyme Activity Mediated by Encephalartos villosus in KwaZulu-Natal Scarp Forest Ecosystems.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {132},
pmid = {41288749},
issn = {1432-184X},
support = {129403//National Research Foundation, South Africa/ ; 138091//National Research Foundation/ ; },
mesh = {*Soil Microbiology ; South Africa ; Soil/chemistry ; Forests ; *Bacteria/classification/enzymology/genetics/isolation & purification/metabolism ; Rhizosphere ; Symbiosis ; Ecosystem ; Microbiota ; },
abstract = {Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.},
}

*Soil Microbiology
South Africa
Soil/chemistry
Forests
*Bacteria/classification/enzymology/genetics/isolation & purification/metabolism
Rhizosphere
Symbiosis
Ecosystem
Microbiota

@article {pmid41288716,
year = {2025},
author = {Chatterjee, A and Ghosh, P and Das, S and Sharaff, M and Mandal, S and Bhattacharya, PM and Chaudhuri, T and Pal, H},
title = {Mangrove derived coactive bacterial inoculant triggered biochemical traits rejuvenating plant cell function under salt stress.},
journal = {Plant cell reports},
volume = {44},
number = {12},
pages = {280},
pmid = {41288716},
issn = {1432-203X},
support = {IGSTC/Call 2019/CirCulTex/19/2020-2021/165//Indo-German Science and Technology Centre/ ; },
mesh = {*Solanum lycopersicum/microbiology/physiology/metabolism/drug effects ; *Salt Stress/physiology ; Plant Roots/microbiology ; *Plant Cells/metabolism ; Salt Tolerance ; },
abstract = {Novel endophytic bacterial consortium promotes the growth of Solanum lycopersicum surviving salt stress by differentially regulating the primary and secondary metabolic pathways. Crop yield is being impacted by global warming, which threatens food security. Salinization of soil or irrigation water is becoming increasingly prevalent in most agricultural terrain, especially around the coast. In India, it is estimated that approximately 10% of additional area is getting salinized, and around 50% of the arable land would be salt-affected by the year 2050. Finding innovative techniques that enable farmers to sustain production in an increasingly saline environment is crucial given the world's population expansion and the depletion of natural resources used in agriculture. Biostimulants are naturally occurring compounds or microorganisms that are used to promote plant functions, such as nutrient absorption, nutrient utilisation efficiency, abiotic stress tolerance, and the overall quality of the resulting agricultural products. In the present work, we evaluated the agronomic effectiveness of a novel formulated biostimulant consisting of four strains of endophytic bacteria isolated from the roots of mangrove plants of Sundarbans in a crop of great interest (Tomato) under controlled conditions and salt stress. Our research has shown that our product had a positive effect on the biochemical parameters in tomato plants under salt stress. The application of our biostimulant also increased osmolyte production and maintained Na[+]/K[+] homeostasis under salt conditions. Similarly, when exposed to salinity, the biostimulant increased the concentration of signature molecules, including primary metabolites, phenolic compounds, polyamines, and phytohormones inside the plant cell. This study enriched our body of knowledge by providing novel perspectives on the mechanism of salt resistance that endophytic microbes provide through symbiosis.},
}

*Solanum lycopersicum/microbiology/physiology/metabolism/drug effects
*Salt Stress/physiology
Plant Roots/microbiology
*Plant Cells/metabolism
Salt Tolerance

@article {pmid41288338,
year = {2025},
author = {Kamel Urmia, H and Koosha, M and Yakhchali, B and Moosa-Kazemi, SH and Oshaghi, MA},
title = {Environmental persistence and transmission dynamics of Serratia AS1 in mosquito habitats: advancing paratransgenesis for malaria control.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0184025},
doi = {10.1128/aem.01840-25},
pmid = {41288338},
issn = {1098-5336},
abstract = {UNLABELLED: Malaria remains a major global health challenge, particularly in developing countries, necessitating innovative control strategies. With rising resistance of Plasmodium to drugs and Anopheles mosquitoes to insecticides, paratransgenesis-using engineered symbiotic bacteria to deliver anti-pathogen molecules-offers a promising alternative. Translating this approach to field applications requires rigorous evaluation under semi-field conditions. We evaluated the environmental stability and transmission dynamics of Serratia AS1-mCherry, a paratransgenesis candidate, in Anopheles stephensi habitats under semi-field conditions in Bandar Abbas, Iran. Serratia AS1 successfully colonized mosquito midguts and ovaries, persisted in larval breeding water for 14 days, and remained stable on sugar-soaked cotton pads for 4-6 days. Transmission routes include transstadial, venereal, and vertical transmission, in addition to adult acquisition from larval habitats (sipping), demonstrating robust colonization and dissemination. Water-based delivery effectively disseminates Serratia AS1 among mosquito populations, highlighting its potential for paratransgenesis-based malaria control. This study establishes the feasibility of using Serratia AS1 with effector molecules in field settings, offering a sustainable strategy for managing vector-borne diseases.

IMPORTANCE: Malaria remains a major health challenge, especially in developing countries where traditional control methods like insecticides and drugs are becoming less effective due to resistance. This study explores a promising new approach called paratransgenesis, which uses genetically modified bacteria to fight malaria. We tested a bacterium called Serratia AS1, which can live inside mosquitoes and spread through their populations. Our experiments showed that Serratia AS1 can survive in mosquito breeding sites and spread effectively among mosquitoes through multiple routes, such as larval water, sugar sources, and even from parent mosquitoes to their offspring. These findings suggest that Serratia AS1 could be used to deliver anti-malaria molecules to mosquitoes in the wild, offering a sustainable and innovative way to control the disease. This work brings us one step closer to using paratransgenesis as a practical tool to reduce malaria transmission and save lives.},
}

@article {pmid41287631,
year = {2025},
author = {Kranawetter, C and Sumner, LW},
title = {Differential root zone secretions and the role of root border cells in rhizosphere manipulation.},
journal = {Phytochemistry reviews : proceedings of the Phytochemical Society of Europe},
volume = {24},
number = {6},
pages = {5639-5658},
pmid = {41287631},
issn = {1568-7767},
abstract = {Root tissues are broadly divided into mature tissue, elongation zone (developing tissue), root tip, and border cells. While each zone contributes individually to the overall root secretion profile, border cells are emphasized in this review due to their specialized secretory functions. Border cells are often overlooked in plant root focused studies, thus excluding an important component of root functionality. Border cells are a specialized cell type surrounding the root apical meristematic region of most plant species, with the exception of the Brassicaceae family that possess border-like cells. Both cell types share the commonality of complete detachment from the root tip and reliance on internal starch reserves to perform metabolic processes. However, border cells release from the root tip as single/individual cells whereas border-like cells separate as cohesive sheets. Furthermore, border cells, but not border-like cells, secrete a complex matrix consisting of mucilage, proteins, DNA, and metabolites. Many of these secreted compounds are bioactive (e.g. secreted mucilage supports microbial growth and DNA physically entangles pathogens) thus mediating symbiosis and pathogen defense. We are interested in metabolites secreted from individual root regions, with a heavy emphasis on those specifically arising from border cells. Border cell metabolite secretion is in need of further investigation, as current research indicates they secrete symbiosis-inducing, allelopathic, and defense oriented metabolites. This review will summarize current literature regarding metabolite secretions by specific root cell types and regions. In particular, it will focus on border cell contributions to the rhizosphere chemistry relative to other root tissue types.},
}

@article {pmid41286654,
year = {2025},
author = {Benmrid, B and Idbella, M and Bonanomi, G and Khourchi, S and Gherardelli, M and Bargaz, A and Cherki, G},
title = {Drought-tolerant rhizobacterial consortia with diverse plant growth promoting traits enhance wheat and faba bean growth under water and low-P availability promising multi-traits.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {771},
pmid = {41286654},
issn = {1471-2180},
support = {AS1-UM6P-Anhalt//OCP Group/ ; AS1-UM6P-Anhalt//OCP Group/ ; AS1-UM6P-Anhalt//OCP Group/ ; },
mesh = {*Triticum/growth & development/microbiology/metabolism ; *Vicia faba/growth & development/microbiology/metabolism ; Droughts ; *Phosphorus/metabolism/deficiency ; Plant Roots/microbiology/growth & development ; Rhizosphere ; *Bacteria/metabolism/classification/genetics ; Water/metabolism ; *Microbial Consortia/physiology ; Soil Microbiology ; Stress, Physiological ; },
abstract = {BACKGROUND: Staple crops like wheat and faba bean are increasingly subjected to multiple and simultaneous stresses, resulting in substantial yield reduction. Although vast available knowledge about the role of root-rhizosphere microbes in enhancing crop tolerance to single stress, few is known about the potential of bacterial consortia rationally assembled from strains with defined and complementary ecological functions to improve crop tolerance to combined drought and phosphorus (P) deficiency. This study evaluated wheat (Triticum durum) or faba bean (Vicia faba) morpho-physiological response to three functionally diverse drought-tolerant bacterial consortia (C7, C8, C9), in greenhouse conditions, under low-P well-watered conditions (rock phosphate (RP), 80% field capacity (FC)) or low-P drought conditions (RP, 40% FC).

RESULTS: Assessment of agro-physiological parameters identified consortium C8 as particularly effective, leading to significant increases in root biomass, leaf area, and shoot inorganic P content, of both wheat and faba bean plants under combined drought and low-P availability. This improvement is likely driven by bacterial traits related to drought tolerance, increased root biomass allocation, and enhanced rhizosphere P availability, as indicated by enhanced physiological traits related to leaf area, photosynthetic efficiency (Fv/Fm ratio), and chlorophyll content. Additionally, soil P availability and acquisition improved in response to bacterial inoculation that positively influenced faba bean nodulation, indicating that these bacterial consortia plausibly increased faba bean symbiotic effectiveness through optimizing P use efficiency as a potential mechanism among others. Additionally, the ability of bacterial consortia to produce phytohormones (e.g. Auxins) could partially explain induced root development and nodulation under water stress, given the key role of these phytohormones in root growth and rhizobia-legume symbiosis establishment.

CONCLUSION: Our findings provide consistent evidence on the effectiveness of bacterial consortia - comprising functionally diverse PGP traits - in enhancing plant growth and nutrient acquisition under stressful conditions.},
}

*Triticum/growth & development/microbiology/metabolism
*Vicia faba/growth & development/microbiology/metabolism
Droughts
*Phosphorus/metabolism/deficiency
Plant Roots/microbiology/growth & development
Rhizosphere
*Bacteria/metabolism/classification/genetics
Water/metabolism
*Microbial Consortia/physiology
Soil Microbiology
Stress, Physiological

@article {pmid41286598,
year = {2025},
author = {Zhang, Y and Wen, H and Li, Q and Lu, Y and Zhang, Z and Sui, L},
title = {From function to omics: endophytic Beauveria bassiana promotes maize growth by activating phytohormone signaling pathways under elevated carbon dioxide.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07763-5},
pmid = {41286598},
issn = {1471-2229},
support = {32271683//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Several entomopathogenic fungal (EPF) species can colonise and establish symbiotic relationships with plants as endophytes, which affects crop growth under elevated carbon dioxide (eCO2) concentrations. However, how EPF facilitates eCO2 in plants is poorly understood, especially at the transcriptional and metabolic levels. Here, the authors used transcriptomics and metabolomics to examine the effects of a widely used EPF, Beauveria bassiana, on maize growth under eCO2, and how it regulated enzyme activity and endogenous hormone metabolism.

RESULTS: Beauveria bassiana colonisation significantly enhanced maize growth across CO₂ concentrations. Key effects include: 39.64% greater leaf area than controls at ambient CO₂ during S3. Significant developmental divergence in leaf area between S3-S4 under eCO₂, 11.8% higher 100-grain weight in eCO₂+Bb vs. eCO₂ alone. Concurrent increases in stress-responsive enzymes and hormones aligned with omics-revealed activation of primary metabolic pathways (ZMA01100) and secondary metabolite biosynthesis pathways (ZMA01110).

CONCLUSIONS: These findings suggested that B. bassiana colonization modulates plant growth under eCO2 by regulating the expression of related genes, and in turn, enzyme activity and hormone metabolism. The findings of the present study offered a theoretical foundation for elucidating the interactions between EPFs and plants under climate change.},
}

@article {pmid41286473,
year = {2025},
author = {Wang, H and Yang, Y and Zhang, H and Chen, X and Zhang, R and Hou, W and Zhang, G},
title = {Symbiotic N-Fixing Bacteria in the Root and Leaf of Typical Alpine Grassland Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {127},
pmid = {41286473},
issn = {1432-184X},
mesh = {Grassland ; *Plant Roots/microbiology ; *Symbiosis ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Tibet ; *Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology ; Nitrogen Fixation ; Phylogeny ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; },
abstract = {Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.},
}

Grassland
*Plant Roots/microbiology
*Symbiosis
*Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics
Tibet
*Nitrogen-Fixing Bacteria/classification/genetics/isolation & purification/physiology
Nitrogen Fixation
Phylogeny
DNA, Bacterial/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Soil Microbiology

@article {pmid41286138,
year = {2025},
author = {Liu, XQ and An, XP and He, WX and Xu, XH and Hashem, A and Abd-Allah, EF and Wu, QS},
title = {Hairy Vetch Intercropping Attenuates Mycorrhizal Benefits to Walnut Growth and Soil Organic Carbon Sequestration via Glomalin.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {128},
pmid = {41286138},
issn = {1432-184X},
support = {SCXX-XZCG-22016//Hubei Province '14th Five-Year' Major Science and Technology Aid Tibet Project/ ; ORF-2025-356//Ongoing Research Funding program, King Saud University, Riyadh, Saudi Arabia/ ; },
mesh = {*Juglans/growth & development/microbiology ; *Mycorrhizae/physiology/growth & development ; *Soil/chemistry ; Soil Microbiology ; *Carbon Sequestration ; Plant Roots/microbiology/growth & development ; Carbon/metabolism/analysis ; Biomass ; *Agriculture/methods ; *Fungal Proteins/metabolism ; *Glycoproteins/metabolism ; },
abstract = {Intercropping is a prevalent soil management strategy within walnut orchards, while its impacts on the functionality of arbuscular mycorrhizal fungi (AMF) in walnuts (Juglans regia) remain unclear, especially concerning soil carbon (C) sequestration via glomalin-related soil protein (GRSP). This study aimed to explore the effects of inoculation with the AMF species Diversispora spurca and intercropping with hairy vetch (Vicia villosa) on walnut biomass accumulation, soil water-stable aggregate (WSA) stability, leaf and root C (Cleaf and Croot) content, soil organic carbon (SOC), GRSP, and GRSP-contained C (CGRSP), in addition to the contribution rate of CGRSP to SOC. The intercropping treatment significantly inhibited root mycorrhizal colonization rate, soil hyphal length, and spore density in AMF-inoculated walnut plants. Individual AMF inoculation, rather than individual intercropping, significantly promoted shoot and root biomass accumulation, WSA stability, SOC, Cleaf and Croot, the levels of purified easily extractable (EEG), difficultly extractable (DEG), and total GRSP (TG), as well as their C contents. The combination treatment (AMF inoculation + intercropping) displayed limited benefits, improving just WSA stability without yielding synergistic advantages over individual treatments. Arbuscular mycorrhizal fungal inoculation significantly increased CGRSP, especially CDEG, while individual intercropping resulted in a reduction of CDEG. The combination treatment elevated both CDEG and CTG, albeit to a lesser extent than AMF alone. The contribution rates of CEEG, CDEG, and CTG to SOC were 0.33% - 0.53%, 1.16% - 1.78%, and 1.49% - 2.31%, respectively. Although AMF inoculation significantly increased the contribution rates of CDEG and CTG to SOC, this effect was diminished when combined with intercropping. Notably, CDEG, rather than CEEG, exhibited a significantly positive correlation with SOC and WSA stability. The findings provide new insights into the mechanisms of SOC sequestration in walnuts grown in controlled environments and offer a theoretical basis for the application of AMF in walnut cultivation.},
}

*Juglans/growth & development/microbiology
*Mycorrhizae/physiology/growth & development
*Soil/chemistry
Soil Microbiology
*Carbon Sequestration
Plant Roots/microbiology/growth & development
Carbon/metabolism/analysis
Biomass
*Agriculture/methods
*Fungal Proteins/metabolism
*Glycoproteins/metabolism

@article {pmid41285821,
year = {2025},
author = {Karimzadeh, S and Safaie, N and Mojerlou, S and Ebrahimi, L},
title = {Identity and diversity of culturable endophytic fungi associated with Capparis spinosa L. in Iran.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41502},
pmid = {41285821},
issn = {2045-2322},
mesh = {*Endophytes/classification/isolation & purification/genetics ; Iran ; *Fungi/classification/isolation & purification/genetics ; *Biodiversity ; Phylogeny ; Plant Roots/microbiology ; },
abstract = {Endophytic fungi play a crucial role in plant health, contributing to stress tolerance, disease resistance, and ecological adaptation. However, the diversity and richness of endophytic fungal communities associated with Capparis spinosa L. in the Alborz, Tehran, and Qom provinces-ranging from semi-arid and slightly temperate to arid and desert climatic conditions-have not yet been investigated. Using morphological and molecular methods, we identified a diverse fungal assemblage comprising 3 phyla, 7 classes, 14 orders, 28 families, and 36 genera. Among the genera shared across all three provinces, Alternaria (28.8%) was the most dominant among the isolates, whereas Simplicillium (1.6%) was the least abundant. Analysis of the isolates using diversity indices revealed that species distribution in all three provinces tended toward evenness, with a similar pattern observed across different tissues. Qom exhibited the highest diversity and richness of fungal species. Additionally, a detailed comparison of different plant tissues revealed that roots consistently harbored the greatest variety and the highest number of isolates compared to stems, leaves, and fruits. Diversity metrics suggest a potential link between climatic gradients and endophyte diversity. These findings enhance our understanding of fungal-plant interactions and provide insights into the microbial contributions to C. spinosa resilience in harsh environmental conditions.},
}

*Endophytes/classification/isolation & purification/genetics
Iran
*Fungi/classification/isolation & purification/genetics
*Biodiversity
Phylogeny
Plant Roots/microbiology

@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}

Single-Cell Analysis/methods
Symbiosis/genetics
*Amoeba/virology/microbiology/genetics
*Microbiota/genetics
Metagenomics/methods
*Ciliophora/virology/microbiology/genetics
Bacteria/genetics/classification
Genomics/methods
Giant Viruses/genetics
Phylogeny
Viruses/genetics/classification

@article {pmid41284260,
year = {2025},
author = {Song, H and Dowdell, K and Delafont, V and Skerlos, S and Raskin, L},
title = {The Neglected Role of Heterotrophic Protists in Engineered Water Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04958},
pmid = {41284260},
issn = {1520-5851},
abstract = {Heterotrophic protists can be considered the dark matter of microbial communities in engineered water systems. They are ubiquitous and ecologically significant yet remain largely overlooked. Although a growing body of research demonstrates their pivotal roles (e.g., predation, symbiosis, and nutrient cycling) in microbial communities in natural ecosystems, their functions in engineered water systems are poorly characterized, and heterotrophic protists are frequently excluded from microbial analyses. This is largely due to methodological constraints that have only recently been overcome. Recent advances in imaging, high-throughput sequencing, and meta-omics approaches, combined with expanding reference databases, have revolutionized studies of protist diversity and functions in a wide range of natural environments. Drawing on research from the fields of protistology, microbial ecology, and environmental microbiology, this review explores how the well-documented ecological roles of heterotrophic protists in natural environments translate to engineered ecosystems, offering insights into their functions in water treatment. We critically evaluate recent literature to synthesize both beneficial roles and potential risks of heterotrophic protists in various water treatment systems, while identifying key knowledge gaps and proposing directions for future research. We advocate for a shift in perspective that recognizes heterotrophic protists as important players and call for their integration into microbial community characterization and ecological frameworks in microbial ecology studies of engineered water systems. This integration will transform our understanding of microbial communities in engineered water systems, ultimately enabling novel, mechanistic, and ecologically informed management strategies.},
}

@article {pmid41282262,
year = {2025},
author = {Geddes, B and Levin, G and Luu, C and Visich, N and Hoselton, S and Lipzen, A and Zhao, S and Li, L and diCenzo, G and Finan, T},
title = {Polyhydroxyalkanoate synthesis by Sinorhizobium meliloti drives a host-specific collapse in symbiosis with Medicago sativa.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7715224/v1},
pmid = {41282262},
issn = {2693-5015},
abstract = {Naturally occurring root-nodule bacteria (rhizobia) vary substantially in their effectiveness at promoting growth of different plant hosts via symbiotic nitrogen fixation. These variations in rhizobial partner quality have important implications for the productivity of nitrogen-fixing symbioses in natural and agricultural ecosystems, yet we have a limited understanding of the genetic basis for this variation. In a case of host-specific reduction in symbiotic effectiveness (N 2 -fixation) with Medicago sativa , we identified the causative genetic elements from the pSymA replicon of Sinorhizobum meliloti HM006 and show them to be involved in polyhydroxyalkanoate (PHA) production in nitrogen-fixing bacteroids. Transfer of this gene region to a strain that forms an effective symbiosis with Medicago sativa resulted in a complete loss of symbiotic N 2 -fixation. We showed the mechanism for symbiotic collapse is the diversion of succinate semialdehyde pools in the bacteroid to gamma-hydroxybutyrate (GHB) by an iron-containing dehydrogenase, GhbD. These findings reveal unexpected impacts of carbon metabolism changes in nodules on symbiont performance and provide a rare example of mechanism for variation in rhizobium partner quality, suggesting that host-specific metabolic incompatibility may be a key player in the variations in partner quality observed in nature.},
}

@article {pmid41281664,
year = {2025},
author = {Lan, X and Zhang, F and Cui, G and Hu, B and Lai, Y and Lin, H and Huang, H and Zhou, D and Yu, M and Yao, G},
title = {Microbiota-directed lactic acid depleting nanoenzyme reactivates antitumor immunity and chemosensitivity in hypoxic tumor.},
journal = {Materials today. Bio},
volume = {35},
number = {},
pages = {102493},
pmid = {41281664},
issn = {2590-0064},
abstract = {The acidification of the tumor microenvironment (TME) remains a major obstacle contributing to malignant progression and impeding therapeutic development. While traditionally attributed to anaerobic glycolysis, increasing evidence suggests that hypoxia-induced colonization of intratumoral symbiotic microbiota, particularly anaerobes, produce lactic acid (LA) metabolites serves as a significant contributor to TME acidification. Although antibiotic-based combination therapies have been explored for the hypoxic tumor treatment, the efficiency was restricted in reversing acidification-induced immunosuppression and chemoresistance. To tackle this challenge, we engineered a delivery platform (TML NPs) for lactate oxidase (LOX) and chemotherapeutic drug tirapazamine (TPZ) by modifying the carrier with metronidazole (MTZ), an antibiotic bearing hypoxia-responsive functional group. By directly targeting the symbiotic anaerobic bacterial metabolism, this strategy introduces a novel paradigm for modulating TME acidification, reversing the LA-mediated suppression of anti-tumor immune responses and chemosensitivity. Our strategy offers a promising translational platform for the precise treatment of TNBC and other hypoxic malignancies.},
}

@article {pmid41280275,
year = {2026},
author = {Qi, X and Zhang, Y and Sun, Z and Wang, G and Ling, F},
title = {A simplified synthetic microbial community enhances resistance of crucian carp (Carassius auratus) to Aeromonas hydrophila infection through host immune activation.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {407-418},
pmid = {41280275},
issn = {2405-805X},
abstract = {Bacterial diseases represent a major bottleneck in the sustainable development of aquaculture. The gut microbiota plays a vital role in host growth and health, including the enhancement of disease resistance. Although substantial progress has been made in elucidating the mechanisms of disease resistance in fish, the precise role of the gut microbiota in enhancing pathogen resistance in aquatic animals remains poorly understood. In this study, crucian carp (Carassius auratus) were used as a model to investigate the role of intestinal microbiota in modulating resistance to Aeromonas hydrophila. Individual crucian carp exhibited distinct clinical phenotypes following A. hydrophila infection. Specifically, significant differences were observed in the composition of the intestinal microbiota between fish displaying mild symptoms and those exhibiting severe phenotypic manifestations (α diversity: p < 0.01; β diversity: p = 0.001). Fecal microbiota transplantation (FMT) experiments demonstrated that fish with mild symptoms conferred enhanced resistance to A. hydrophila when their intestinal contents were transplanted into other individuals (p = 0.006). Further microbial analysis identified Cetobacterium (p = 0.013), Paraclostridium (p < 0.01), and Pseudomonas (p < 0.01) as key differential taxa. A simplified microbial community comprising these three strains was subsequently constructed. Feeding experiments confirmed that administration of this community significantly improved host resistance to A. hydrophila (p < 0.05) by activating intestinal immune responses and reinforcing the gut barrier. Overall, our findings underscore the potential of the microbial community as a novel strategy for disease prevention and control in aquaculture, providing a theoretical foundation for the development of microbiome-based therapies in fish health management.},
}

@article {pmid41279359,
year = {2025},
author = {Chi, X and Wang, CH and Parisotto, YF and Nyberg, WA and Cabric, V and Gelineau, A and Cao, Y and Owen, DL and Ambjörnsson, J and Mathis, D and Eyquem, J and Brown, CC and Benoist, C},
title = {Decoding Peripheral Tolerance: TCR Rules for pTreg differentiation in the Gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.20.683415},
pmid = {41279359},
issn = {2692-8205},
abstract = {Peripheral differentiation of regulatory T cells (pTregs) promoted by foreign antigens encountered in barrier tissues is considered a unique contributor to immunological tolerance to obligate non-self, like food or symbiotic microbes. The relative importance of adaptive recognition via the T cell receptor (TCR) vs environmental small-molecule or neuroimmune cues, is poorly understood. We leverage CRISPR-based TCR editing to perform in primary T cells in vivo , with a large panel of TCRs, a screen to assess pTreg differentiation induced by self, microbial, or dietary antigens. All antigen classes drive pTreg differentiation, which varies with the origin of the TCR: TCRs derived from Tregs enable pTreg differentiation much more effectively than those from Tconv. TCRs recognizing self, microbial, or dietary antigens elicit distinct pTreg phenotypes, Helios[+], RORγ[+], or both. Mechanistically, these trace to different types of antigen-presenting-cell involved. That Treg-derived TCRs preferentially drive tolerogenic fate speaks to preferential drivers of tolerogenic therapy.},
}

@article {pmid41279009,
year = {2025},
author = {Morgese, EA and Ferrell, BD and Toth, SC and Polson, SW and Wommack, KE and Fuhrmann, JJ},
title = {Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.06.680108},
pmid = {41279009},
issn = {2692-8205},
abstract = {Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts' genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. elkanii strains USDA94 and USDA31, and B. diazoefficiens strain USDA110. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ∼70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens displayed podophage-like morphology, greater genetic diversity, and divided into two distinct species. Although no phages were recovered against B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware isolates showed susceptibility during the host range assay. The phage genomes demonstrated features predicting phenotypes. Terminase genes predicted headful packaging among the phages which is critical for generalized transduction. The B. elkanii phages all carried tmRNA genes capable of recruiting stalled ribosomes and both phage groups carried DNA polymerase A indicating greater control of phage genome replication. State-of-the-art structural annotation revealed a tail fiber gene within a phage genome having the highest proportion (80.77%) of unknown genes. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.},
}

@article {pmid41278752,
year = {2025},
author = {Lubin, MB and Teixeira, DH and Belin, BJ},
title = {Characterization of chemotaxis in soybean symbiont Bradyrhizobium diazoefficiens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682368},
pmid = {41278752},
issn = {2692-8205},
abstract = {UNLABELLED: Symbiotic relationships between nitrogen-fixing soil bacteria and legumes provide nearly half of all biologically fixed nitrogen on Earth, playing a crucial role in sustainable agriculture. These relationships rely on bacterial navigation of complex, dynamic soil environments to reach their plant hosts. Central to this behavior are bacterial motility and chemotaxis, the ability to sense and move toward host-derived signals in the rhizosphere. In the soybean symbiont Bradyrhizobium diazoefficiens USDA110, motility is controlled by dual flagellar systems, and this strain contains three putative but uncharacterized chemotaxis operons (che1 , che2 , and che3). Using targeted deletions of all three predicted cheA genes, we show that cheA2 is the primary driver of chemotaxis toward soybean seed exudate in soft agar assays, and that the greater contribution of cheA2 vs. cheA1 in soft agar chemotaxis is due to its genomic context. Interestingly, we also found that B. diazoefficiens mutants that are incapable of chemotaxis in semisolid media retain wild type-like swimming speeds in aqueous media. These findings provide insight into how the agricultural inoculant B. diazoefficiens coordinates its chemosensory systems to respond to its host plant.

IMPORTANCE: Chemotaxis is crucial for the establishment of beneficial plant-microbe associations, yet mechanistic studies of chemotaxis have been limited to a handful of soil bacterial models, namely Azospirillum brasilense , Sinorhizobium meliloti , and Rhizobium leguminosarum . These three models represent only a fraction of the diversity found among plant- beneficial bacteria and agricultural inoculants. The soybean symbiont Bradyrhizobium diazoefficiens USDA110 is a commonly used soybean inoculant with exceptional nitrogen fixation efficiency, but the genetic control of chemotaxis in B. diazoefficiens has not been examined. Establishing B. diazoefficiens as a model of chemotaxis provides an opportunity to understand how multiple chemotaxis systems coordinate root colonization in this major agricultural symbiont and can enable comparative analyses of plant-microbe recognition strategies across agricultural bacteria.},
}

@article {pmid41278148,
year = {2025},
author = {Dely, A and Racicot, R and Samples, R and Giddings, LA},
title = {Draft genome sequence and metabolomics data for Streptomyces sp. ADLamb9 isolated from the rhizosphere of Lavandula dentata.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112199},
pmid = {41278148},
issn = {2352-3409},
abstract = {Iron-chelating molecules or siderophores play pivotal roles in soil ecosystems, particularly in facilitating plant iron uptake as well as the phytoremediation of metal-polluted environments. Lavandula dentata, commonly referred to as French Lavender, is a valuable species for siderophore production due to its ability to thrive in iron-deficient Mediterranean soils by forming symbiotic relationships with siderophore-producing rhizosphere microbes. Here, we used a Chrome Azurol S (CAS) overlay assay to isolate a yellow-pigmented L. dentata rhizosphere siderophore-producing bacterium. This isolate also demonstrated antibacterial and antifungal activities against Bacillus subtilis and Aspergillus flavus, respectively. Genomic sequencing revealed that the isolate was Streptomyces sp. ADLamb9 with a genome size of 8.2 Mb and 71.77% GC content. antiSMASH analysis of the Streptomyces sp. ADLamb9 genome identified four putative siderophore biosynthetic gene clusters as well as the catecholate siderophore mirubactin. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) masses consistent with desferrioxamine B (561.3604 m/z), IC202C (517.3342 m/z), mirubactin (605.2207 m/z), as well as previously unreported desferrioxamine A1C. Notably, the presence of the rare earth element cerium differentially affected the accumulation of catecholate and hydroxamate siderophores, highlighting our incomplete understanding of the complex regulation and relationship between siderophore biosynthesis genes. These datasets, deposited at NCBI under the BioProject accession number PRJNA1224804, contribute to the broader scientific understanding of metabolite diversity and genomic features of Streptomyces sp. ADLamb9, providing insight into its use in bioremediation, especially in the presence of rare earth elements.},
}

@article {pmid41277186,
year = {2025},
author = {Sinha, A and Kumar, S},
title = {Symbiotic Relationships Between Arbuscular Mycorrhizal Fungi and Essential Oil-Producing Herbs: A Review of Recent Advances.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70127},
doi = {10.1002/jobm.70127},
pmid = {41277186},
issn = {1521-4028},
support = {//The authors received no specific funding for this work./ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) significantly impact on the growth, nutritional intake, and secondary metabolite synthesis of essential oil-producing plants by forming crucial symbiotic relationships with their roots. Recent research findings that demonstrate the diverse functions of AMF in improving the amount and chemical makeup of essential oils are compiled in this article. In sustainable agriculture, particularly in organic farming systems that utilize minimal synthetic inputs, AMF and medicinal herbs have demonstrated a positive relationship. AMF also supports ecological stability by promoting biodiversity and enhancing soil structure. The molecular and pharmacological mechanisms underlying these plant-fungal interactions are still not fully known, however. This study highlights the need for further research into the mechanisms of action of AMF, the development of effective inoculation methods, and the evaluation of novel herb-fungus combinations. It also reveals present research gaps. These revelations will open the door to more environmentally friendly farming methods and the efficient use of AMF in the manufacture of essential oils. AMF and medicinal plants have a promising interaction in sustainable agriculture, especially in organic farming systems that employ fewer synthetic inputs. Additionally, AMF improves soil structure and encourages biodiversity, both of which support ecological stability.},
}

@article {pmid41276973,
year = {2025},
author = {Luo, X and Yang, X and He, L and Wang, K and Gao, Y and Zhang, J and Yang, L and Li, Z and Zhao, X and Zhao, R and Zhao, S},
title = {Interaction Mechanisms between 6:2 Fluorotelomer Sulfonic Acid (6:2 FTSA) and Soil-Soybean System: Insight from Biodegradation, Phytotoxicity, and Microbial Shifts.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11903},
pmid = {41276973},
issn = {1520-5118},
abstract = {As an important perfluorooctanesulfonate (PFOS) substitute, 6:2 fluorotelomer sulfonic acid (6:2 FTSA) has been widely detected in soil. However, the interaction mechanisms between 6:2 FTSA and the soil-plant system are still unknown. Here, we explored the biodegradation, phytotoxicity, and microbial impact of 6:2 FTSA in a soil-soybean system. The biodegradation of 6:2 FTSA in plants was mediated by both enzymes and coexisting microorganisms. 6:2 FTSA (2.97 nmol/g) inhibited soybean growth and caused oxidative damage, while soybeans enhanced their stress tolerance and metabolism of 6:2 FTSA by modulating genes involved in fatty acid metabolism, hormone signaling, oxidative stress, xenobiotic detoxification, and transmembrane transport. 6:2 FTSA affected rhizospheric and root endophytic microbial communities, with symbiotic fungi being more sensitive to 6:2 FTSA stress than bacteria. Five 6:2 FTSA-degrading rhizospheric and endophytic bacterial strains belonging to genera Acinetobacter, Rhodococcus, and Klebsiella were isolated and identified, with the rhizosphere bacteria exhibiting more effective degradation. Our findings reveal the ecological risks and detoxification mechanisms of emerging PFOS alternatives in soil-crop systems.},
}

@article {pmid41276563,
year = {2025},
author = {Thériault, V and De la Rosa, CMA and Miard, S and Taubert, S and Picard, F},
title = {Impact of bacterial inactivation methods on Caenorhabditis elegans feeding and healthspan.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-27444-5},
pmid = {41276563},
issn = {2045-2322},
support = {RGPIN-2024-06781//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Accurate bacterial inactivation methods are essential for nutritional and microbiota studies in Caenorhabditis elegans, to determine whether the observed effects arise from nutrients provided by ingested bacteria or from active symbiotic interactions. However, some inactivation methods alter bacterial palatability, complicating conclusions about their direct impact. We aimed to identify an effective method for inactivating the bacterial strain Escherichia coli OP50, the standard food source for most C. elegans experiments, that preserves normal behavior and physiology in C. elegans. We compared heat inactivation (65 °C for 35 min) with 0.5% paraformaldehyde (PFA) inactivation. Worms fed PFA-inactivated bacteria showed no food aversion, and maintained wild-type pharyngeal pumping levels, fertility rates, and lipid accumulation, closely resembling the behavior and physiology of worms fed alive E. coli OP50. In contrast, heat‑inactivated bacteria elicited strong food avoidance, reduced pumping activity, activation of the mitochondrial unfolded protein response (UPR[mt]), decreased lipid stores and fertility, and increased survival relative to the other groups. These findings demonstrate that 0.5% PFA inactivation more accurately preserves C. elegans physiological and behavioral traits than heat inactivation, making it a more suitable method for microbiota and nutritional studies.},
}

@article {pmid41276306,
year = {2025},
author = {Tian, L and Gupta, A and Li, W and Wang, G and Jiang, D and Yan, Y and Jia, Z and Tran, LP and Tian, C},
title = {Utilization of arbuscular mycorrhizal fungi symbiosis-related genes from host plants in biotechnology for sustainable agriculture.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/07388551.2025.2581883},
pmid = {41276306},
issn = {1549-7801},
abstract = {In recent years, interest in the role of nutrient cycling in sustainable agriculture has significantly increased. The potential of arbuscular mycorrhizal (AM) fungi (AMFs) in nutrient cycling and plant growth improvement has long been recognized. However, there have been only a few studies on the identification and exploration of AM symbiosis-related plant genes for sustainable agriculture. We have developed a new constructive model for using host plant-derived AM symbiosis-related genes to improve breeding and AMF utilization for sustainable agriculture, particularly in the context of climate change. This model include: 1) the discovery of AM symbiosis-related genes in crop wild-relatives for molecular breeding and 2) the screening and propagation of AMFs that can help improve water-use efficiency and nutrient-use efficiency by crops, thereby reducing chemical fertilizer use in agricultural production. The first approach uniquely facilitates the identification of host plant-derived AM symbiosis-related genes, such as CHITIN ELICITOR RECEPTOR KINASE 1 (OsCERK1) from Dongxiang (DY) wild rice (Oryza rufipogon) (OsCERK1DY), MILDEW RESISTANCE LOCUS 1 (MLO1) from wild barley (Hordeum spontaneum), and WRKY60 from wild soybean (Glycine soja), for breeding purposes. The second one involves identifying soil-borne AMF species, such as Rhizophagus intraradices and Glomus mosseae for practical applications in the field. This suggestive model presents an emerging biotechnological potential for engineering climate-resilient crops.},
}

@article {pmid41275102,
year = {2025},
author = {Bruzzese, DJ and Gstöttenmayer, F and Weiss, BL and Khalil, H and Mach, RL and Abd-Alla, AMM and Aksoy, S},
title = {Comparative genomics and transcriptomics of the Spiroplasma glossinidia strain sGff reveal insights into host interaction and trypanosome resistance in Glossina fuscipes fuscipes.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12351-w},
pmid = {41275102},
issn = {1471-2164},
support = {R21AI163969/NH/NIH HHS/United States ; R21AI163969/NH/NIH HHS/United States ; D42017//International Atomic Energy Agency/ ; },
}

@article {pmid41274117,
year = {2025},
author = {Imai, Y and Kimura, S and Kitajima, S and Sadato, N and Chiba, R and Hibino, H and Adachi-Akahane, S},
title = {Toward the promotion of "One Health" - part I: How do humans work to live together with humans, other organisms, and xenobiotics on Earth?.},
journal = {The journal of physiological sciences : JPS},
volume = {76},
number = {1},
pages = {100050},
doi = {10.1016/j.jphyss.2025.100050},
pmid = {41274117},
issn = {1880-6562},
abstract = {Thirty years from now, society will be transformed by dramatic advances in digital transformation, life infrastructure, and personalized medicine. People will communicate seamlessly in virtual spaces, and older adults will enjoy more fulfilling lives. Nevertheless, increasingly complex lifestyles will place immense pressure on ecosystems, affecting the environment and organisms and leading to serious health challenges. To address these issues, the Japanese Association of Anatomists, the Physiological Society of Japan (PSJ), and the Japanese Pharmacological Society have launched a collaborative initiative on "One Health". This framework aims to integrate the protection of flora and fauna with the health of humans, animals, and the planet, extending even to outer space. In the symposium held at 2025 APPW congress cohosted by PSJ, experts from multiple disciplines discussed how humans can coexist with microbes, xenobiotics, humans, and robots on Earth, fostering a sustainable and resilient future. This article summarizes this One Health symposium.},
}

@article {pmid41273130,
year = {2025},
author = {Zhang, XY and Li, DG},
title = {Immunoglobulin G and Aging: Biological Functions and Its Crosstalk with the Gut Microbiota.},
journal = {Rejuvenation research},
volume = {},
number = {},
pages = {},
doi = {10.1177/15491684251396176},
pmid = {41273130},
issn = {1557-8577},
abstract = {Aging is characterized by a progressive decline in physiological integrity, often accompanied by chronic inflammation and immune dysregulation. Immunoglobulin G (IgG), a key effector of humoral immunity, undergoes substantial structural and functional remodeling with age, particularly through changes in its glycosylation profile. These modifications shift IgG toward a proinflammatory state, linking it to inflammaging and multiple age-related diseases. This review synthesizes recent advances in understanding how IgG contributes to immune aging, with a specific focus on its glycosylation-dependent functions, tissue accumulation, and bidirectional crosstalk with the gut microbiota. We also highlight the potential of IgG as a biomarker and therapeutic target in aging-related interventions. We discuss the dual functional architecture of IgG and how age-related glycan shifts-namely, increased agalactosylation, afucosylation, and bisecting N-acetylglucosamine (GlcNAc)-enhance binding to activating Fcγ receptors, amplifying proinflammatory signaling. Experimental studies demonstrate that IgG accumulation in adipose tissue contributes to metabolic dysfunction via Neonatal Fc Receptor (FcRn)-dependent pathways. Additionally, sex hormones modulate IgG glycosylation patterns, partially explaining sex-specific differences in immune aging. The concept of "glycan clocks" has emerged as a tool to assess biological age and intervention responsiveness. Moreover, the gut microbiota plays a critical role in shaping the IgG repertoire, and aging disrupts this IgG-microbiota axis, resulting in altered mucosal immunity and systemic inflammation. Interventions targeting this axis-including microbiota modulation and glycoengineering-offer promising translational avenues for immune rejuvenation. Finally, we review emerging therapeutic strategies that leverage the gut-immune interface to mitigate aging-associated cardiovascular and metabolic diseases. IgG is not merely a biomarker but an active participant in the aging process, functioning at the intersection of immune regulation, microbial symbiosis, and systemic inflammation. Its age-associated transformation reflects broader changes in host immunity and highlights new opportunities for precision interventions in immunosenescence.},
}

@article {pmid41272488,
year = {2025},
author = {Wang, R and Pan, H},
title = {Identification and functional evaluation of cyclin-dependent kinase genes reveals that CDKB1;1 and CDKB2;2 contribute to the balance of mitosis and endoreduplication in Medicago truncatula nodule.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1617},
pmid = {41272488},
issn = {1471-2229},
mesh = {*Medicago truncatula/genetics/enzymology/microbiology ; *Mitosis/genetics ; *Root Nodules, Plant/genetics ; *Cyclin-Dependent Kinases/genetics/metabolism ; *Endoreduplication/genetics ; *Plant Proteins/genetics/metabolism ; Nitrogen Fixation/genetics ; Gene Expression Regulation, Plant ; Symbiosis ; Protein Interaction Maps ; },
abstract = {BACKGROUND: Cyclin-dependent kinases (CDKs) critically regulate plant cell cycle transitions, including mitosis-to-endoreduplication switches essential for growth and adaptation. In Medicago truncatula, nodules form through symbiotic nitrogen fixation with rhizobia. The terminal differentiation of bacteroids within nodule cells is critical for efficient nitrogen fixation. To maintain and optimize the functionality of these differentiated symbiosomes, host nodule cells undergo repeated rounds of endoreduplication. However, which CDKs are involved in regulating endoreduplication in nodule cells to support effective symbiotic nitrogen fixation remains largely unknown.

RESULTS: We identified and characterized 29 CDK genes (15 CDKs and 14 CDKLs) classified into eight conserved subgroups. These genes displayed diverse exon/intron structures and protein motifs, with CDKA, CDKB, and CDKL subfamilies showing strong conservation with Arabidopsis thaliana. Expression analysis revealed specific downregulation of CDKB1;1, CDKB2;2, and CDKL13 in nodule infection to fixation zones. Protein-protein interaction (PPI) network and Gene ontology (GO) analyses demonstrated CDKB1;1 and CDKB2;2 involvement in cell cycle regulation. Overexpression of CDKB1;1 or CDKB2;2 disrupted endoreduplication and nitrogen fixation, with CDKB1;1 having the most pronounced effect, while CDKL13 appeared dispensable for symbiosis.

CONCLUSION: Our study presents the comprehensive genome-wide analysis of the CDK gene family in M. truncatula, demonstrating that the essential role of CDKB1;1 and CDKB2;2 downregulation in symbiotic nitrogen fixation and endoreduplication offers new insights into cell cycle regulation in nodules. It also identifies potential targets for improving nitrogen fixation efficiency in legumes.},
}

*Medicago truncatula/genetics/enzymology/microbiology
*Mitosis/genetics
*Root Nodules, Plant/genetics
*Cyclin-Dependent Kinases/genetics/metabolism
*Endoreduplication/genetics
*Plant Proteins/genetics/metabolism
Nitrogen Fixation/genetics
Gene Expression Regulation, Plant
Symbiosis
Protein Interaction Maps

@article {pmid41271942,
year = {2025},
author = {Dmitrieva, M and Shelkovnikova, V and Morgunova, M and Malygina, E and Imidoeva, N and Belyshenko, A and Telnova, T and Vavilina, T and Konovalov, A and Batalova, A and Lipatova, O and Listopad, A and Axenov-Gribanov, D},
title = {Genetic and biotechnological potential of thermophilic Streptomyces sp. isolated from Baikal freshwater psychrophilic sponge.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41403},
pmid = {41271942},
issn = {2045-2322},
support = {FZZE-2024-0003//Ministry of Science and Higher Education of the Russian Federation/ ; FZZE-2024-0013//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Streptomyces/genetics/isolation & purification/metabolism ; *Porifera/microbiology ; Animals ; Fresh Water/microbiology ; Biotechnology/methods ; Biological Products/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Temperature ; Phylogeny ; },
abstract = {Microorganisms inhabiting extreme environmental conditions receive special attention because they possess different adaptations to adverse conditions. Currently, their biotechnological potential and ability to isolate biologically active metabolites have increased. The increasing mortality due to different diseases has become particularly important as one of the notable challenges in modern healthcare. This highlights the necessity of discovering new producers of natural products (NPs). The aim of this study was to evaluate the genetic and biotechnological potential through the assessment of NP synthesis and genome annotation of the thermophilic strain Streptomyces sp. LPB2020-019-1HS. The thermophilic strain was isolated from the Baikal endemic cold water sponge Lubomirskia baikalensis. Subsequently, Streptomyces sp. LPB2020-019-1HS was cultivated at six temperatures ([Formula: see text]C, [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C) in twelve nutrient media with different compositions (nutrient rich and nutrient poor). Using high-performance liquid chromatography and mass spectrometry approaches, the synthesis of compounds by the strain was assessed at [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C. Antimicrobial activity was evaluated at all temperatures (from [Formula: see text] to [Formula: see text]C). We demonstrated the presence of antibiotic activity against Bacillus subtilis for strains cultivated at 28 °C, [Formula: see text]C, and [Formula: see text]C. Additionally, we observed activity against Mycobacterium smegmatis when the strain was cultivated at [Formula: see text]C, [Formula: see text]C, [Formula: see text]C, and [Formula: see text]C. Furthermore, the strain exhibited activity against Escherichia coli, Pseudomonas putida, and Candida glabrata when cultured at [Formula: see text]C. Overall, we found that Streptomyces sp. LPB2020-019-1HS produces a family of NPs related to Nocardamine and hypothesized that freshwater Actinobacteria have mechanisms for chelating iron ions, making them available for plants/sponges or other symbiotic organisms. Therefore, our research findings underscore the importance of studying extremophilic microorganisms from Lake Baikal in the context of developing new pharmaceuticals and biotechnological solutions for contemporary healthcare challenges.},
}

*Streptomyces/genetics/isolation & purification/metabolism
*Porifera/microbiology
Animals
Fresh Water/microbiology
Biotechnology/methods
Biological Products/metabolism/pharmacology
Anti-Bacterial Agents/pharmacology
Temperature
Phylogeny

@article {pmid41271671,
year = {2025},
author = {Shahul Hameed, UF and Balakrishna, A and Wang, JY and Alvarez, D and Momin, AA and Schwarzenberg, A and Al-Babili, S and Arold, ST},
title = {Molecular Basis for Catalysis and Regulation of the Strigolactone Catabolic Enzyme CXE15.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10290},
pmid = {41271671},
issn = {2041-1723},
support = {BAS/1/1056-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Lactones/metabolism ; *Arabidopsis/enzymology/genetics/metabolism ; *Arabidopsis Proteins/metabolism/chemistry/genetics ; Reactive Oxygen Species/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Gene Expression Regulation, Plant ; Catalysis ; *Plant Growth Regulators/metabolism ; Oxidation-Reduction ; Protein Multimerization ; },
abstract = {Strigolactones (SLs) are pivotal plant hormones involved in developmental, physiological, and adaptive processes. SLs also facilitate symbiosis with arbuscular mycorrhizal fungi and trigger germination of root parasitic Striga plants. The carboxylesterase CXE15, recently identified as the SL catabolic enzyme in Arabidopsis thaliana, plays a crucial role in regulating SL levels. Our study elucidates the structural and regulatory mechanisms of CXE15. We present four crystal structures capturing the conformational dynamics of CXE15, revealing a unique N-terminal extension (Nt) that transitions from a β-sheet in monomers to an intertwined helical structure in dimers. Only the dimeric form is catalytically active, as it forms a hydrophobic cavity for SLs between its two active sites. The moderate dimerisation affinity allows for genetic regulation through protein expression levels. Additionally, we identify an environment-controlled regulation mechanism. Under oxidising conditions, a disulphide bond forms between Cys14 of the two monomers, blocking the active site and inhibiting SL cleavage. This redox-sensitive inhibition of SL catabolism, triggered by reactive oxygen species (ROS) in response to abiotic stress, suggests a mechanism for maintaining high SL levels under beneficial conditions. Our findings provide molecular insights into the regulation of SL homeostasis and catabolism under stress conditions.},
}

*Lactones/metabolism
*Arabidopsis/enzymology/genetics/metabolism
*Arabidopsis Proteins/metabolism/chemistry/genetics
Reactive Oxygen Species/metabolism
Catalytic Domain
Crystallography, X-Ray
Gene Expression Regulation, Plant
Catalysis
*Plant Growth Regulators/metabolism
Oxidation-Reduction
Protein Multimerization

@article {pmid41270733,
year = {2025},
author = {Wei, Z and Lan, Y and Meng, L and Wang, H and Li, L and Li, Y and Zhang, N and Lu, R and Cui, Z and Song, Y and Wang, Y and Li, Y and Yue, Z and Fan, G and Li, Q and Gu, Y and Liu, S and Qian, PY and Meng, L and Shao, C},
title = {Hologenomic insights into the molecular adaptation of deep-sea coral Bathypathes pseudoalternata.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.020},
pmid = {41270733},
issn = {1934-6069},
abstract = {Deep-sea coral ecosystems support biodiversity and nutrient cycling through interactions with symbionts. However, their molecular mechanisms remain unexplored. Here, hologenomic analyses of Bathypathes pseudoalternata are applied to uncover molecular adaptations underpinning host-symbiont interactions. Genomic evidence reveals that B. pseudoalternata exhibits adaptations in nutrient transport, immune response, and lysosomal digestion, reflecting its genomic adjustments for a stable symbiosis. Candidatus Nitrosopumilus bathypathes (78.43% ± 3.65%) is inferred to oxidize host-derived ammonia to synthesize amino acids and vitamins to provision the host. The presence of CRISPR-Cas and restriction-modification (R-M) systems suggests that Ca. Bathyplasma bathypathes and Ca. Thalassoplasma bathypathes (10.68% ± 2.99%) may protect the host from viral infections. Ca. Bathybacter bathypathes (8.39% ± 1.53%) is hypothesized to synthesize heme, lipoic acid, and glutathione, which serve dual functions as antioxidants and nutrients. These findings collectively provide insights into how the hologenome contributes to the survival of B. pseudoalternata in the extreme environment.},
}

@article {pmid41267536,
year = {2025},
author = {Zhou, J and Zhang, W and Guo, Q and Liu, X and Wei, C},
title = {Initially Coexisting Endosymbionts Migrate Into Different Tissues During Ontogeny of Host Cicadas.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70185},
doi = {10.1111/1462-2920.70185},
pmid = {41267536},
issn = {1462-2920},
support = {32270496//National Natural Science Foundation of China/ ; 2025KYCXZ05//Northwest A&F University Doctoral Candidates' Independent Innovation Research Project Funding/ ; },
mesh = {*Symbiosis ; *Hemiptera/microbiology/growth & development ; Animals ; *Fungi/physiology ; },
abstract = {Endosymbionts play pivotal roles in driving ecological and evolutionary diversification of many insects, yet the morphogenesis and evolutionary origin of their specialised symbiotic organs (e.g., bacteriomes) remain poorly understood. Here we investigated the bacteriome morphogenesis in Cicadidae using microscopy-based methods. We revealed that bacteriomes originate either from both the original bacteriocytes that emerged after anatrepsis and the novel bacteriocytes that appeared during katatrepsis, or solely from the latter. Bacteriomes expand via "budding" proliferation to increase the bacteriome unit number, and bacteriome developmental patterns closely correlate with the presence/absence of the yeast-like fungal symbionts (YLS) and their colonisation dynamics. The obligate endosymbiont Karelsulcia and YLS, coexisting in bacteriomes during early stages of host ontogeny, may compete for ecological niches, potentially resulting in translocation of YLS into fat bodies. This indicates that bacteriomes may have initially functioned as immune organs like fat bodies, but evolved specifically for accommodating bacterial endosymbionts. The translocation of YLS from bacteriomes to fat bodies during the later development of host cicadas indicates that immune-mediated regulation occurs in such symbiotic organs as host insects mature. This study sheds light on how symbiont-host interactions shape the symbiotic organogenesis, which provides insights into adaptive evolution of specialised symbiotic organs in plant sap-feeding insects.},
}

*Symbiosis
*Hemiptera/microbiology/growth & development
Animals
*Fungi/physiology

@article {pmid41266970,
year = {2025},
author = {Jin, L and Xu, Q and Miao, C and Zhan, J and Zhang, Y and Li, M and Cheng, J and Liu, P and Yang, Y and Zhou, H and Hu, Z and Li, F and Wu, C},
title = {Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07765-3},
pmid = {41266970},
issn = {1471-2229},
support = {110202102033//the Key Grant of China National Tobacco Corporation, China/ ; },
}

@article {pmid41266614,
year = {2025},
author = {Wiles, EL and Kakumanu, ML and Schal, C},
title = {Wolbachia-supplemented B-vitamins are critical for blood digestion in the bed bug Cimex lectularius.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40962},
pmid = {41266614},
issn = {2045-2322},
support = {2023348287//National Science Foundation Graduate Research Fellowship Program/ ; NC02639//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Bedbugs/microbiology/physiology/metabolism ; *Wolbachia/physiology ; *Riboflavin/pharmacology/metabolism ; *Digestion ; Symbiosis ; *Vitamin B Complex/pharmacology ; Biotin/pharmacology ; Female ; },
abstract = {Wolbachia, a bacterial endosymbiont, acts as an obligate nutritional mutualist in the bed bug, Cimex lectularius. Wolbachia in C. lectularius (wCle) supplements B-vitamins, namely riboflavin (B2) and biotin (B7), which are deficient in the bed bug's diet of vertebrate blood. Experimental elimination of wCle significantly impairs fitness in bed bugs, resulting in slow development, low egg production and egg hatch rate, and smaller adult body size. Although this obligatory symbiosis has been well-documented, the specific physiological mechanisms by which wCle-supplemented B-vitamins promote bed bug fitness remain unclear. We hypothesized that B-vitamin deficiency impairs digestion in aposymbiotic bed bugs, and in this study we investigated the effects of wCle elimination on three digestive processes in the bed bug - diuresis, erythrocyte (red blood cell) lysis, and protein catabolism. Our results show that wCle elimination significantly slows both diuresis and protein catabolism. We also demonstrate that riboflavin is critical for the breakdown of hemoglobin, the main protein component of red blood cells, but not albumin, the main protein component of plasma. We propose that the lack of wCle-supplemented riboflavin results in systemic protein deficiency, driving various fitness-related deficits in aposymbiotic bed bugs. These findings enhance our understanding of bed bug digestive physiology and the wCle-bed bug nutritional mutualism, with broader implications for other blood-feeding arthropods.},
}

Animals
*Bedbugs/microbiology/physiology/metabolism
*Wolbachia/physiology
*Riboflavin/pharmacology/metabolism
*Digestion
Symbiosis
*Vitamin B Complex/pharmacology
Biotin/pharmacology
Female

@article {pmid41266521,
year = {2025},
author = {Zhou, Y and Zhu, P and Xia, Y and Hassan, Z},
title = {The mutualistic symbiosis of public and scientific attention in science communication.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41151},
pmid = {41266521},
issn = {2045-2322},
support = {22YB013//Jiangxi Provincial Education Science '14th Five-Year Plan' 2022 General Topic: Research on Red Gene Inheritance of Contemporary College Students Based on Heart Stream Experience/ ; 2023JSYJC20//Public Security Ministry Technical Research Program/ ; G2024507002//Hebei Natural Science Foundation: Research on Modeling of Public Opinion Risks in Online Communities and Intelligent Governance Algorithms/ ; },
mesh = {Humans ; *Symbiosis ; *COVID-19/epidemiology ; Models, Theoretical ; *Communication ; *Information Dissemination/methods ; *Science ; *Scholarly Communication ; },
abstract = {This study examines the bidirectional tension between public and scientific attention amid informatization, analyzing their mutualistic symbiosis to address science communication challenges. We constructed a mathematical model of mutualistic symbiosis in their relationship was developed based on the Logistic Model. Subsequently, numerical simulations were employed to investigate the evolutionary trends and patterns of scientific attention, public attention, and the effectiveness of science communication under varying modes of public attention and initial values of scientific attention. Furthermore, using "COVID-19" as a case study, an empirical analysis was conducted on to assess the correlation between public attention and scientific attention and evaluate the constructed mathematical Model, verifying its scientific validity and effectiveness. This study underscores the critical role of science communication in fostering advantageous interactions between scientific and public attention. Nonetheless, it is imperative to adopt tailored science communication strategies that accommodate diverse public attention modes and initial levels of scientific attention while selecting appropriate symbiotic models for specific contexts. This proposed approach ensures the effective dissemination of scientific information and fosters a robust science communication ecosystem.},
}

Humans
*Symbiosis
*COVID-19/epidemiology
Models, Theoretical
*Communication
*Information Dissemination/methods
*Science
*Scholarly Communication

@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}

Animals
*Enterococcus faecalis/physiology/genetics
Bees/virology/microbiology
*Symbiosis
Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Larva/virology/microbiology
Apoptosis

@article {pmid41265612,
year = {2025},
author = {Ranjbar, M and Ahmadpour, M and Kiani, M and Govahi, M},
title = {Myco-macromolecular symbiosis: Chitosan-folate ZnO nanoplatforms from Trametes versicolor for dual-functional oncological and antibacterial therapy.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149140},
doi = {10.1016/j.ijbiomac.2025.149140},
pmid = {41265612},
issn = {1879-0003},
abstract = {The increasing prevalence of antibiotic-resistant bacteria and cancer necessitates the development of novel, targeted therapeutic strategies. This study aimed to develop a multifunctional nanoplatform combining antibacterial and anticancer properties through green synthesis and strategic surface functionalization. Zinc oxide nanoparticles (ZnO NPs) were biosynthesized using Trametes versicolor extract as a reducing and capping agent, then surface-functionalized with chitosan (Cs) for enhanced biocompatibility and conjugated with folic acid (FA) for targeted delivery. The NPs were characterized using multiple analytical techniques and evaluated for antibacterial activity against Gram-positive (Bacillus subtilis, Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. Cytotoxicity was assessed in cancer cells (MDA-MB-231) and normal cells (MCF-10 A), followed by gene expression analysis of key oncogenic and apoptotic markers. Characterization confirmed the formation of crystalline, core-shell structures with successful ligand attachment. Cs-ZnO NPs demonstrated significantly enhanced antibacterial activity against all tested bacterial strains compared to bare ZnO NPs. FA-Cs-ZnO NPs exhibited selective cytotoxicity toward cancer cells while maintaining biocompatibility with normal cells. Gene expression analysis revealed down-regulation of cancer stemness genes (CD44, SOX2) and proliferation markers (mTOR, β-catenin), coupled with up-regulation of the apoptotic marker Caspase 3. This green-synthesized, dual-functional nanoplatform demonstrates promising potential for combined antibacterial and targeted anticancer therapy, warranting further in vivo evaluation for clinical translation.},
}

@article {pmid41265272,
year = {2025},
author = {Jia, J and Xue, X and Wang, Z and Xiong, X and Hu, H and Wu, C},
title = {Phycosphere as a hotspot of antibiotic resistomes in aquatic environments.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140513},
doi = {10.1016/j.jhazmat.2025.140513},
pmid = {41265272},
issn = {1873-3336},
abstract = {Algal-bacterial interactions represent fundamental ecological processes in aquatic environments, crucially governing nutrient cycling and energy flow within food webs. Beyond their ecological roles, the algal phycosphere has recently been identified as a critical hotspot for the proliferation and enrichment of antibiotic resistance genes (ARGs). It's reported that the total abundance of ARGs in the phycosphere of microalgae is up to 47-fold higher than in the surrounding water. However, a systematic understanding of how the phycosphere drives ARG dynamics in aquatic ecosystems remains limited. This review synthesizes current evidence to evaluate the mechanisms by which algae influence ARG proliferation within aquatic ecosystems. Findings indicate that in the phycosphere, algal-bacterial interactions shape ARG fate by modulating bacterial community composition. The symbiotic bacteria are specifically enriched in the phycosphere and play important roles in the proliferation of ARGs. Furthermore, exogenous factors (e.g., nutrients, antibiotics, microplastics, and warming) alter these interactions, thereby changing the phycospheric bacterial community and further affecting ARG evolution. Algal blooms typically enhance the dominance of key ARG hosts, promoting aquatic ARG proliferation. The review concludes by outlining research priorities essential for advancing mechanistic insights into algal-associated ARG dynamics.},
}

@article {pmid41265199,
year = {2025},
author = {Li, X and Shi, F and Zhou, M and Su, H and Liu, X and Wei, Y and Wang, F},
title = {Arbuscular mycorrhizal fungi change toxic effects of different types of microplastics on Lactuca sativa L. by influencing plant metabolic processes.},
journal = {Ecotoxicology and environmental safety},
volume = {307},
number = {},
pages = {119443},
doi = {10.1016/j.ecoenv.2025.119443},
pmid = {41265199},
issn = {1090-2414},
abstract = {Soil microplastics (MPs) pollution is becoming more serious, and symbiotic microorganisms in soil-plant systems may influence the environmental behavior and related plant responses to MPs stress. In this study, common primary plastic products were broken down into MPs to investigate the toxic effects and migration behavior of MPs on lettuce (Lactuca sativa L.) in the presence of arbuscular mycorrhizal fungi (AMF). Our findings show that symbiotic AMF reduce the uptake and toxic effects of polyethylene terephthalate (PET) by increasing nucleotide metabolism and zeatin biosynthesis, resulting in a 20.64 % drop in PET uptake and an 11.43 % increase in lettuce biomass. In contrast, AMF promoted the absorption of polypropylene (PP) and polystyrene (PS) by lettuce, inhibiting ascorbate metabolism and lysine biosynthesis, and causing poorer lettuce growth. The positive regulatory effect of AMF on the nutritional quality and health status of plants under PET stress shows that AMF have the potential to alleviate the toxicity of MPs to lettuce in farmland and to remediate the MPs-related pollution in agricultural areas.},
}

@article {pmid41262929,
year = {2025},
author = {Asatulloev, T and Yusupov, Z and Cai, L and Chen, Q and Gurung, B and Tojibaev, KS and Sun, W},
title = {Comparative root associated microbial community analysis of Oreocharis mileensis, a resurrection plant species with extremely small populations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692695},
pmid = {41262929},
issn = {1664-302X},
abstract = {Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting and drought associated microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five populations of Oreocharis mileensis, a resurrection plant, during hydrated and dehydrated states to examine population-level microbiome differences or affinity, identify microorganisms that may assist during plant desiccation, and assess their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, and endosphere) but exhibited only moderate drought-induced changes, suggesting that O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa varied relatively between populations, reflecting niche specialization and host genotype. Drought increased bacterial alpha diversity while reducing beta diversity, indicating homogenization driven by stress-tolerant taxa such as Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (e.g., Microlunatus, Rubrobacter) and other drought-resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought conditions. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. Overall, this study expands our understanding of microbiome assembly in resurrection plants and highlights candidate microbes for microbiome engineering to enhance crop stress tolerance.},
}

@article {pmid41262890,
year = {2025},
author = {Chuang, PS and Hsu, TC and Lu, CY and Yu, SP and Liu, PY and Lim, SL and Chen, YH and Chiou, YJ and Yang, SH and Wang, PL and Tang, SL},
title = {Metabolic interactions between coral animal and endolithic bacterial communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf193},
pmid = {41262890},
issn = {2730-6151},
abstract = {Coral skeletons constitute sources of nutrients and energy for holobiont. Although bacteria predominate in endolithic microbiomes of corals, their ecological functions have long been masked by those of symbiotic microalgae. In the skeleton of Isopora palifera, previous studies showed the absence of microalgae and a green layer dominated by green sulfur bacteria. This system, which excludes a contribution from microalgae, provides a perfect model for studying the role of endolithic bacteria in corals. Using this model, we examined the metabolite profile and translocation of organic matter between coral tissue and skeleton. Chromatography-time-of-flight-mass spectrometry and ultra-high-performance liquid chromatography tandem mass spectrometry revealed distinct metabolic profiles in tissue and different skeletal layers. A stable isotope incubation experiment further demonstrated [13]C translocation between tissue and the green layer, but no translocation of [15]N. These findings suggest communication between the two compartments that is generally carbon-based, possibly in the form of carbohydrates and bioactive compounds, such as corticosterone and domoic acid. Nevertheless, some nitrogenous compounds appear to have an endolithic source, indicating a possible contribution of the skeleton to coral animal. Notably, antibiotic treatment greatly increased [15]N translocation in the tissue but not in the green layer. This highlights an important role of bacteria in nitrogen cycling in the holobiont and in establishing the nitrogen-limiting green layer. Altogether, this study provides the first data about coral skeletal metabolomes. Based on these findings, we propose a model of interactions between coral animal and skeletal bacterial communities, offering a new perspective on the ecological role of endolithic bacteria in corals.},
}

@article {pmid41261892,
year = {2025},
author = {Ma, M and Michalik, A and Deng, J and Hu, Y and Łukasik, P},
title = {Contrasting genomic trajectories of Bartonellaceae symbionts of planthoppers.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf216},
pmid = {41261892},
issn = {1759-6653},
abstract = {Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in the family Bartonellaceae (Hyphomicrobiales), notorious for also including virulent vertebrate pathogens. Here we show that Bartonellaceae phylogenetically placed within the clade that has only encompassed ant symbionts to date - Candidatus genus Tokpelaia - have established as symbionts in four different clades of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Genome size and contents indicate different levels of integration of these strains into the planthopper biology and their diverse roles. Symbionts infecting one of the clades have some of the largest genomes among Bartonellaceae, at ca. 2 Mb, two others are under 700 kb, and the fourth is reduced to barely 158 kb. The planthopper-associated Tokpelaia strains with larger genomes, similarly to ant symbionts, encode multiple amino acid and vitamin biosynthesis genes, complementing the degraded nutritional capabilities of their hosts' ancient heritable endosymbionts. Strikingly, the smallest Tokpelaia genome lacks any genes linked to essential amino acid biosynthesis, in contrast to all other known insect-associated bacteria with genomes of comparable size. We identified a single vitamin biosynthesis gene and iron-sulfur cluster assembly genes as its only putative contributions to the host biology. Our results broaden the host spectrum of non-pathogenic Bartonellaceae, indicating that they have contributed to nutrition and symbiotic consortium function in diverse diet-restricted host clades. They also highlight an unexpectedly broad range of evolutionary outcomes for this important bacterial group.},
}

@article {pmid41261810,
year = {2025},
author = {Peng, L and Yang, Y and Martin, FM and Yuan, Z},
title = {Endophytes with mycorrhizal potentials: biological and ecological implications.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70772},
pmid = {41261810},
issn = {1469-8137},
support = {2022YFD2201900//National Key Research and Development Program of China/ ; 32471839//National Natural Science Foundation of China/ ; CAFYBB2023QC001-02//Fundamental Research Funds for the Central Nonprofit Research of Chinese Academy of Forestry/ ; Z25C010004//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {Generally, the root mycobiome is dominated by endophytic and mycorrhizal fungi with mutualistic potential to enhance plant fitness. In some cases, however, the distinction between the two biotrophic guilds is challenged by the ability of several endophytic fungi to colonize roots and transfer nutrients to the plants. With more research on harnessing plant-endophyte combinations using a gnotobiotic system, more endophytes endowed with mycorrhizal-like traits have been identified. They often benefit nonmycorrhizal plants by employing a set of responses to nutrient deficiency similar to those from mycorrhizal plants, orchestrate the development of ectomycorrhizal-like structures under controlled conditions, and share genetic traits with true mycorrhizal fungi, such as a lower content of plant cell wall-degrading enzymes and gene networks reminiscent of mutualistic interactions. Based on these characteristics, we propose the term 'mycorrhizal-like endophytes' to describe these fungi, which likely represent a transitional state along the endophyte-mycorrhizal mutualistic continuum.},
}

@article {pmid41261196,
year = {2025},
author = {Yu, WQ and Qiu, H and Sun, YP and Zhao, MW and Shi, L},
title = {Microorganisms' perception, scavenging, and adaptation to reactive oxygen species signals in microbe-plant interactions.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {466},
pmid = {41261196},
issn = {1573-0972},
support = {No. CARS20//the China Agriculture Research System of the MOF and MARA/ ; (2024)171//the Project of Science and Technology Programs of Guizhou Province/ ; },
mesh = {*Reactive Oxygen Species/metabolism ; *Plants/microbiology/metabolism ; Symbiosis ; Signal Transduction ; Oxidative Stress ; Antioxidants/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; Adaptation, Physiological ; Plant Immunity ; },
abstract = {Plant-microbial interactions represent a complex biological process in which reactive oxygen species (ROS) play central roles in both plant immunity and symbiosis establishment. ROS act as defense signaling molecules to activate immune responses and as symbiotic cues to regulate microbial colonization. To cope with plant-derived ROS, microbes have evolved sophisticated sensing and scavenging mechanisms; however, a systematic understanding of these responses remains limited. Recent advances in molecular biology and genetics have revealed that microbes can directly sense ROS via transcription factors or indirectly perceive oxidative stress through bio macromolecular damage. They maintain intracellular redox homeostasis through enzymatic antioxidant systems-including catalase (CAT), superoxide dismutase (SOD), and peroxiredoxin/thioredoxin (Prx/Trx)-as well as non-enzymatic mechanisms such as melanin and extracellular polysaccharides. This review systematically summarizes microbial ROS perception and scavenging strategies, highlighting functional distinctions and evolutionary adaptations in pathogenic infection versus symbiosis. These insights provide a theoretical framework for understanding plant-microbial interactions and suggest potential ROS-related strategies for improving agricultural productivity and ecological resilience.},
}

*Reactive Oxygen Species/metabolism
*Plants/microbiology/metabolism
Symbiosis
Signal Transduction
Oxidative Stress
Antioxidants/metabolism
Oxidation-Reduction
*Bacteria/metabolism
Adaptation, Physiological
Plant Immunity

@article {pmid41257969,
year = {2025},
author = {Arenas, F and Marqués-Gálvez, JE and Guarnizo, ÁL and Andreu-Ardil, L and Morte, A and Navarro-Ródenas, A},
title = {Winter soil mycelium dynamics of Terfezia claveryi are shaped by rainfall and temperature in Mediterranean shrublands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40727},
pmid = {41257969},
issn = {2045-2322},
support = {145/MSJD/22//Ministerio de Ciencia, Innovación y Universidades/ ; 123/MTAI/22//Ministerio de Ciencia, Innovación y Universidades/ ; R.D. 103/2019//Universidad de Murcia/ ; MCIN/AEI/10.13039/50110001103//Ministerio de Ciencia e Innovación/ ; PRTR-C17.I1//Fundación Séneca/ ; },
abstract = {UNLABELLED: Shrubland ecosystems play a crucial role in Mediterranean forests, contributing to soil protection, biodiversity conservation, carbon sequestration, and ecosystem restoration. In semi-arid regions, mycorrhizal woody plants such as Helianthemum spp. form ectendomycorrhizal symbiosis with edible desert truffles, representing an emerging and sustainable crop with significant potential for rural development and economic diversification. Significant progress has been made in the breeding of Terfezia claveryi Chatin, but key aspects of its life cycle, such as the temporal and spatial behaviour of the soil mycelium, remain underexplored. This study aimed to investigate the seasonal dynamics of T. claveryi soil mycelium in plantations and wild areas of the Region of Murcia (Spain) using real-time quantitative PCR. The relationship between fungal biomass and host plant phenology and environmental parameters was also investigated. Our results showed that T. claveryi soil mycelium was higher in plantations than in wild areas, and in Xerolls than in Orthents soils. Fungal dynamics lacked seasonal or annual patterns; however winter mycelium showed a strong correlation with preceding agroclimatic variables, especially precipitation and maximum temperature. This research sheds light on the ecological processes underlying the desert truffle shrublands and offers practical implications for optimising T. claveryi cultivation strategies and promoting ecosystem restoration.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-24621-4.},
}

@article {pmid41259095,
year = {2025},
author = {Morel Revetria, MA and Sanjuan, J and Berriel, V and Velázquez, E},
title = {Bradyrhizobium monzae sp. nov. isolated from a root nodule of the introduced legume Crotalaria ochroleuca in Uruguay.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006973},
pmid = {41259095},
issn = {1466-5034},
mesh = {*Bradyrhizobium/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Root Nodules, Plant/microbiology ; *Crotalaria/microbiology ; Uruguay ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; Base Composition ; Genome, Bacterial ; Fatty Acids/chemistry ; },
abstract = {A strain, namely Oc8[T], was isolated from a root nodule of Crotalaria ochroleuca in Uruguay. This strain induced effective nodules in roots of Crotalaria ochroleuca, Crotalaria juncea, Crotalaria spectabilis and Cajanus cajan. Oc8[T] belongs to the genus Bradyrhizobium according to the results of the 16S rRNA gene sequence analysis, and it forms an independent lineage within a cluster encompassing 13 described species of this genus. From them, the type strains closest related to the strain Oc8[T] with more than 99.5% similarity in 16S rRNA gene sequence were those of Bradyrhizobium ganzhouense, Bradyrhizobium cytisi, Bradyrhizobium guangdongense and Bradyrhizobium rifense (99.71%, 99.65%, 99.60% and 99.57%, respectively). A genome-based phylogeny showed that B. ganzhouense JCM 19881[T], B. cytisi CTAW11[T] and B. rifense CTAW71[T] were the closest type strains to the strain Oc8[T]. Values lower than the species cutoff of 95% and 70% were found after average nucleotide identity and digital DNA-DNA hybridization calculation between the genome of the strain Oc8[T] and those available genomes of the closest related Bradyrhizobium species. These results, together with those of the symbiotic nodC gene analysis, support the affiliation of this strain to the symbiovar cyanophyllae of a new species of Bradyrhizobium for which the name Bradyrhizobium monzae sp. nov. is proposed. The type strain is Oc8[T] (=LMG 33261[T]=CECT 30885[T]).},
}

*Bradyrhizobium/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Phylogeny
*Root Nodules, Plant/microbiology
*Crotalaria/microbiology
Uruguay
DNA, Bacterial/genetics
Bacterial Typing Techniques
Sequence Analysis, DNA
Nucleic Acid Hybridization
Base Composition
Genome, Bacterial
Fatty Acids/chemistry

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41257557,
year = {2025},
author = {Ehsanzadeh, P and Feizabadi, S and Razmjoo, J},
title = {Enhanced grain yield of mycorrhizae-inoculated modern and ancient wheats across different salinities: the gains stem from physiological, photosynthetic, and root attributes.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1597},
pmid = {41257557},
issn = {1471-2229},
mesh = {*Triticum/microbiology/growth & development/physiology/genetics ; *Mycorrhizae/physiology ; Photosynthesis ; Salinity ; Plant Roots/microbiology/physiology/growth & development ; Edible Grain/growth & development ; Symbiosis ; *Glomeromycota/physiology ; Genotype ; },
abstract = {The current salinization of soils and water resources not only reduces crop yield, but it may also alter the known beneficial symbiotic relationships in the rhizosphere of different plant species, including different types of wheat. Shedding light on the symbiotic association of the mycorrhizae (AMF) and ancient wheats under saline conditions may pave the way for tackling salt-induced penalties of wheat grain yield and, hence, solving the current global food security concerns. A two-year field experiment and a pot experiment were carried out, where 10 and 11 wheat genotypes (including modern bread and durum and ancient spelt and emmer wheats), respectively, were exposed to 0 -120 mM NaCl salinity and either left uninoculated or inoculated with AMF (Funnelliformis mosseae). Salinity suppressed plant chlorophylls by up to 20%, carotenoids by 33%, relative water content by 16%, K and P concentrations by 17 and 35%, respectively, grain yield by 19%, total plant dry mass by 7%, root length by 37%, volume by 49%, area by 35%, and root branching by 41%, while increasing Na accumulation by 35%, and proline concentration by 72%. The negative effects of salinity tended to be milder in some of the ancient emmer and spelt wheat genotypes. AMF inoculation ameliorated the adverse effects of salinity on photosynthetic attributes, rooting traits, grain yield components, total dry mass (7%), leaf relative water content (5%), K (21%) and P (23%) concentrations, while reducing the Na (6%) concentration under both saline and non-saline conditions. The maintained chlorophyll levels, root development, K and P concentrations, and total dry mass of the salt-stressed ancient emmer (and to a lesser extent spelt) genotypes were further sustained by AMF inoculation. Overall, findings from the field and pot experiments showed that AMF inoculation is effective in ameliorating salt damages in wheat. These findings depict AMF inoculation of ancient emmer, spelt, and Khorasan wheats as a promising practical strategy for tackling the ever-increasing threats of salt stress to wheat production and food security.},
}

*Triticum/microbiology/growth & development/physiology/genetics
*Mycorrhizae/physiology
Photosynthesis
Salinity
Plant Roots/microbiology/physiology/growth & development
Edible Grain/growth & development
Symbiosis
*Glomeromycota/physiology
Genotype

@article {pmid41256368,
year = {2025},
author = {Gao, A and Newhart, V and Flory, M and Alam, A},
title = {Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.679439},
pmid = {41256368},
issn = {2692-8205},
abstract = {The mammalian intestine harbors a highly complex, very diverse, and numerically vast community of symbiotic microorganisms, which profoundly influence the development and maintenance of the intestinal barrier function. Alterations in microbial composition, known as dysbiosis, are observed in Inflammatory Bowel Disease (IBD), colorectal cancer (CRC), and gastrointestinal infections; however, the exact causal relationship between these changes and the resolution of intestinal inflammation and the repair of damaged mucosa remains unclear. Notably, IBD is not only marked by dysbiosis but also by changes in microbial metabolic pathways and metabolite landscape in the intestinal lumen. The small molecules and microbial metabolites present in the intestinal lumen have emerged as potential regulators of gut pathology, cancer, and mucosal repair. Investigating how altered microbiota and microbial metabolic activities influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. This knowledge can be harnessed to promote intestinal homeostasis, prevent relapse, and prolong remission of IBD. To dissect the complex interplay between the gut microbiome and IEC, we focused on the overrepresented bacterium Bacteroides thetaiotaomicron . Here, we show that B. thetaiotaomicron and Akkermansia muciniphila , the dominant members of gut microbiota, expand during the repair & resolution phase of the chemically induced acute murine colitis. Furthermore, our bioinformatics analysis demonstrated that the elevated relative abundance of B. thetaiotamicron was also accompanied by rewiring of bacterial metabolic programs towards the essential amino acid metabolism, polyamine synthesis and utilization, stress response mechanisms, cell envelope biogenesis, and nutrient scavenging. Our RNA sequencing and transcriptomic analysis of primary human colonic epithelial cells cocultured with B. thetaiotaomicron showed that B. thetaiotaomicron stimulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. Our study emphasizes the crucial functions of the gut microbiome and metabolic activities in regulating the functions of intestinal epithelial cells during the repair of injured gut mucosa. Thus, these microorganisms and their metabolism hold promise as potential therapeutic agents.},
}

@article {pmid41254159,
year = {2025},
author = {Guo, J and Chu, L and Ye, X and King, WL and Shao, J and Wang, Z and Liu, J and Chen, C and Yu, M},
title = {Low soil phosphorus and high symbiotic fungal richness inhibits plant aboveground biomass in fragmented forests in China.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1598},
pmid = {41254159},
issn = {2399-3642},
support = {32101269//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31930073//National Natural Science Foundation of China (National Science Foundation of China)/ ; LQ22C030002//Science and Technology Department of Zhejiang Province/ ; },
mesh = {*Phosphorus/analysis ; China ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Biomass ; *Soil Microbiology ; *Biodiversity ; *Fungi/physiology ; Rhizosphere ; },
abstract = {Habitat fragmentation is a major threat to biodiversity, and it usually leads to microclimate variations. Habitat quality (e.g. nutrients and moisture) and fungal symbioses play important roles in plant growth and ecosystem productivity. However, the impact of habitat fragmentation on plant aboveground biomass (AGB) is unclear. We examined the soil nutrients, rhizosphere fungal richness, and the AGB of 10 woody plant species on 10 islands of the same age but varying in size and isolation, in a land-bridge island system of subtropical China. Here we show that island size, soil nutrients, and fungal symbioses are key factors driving plant growth patterns in a fragmented island system. Plant AGB is positively correlated with soil phosphorus (P) but negatively correlated with richness of symbiotic fungi, suggesting that P content is more impactful than fungal symbiosis on plant growth in subtropical fragmented forests. Across all islands, low soil P and high symbiotic fungal richness lead to decreased plant AGB on small islands. These findings highlight the critical role of environmental filtering in shaping plant development within island fragments.},
}

*Phosphorus/analysis
China
*Forests
*Symbiosis
*Soil/chemistry
*Biomass
*Soil Microbiology
*Biodiversity
*Fungi/physiology
Rhizosphere

@article {pmid41254011,
year = {2025},
author = {Medina, S and Medrano-Padial, C and Guillén, S and Pérez-Través, L and Pérez-Novas, I and Periago, P and García-Viguera, C and Domínguez-Perles, R},
title = {SCOBY-based, innovative, and sustainable production of gallic acid from sucrose towards multipurpose applications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40536},
pmid = {41254011},
issn = {2045-2322},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación,Spain/ ; },
mesh = {*Gallic Acid/metabolism ; Fermentation ; *Sucrose/metabolism ; *Bacteria/metabolism ; *Kombucha Tea/microbiology ; *Yeasts/metabolism ; },
abstract = {Kombucha is a traditional beverage obtained from the fermentation of sugared tea by a symbiotic culture of bacteria and yeast (SCOBY), whose metabolism contributes significantly to the phytochemical composition and health-promoting properties of the final product. Among the phenolics present, gallic acid stands out as a multifunctional molecule with antioxidant, anti-inflammatory, and cardio-protective activities, making it a compound of growing interest for the development of functional foods, nutraceuticals and cosmetics. While gallic acid in kombucha has typically been attributed to plant-derived precursors, its potential de novo microbial origin has remained largely unexplored. In this work, robust evidence supports that SCOBY can synthesise gallic acid directly from sugars, without the contribution of tea or other plant materials. Metabolomic analyses combined with physicochemical characterisation (pH, ethanol, acetic acid, total soluble solids, sucrose, glucose, and fructose) revealed a linear increase in gallic acid production under standard fermentation conditions, associated with the microbial community's tolerance to high sugar concentrations and its metabolic capacity to generate bioactive phenolics. This finding highlights a previously unrecognised role of SCOBY as a natural cell factory for gallic acid production. In contrast to metabolic engineering approaches in model microorganisms such as Escherichia coli or Pseudomonas, our study demonstrates that a non-engineered microbial consortium can achieve this transformation simply and sustainably. These results open a novel route for the plant-free biosynthesis of gallic acid with potential applications across the food, cosmetic, and pharmaceutical industries.},
}

*Gallic Acid/metabolism
Fermentation
*Sucrose/metabolism
*Bacteria/metabolism
*Kombucha Tea/microbiology
*Yeasts/metabolism

@article {pmid41253823,
year = {2025},
author = {Zhou, J and Guo, Q and Han, X and Zhang, W and Huang, Z and Dietrich, CH and Wei, C},
title = {Genome degradation results in nested symbiosis and endosymbiont replacement in cicadas.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10104},
pmid = {41253823},
issn = {2041-1723},
mesh = {*Symbiosis/genetics ; *Hemiptera/microbiology/genetics ; Phylogeny ; Animals ; *Genome, Bacterial ; },
abstract = {Gradual genome degradation and fragmentation in primary nutritional endosymbionts have required symbiont-dependent hosts periodically to replace such symbionts over evolutionary timescales, yet the processes involved in de novo emergence of endosymbiosis and symbiont replacement are challenging to ascertain. Here we show that phylogenetic relationships of two ancient vertically-transmitted bacterial endosymbionts of cicadas, Hodgkinia and Karelsulcia, mirror host phylogeny, particularly indicating a single ancestral infection of cicadas by Hodgkinia with subsequent host-symbiont codiversification before being replaced by yeast-like fungal symbionts (YLS). We demonstrate a case of co-existence of Hodgkinia with Karelsulcia and a YLS, representing an advanced ongoing symbiont replacement process. In some individuals of the cicada Chremistica ochracea, the Hodgkinia is highly degenerated but colonizes (instead of neighboring) its partner Karelsulcia. The physical fusion of these two bacterial endosymbionts yields a nested symbiosis while the new YLS is recruited, probably preserving essential metabolic pathways necessary for host nutrition and facilitating continued vertical symbiont transmission. Such fusion may have provided refuge for the degrading bacterial endosymbiont and delayed symbiont replacement. Our study sheds light on adaptive and non-adaptive evolutionary mechanisms involved in symbiont loss and replacement, offering fresh insights into endosymbiotic origins of cellular organelles.},
}

*Symbiosis/genetics
*Hemiptera/microbiology/genetics
Phylogeny
Animals
*Genome, Bacterial

@article {pmid41253704,
year = {2025},
author = {Zecua-Ramirez, P and Dunken, N and Charura, NM and Llamas, E and De Quattro, C and Mandel, A and Langen, G and Dagdas, Y and Zuccaro, A},
title = {Autophagy restricts symbiosis-associated cell death and regulates colonization by Serendipita indica in Arabidopsis.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf590},
pmid = {41253704},
issn = {1532-2548},
abstract = {Endophytic colonization of Arabidopsis (Arabidopsis thaliana) by the beneficial root endophyte Serendipita indica is characterized by an initial biotrophic phase, followed by a confined host cell death phase that facilitates fungal accommodation. However, the host molecular pathways that restrict S. indica proliferation and regulate symbiosis-associated cell death remain largely unknown. Our study demonstrates that autophagy, a key cellular degradation pathway that maintains homeostasis, is locally activated during colonization and is required to limit fungal proliferation and immunometabolic stress. Autophagy-deficient mutants exhibit elevated basal root cell death, increased colonization, and hypersensitivity to the fungal-derived purine metabolite 2'-deoxyadenosine (dAdo), an immunometabolic signal that modulates host cell viability and reprograms immune and metabolic responses via ENT3 (equilibrative nucleoside transporter 3)-mediated uptake. In ent3 and atg5 ent3 mutants, suppression of dAdo import reduces S. indica-induced cell death, confirming the central role of ENT3-mediated uptake. Despite increased colonization and stress sensitivity, autophagy-deficient plants retain S. indica-mediated root growth promotion, indicating that mutualistic benefits can occur independently of immunometabolic stress resilience. Based on these findings, we propose that autophagy-mediated pro-survival responses are essential for maintaining symbiotic homeostasis by integrating immunometabolic signals and preserving host cell viability.},
}

@article {pmid41253152,
year = {2025},
author = {Li, Y and Qiu, J and Liu, Z and Xiao, H and Wang, B and Dong, Y and Xiao, Y and Wang, Q and Dong, J and Cui, M},
title = {Phytate enhances gut Parasutterella colonization to alleviate radiation injury.},
journal = {Cell chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chembiol.2025.10.009},
pmid = {41253152},
issn = {2451-9448},
abstract = {Food as medicine shows promise for disease intervention or treatment. Here, we found phytate, an active ingredient of plant-based diets, exhibits properties in mitigating radiotherapy-related complications. Oral gavage of phytate restored hematogenic organ atrophy, elevated peripheral blood neutrophils and white blood cells, reduced inflammation, and improved gastrointestinal (GI) integrity in irradiated mice. Phytate intake modulated the gut microbiota, facilitating the colonization of symbiotic Parasutterella in GI tract, thus combating intestinal radiation toxicity. In vitro assays and untargeted metabolomics identified 3-phenyllactic acid (PLA) and N-acetyl-L-leucine (NL) as functional metabolites produced by Parasutterella. In vitro, ex vivo, and in vivo models showed that PLA induces M2-like polarization in macrophages, while NL reduced oxidative stress, both counteracting radiation toxicity and working synergistically. Our findings offer mechanistic insights into phytate for alleviating radiation-associated complications and suggest that Parasutterella and its metabolites might be employed as promising probiotics or postbiotics for cancer patients undergoing radiotherapy.},
}

@article {pmid41251823,
year = {2025},
author = {Della Mónica, IF and Godeas, AM and Scervino, JM},
title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {66},
pmid = {41251823},
issn = {1432-1890},
support = {UBACyT 20020220400300BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 01283-2021//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PINI 04/B253//Fundación de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; },
mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.},
}

*Mycorrhizae/physiology/enzymology
*Symbiosis
Plant Roots/microbiology
*Phosphorus/metabolism
Acid Phosphatase/metabolism
*Phosphoric Monoester Hydrolases/metabolism
Daucus carota/microbiology
*Glomeromycota/physiology/enzymology
*Phosphates/metabolism

@article {pmid41251487,
year = {2025},
author = {Kennedy, SJ and Risser, DD and Paul, BG},
title = {Diel expression dynamics in filamentous cyanobacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0377924},
doi = {10.1128/mbio.03779-24},
pmid = {41251487},
issn = {2150-7511},
abstract = {Filamentous cyanobacteria of the Nostocaceae family can differentiate into multicellular forms to adapt to environmental stresses, and members can establish symbiosis with various embryophytes. Representative laboratory strains are typically grown under continuous light to maintain stable metabolic conditions; however, this departure from a natural diel cycle can result in extended stress. Early genomic examination of Nostoc punctiforme suggests the genetic potential for a circadian clock, but we lack insight into global cellular dynamics through the natural diel cycle for this model organism. Here, we comprehensively assess changes in expression of core cellular processes and the mobilome of accessory genetic elements during diel growth of N. punctiforme PCC 73102. The primary transcriptome confirmed that multicellular cyanobacteria precisely coordinate photosynthesis and carbon assimilation for cell division during the day, while control of DNA recombination and repair appeared to be sequestered to darkness. Moreover, we expanded the known repertoire of light-sensing proteins to uncover a putative regulator of circadian rhythm that itself exhibits striking oscillation between day-night expression. This was in sharp contrast to the arrhythmic pattern observed for a homolog of the canonical circadian input kinase in unicellular cyanobacteria. Looking beyond cellular coordination of diel growth, we uncovered dynamic mobile elements and, notably, targeted hypermutation by retroelements that are likely maintained for conflict mitigation, which is crucial for a multicellular lifestyle.IMPORTANCEModel strains of filamentous cyanobacteria are typically cultivated under controlled laboratory conditions that poorly reflect the natural environment, including growth under constant light. Our study addresses this discrepancy to provide a new benchmark for investigating gene expression in the model organism, Nostoc punctiforme. By analyzing changes in the global transcriptome over a diel cycle, we found a clear partition of cellular processes between periods of light and darkness, with metabolism dominating in the light and cell maintenance and repair processes dominating in the dark. In addition, an active mobilome of genetic elements was uncovered with dynamic expression patterns throughout a diel cycle. Our findings highlight the importance of considering diel cycles in cyanobacterial research and provide new insight into the regulatory complexity, genome plasticity, and adaptive mechanisms of these ecologically important organisms. Our study reinforces the need to consider the natural diel cycle in laboratory models of filamentous cyanobacteria, bringing new insights into their regulatory complexity and revealing adaptive drivers of genome plasticity that may enable members of Nostoc to occupy a wide variety of ecosystems.},
}

@article {pmid41251484,
year = {2025},
author = {Hamm, JN},
title = {Nutrient availability affects optimal growth strategy in predatory DPANN.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0147525},
doi = {10.1128/msystems.01475-25},
pmid = {41251484},
issn = {2379-5077},
abstract = {The DPANN archaea comprise a major microbial lineage that appears to be primarily host dependent. Despite the relative ubiquity of DPANN archaea across the biosphere, our understanding of their ecological role is limited due to the absence of cultivated representatives for most DPANN lineages. The majority of cultivated DPANN species are characterized as mildly parasitic ectosymbionts due to reliance on physical interactions with host cells. However, Candidatus Nanohaloarchaeum antarcticus has been reported to adopt a predatory lifestyle, resulting in the lysis of large numbers of host cells. The factors influencing DPANN-host interactions that drive Ca. Nha. antarcticus to adopt an aggressive lifestyle, although other DPANN appear not to, remain unclear. Here, I present a framework for understanding the ecological pressures specific to the Ca. Nha. antarcticus-Halorubrum lacusprofundi system and why a more aggressive, predatory lifestyle improves population persistence compared with a lifestyle more similar to other DPANN.},
}

@article {pmid41251315,
year = {2025},
author = {Yurchenko, OV and Chernyshev, AV},
title = {Spermatozoon Ultrastructure in the Symbiotic Hoplonemertean, Malacobdella japonica Takakura, 1897.},
journal = {Journal of morphology},
volume = {286},
number = {11},
pages = {e70101},
doi = {10.1002/jmor.70101},
pmid = {41251315},
issn = {1097-4687},
mesh = {Male ; Animals ; *Spermatozoa/ultrastructure ; Symbiosis ; Mitochondria/ultrastructure ; *Invertebrates/ultrastructure/physiology ; Acrosome/ultrastructure ; Microscopy, Electron, Transmission ; Cell Nucleus/ultrastructure ; },
abstract = {The sperm morphology of Malacobdella japonica, a symbiotic nemertean living in the clam Spisula sachalinensis, has been examined using light and electron microscopy. In this species, the structure of the elongated spermatozoon, consisting of a straight head and a posteriorly oriented flagellum, is similar to that of Malacobdella grossa, as previously studied. In both species, the sperm head has an acrosomal complex, an elongated nucleus, and a neck region. The small acrosomal complex, including a thimble-like acrosomal vesicle, a post-acrosomal ring of electron-dense material, and a subacrosomal space, is located asymmetrically at the anterior end of the nucleus. However, there are some differences between the species in the structure and organization of the mitochondrial compartment. In M. grossa, the mitochondria are elongated along the nucleus and remain separate all along their length. In M. japonica, the mitochondria merge at the base of the neck region, forming a ring around the distal centriole. Above this area, they remain separate, similarly to the pattern observed in M. grossa. This finding suggests M. japonica to be an intermediate stage between M. grossa, distinguished by its unique separate mitochondria, and other hoplonemerteans that have a single, ring-like mitochondrion. We assume that the ultrastructure of spermatozoa in symbiotic nemerteans is shaped rather by the mode of fertilization than by their lifestyle. With external fertilization, without forming clutches, the lifestyle does not lead to the development of highly modified spermatozoa.},
}

Male
Animals
*Spermatozoa/ultrastructure
Symbiosis
Mitochondria/ultrastructure
*Invertebrates/ultrastructure/physiology
Acrosome/ultrastructure
Microscopy, Electron, Transmission
Cell Nucleus/ultrastructure

@article {pmid41250913,
year = {2025},
author = {Xu, H and Huang, S and Wang, J and Wang, T and Han, Q and Wu, K and Gao, Z and Shi, X and Tu, T and Wang, M and Huang, L and Chen, J and Liu, Y and Zhang, Y and Lin, G and Chen, Z and Chen, X},
title = {Soybean Auxin Transporter PIN3 Regulates Nitrate Acquisition to Improve Nitrogen Use and Seed Traits.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e11907},
doi = {10.1002/advs.202511907},
pmid = {41250913},
issn = {2198-3844},
support = {2022YFA0912100//National Key Research, Development Program of China/ ; 32222009//National Natural Science Foundation-Outstanding Youth Foundation/ ; 133-725025010B//Funding for a World-Class Plant Protection Discipline/ ; 32300277//National Natural Science Foundation of China -Youth Fund Project/ ; 2022J01161//Natural Science Foundation of Fujian/ ; 2023J01482//Natural Science Foundation of Fujian/ ; SKLJPR2505//Joint Research Program of State Key Laboratory of Agricultural and Forestry Biosecurity/ ; },
abstract = {Enhancing nitrogen-use efficiency is essential for boosting crop yields and advancing sustainable agriculture, particularly in the absence of synthetic fertilizers. Despite the inherent nitrogen-fixation capacity of the staple legume crop soybean (Glycine max) by symbiotic rhizobia, improving nitrogen use has been challenging. Here, a role for the auxin-efflux transporters PIN3a and PIN3b in soybean nitrate acquisition is uncovered. PIN3a/b localizes to the plasma membrane, and high environmental nitrate induces PIN3a degradation and its accumulation at cell junctions. Disrupting PIN3 homologs results in auxin over-accumulation, impairs pavement-cell polarity, and enhances signaling via the transcription factors ARF and STF3/4. These transcription factors separately bind to and activate the NPF2.13 promoter, thereby strengthening nitrate uptake. pin3ab and pin3abd mutants have enhanced nitrate acquisition and resistant to high nitrate on pavement-cell growth. The elevated nitrogen accumulation translates to higher oil contents in pin3ab mutant seeds in an elite cultivar background across multiple years and field locations. The findings shed light on the regulation of nitrate uptake in crop-plant development and demonstrate the unexpected potential of manipulating auxin transporters to enhance soybean nitrogen-use efficiency and agronomic performance.},
}

@article {pmid41249874,
year = {2025},
author = {Ruan, HQ and Li, CL and Dong, YJ and Yu, X and Ye, SM and Zhang, HY and Liu, J and Guo, RP and Zeng, W and Song, L and Xie, ZP and Staehelin, C},
title = {Exo-oligosaccharide signaling in Lotus japonicus roots promotes synthesis and secretion of symbiotic phenylpropanoids resulting in increased production of Nod factors in rhizobia.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70719},
pmid = {41249874},
issn = {1469-8137},
support = {//Guangdong Provincial Key Laboratory of Plant Stress Biology/ ; 10251027501000014//Guangdong Natural Science Foundation/ ; 31670241//National Natural Science Foundation of China/ ; //Science Foundation of the State Key Laboratory of Biocontrol/ ; },
abstract = {Besides lipo-chitooligosaccharidic Nod factors (NFs), rhizobial exo-oligosaccharides (EOS), derived from exo-polysaccharides (EPS), are symbiotic signals that promote nodule formation on legume roots. However, plant genes regulated by EOS signaling remain unidentified. Here, we used purified EPS and the rhizobial glycanase ExoK to produce EOS in vitro. EOS was applied to Lotus japonicus roots to identify genome-wide gene expression changes. Mutants of Sinorhizobium sp. NGR234 and L. japonicus were used to investigate the symbiotic roles of EOS and NFs. Transcriptomic analysis showed that EOS induced the expression of many phenylpropanoid biosynthesis genes, among other transcriptome alterations. EOS signaling occurred in both L. japonicus wild-type plants and mutants with impaired NF signaling, but not in epr3 mutant plants defective in the EOS receptor. Root exudates from EOS-treated plants showed increased genistein levels and enhanced activation of nodulation genes in NGR234, leading to higher NF production. Further experiments demonstrated that both EOS and NFs upregulate the expression of genes involved in flavonoid synthesis. Inoculation tests with NGR234 and its mutants revealed that EOS, rather than EPS, plays a role in promoting infection thread development in L. japonicus. In conclusion, we identified L. japonicus genes regulated by EOS signaling and found that EOS can stimulate the production of symbiotic phenylpropanoids that upregulate NF synthesis in rhizobia.},
}

@article {pmid41247772,
year = {2025},
author = {Rawlings, TM and Guttridge, SA and Lucas, ES},
title = {New models of implantation: towards a whole better than the sum of parts.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deaf223},
pmid = {41247772},
issn = {1460-2350},
support = {//Next-Generation Fellowship at the Loke Centre for Trophoblast Research, University of Cambridge/ ; SBF0010\1091//Academy of Medical Sciences Springboard/ ; },
abstract = {Recent advances in the development of stem-cell-based embryo models and endometrial assembloids have fuelled understanding of their respective biology. However, a faithful combined approach is required to truly advance our understanding of implantation processes. This mini-review considers the most recent developments in producing reliable in vitro models of the human endometrium and human embryo, and the next steps required to combine their respective potential. While the fundamental biology of implantation is the primary driver of in vitro model development, the combined effort of embryo and endometrial models to generate new models of implantation provides the opportunity to manipulate either compartment to further understand the aetiologies of reproductive dysfunction. Through combining both systems, their efforts are symbiotic, each extending the relevance and utility of their counterpart to generate a whole greater than the sum of its parts.},
}

@article {pmid41247017,
year = {2025},
author = {Carpentier, J and Derocles, SA and Chéreau, S and Marquer, B and Linglin, J and Lebreton, L and Legeai, F and Vannier, N and Cortesero, A and Mougel, C},
title = {Contrasting glucosinolate profiles in rapeseed genotypes shape the rhizosphere-insect continuum and microbial detoxification potential in a root herbivore.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0126925},
doi = {10.1128/msystems.01269-25},
pmid = {41247017},
issn = {2379-5077},
abstract = {Plant secondary metabolites are key mediators of plant-insect-microbiome interactions, yet their role in structuring functionally relevant insect-associated microbial communities remains poorly understood. Here, we combined a factorial experiment using Brassica napus genotypes differing in glucosinolate (GLS) content with distinct succession to investigate the eco-evolutionary dynamics of the microbiota of the root herbivore Delia radicum. Amplicon sequencing and microbial culturing revealed that both rhizospheric and gut microbial communities are shaped by plant genotype and soil legacy, with a subset of bacterial taxa shared across compartments. Notably, Pseudomonas brassicacearum, harboring the isothiocyanates (ITC) detoxifying gene saxA, was consistently recovered from both plant and insect habitats. Functional assays confirmed its capacity to degrade 2-phenylethyl isothiocyanate (PEITC), a major toxic GLS hydrolysis product. Other gut-derived microbial isolates exhibited heterogeneous responses to PEITC, ranging from growth inhibition, promotion, or growth recovery after a prolonged lag phase. Despite the toxicity of ITC, insect fitness proxies were enhanced on GLS +plants, suggesting microbiota-mediated adaptation to host chemical defenses. Our findings reveal a plant genotype-specific filtering of environmentally acquired microbes and highlight the role of detoxifying symbionts in Delia radicum performance.IMPORTANCEUnderstanding how herbivorous insects adapt to plant chemical defenses is important in the context of new agricultural practices. This study highlights that the host plant genotype shapes not only rhizospheric and gut microbial communities but also promotes the acquisition of symbiotic bacteria capable of detoxifying harmful isothiocyanates. These findings reveal a functional microbial pathway for insect adaptation to plant defenses, with potential implications for pest management strategies. By uncovering the role of plant-associated microbiota, the acquisition of beneficial microbes, and their functional contributions to host fitness, this work provides a foundation for innovative agroecological approaches that leverage plant-microbe-insect interactions.},
}

@article {pmid41247016,
year = {2025},
author = {Beilinson, V and Chen, GY and Hargadon, AC and Ruby, EG and McFall-Ngai, MJ},
title = {Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0049825},
doi = {10.1128/msystems.00498-25},
pmid = {41247016},
issn = {2379-5077},
abstract = {UNLABELLED: Understanding the cause and consequences of bacterial strain variation remains a challenge in the study of symbioses. While the diverse reactions of the host immune system to strain variants have been well studied in pathogenesis, much less is known about how strain variation influences beneficial associations. From the complex vertebrate gut microbiome to the more tractable invertebrate models of symbiosis, the host's cellular and molecular responses to this diversity remain largely a mystery. Here, we explore strain diversity in Vibrio fischeri, the bioluminescent bacterial symbiont of the Hawaiian bobtail squid, Euprymna scolopes. Phylogenetic analyses of the genomes of 62 V. fischeri strains, including 50 light organ-associated and 12 planktonic isolates, revealed several genes that were absent in planktonic strains, but uniformly present in symbiotic ones. To better understand the consequences of this diversity to the host, we selected five light-organ associated strains: three from E. scolopes but having different combinations of colonization factors, one from a congeneric squid host, and one from a marine fish. We colonized juvenile E. scolopes with these strains and, using RNAseq, found that (i) the most similar host transcriptomic responses occurred among the native E. scolopes strains, (ii) intermediate was the strain from the related squid, and (iii) least similar was the fish strain. Importantly, native strains downregulated immune-related genes more than non-native ones. Finally, host development was atypical or delayed when colonized by non-native strains. These experiments point the way to more targeted studies of the mechanisms underlying host responses to symbiont strain diversity.

IMPORTANCE: Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of host tissues to differences between the strains present in an animal's normal microbiome. We use a natural, species-specific, symbiosis to explore the influence of strain-level differences on host gene expression and morphogenesis. Analysis of symbiotic strains from squids and fishes, as well as free-living strains, shows that the carriage of colonization determinants, while critical to competitive success among strains of a species, has a minimal effect on the transcriptional response of the host. We provide evidence that a more important driver of normal gene expression during the development of symbiosis is the history of a strain's co-diversification with its host species. Such studies, using simple invertebrate models, allow the recognition of otherwise obscured interactions underlying the more complex microbiomes of vertebrates.},
}

@article {pmid41246383,
year = {2025},
author = {Panthalil, BS and Vogts, A and Benavides, M and Harke, MJ and Hassenrück, C and Subramaniam, A and Montoya, JP and Voss, M},
title = {Novel pennate diatom symbionts support high N2 fixation rates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf190},
doi = {10.1093/ismeco/ycaf190},
pmid = {41246383},
issn = {2730-6151},
abstract = {Diazotrophy is the most important nitrogen source in the oligotrophic surface ocean, but the organisms involved and their contributions are incompletely understood due to limited observations. Only diazotrophic organisms possess the nifH gene to reduce dinitrogen to ammonium, but their distribution and activity can only be quantified through sampling and experiments during research cruises. Some recent studies document small diatoms with symbionts able to fix nitrogen, a new source of biologically available nitrogen in addition to the well-known cyanobacterial species such as Trichodesmium or symbionts of haptophytes (UCYN-A) and diatoms (Diatom-Diazotroph Associations, or DDAs). Here, we document a very active symbiosis between small pennate diatoms such as Mastogloia and Haslea with rhizobial and cyanobacterial symbionts in waters of the Western tropical North Atlantic influenced by the Amazon River plume. We used NanoSIMS analysis of [15]N2 tracer experiments to quantify high rates of nitrogen fixation in generally abundant, symbiont-bearing pennate diatoms. This newly described symbiosis may contribute a previously unquantified flux of biologically available nitrogen to oceanic systems. Pennate diatoms and their symbionts may close a key gap in our understanding of the supply of nutrients to the ocean and provide a previously unknown biological sink for carbon dioxide.},
}

@article {pmid41246320,
year = {2025},
author = {Dey, P},
title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674913},
doi = {10.3389/fimmu.2025.1674913},
pmid = {41246320},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; },
abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Humans
Dysbiosis
Mice, Knockout
*Intestines/microbiology/immunology
*Intestinal Mucosa/metabolism/microbiology/immunology
*Host Microbial Interactions/genetics
Mice

@article {pmid41245697,
year = {2025},
author = {San-Blas, E and Morales-Montero, P and Bastidas, B and Půža, V and Machado, RAR},
title = {Heterorhabditis caligo n. sp. (Rhabditida: Heterorhabditidae): A New Entomopathogenic Nematode from Pichilemu Sand Dunes, Chile.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250045},
doi = {10.2478/jofnem-2025-0045},
pmid = {41245697},
issn = {0022-300X},
abstract = {During a survey of the nematode biodiversity in the Petrel wetland (central Chile), a population of Heterorhabditis sp. was found in the coastal dune samples. Morphological, morphometric, and molecular studies indicated that this nematode belonged to the megidis group, and represented a novel species, which we named Heterorhabditis caligo n. sp. This nematode species resembles H. marelatus but it is different in the morphometrics of its infective juvenile in the following ways: pharynx length (135-150 μm vs. 120-138 μm), and the position of the excretory pore from the anterior end (105-128 μm vs. 81-113 μm). In males, the fourth and eighth pairs of the bursal papillae are shorter and do not reach the edge of the bursa in H. caligo n. sp., whereas all the papillae in H. marelatus reach the edge of the bursa. The excretory pore of amphimictic females of H. caligo n. sp. is located more posteriorly than in those of H. marelatus 193 (169-224) μm vs. 157 (139-178) μm, respectively. Phylogenetic analyses of the genus based on whole nuclear and mitochondrial genome sequences and on five gene markers showed a clear separation of Heterorhabditis caligo n. sp. from the other species, placing it within the megidis group.},
}

@article {pmid41242729,
year = {2025},
author = {Takeguchi, Y and Shibuya, R and Kondo, M and Betsuyaku, E and Itakura, M and Minamisawa, K and Sugawara, M and Betsuyaku, S},
title = {Unipolar Polysaccharide-mediated Attachment of the N2O-reducing bacterium Bradyrhizobium ottawaense SG09 to Plant Roots.},
journal = {Microbes and environments},
volume = {40},
number = {4},
pages = {},
doi = {10.1264/jsme2.ME25043},
pmid = {41242729},
issn = {1347-4405},
mesh = {*Bradyrhizobium/genetics/physiology/metabolism ; *Plant Roots/microbiology ; Symbiosis ; Arabidopsis/microbiology ; *Nitrous Oxide/metabolism ; *Bacterial Adhesion ; Glycine max/microbiology ; *Polysaccharides, Bacterial/metabolism/genetics ; Multigene Family ; },
abstract = {Agricultural soils are an important source of nitrous oxide (N2O), which has greenhouse and ozone-depleting effects. Bradyrhizobium ottawaense SG09 is a nitrogen-fixing rhizobium with high N2O-reducing activity. Rhizobia form symbiotic nodules in leguminous plants. The initial physical attachment of bacteria to plant roots is a critical step in the establishment of symbiotic interactions. In the present study, we performed a microscopic anal-ysis using DsRed-expressing B. ottawaense SG09. We revealed that B. ottawaense SG09 attached to both the root surface and root hairs via single cellular poles. This polar attachment was observed not only to the symbiotic host soybean, but also to non-leguminous plants, such as Arabidopsis, rice, corn, and wheat. We identified and analyzed the unipolar polysaccharide (upp) gene cluster, which is proposed to be involved in the polar attachment of rhizobia, in the genome of B. ottawaense SG09. We established an Arabidopsis-based interaction assay and demonstrated that uppC and uppE play a critical role in attachment to both the root surface and root hairs.},
}

*Bradyrhizobium/genetics/physiology/metabolism
*Plant Roots/microbiology
Symbiosis
Arabidopsis/microbiology
*Nitrous Oxide/metabolism
*Bacterial Adhesion
Glycine max/microbiology
*Polysaccharides, Bacterial/metabolism/genetics
Multigene Family

@article {pmid41242215,
year = {2025},
author = {Liu, X and Yu, J and Liu, Y and Tan, L and Fu, M and Chen, Y and Xia, L and Zhang, S},
title = {Sexual dimorphism in arbuscular mycorrhizal fungal-assisted zinc detoxification: female poplars emerge as superior phytoremediator through lignin-flavonoid pathways.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt D},
pages = {110751},
doi = {10.1016/j.plaphy.2025.110751},
pmid = {41242215},
issn = {1873-2690},
abstract = {Zinc (Zn) is an essential micronutrient but becomes cytotoxic at elevated levels. Arbuscular mycorrhizal (AM) fungi are known to enhance plant tolerance to potential toxic elements, but it is unclear how AM symbiosis mediates the sexually dimorphic responses to Zn toxicity in dioecious poplars. In this study, female and male Populus cathayana inoculated with Funneliformis mosseae were used to investigate the mechanisms of AM symbiosis to alleviate Zn toxicity. The results showed that non-mycorrhizal males exhibited greater resistance to Zn toxicity than females, primarily through the synthesis of organic acids. However, AM symbiosis altered defense strategies in both sexes, enhancing Zn tolerance through cysteine- and ethylene-mediated pathways. In female roots, AM symbiosis increased lignin (34.00 %) and flavonoid (77.47 %) accumulation, thereby enhancing Zn resistance and alleviating oxidative stress. Critically, AM symbiosis significantly upregulated the expression of metal chelation and transport genes (PcMT1d, PcZIP6 and PcZIP7) in females, resulting in higher Zn uptake and translocation efficiency. Zn accumulation in females increased by 44.26 %, while soil available Zn decreased by 44.19 %, highlighting their potential for phytoremediation. Therefore, this study clarifies the sexually differential mechanisms to Zn resistance in P. cathayana, and reveals the promising application of female P. cathayana and AM fungi in the remediation of Zn-contaminated soils.},
}

@article {pmid41241951,
year = {2025},
author = {Van Nynatten, A and Cunning, R and Tietjen, KL and Baum, JK},
title = {Marine Heatwaves Transform Coral Symbioses With Enduring Effects.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70263},
doi = {10.1111/ele.70263},
pmid = {41241951},
issn = {1461-0248},
support = {//British Columbia Knowledge Development Fund/ ; //Rufford Foundation/ ; //Pew Charitable Trusts/ ; NFRFT-2020-00073-BIOSCAN//New Frontiers in Research Fund (NFRF)/ ; //Natural Sciences and Engineering Research Council of Canada/ ; OCE-1446402//National Science Foundation (NSF) RAPID grant/ ; 10.13039/100000001//National Science Foundation (NSF) RAPID grant/ ; //National Geographic Society/ ; 10.13039/501100000196//Canada Foundation for Innovation (CFI)/ ; //Centre for Asia-Pacific Initiatives, University of Victoria/ ; //University of Victoria Centre for Asia-Pacific Initiatives/ ; //David and Lucile Packard Foundation/ ; },
mesh = {Animals ; *Symbiosis ; *Anthozoa/physiology ; *Coral Reefs ; Climate Change ; *Hot Temperature ; *Extreme Heat/adverse effects ; },
abstract = {Climate change-amplified extreme weather events are reshaping ecological communities globally. On coral reefs, heatwaves typically disrupt the obligate coral-algal symbiosis, with symbiont identity a prime determinant of coral resilience to these thermal extremes. Yet, whether heatwaves have long-term effects on coral symbioses remains unclear due to a lack of longitudinal symbiont data. Here, we report on a decadal coral symbiont survey (2013-2023), spanning the most prolonged tropical marine heatwave on record (2015-2016) and its aftermath. Concomitant with mass coral mortality, we document wholesale transformation of the symbiont assemblages in two coral species, the legacy of which was persistent for 7 years post heatwave. We also found evidence suggestive of a symbiont's local extinction, of local human disturbance impeding symbiont recovery, and of new coral recruits hosting symbiont assemblages distinct from survivors. Our study demonstrates heatwaves can have long-lasting impacts on symbioses raising concern for coral resilience to future heatwaves.},
}

Animals
*Symbiosis
*Anthozoa/physiology
*Coral Reefs
Climate Change
*Hot Temperature
*Extreme Heat/adverse effects

@article {pmid41240368,
year = {2025},
author = {Song, JH and Agake, SI and Tanabata, S and Cui, Y and Su, L and Montes-Luz, B and Xu, D and Stacey, G},
title = {Phloem-specific translational regulation of soybean nodulation: insights from a phloem-targeted TRAP-Seq approach.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf570},
pmid = {41240368},
issn = {1532-2548},
abstract = {Soybean (Glycine max) root nodulation is a symbiotic process that requires complex molecular and cellular coordination. The phloem plays a crucial role not only in nutrient transport but also in long-distance signaling that regulates nodulation. However, the molecular mechanisms underlying phloem-specific regulation during nodulation remain poorly characterized. Here, we developed a phloem-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) system to investigate the translational dynamics of phloem-associated genes during nodulation. Using a phloem-specific promoter (Glyma.01G040700) combined with the GAL4-UAS amplification system, we successfully captured the translatome of soybean root phloem at early (72 hours post-inoculation, hpi) and late (21 days post-inoculation, dpi) nodulation stages. Differential expression analysis revealed dynamic translational reprogramming, with 2,636 differentially expressed genes (DEGs) at 72 hpi and 8,422 DEGs at 21 dpi. Gene ontology and pathway enrichment analyses showed stage-specific regulatory shifts, including early activation of ethylene and defense pathways and late-stage enhancement of nutrient transport and vascular development. Transcription factor analysis identified GmbHLH121 as a key phloem-specific regulator of nodulation. Functional validation using RNAi knockdown and overexpression experiments demonstrated that GmbHLH121 negatively regulates nodule formation, likely acting downstream of or independently from early nodulation signaling pathways. Additionally, we uncovered dynamic regulation of cell wall-modifying enzyme (PME and PMEI) in the phloem, implicating their role in modulating plasmodesmata (PD) permeability and facilitating symplastic connectivity during nodulation. Our findings highlight the critical role of phloem-mediated translational regulation in coordinating root nodulation, emphasizing the phloem as an active regulatory hub for long-distance signaling and symbiotic efficiency.},
}

@article {pmid41240364,
year = {2025},
author = {Khan, M},
title = {Gatekeeping symbiosis: Autophagy shapes Serendipita indica -Arabidopsis thaliana Interaction.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf593},
pmid = {41240364},
issn = {1532-2548},
}

@article {pmid41240200,
year = {2025},
author = {Bashir, S and Zargar, SM and Husaini, AM},
title = {Epigenetic-modifications induced by plant-microbial interactions modulate plant immunity, Defense-response and mutualistic associations.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {86},
pmid = {41240200},
issn = {1573-4978},
mesh = {*Plant Immunity/genetics ; *Epigenesis, Genetic/genetics ; *Symbiosis/genetics ; *Plants/microbiology/genetics/immunology ; Mycorrhizae ; Gene Expression Regulation, Plant ; Plant Diseases/microbiology/genetics/immunology ; },
abstract = {Plants live in intricate ecological niches where they are in continual contact with a wide variety of microorganisms, including both beneficial symbionts and dangerous diseases. For plants to survive and be healthy, they must be able to discriminate between these various microorganisms and deploy the proper defenses. Recent studies show that epigenetic processes, in addition to traditional signaling pathways, are essential for regulating how plants react to microbial interactions. The comprehensive summary examines how epigenetic changes control plant immunity by regulating pattern-triggered immunity (PTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), and defense priming. Additionally, we explore the role that these epigenetic variables play in the establishment and maintenance of mutualistic relationships with beneficial microbes such as plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and rhizobia. The paper also highlights how chromatin-based regulatory mechanisms and non-coding RNA (ncRNA) networks, such as microRNAs, small interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), facilitate two-way communication between microorganisms and plants. Recent developments in high-throughput sequencing and functional genomics have revealed the plasticity and memory capacity of the plant epigenome, providing intriguing opportunities for crop enhancement. Researchers are exploring the ability of epigenome editing techniques, such as synthetic transcriptional regulators and CRISPR-dCas9-based systems, to accurately modify stress-responsive genes. This review highlights the potential of epigenetic engineering as a sustainable strategy for enhancing plant immunity, stress tolerance, and symbiotic efficiency by elucidating the epigenetic frameworks that regulate interactions between microbes and plants.(Fig. 1).},
}

*Plant Immunity/genetics
*Epigenesis, Genetic/genetics
*Symbiosis/genetics
*Plants/microbiology/genetics/immunology
Mycorrhizae
Gene Expression Regulation, Plant
Plant Diseases/microbiology/genetics/immunology

@article {pmid41239036,
year = {2025},
author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA},
title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41239036},
issn = {1618-1905},
abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.},
}

@article {pmid41238942,
year = {2025},
author = {Cummings, J and Dahlin, KJ and Gross, E and Hauenstein, JD},
title = {Routing Functions for Parameter Space Decomposition to Describe Stability Landscapes of Ecological Models.},
journal = {Bulletin of mathematical biology},
volume = {87},
number = {12},
pages = {177},
pmid = {41238942},
issn = {1522-9602},
support = {2316455//Directorate for Mathematical and Physical Sciences/ ; 1945584//Division of Mathematical Sciences/ ; 2331400//Division of Mathematical Sciences/ ; 00005696//Simons Foundation/ ; },
abstract = {Changes in environmental or system parameters often drive major biological transitions, including ecosystem collapse, disease outbreaks, and tumor development. Analyzing the stability of steady states in dynamical systems provides critical insight into these transitions. This paper introduces an algebraic framework for analyzing the stability landscapes of ecological models defined by systems of first-order autonomous ordinary differential equations with polynomial or rational rate functions. Using tools from real algebraic geometry, we characterize parameter regions associated with steady-state feasibility and stability via three key boundaries: singular, stability (Routh-Hurwitz), and coordinate boundaries. With these boundaries in mind, we employ routing functions to compute the connected components of parameter space in which the number and type of stable steady states remain constant, revealing the stability landscape of these ecological models. As case studies, we revisit the classical Levins-Culver competition-colonization model and a recent model of coral-bacteria symbioses. In the latter, our method uncovers complex stability regimes, including regions supporting limit cycles, that are inaccessible via traditional techniques. These results demonstrate the potential of our approach to inform ecological theory and intervention strategies in systems with nonlinear interactions and multiple stable states.},
}

@article {pmid41238653,
year = {2025},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Obrępalska-Stęplowska, A},
title = {Bacteria associated with the cereal leaf beetle act as the insect's allies in adapting to protease inhibitors, but impair its development in laboratory condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39944},
pmid = {41238653},
issn = {2045-2322},
support = {UMO-2020/37/N/NZ9/02577//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Coleoptera/microbiology/growth & development/drug effects ; Larva/microbiology/growth & development/drug effects ; *Protease Inhibitors/pharmacology ; *Bacteria ; Microbiota ; *Adaptation, Physiological ; Edible Grain/parasitology ; },
abstract = {Oulema melanopus [L.] (cereal leaf beetle, CLB) is one of the most serious cereal pests. Plant protease inhibitors (PIs) are known for their insecticidal properties. The role of CLB-associated bacteria in insect adaptation to PIs is not yet known. We investigated the role of CLB-associated bacteria in adaptation to PIs, and whether the reduction of bacteria will affect the CLB development. We found a decrease in proteases activity in insects with a diminished bacterial community compared to those with an intact bacterial community. Thus, the study showed that the CLB-associated bacteria participate in the adaptation of CLB larvae to PIs. On the other hand, regardless of the type of PI used, ultimately a higher survival rates were recorded for larvae with a reduced bacterial community compared to insects with a natural microbiome in laboratory conditions. In such conditions, higher larval survival rates and a higher percentage of larvae reaching the pupal and imago stages were recorded in insects whose bacterial community was reduced. Since the CLB bacterial microbiome showed a negative impact on the development of the insect's host and its survival in response to PIs in laboratory conditions, it can be concluded that CLB-associated bacteria can be an ally of its insect host, but also an adversary when conditions are not optimal for symbiosis.},
}

Animals
*Coleoptera/microbiology/growth & development/drug effects
Larva/microbiology/growth & development/drug effects
*Protease Inhibitors/pharmacology
*Bacteria
Microbiota
*Adaptation, Physiological
Edible Grain/parasitology

@article {pmid41238138,
year = {2025},
author = {Bae, S and Ha, GS and Cheong, DY and Baek, G},
title = {Evaluating the potential of treating organic acid-pretreated mixed fruit waste in a 13-L microbial electrolysis cell.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133641},
doi = {10.1016/j.biortech.2025.133641},
pmid = {41238138},
issn = {1873-2976},
abstract = {Microbial electrolysis cells (MECs) offer a sustainable approach to producing hydrogen (H2) from organic waste. However, industrialization of MECs is hindered by a low H2 production rate (HPR), mainly due to inefficient mass transfer between microbes and electrodes. To overcome this limitation, efficient dual-chamber MEC reactor design and evaluation of various substrate applicability are essential. In this study, we investigated the potential of mixed fruit waste (MFW) as an MEC substrate and its impact on microbial community dynamics in a multi-stack MEC reactor designed for H2 production. To enhance microbial utilization, MFW was pretreated with eco-friendly organic acids (i.e., citric acid), achieving a high carbohydrate extraction efficiency of 82 %. Physicochemical analyses of MFW before and after pretreatment confirmed effective hydrolysis. MEC operation with 25 % MFW extract achieved a high chemical oxygen demand (COD) removal efficiency of 77 % and a maximum current density of 0.71 A/m[2] (16.36 A/m[3]). Organic components in the MFW extract, including 5-hydroxymethylfurfural (HMF) and furan derivatives, were completely decomposed during MEC operation. Notably, microbial community analysis revealed distinct spatial distributions across the anode's vertical positions. Fermentative bacteria predominated in the bottom section, while electroactive genera such as Geobacter and Comamonas dominated the top section, likely due to the upward flow and recirculation of the organic substrate introduced at the bottom. The proposed multi-stack MEC process enhanced substrate utilization and microbial symbiosis interactions, highlighting its potential for industrial-scale applications.},
}

@article {pmid41234736,
year = {2025},
author = {Zhang, Q and Ma, S and Wang, R and Li, L and Zhang, Q and Ju, M and Gu, P},
title = {Diversity and drivers of arbuscular mycorrhizal fungi in the rhizosphere soil of wine grape in the eastern foot of Helan Mountain in Ningxia of China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1700411},
pmid = {41234736},
issn = {1664-302X},
abstract = {INTRODUCTION: Arbuscular mycorrhizal fungi (AMF) are symbiotic microorganisms that exert positive effects on their host plants. However, their colonization and community diversity in wine grapes remain unclear.

METHODS: This study investigated roots and rhizosphere soils from Cabernet Sauvignon grapevines in vineyards in seven ecological regions at the eastern foot of the Helan Mountains in Ningxia, China. We employed Illumina MiSeq high-throughput sequencing to analyze AMF community composition and diversity in the rhizosphere soil, and examined the effects of soil factors on AMF communities.

RESULTS: The results showed that the grapevine root system was colonized by AMF, with significant spatial heterogeneity in colonization rates and spore densities across the sample plots. Differences in the diversity of the AMF communities in the rhizosphere soil of wine grapes in the different sample plots were observed, and these AMF communities were further divided into three groups. In total, 168 operational taxonomic units were detected in the rhizosphere soil, corresponding to 40 AMF species from five orders, seven families, and seven genera. The Glomus and Glomus melanosporum were the dominant genus and species, respectively. Claroideoglomus and Glomus were identified as biomarkers. Soil pH and organic matter were key factors influencing AMF colonization, abundance, diversity, and community composition.

DISCUSSION: The grape rhizosphere in this region hosts a rich diversity of AMF. This finding provides a reference for the protection and commercial cultivation of AMF in wine grape rhizospheres.},
}

@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.

RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.

CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}

*Anthozoa/microbiology
Animals
*Symbiosis
*Nitrogen Cycle
Metagenomics/methods
Microbiota
Brazil
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
In Situ Hybridization, Fluorescence