@article {pmid40962294,
year = {2025},
author = {Bithell, SL and Asif, MA and Chowdhury, J and Kamiri, AK and Snijders, F and Harden, S and Plett, KL and Plett, JM},
title = {Genetic Insights Into Pathways Supporting Optimized Biological Nitrogen Fixation in Chickpea and Their Interaction With Disease Resistance Breeding.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70514},
doi = {10.1111/ppl.70514},
pmid = {40962294},
issn = {1399-3054},
support = {DAN00172//Grains Research and Development Corporation/ ; DAN00213 (BLG205)//Grains Research and Development Corporation/ ; },
mesh = {*Cicer/genetics/microbiology/metabolism ; *Nitrogen Fixation/genetics/physiology ; *Disease Resistance/genetics ; Quantitative Trait Loci/genetics ; *Plant Diseases/microbiology/genetics ; Mesorhizobium/physiology ; *Plant Breeding ; Symbiosis/genetics ; Genotype ; Phytophthora/physiology ; Gene Expression Regulation, Plant ; },
abstract = {In chickpea (Cicer arietinum), a globally important grain legume, improvements in yield stability are required to address food security and agricultural land loss. One approach is to improve both nutrient acquisition through symbiosis with rhizobial bacteria and biotic stress resistance. To support the simultaneous selection of multiple beneficial traits, we sought to identify quantitative trait loci (QTL) and genes linked to improved plant-microbe symbiosis both under symbiosis-promotive growth conditions and when pathogens are present. Our aims were to use the chickpea-Mesorhizobium rhizobial model to identify QTL associated with biological nitrogen fixation (BNF) and nutrient acquisition and understand factors promotive of sustained BNF under biotic stress through the impact of Phytophthora root rot (PRR) on BNF across chickpea genotypes on host gene expression. Using two chickpea × C. echinospermum recombinant inbred line (RIL) populations, we identified QTL associated with BNF and several associated with macro- and micro-nutrient status of chickpea. From within a set of the most PRR-resistant RIL (n = 70), we successfully identified RIL with both high PRR resistance and N sourced from BNF. In conditions of the tripartite (host:rhizobia:pathogen) interaction, while there was no consistent pathogen impact on the abundance of Mesorhizobium in nodules, PRR-resistant genotypes maintained a higher activity of their N-assimilation genes, while susceptible genotypes repressed these genes. This improved understanding of the genetic support of BNF in chickpea will allow selection for material that maintains higher BNF and is more disease resistant, which together may improve yield stability in chickpea.},
}

*Cicer/genetics/microbiology/metabolism
*Nitrogen Fixation/genetics/physiology
*Disease Resistance/genetics
Quantitative Trait Loci/genetics
*Plant Diseases/microbiology/genetics
Mesorhizobium/physiology
*Plant Breeding
Symbiosis/genetics
Genotype
Phytophthora/physiology
Gene Expression Regulation, Plant

@article {pmid40962161,
year = {2025},
author = {Lin, LB and Cao, X and Shi, W and Shen, D and Wang, MN and Wang, JY and Ning, JH and Hu, JY and Duan, DZ and Wang, XL and Xiao, J},
title = {Acroeremophilanes A-I, eremophilane-type sesquiterpenoids from the Sinomenium acutum-derived symbiotic fungus Acrocalymma cycadis.},
journal = {Phytochemistry},
volume = {},
number = {},
pages = {114677},
doi = {10.1016/j.phytochem.2025.114677},
pmid = {40962161},
issn = {1873-3700},
abstract = {This study separated nine previously undescribed highly oxygenated eremophilane sesquiterpenoids, designated as acroeremophilanes A-I (1-9), as well as three identified analogs (10-12), in the symbiotic fungus Acrocalymma cycadis derived from Sinomenium acutum. Structural elucidation of the metabolites was achieved using 1D and 2D NMR; HR-ESI-TOF-MS; single-crystal X-ray diffraction; and ECD spectra calculations. Notably, acroeremophilane A (1) was identified as an unusual chlorinated nor-eremophilane sesquiterpenoid incorporating an α,β-unsaturated ketone unit with an enol fragment. Acroeremophilanes F-H (6-8) were characterized as rare glycosylated eremophilane sesquiterpenoids derived from the symbiotic fungus. The in vitro cytotoxicities showed that C-1 substituted chlorinated eremophilane sesquiterpenoids displayed obvious cytotoxicity, in which acroeremophilane C (3) exhibited potent cytotoxicity to HeLa and A549 cells, and IC50 values were 2.89 and 4.55 μM, separately. The results of the apoptosis assays indicated that compound 3 primarily induces apoptotic cell death.},
}

@article {pmid40961934,
year = {2025},
author = {Zhang, X and Jin, X and Li, J and Dini-Andreote, F and Li, H and Khashi U Rahman, M and Du, M and Wu, F and Wei, Z and Zhou, X and van der Heijden, MGA and Rillig, MC},
title = {Common mycorrhizal networks facilitate plant disease resistance by altering rhizosphere microbiome assembly.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.08.016},
pmid = {40961934},
issn = {1934-6069},
abstract = {Arbuscular mycorrhizal fungi can interconnect the roots of individual plants by forming common mycorrhizal networks (CMNs). These symbiotic structures can act as conduits for interplant communication. Despite their importance, the mechanisms of signal transfer via CMNs and their implications for plant community performance remain unknown. Here, we demonstrate that CMNs act as a pathway to elicit defense responses in healthy receiver plants connected to pathogen-infected donors. Specifically, we show that donor plants infected by the phytopathogen Botrytis cinerea transfer jasmonic acid via CMNs, which then act as a chemical signal in receiver plants. This signal transfer to receiver plants induces shifts in root exudates, promoting the recruitment of specific microbial taxa (Streptomyces and Actinoplanes) that are directly linked to the suppression of B. cinerea infection. Collectively, our study reveals that CMNs act as interplant chemical communication conduits, transferring signals that contribute to plant disease resistance via modulation of the rhizosphere microbiota.},
}

@article {pmid40961931,
year = {2025},
author = {Li, L and Yang, Q and Liu, M and Lin, S and Hua, W and Shi, D and Yan, J and Shi, X and Hoffmann, AA and Zhu, B and Liang, P},
title = {Symbiotic bacteria mediate chemical-insecticide resistance but enhance the efficacy of a biological insecticide in diamondback moth.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.09.022},
pmid = {40961931},
issn = {1879-0445},
}

@article {pmid40961929,
year = {2025},
author = {Fang, J and Wang, X and Li, L and Liu, J and Fang, L and Xiao, Y and Wang, Y and Fang, Z},
title = {A sucrose transporter from Gongronella butleri w5 mediates plant-fungus-bacteria interaction.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.043},
pmid = {40961929},
issn = {1879-0445},
abstract = {Beneficial fungi in the plant rhizosphere connect plants and soil bacteria by releasing carbon sources as a bridge. Sucrose, a direct product of plant photosynthesis, plays a crucial role in this process. Here, we report that the sucrose transporter (SUT) protein GspSUT1 worked as a key regulator in the plant-beneficial fungus Gongronella butleri w5 (w5) and promoted plant growth by modulating carbon allocation during plant-fungus-bacteria interactions. The GspSUT1 expression was upregulated during the w5-plant interaction, accompanied by a decrease in sucrose in the root of Actinidia chinensis var. Chinensis "Hongyang." Knocking down the expression level of GspSUT1 through host-induced gene silencing (HIGS) led to the accumulation of sucrose in the plant root and a reduction in the release of monosaccharides into the environment, which in turn decreased the abundance of soil nitrogen-fixing bacteria and lowered the available nitrogen content in the soil, thereby weakening the ability of w5 to promote plant growth. Our research suggested that GspSUT1 from w5 played a crucial role in promoting plant growth and proved that the SUTs in beneficial fungi can influence soil microbial composition by regulating carbon allocation during plant-fungus-bacteria interactions, thereby improving soil nutrient availability and promoting plant growth.},
}

@article {pmid40961676,
year = {2025},
author = {Ma, J and Sun, H and Ji, Y and He, Q and Chen, L and Han, Y and Bi, P and Zhu, L},
title = {Niche differentiation drives microbial community assembly in an anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) system: Insights into Anammox self-enrichment.},
journal = {Water research},
volume = {288},
number = {Pt A},
pages = {124615},
doi = {10.1016/j.watres.2025.124615},
pmid = {40961676},
issn = {1879-2448},
abstract = {Integrating anammox into the anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) process presents a promising strategy for low-carbon wastewater treatment. Operating under low dissolved oxygen (DO) conditions, the AOA-AGS system enables in situ enrichment of anaerobic ammonia-oxidizing bacteria (AnAOB) via sludge granulation. This study addresses two key questions: how to drive AnAOB self-enrichment during AGS formation and how microbial aggregates of different sizes contribute to the balance between nitrogen and phosphorus removal. In an AOA-AGS sequencing batch reactor (SBR) operated at a DO concentration of 0.30 mg/L, AnAOB self-enrichment was successfully achieved (0-1.25 %). The system demonstrated efficient and stable nutrients removal, with removal efficiencies of chemical oxygen demand (COD), total inorganic nitrogen (TIN), and total phosphorus (TP) reaching 88.70 ± 4.96 %, 84.24 ± 3.59 %, and 96.76 ± 1.67 %, respectively. Microbial community assembly was primarily governed by deterministic processes, with niche differentiation facilitating the enrichment of AnAOB. The granular sludge exhibited a broader niche breadth (0.6596) compared to flocculent sludge (0.5885), supporting the coexistence of AnAOB and other functional microorganisms. Co-occurrence network analysis revealed cooperative or symbiotic relationship among functional bacteria (positive correlations accounted for 54.89 %), with 10 keystone taxa collectively shaping microbial community and function. Functionally, large granules (500-2000 μm) exhibited greater anammox capacity, and large flocs (100-200 μm) and small granules (200-500 μm) contributed to simultaneous nitrification and endogenous denitrification (SNED), whereas small flocs (<100 μm) exhibited stronger phosphorus metabolism potential. Phosphorus-rich flocs were selectively discharged, while AnAOB were effectively retained within granules. These findings offer practical insights for optimizing AOA-AGS system and advancing energy-efficient wastewater treatment technologies.},
}

@article {pmid40961203,
year = {2025},
author = {Girard, EB and Del Rio-Hortega, L and Pratama, AMA and Volkenandt, S and Macher, JN and Wilken, S and Renema, W},
title = {Specific host-algae relationship, yet flexible bacterial microbiome, in diatom-bearing foraminifera.},
journal = {Science advances},
volume = {11},
number = {38},
pages = {eadx4098},
doi = {10.1126/sciadv.adx4098},
pmid = {40961203},
issn = {2375-2548},
mesh = {*Diatoms/microbiology/genetics ; *Foraminifera/microbiology/physiology ; *Microbiota ; Symbiosis ; *Bacteria/genetics/classification ; Ecosystem ; Phylogeny ; },
abstract = {Whether the adaptive strategies of marine mixotrophs, organisms that combine heterotrophic and autotrophic nutrition, in response to global change are rooted in their symbiotic relationships is debated, especially for larger benthic foraminifera. Despite their importance in the ecosystem, there are controversial findings regarding the specificity of their algal endobionts, preventing a deeper understanding of their adaptive strategies. Using single-cell metabarcoding on 243 diatom-bearing foraminifera specimens from Indonesia, we found one highly dominant diatom strain in each foraminiferal host species bearing at least 90% of the reads in a majority of host species, whereas the bacterial community was very flexible, with only 25% of the variation explained by water depth, substrate type, location, and host species. Our results suggest that the adaptive strategy of the foraminiferal holobiont rather lies within its bacterial endobiome. Its dynamism likely facilitates the adaptive potential of foraminifera, supporting their proliferation across different environmental settings.},
}

*Diatoms/microbiology/genetics
*Foraminifera/microbiology/physiology
*Microbiota
Symbiosis
*Bacteria/genetics/classification
Ecosystem
Phylogeny

@article {pmid40960226,
year = {2025},
author = {Zhao, X and Ren, Z and Cao, D and Shao, Z and Liu, M and Huang, Y},
title = {Pre-Colonization of Bacillus siamensis on Ocular Surface Mitigates Fusarium keratitis Through Direct Antifungal Activity and Pre-Activation of NF-κB Pathway.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {12},
pages = {38},
doi = {10.1167/iovs.66.12.38},
pmid = {40960226},
issn = {1552-5783},
mesh = {Animals ; Mice ; *NF-kappa B/metabolism ; *Eye Infections, Fungal/microbiology/metabolism ; *Bacillus/physiology ; *Fusariosis/microbiology/metabolism ; *Keratitis/microbiology/metabolism ; *Fusarium/isolation & purification ; *Antifungal Agents/pharmacology ; Humans ; Signal Transduction ; Male ; Female ; Disease Models, Animal ; Tomography, Optical Coherence ; *Corneal Ulcer/microbiology ; Blotting, Western ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; *Cornea/microbiology ; },
abstract = {PURPOSE: Fungal keratitis (FK) is a severe ocular disease that leads to corneal ulceration and permanent vision loss. The ocular surface microbiota comprises beneficial symbiotic and pathogenic bacteria. Therefore, this study aimed to isolate beneficial bacterial strains from the ocular surface and evaluate their effect on Fusarium infections.

METHODS: Alterations in the ocular surface microbiota of patients with FK were analyzed using 16S rRNA sequencing. Candidate bacteria were isolated from mouse eyeballs and evaluated for antifungal activity. Quantitative PCR (qPCR) and culture were used to determine the colonization efficiency of Bacillus siamensis (B. siamensis). In addition, its biological safety was assessed. The effects of B. siamensis pre-colonization on Fusarium keratitis were evaluated using slit-lamp examination, clinical scoring, optical coherence tomography, hematoxylin and eosin staining, and RNA sequencing. Western blotting and RT-qPCR were used to assess its effects of on NF-κB signaling and inflammation, whereas flow cytometry was used to measure changes in immune cell populations following B. siamensis pre-colonization.

RESULTS: Ocular surface microbiota of patients with FK had significantly low levels of Bacilli. B. siamensis exhibited significant direct antifungal activity with minimal toxicity. Pre-colonization with B. siamensis mitigated FK-associated corneal edema and opacity, structural damage, inflammation, and fungal burden. Additionally, it enhanced ocular surface immunity into a "pre-immune" state by activating NF-κB pathway in healthy mice cornea.

CONCLUSIONS: B. siamensis on the ocular surface can directly engulf Fusarium hyphae and secrete antifungal substances to exert antifungal effects. Moreover, it enhanced ocular surface immunity into a "pre-immune" state by activating NF-κB pathway to facilitate rapid immune response.},
}

Animals
Mice
*NF-kappa B/metabolism
*Eye Infections, Fungal/microbiology/metabolism
*Bacillus/physiology
*Fusariosis/microbiology/metabolism
*Keratitis/microbiology/metabolism
*Fusarium/isolation & purification
*Antifungal Agents/pharmacology
Humans
Signal Transduction
Male
Female
Disease Models, Animal
Tomography, Optical Coherence
*Corneal Ulcer/microbiology
Blotting, Western
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
*Cornea/microbiology

@article {pmid40960018,
year = {2025},
author = {Wang, Y and Hu, S and Zhu, F and Li, X and You, L and Chen, Z and Hu, B and Zhao, F},
title = {Mitigating Ecological Risks: Role of Arbuscular Mycorrhizal Symbiosis in Translocation and Transformation of Per- and Polyfluoroalkyl Substances in Constructed Wetlands.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06131},
pmid = {40960018},
issn = {1520-5851},
abstract = {Arbuscular mycorrhizal fungi (AMF) are increasingly recognized for their potential to remediate per- and polyfluoroalkyl substances (PFASs) in constructed wetlands (CWs), but their mechanisms in affecting PFAS removal remain unclear. This study aims to elucidate AMF's impacts on PFAS removal and their role in mitigating the environmental risks posed by residual PFASs in the effluent. The results indicated that the primary removal pathways of PFASs in CWs were substrate adsorption and microbial degradation, while plant uptake contributed minimally (0.2-0.3%). AMF enhanced host plant absorption and translocation of PFASs, thereby increasing PFAS accumulation in plant tissues. Additionally, AMF promoted the enrichment of key microbes (e.g., Chloroflexi and Proteobacteria), which stabilized and enhanced the activity of the rhizosphere microbial network, facilitating PFAS biotransformation and degradation. Through the reinforcement of microbial degradation, substrate adsorption, and plant uptake pathways, AMF symbiosis significantly enhanced PFAS removal, increasing efficiency by 10.5-13.3% compared to treatments without AMF. Notably, long-chain (C > 7) PFASs pose higher ecological risks compared to short-chain (C ≤ 7) PFASs. AMF effectively reduced the ecological risks associated with residual PFASs and their metabolites in the effluent. The results highlight AMF's potential to improve PFAS removal in CWs and offer valuable insights for developing sustainable, high-efficiency pollution control strategies.},
}

@article {pmid40959591,
year = {2025},
author = {Ye, X and Yigitcanlar, T and Goodchild, M and Huang, X and Li, W and Shaw, SL and Fu, Y and Gong, W and Newman, G},
title = {Artificial intelligence in urban science: why does it matter?.},
journal = {Annals of GIS},
volume = {31},
number = {2},
pages = {181-189},
pmid = {40959591},
issn = {1947-5683},
abstract = {Urban science aims to explain, discover, understand, and generalize (EDUG) complex, human-centric systems, emphasizing societal context and sustainability. However, integrating artificial intelligence (AI) into urban science presents challenges, including data availability, ethical considerations, and the 'black-box' nature of many AI models. Despite these limitations, AI offers significant opportunities for urban management and planning by leveraging vast, multimodal datasets to optimize infrastructure, predict trends, and enhance resilience. Techniques such as explainable AI and knowledge-driven approaches have begun addressing transparency concerns, aligning AI outputs with urban science's emphasis on interpretability. Urban science reciprocally contributes to AI development by embedding contextual awareness and human-centric insights, enhancing AI's ability to navigate urban complexities. Examples include digital twins for real-time urban analysis and generative AI for inclusive urban modelling. This opinion piece advocates for fostering a symbiotic relationship between AI and urban science, emphasizing co-learning and ethical collaboration. By integrating technical innovation with societal needs, the convergence of AI and urban science - termed the 'New Urban Science' - promises smarter, equitable, and sustainable cities. This paradigm underscores the transformative potential of aligning AI advancements with urban science's foundational goals.},
}

@article {pmid40959553,
year = {2025},
author = {Ottaway, M and Swinnen, J and Verhaevert, K and Ruytinx, J},
title = {Impact of sublethal zinc exposure on ectomycorrhizal Laccaria bicolor x poplar symbiosis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1656580},
pmid = {40959553},
issn = {1664-462X},
abstract = {Soil Zn pollution is a widespread problem that is impacting on plant growth and production. Several tree species can rely on fungal ectomycorrhizal symbionts to mitigate toxicity effects to some extent. Here, we explored the impact of Zn pollution on L. bicolor and its ectomycorrhizal symbiosis with Populus tremula x alba. Next to growth and morphological parameters in sublethal Zn exposure, we investigated responses of symbiosis marker genes, reactive oxygen species scavenging enzymes and Zn transporters in presence and absence of a host plant. Our results indicate that the ECM symbiosis development is maintained in excess Zn conditions despite a reduction in fungal and plant growth. Symbiosis marker gene expression showed sensitivity to Zn excess, even when the fungus was cultured in absence of a host. Zn-induced transcriptional responses of ROS scavenging enzymes and Zn transporters were mainly restricted to mycelia in presence of a host and less prevalent without host. Establishment of new homeostatic equilibria, in particular in presence of a host, seem essential to maintain symbiosis, protect the host and adapt physiologically to Zn pollution. This research furthers our understanding of how resilient plant-fungal symbiotic interactions are, and the interplay between both partners in changing environmental conditions.},
}

@article {pmid40959550,
year = {2025},
author = {Mahto, RK and B S, C and Singh, RK and Kumar, A and Kumar, S and Yadav, R and Dey, D and Hamwieh, A and Kumar, R},
title = {Symbiotic nitrogen fixation for sustainable chickpea yield and prospects for genome editing in changing climatic situations.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1621191},
pmid = {40959550},
issn = {1664-462X},
abstract = {Chickpea (Cicer arietinum L.) is a vital/essential legume crop valued for its nutritional, agricultural, and economic importance, with a relatively large genome size of approximately 738 megabases. Chickpea roots establish symbiotic relationships with soil microorganisms, resulting in the formation of root nodules essential for biological nitrogen fixation. In this study, 20 chickpea genotypes were selected from a genome-wide association panel to assess nodulation traits under eight different treatment combinations involving biofertilizers (Rhizobium, vesicular-arbuscular mycorrhiza - VAM) and inorganic fertilizers (NPK) using a randomized block design with three replications. Pre-planting soil preparation included the application of fertilizers and biofertilizers. Comprehensive analyses including descriptive statistics, correlation, path analysis, principal component analysis, agglomerative hierarchical clustering, and gene expression studies were conducted. Among treatments, the NPK+Rhizobium combination significantly enhanced nodulation across genotypes, while the Rhizobium+VAM (T7) treatment identified ICC-9085 as a superior donor for the number of nodules, aiming for sustainable chickpea productivity. Gene expression profiling through qRT-PCR revealed that the RZ+VAM treatment notably upregulated several key genes, including CaNFP, GST, Leghemoglobin, Nodulin6, and CaLYK3, with CaNFP emerging as a pivotal regulator of nodulation. The marked upregulation of CaNFP underlines its potential as a target for enhancing symbiotic efficiency. The availability of the chickpea draft genome opens new avenues for employing genome editing tools such as CRISPR/Cas systems. Targeted editing of the CaNFP gene offers a promising strategy to improve nodule formation, nitrogen fixation, and overall plant vigor. Integrating CaNFP gene through genome editing with potential genotypes and use of microbial treatments can accelerate the development of elite chickpea cultivars, enhancing productivity while reducing reliance on chemical fertilizers and supporting sustainable agricultural practices.},
}

@article {pmid40959220,
year = {2025},
author = {Zhang, J and Yin, Y and Wang, Y and Luo, S and Li, Y and Zhao, W and Cao, P and Liu, Y and Ma, H},
title = {Analysis of the community composition and diversity of endophytes in extremely spicy industrial chili peppers from Tibet using high-throughput sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1630090},
pmid = {40959220},
issn = {1664-302X},
abstract = {Industrial chili peppers contain more than 100 times the capsaicin content of common chili peppers; these peppers are primarily used for industrial processing and capsaicin extraction. Chili peppers thrive in warm temperatures, require plenty of sunlight, and are drought-resistant; therefore, making the high-altitude climate of Tibet ideal for their cultivation. Endophytes are microorganisms that can inhabit healthy plants at various stages of their life cycle. Through long-term co-evolution, endophytes and host plants establish a mutually beneficial symbiotic relationship, which assists plants in secondary metabolite production. This study investigated the differences in endophyte community structure across various lines of industrial chili peppers. It also explored the relationship between capsaicinoids and endophyte community composition in high-altitude habitats of Tibet using high-throughput sequencing to obtain fundamental data on industrial chili pepper endophytes. The results showed that the diversity of endophyte communities was characterized by conservatism among groups and that the composition and community structure of endophyte communities were specific to different groups. Community composition analysis revealed that there were generally consistent dominant phyla of endophytic microorganisms in industrial chili peppers, although differences in their relative abundance percentage were observed. Bacterial community composition at the genus level was less affected by capsaicin concentration across different groups; however, the fungal community composition at the genus level was more responsive to capsaicinoid concentrations than that of bacteria. Bacterial communities from four different chili pepper varieties showed significant differences in the enrichment of genera. Fungi were differentially enriched in two groups: the td1 group with high capsaicin concentrations and the sylj group with low capsaicin concentrations. Among the four groups, endophytic bacteria exhibited the highest percentage of genes associated with unknown functions, while fungal trophic patterns had the most significant percentage of unknown trophic types. Overall, this study provides a valuable reference for the efficient cultivation and utilization of industrial chili peppers in Tibet.},
}

@article {pmid40958419,
year = {2025},
author = {Zhang, W and Liu, W and Wang, K and Cheng, H and Bai, X and Zhang, J and Wei, G and Chen, J},
title = {Persulfidation of host NADPH oxidase RbohB by rhizobial 3-mercaptopyruvate sulfurtransferase maintains redox homeostasis and promotes symbiotic nodulation in soybean.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.09.013},
pmid = {40958419},
issn = {1752-9867},
abstract = {Reactive oxygen species (ROS) play a crucial role in various stages of legume-rhizobium symbiosis, from initial nodulation signaling to nodule senescence. However, how rhizobial redox-related proteins regulate symbiotic nodulation in legumes remains largely unknown. By combining transcriptomics, proteomics, and biochemical and molecular genetics, we investigated the role of the Sinorhizobium fredii Q8 enzyme 3-mercaptopyruvate sulfurtransferase (3MST). Although 3MST was not the primary source of hydrogen sulfide (H2S) under our conditions, its absence significantly disrupted symbiotic nodule development, redox homeostasis, infection capacity, and nitrogen fixation efficiency in soybean. We identified host plasma membrane-localized NADPH oxidase (RbohB) as a pivotal regulator that activates immune responses during nodule development. Notably, 3MST localized to the nucleoid and cytoplasmic membrane and was secreted during nodulation, where it interacted with RbohB and persulfidated Cys791 to suppress NADPH oxidase activity. This 3MST-mediated regulation maintained symbiotic redox balance and promoted nodule development. Genetic analysis of soybean involving RbohB overexpression, RNA interference and site-directed mutagenesis at Cys791 supported the model, linking the 3MST-RbohB interaction to effective rhizobial colonization and improved plant growth. Collectively, our findings shed light on a rhizobium-host redox pathway in which a rhizobial sulfurtransferase modulates RbohB via persulfidation to promote nodulation.},
}

@article {pmid40958172,
year = {2025},
author = {Saidi, R and Idbella, M and Ndiaye, PA and Ibnyasser, A and Houasli, C and Rchiad, Z and Miftah Kadmiri, I and Daoui, K and Bargaz, A},
title = {Genotype and Phosphorus Availability Shape Chickpea Symbiotic Efficiency and Rhizosphere Microbiome Composition, Driving Contrasting Agro-Physiological Responses.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70181},
pmid = {40958172},
issn = {1365-3040},
support = {//This study was financially supported by OCP Foundation at UM6P through UGF (Unité de Gestion des Fonds) within the sustainable agriculture R&D programme between Mohammed VI Polytechnic University (UM6P) and Agronomic Research Institute (INRA) in Morocco./ ; },
abstract = {Co-inoculation of grain legumes, including chickpea, with nitrogen-fixing and phosphate-solubilising bacteria (PSB) improves symbiotic efficiency and plant productivity under low-P availability. However, the extent of chickpea's responsiveness to inoculation and their reliance on symbiotic nitrogen (N) fixation remains intricately influenced by plant genotypic diversity and the associated rhizosphere microbiome under different P levels. This study evaluated the agro-physiological, symbiotic and microbial traits of two Moroccan winter chickpea (Cicer arietinum) varieties (Arifi and Bochra) under low-P conditions represented by three rock-P levels (0, 25, 50 and 75 kg P2O5 ha[-1]) and co-inoculation with Mesorhizobium ciceri and Rhanella aceri (PSB). Results showed that inoculation at rock-P levels ≥ 50 kg P2O5 ha[-1], significantly improved symbiotic traits, plant biomass and nutrient uptake in both varieties, with Bochra exhibiting superior performance. At 75 kg P2O5 ha[-1] of rock-P, Bochra exhibited a strong correlation between root morphological traits and P-related rhizosphere traits. Results further highlighted Bochra's robust response to inoculation under 75 kg P2O5 ha[-1] rock-P, driven by its ability to shape the rhizobacterial community composition, where Mesorhizobium dominated and significantly influenced plant and rhizosphere traits. More notably in Bochra than Arifi, rhizobacterial species richness and community composition correlated strongly with nodule traits, plant traits and rhizosphere P-related parameters. These findings elucidate the significant contribution of the rhizosphere bacterial community to the symbiotic performance of Mesorhizobium-inoculated chickpea, which remains both genotype- and P-dependent.},
}

@article {pmid40957907,
year = {2025},
author = {Purahong, W and Tanunchai, B and Ji, L and Stellmach, H and Hilman, B and Schulze, ED and Hause, B and Tarkka, M and Buscot, F and Herrmann, S},
title = {Plasticity of symbiotroph-saprotroph lifestyles of Piloderma croceum associated with Quercus robur L.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1344},
pmid = {40957907},
issn = {2399-3642},
mesh = {*Quercus/microbiology ; *Symbiosis ; *Mycorrhizae/physiology ; Plant Roots/microbiology ; Wood/microbiology ; *Basidiomycota/physiology ; Mycelium/growth & development ; },
abstract = {Besides their symbiotic association with tree rootlets, ectomycorrhizal (EM) fungi have been commonly detected in nature in deadwood and plant debris of various tree species. However, their potential dual roles as symbiotrophs and saprotrophs are still debated. Here, we provide evidence from a series of experiments on the plasticity of symbiotrophic-saprotrophic lifestyles of the ectomycorrhizal fungus Piloderma croceum associated with Quercus robur L. Specifically, we find that P. croceum efficiently colonizes deadwood of oak in an experimental system without living oak. Results based on the productions of hydrolytic enzymes and corticrocin as well as the [14]C content in deadwood and mycelium of P. croceum demonstrate its capability of wood decomposition and assimilation of C from the decomposing wood. Our results also show that in presence of wood pieces colonized by saprotrophic mycelium of P. croceum, the roots of oak plants develop true EM symbiosis with Hartig net formation. Collectively, our results indicate a role for mycelium growing in deadwood as an underestimated EM fungus propagule bank, suggesting that deadwood and other decomposing plant material may indirectly influence the productivity of forest ecosystems by contributing to the recruitment of mycorrhizal fungi, thereby enhancing plant nutrient acquisition.},
}

*Quercus/microbiology
*Symbiosis
*Mycorrhizae/physiology
Plant Roots/microbiology
Wood/microbiology
*Basidiomycota/physiology
Mycelium/growth & development

@article {pmid40961498,
year = {2024},
author = {French, KB and Herrera, MJ and German, DP},
title = {Sea Urchin Larvae (Strongylocentrotus purpuratus) Select and Maintain a Unique Microbiome Compared to Environmental Sources.},
journal = {The Biological bulletin},
volume = {247},
number = {1},
pages = {56-73},
doi = {10.1086/736931},
pmid = {40961498},
issn = {1939-8697},
mesh = {Animals ; Larva/microbiology/growth & development ; *Microbiota ; *Strongylocentrotus purpuratus/microbiology/growth & development ; Symbiosis ; Ecosystem ; Seawater ; Bacteria/classification/isolation & purification ; },
abstract = {AbstractMany organisms may rely on microbes that seed the host body and are typically maintained as a consortial symbiosis. Marine invertebrates have highly diverse microbiomes and offer many different life history traits across which to explore the members and functions of these symbionts but are largely absent from the holobiont and microbiome literature compared to humans and vertebrates. We tracked the microbiome of Strongylocentrotus purpuratus larvae and examined the role of vertical transmission via gametes and the role of horizontal transmission via diet and seawater for seeding the developing larvae with microbes potentially critical to holobiont health and fitness. We used 16S short-read sequencing to track the composition and relative abundances of bacteria associated with diet (microalgae) and with habitat (filtered seawater), as well as with S. purpuratus gametes and larvae under standard lab rearing conditions. The larval microbiome differed across developmental stages and between filtered seawater and algae, and specific bacterial taxa were associated with those differences. In this experiment, developing larvae selected and maintained a unique microbiome compared to their diet and habitat. Eggs were a potentially significant source of vertical transmission during embryonic development (genus Psychromonas), while horizontal transmission via filtered seawater was the main contributor to larval feeding stages, suggesting that filtered seawater is likely the most important source of potential symbionts. Gaining new insights into how marine invertebrate larval microbiomes are seeded and with what taxa is important for endangered-species aquaculture and for ecosystem restoration and management to protect inoculation sources for early-life stage organisms.},
}

Animals
Larva/microbiology/growth & development
*Microbiota
*Strongylocentrotus purpuratus/microbiology/growth & development
Symbiosis
Ecosystem
Seawater
Bacteria/classification/isolation & purification

@article {pmid40957508,
year = {2025},
author = {Maake, MM and Beukes, CW and Van Der Nest, MA and Avontuur, JR and Muema, EK and Stępkowski, T and Venter, SN and Steenkamp, ET},
title = {Argyrolobium legumes from an African centre of endemism associates with novel Bradyrhizobium species harbouring unique sets of symbiosis genes.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108471},
doi = {10.1016/j.ympev.2025.108471},
pmid = {40957508},
issn = {1095-9513},
abstract = {Given that several, mainly endemic South African Genisteae genera occupy basal positions in legume phylogenetic trees, this region of Africa is considered a primaeval centre of diversification of this legume tribe. Despite the importance of South Africa in Genisteae evolution, almost all studies have focused on rhizobia nodulating Genisteae species in their centres of diversity in either the Mediterranean Basin or the Americas. Therefore, this study aimed to identify and characterize rhizobial strains associated with Argyrolobium species native to areas of the Grassland biome associated with the Great Escarpment, which dominates the subcontinent's eastern landscape and compare these to bradyrhizobia nodulating Genisteae in the remaining centres of diversity. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB) separated the 18 Bradyrhizobium strains examined into five well-supported groups. Three of these were conspecific with B. arachidis, B. brasilense/B. australafricanum and B. ivorense, while the remaining two appeared to be new to science. After confirming their novelty using Average Nucleotide Identity, a metric for genome relatedness, and certain phenotypic traits, we recognized them as novel species for which we proposed the names B. spitzkopense sp. nov. (Arg816[Ts]) and B. mpumalangense sp. nov. (Arg237L[Ts]). Phylogenetic analyses of nodA gene sequences showed that about half of the strains examined, irrespective of their species identity, harboured alleles known only from the Grassland biome along the Great Escarpment that previously were detected in Bradyrhizobium strains nodulating Crotalarieae genera endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique nodA alleles typically encode the nodH gene, the product of which adds a sulfate moiety to the Nod factor (the signalling molecule for establishing the nitrogen-fixing symbiosis). The remaining strains had nodA alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, their genomes lacked nodH but encoded nodZ the gene involved in the fucosylation of the Nod factor. Our findings therefore showed that the root nodules of Genisteae (and its sister tribe Crotalarieae) native to the Grassland biome along the Great Escarpment are often related Bradyrhizobium strains that, however, are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas.},
}

@article {pmid40957209,
year = {2025},
author = {Feng, Y and Jiang, C and Zhang, W and Gong, L and Sun, L},
title = {Single and mixture toxicity effects of legacy and emerging per- and polyfluoroalkyl substances on submerged plants and epiphytic biofilms.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139862},
doi = {10.1016/j.jhazmat.2025.139862},
pmid = {40957209},
issn = {1873-3336},
abstract = {Although per- and polyfluoroalkyl substances (PFASs), often referred to as "forever chemicals," pose persistent threats to aquatic ecosystems, the effects of multiple PFAS types on submerged macrophyte-biofilm symbiotic systems remain poorly understood. In this study, we systematically investigated the impacts of single and combined exposures to both legacy and emerging PFAS on submerged macrophytes, biofilms, and associated microbial risks. Our results show that the growth of Vallisneria natans was inhibited under both single and mixed PFAS stress. Photosynthetic performance and nutrient uptake in V. natans were variably affected depending on the PFAS type. Emerging PFAS were more likely to induce oxidative stress, with malondialdehyde content increasing by 36.7 % under hexafluoropropylene oxide dimer acid exposure. Notably, PFAS stress significantly altered biofilm morphology and microbial community composition, including enrichment of several human bacterial pathogens. Additionally, PFAS exposure promoted the enrichment of antibiotic resistance genes (ARGs), and the increased abundance of mobile genetic elements suggested a higher potential for horizontal gene transfer. Co-occurrence network analysis further revealed that potential ARG hosts were affected under PFAS stress.},
}

@article {pmid40956093,
year = {2025},
author = {Zhao, X and Cai, M and Yin, S and Zhou, Z and Yang, J and Shen, Y and Xia, Z and Tang, Q and Yang, G and Yi, S and Gao, Q},
title = {Interaction of host gene-gut microbiota in male grading of Macrobrachium rosenbergii.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/spectrum.01290-25},
pmid = {40956093},
issn = {2165-0497},
abstract = {UNLABELLED: The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a crustacean of high nutritional and economic value, is crucial for aquaculture. During the same growth cycle, male GFPs develop into three distinct forms: small males, orange claw males, and blue claw males. These morphotypes display varying social behaviors, which severely constrain their industrial development. To address this, this study collected male GFP samples at critical developmental time points (100, 110, and 120 days post-hatching) for phenotypic trait measurement and analysis to obtain external morphological data. Through gut microbiota diversity analysis, we identified key gut bacteria (Lactococcus garvieae and Lactobacillus taiwanensis) influencing male morphotype differentiation. Transcriptomic analysis revealed host Kyoto Encyclopedia of Gene and Genome pathways and key genes (Wnt-6, CTSB, CTSL, PPAE, and TP53) associated with morphotype differentiation. The interactions among phenotypic traits, gut microbiota, and key genes were systematically studied through association analysis. Weighted gene co-expression network analysis was employed to construct co-expression modules, from which critical gene modules influencing phenotypic variation were identified. Through association network analysis, we established an "Achromobacter-CD-TRINITY_DN93139_c0_g2 (calpain clp-1)" interaction model. Our findings provide novel insights into the genetic enhancement of GFPs and offer guidelines for future research regarding gut symbiotic bacteria and breeding initiatives.

IMPORTANCE: Male Macrobrachium rosenbergii (giant freshwater prawn [GFP]) in the same growth cycle will develop into small males, orange claw males, and blue claw males. This individual heterogeneity in growth significantly impacts the benefits of aquaculture. However, the factors influencing the differentiation of male GFP morphotype remain unclear. This study analyzed the phenotypic data of various GFP levels, the structure of the intestinal microbiota, and the differential genes within the gonadal transcriptome at critical time points of male GFP-level type differentiation. The aim was to explore the potential role of intestinal microbiota and differential genes in this phenomenon. This study offers new insights into the research on the phenomenon of male GFP-level type differentiation.},
}

@article {pmid40954993,
year = {2025},
author = {Park, SL and Kim, MS and Kim, TH},
title = {Gut Microbiome and Estrogen.},
journal = {Journal of menopausal medicine},
volume = {31},
number = {2},
pages = {95-101},
doi = {10.6118/jmm.24024},
pmid = {40954993},
issn = {2288-6478},
support = {/SCH/Soonchunhyang University/Korea ; },
abstract = {Estrogens are steroid hormones that are involved in regulating the growth, development, and functioning of the human reproductive system as well as in controlling the neuroendocrine, skeletal, adipogenesis, and cardiovascular systems. Estrogen is released into the bloodstream in two different states: as a free hormone or in association with proteins such as sex hormone-binding globulin or albumin. Unbound estrogen, which is not bound to proteins, can freely pass through cell membranes without any regulatory constraints. The microbiome is a distinct microbial population that inhabits a well-defined environment characterized by specific physio-chemical properties. It engages in a symbiotic relationship with the host, assisting in internal equilibrium regulation and immune reaction modulation. Over the years, several research investigations have underscored the importance of the microbiome in promoting wellness and preventing illnesses. An alteration in the microbiome, also known as dysbiosis, can disrupt bodily processes and contribute to the onset of ailments such as cardiovascular disorders, cancers, and respiratory conditions. The microbiome plays a crucial role in maintaining human health. Several elements affect the balance of the intestinal microecological system such as dietary habits, medication usage, pathogens, and endocrine factors. Recent research has indicated a disparity between genders in the prevalence of certain diseases associated with the microbiome, with sex hormones playing a crucial role in affecting specific health conditions.},
}

@article {pmid40951973,
year = {2025},
author = {Ser, SL and Ware-Gilmore, F and Dennington, NL and Miller, A and McNulty, BP and Harris, ML and Jones, MJ and Hall, MD and Sgrò, CM and Shea, K and McGraw, EA},
title = {Repeated thermal stress exposure in Aedes aegypti co-infected with Wolbachia and dengue virus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0012925},
doi = {10.1128/msphere.00129-25},
pmid = {40951973},
issn = {2379-5042},
abstract = {UNLABELLED: Climate change is increasing the frequency and intensity of heatwaves, affecting the thermal tolerance of mosquitoes and potentially influencing the efficacy of the biological control agent, Wolbachia. This study investigates the impact of repeated thermal stress on Aedes aegypti mosquitoes co-infected with Wolbachia and dengue virus (DENV). We exposed infected mosquitoes (singly and in co-infection) to varying intensities, frequencies, and durations of thermal stress to assess their thermal sensitivity via a "knockdown assay" compared to uninfected controls. Our results demonstrate that co-infection with Wolbachia and DENV significantly increases thermal sensitivity, with mosquitoes exhibiting a twofold faster median knockdown time than either singly infected or uninfected controls in most cases. A comparison of mosquitoes with no prior heat exposure to those given a single exposure revealed some evidence of heat hardening, or a slight lengthening of time to knockdown. Additional exposures provided no substantial benefit, however. Extended thermal stress (60 mins) also significantly reduced DENV loads, while Wolbachia loads remained stable, indicating that prolonged heat may disrupt viral replication without affecting bacterial symbiosis. These findings suggest that heatwaves could lower vector competence and disproportionately affect DENV-infected mosquitoes in Wolbachia-release areas, with implications for biocontrol strategies. Field studies should explore how infection affects mosquitoes' ability to modulate thermal exposure behaviorally, providing insights for optimizing Wolbachia-based control efforts.

IMPORTANCE: Dengue virus (DENV), spread by the mosquito Aedes aegypti, is a major global health threat affecting millions of people. This study examines how repeated exposures to heat stress affect the thermal tolerance of mosquitoes infected with DENV and/or Wolbachia, a bacterium used for biological control. These repeated exposures mimic the experience of mosquitoes in the wild experiencing heatwaves of increasing frequency under climate change. Our research shows that Ae. aegypti co-infected with Wolbachia and DENV is more susceptible to thermal stress than singly infected or uninfected mosquitoes. We also demonstrate that multiple independent thermal stress exposures do not exacerbate the effect of infection. Understanding these interactions is essential for predicting how climate change may affect dengue transmission and the resilience of Wolbachia-based interventions.},
}

@article {pmid40951533,
year = {2025},
author = {Nie, Y and Shi, Y and Yang, Y},
title = {Gut Microbiota: Implications in Pathogenesis and Potential Therapeutic Target in Primary Biliary Cholangitis.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {9},
pages = {776-784},
pmid = {40951533},
issn = {2310-8819},
abstract = {Primary biliary cholangitis (PBC) is a chronic progressive autoimmune disorder characterized by small non-purulent intrahepatic bile duct destruction (ductopenia) and cholestasis. While the etiology of PBC remains unclear, it is believed to involve genetic-environmental interactions. Emerging evidence highlights gut microbiota dysbiosis in PBC patients, with increased symbiotic bacteria and decreased pathogenic bacteria. Microbial alterations potentially influence disease pathogenesis through multiple mechanisms, including immune dysregulation, intestinal barrier damage, BA metabolic dysregulation, and cholestasis. These findings suggest that the gut microbiota can serve not only as a non-invasive biomarker for diagnosis and prognosis evaluation but also as a therapeutic target for the disease. In this review, we summarize changes in PBC patients' gut microbiota, explain how these changes affect disease occurrence and development, and discuss treatment methods with potential clinical value that intervene in gut microbiota.},
}

@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}

@article {pmid40950589,
year = {2025},
author = {Li, YH and Yang, M and Wei, TS and Chen, HG and Gong, L and Wang, Y and Gao, ZM},
title = {Survival strategies for the microbiome in a vent-dwelling glass sponge from the middle Okinawa Trough.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1636046},
pmid = {40950589},
issn = {1664-302X},
abstract = {The adaptive mechanisms of sponge microbiomes to harsh deep-sea environments, including hydrothermal vents and cold seeps, remain unclear. Here, we used metagenomics to investigate the microbiome of an undescribed vent-dwelling glass sponge from the middle Okinawa Trough, probably representing a novel species within the family Bolosominae. Eleven high-quality prokaryotic metagenome-assembled genomes (MAGs) were retrieved, none assignable to known species, with two representing new genera. Dominant MAGs included sulfur-oxidizing bacteria (SOB) and ammonia-oxidizing archaea, followed by methane-oxidizing bacteria (MOB) and nitrite-oxidizing bacteria. Global distribution analysis suggested that most MAGs were sponge-specific symbionts. Comparative genomics revealed functional redundancy among SOB and early-stage genome reduction in a unique MOB lineage. Additionally, a total of 410 viral contigs were identified, most exhibiting a lytic lifestyle and forming distinct clades from known viruses. Our work expands understanding of the diversity and novelty of deep-sea sponge-associated prokaryotes and viromes, and suggests their niche adaptation to hydrothermal fluid environments.},
}

@article {pmid40948583,
year = {2025},
author = {Corning, C and Dolatmoradi, M and Tran, TH and Stacey, G and Szente, L and Samarah, LZ and Vertes, A},
title = {Degree of polymerization and spatial distributions of acyclic and cyclic oligohexoses in soybean root nodules uncovered by MALDI and nanophotonic laser desorption ionization mass spectrometry.},
journal = {Materials today. Bio},
volume = {32},
number = {},
pages = {101776},
pmid = {40948583},
issn = {2590-0064},
abstract = {In the symbiotic relationship of legumes and rhizobia, disaccharides, mostly sucrose, are produced by the plant and provided as energy and carbon sources for the bacteria. The microbes, in turn, store these carbohydrates as acyclic oligohexoses to buffer fluctuations in supply. Simultaneously, cyclic oligohexoses (β-glucans) of varying sizes and structures are synthesized by nitrogen-fixing soil bacteria both in free living form and in legume root nodules. In the bacteroids, transformed from Bradyrhizobium japonicum strain USDA110 in soybean (Glycine max) root nodules, glucose units are attached by glycosidic bonds and are known to contain degrees of polymerization with 10 ≤ n ≤ 13 repeat units in branched cyclic structures. Whereas cyclic β-glucans (CβGs) are thought to facilitate bacterial adaptation and legume-rhizobia symbiosis, information on their ring sizes, branching from the ring structures, and their spatial distributions within the nodules is scarce. Here we demonstrate that using mass spectrometry (MS), based on matrix-assisted laser desorption ionization (MALDI) and laser desorption ionization (LDI) from emerging silicon nanopost array (NAPA) nanophotonic platforms, the presence of a wider array of potentially cyclic oligohexoses can be discovered with degrees of polymerization in the 2 ≤ n ≤ 14 residue range. On the low end of the oligomer size distribution, the cyclic nature of CYn with n < 10 can be increasingly questioned based on the large strain such macrocycles would exhibit and the DP control during the CβG synthesis by the glucan phosphorylase involved in their synthesis. At the same time, acyclic oligohexoses with a degree of polymerization of 2 ≤ n ≤ 13 were also detected. Tandem MS with collision induced dissociation (CID) indicated that the cyclic structure with n = 12 contained a branching residue. It detached from the macrocycle at lower collision energies (70 instrument units), whereas the rings themselves fragmented at higher energies (90 instrument units). We also prove that the spatial distributions of acyclic and cyclic oligohexoses in the G. max nodules can be captured by MS imaging (MSI) based on MALDI and NAPA-LDI. The acyclic species were more abundant in the infection zone, whereas the cyclic oligohexoses appeared more concentrated in the inner cortex and in the root vasculature. At some locations, possibly in the vascular bundles surrounding the nodule and traversing the root, the cyclic oligohexoses were especially abundant. The distributions of acyclic oligohexoses were also mapped in the nodule sections. These linear or branching molecules were abundant in the infection zone, where the cyclic oligohexoses were less concentrated or absent.},
}

@article {pmid40947489,
year = {2025},
author = {Liu, Z and Hu, B and Flemetakis, E and Haensch, R and Franken, P and Rennenberg, H},
title = {Convergent evolution and adaptive diversification of root symbioses.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70077},
pmid = {40947489},
issn = {1469-185X},
support = {cstc2021ycjh-bgzxm0002//Chongqing Municipal Science and Technology Bureau/ ; cstc2021ycjh-bgzxm0020//Chongqing Municipal Science and Technology Bureau/ ; },
abstract = {Mutualistic symbioses between plants and microorganisms have served as a cornerstone for terrestrial ecosystem establishment since the colonization of land by plants ca. 470 million years ago (Ma). These mutualisms diversified in symbiont partners and ecological functions in response to dynamic environmental shifts, with root-based architectures emerging later as a key adaptive innovation. Phylogenomic analyses reveal a conserved common symbiotic signalling pathway (CSSP) through the mycorrhizal-actinorhizal-rhizobial (MAR) evolutionary trajectory, underscoring convergent evolutionary mechanisms that facilitated the repeated emergence of mutualistic root-microbe interactions. Despite this shared foundation, recent studies highlight lineage-specific adaptations in symbiont recognition, immune evasion, and nutrient exchange, reflecting divergent evolutionary pressures and ecological niches. For instance, actinorhizal symbioses, although understudied compared to legume-rhizobia systems, exhibit unique adaptations in host specificity and nitrogen-fixation efficiency, offering untapped potential for sustainable agriculture and reforestation. This review synthesizes information from different disciplines to elucidate the origin and diversification of root symbioses, emphasizing molecular innovations and ecological drivers that shaped their evolution. We further explore the role of environmental pressures, such as resource availability and climate change, in driving the adaptive diversification of these symbiotic relationships. By integrating evolutionary, molecular, and ecological perspectives, this work advances our understanding of root symbioses as dynamic systems shaped by both conserved mechanisms and context-dependent adaptations.},
}

@article {pmid40909553,
year = {2025},
author = {Pujhari, S and Heebner, J and Raumann, E and Zhong, T and Rasgon, JL and Swulius, MT and Shaffer, CL and Kaplan, M},
title = {In situ architecture of the endosymbiont Wolbachia pipientis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40909553},
issn = {2692-8205},
support = {P20 GM130456/GM/NIGMS NIH HHS/United States ; R01 AI116636/AI/NIAID NIH HHS/United States ; R35 GM157116/GM/NIGMS NIH HHS/United States ; },
abstract = {Hidden within host cells, the endosymbiont Wolbachia pipientis is the most prevalent bacterial infection in the animal kingdom. Scientific breakthroughs over the past century yielded fundamental mechanisms by which Wolbachia controls arthropod reproduction to shape dynamic ecological and evolutionary trajectories. However, the structure and spatial organization of symbiont machineries that underpin intracellular colonization and orchestrate maternal inheritance remain unknown. Here, we used cryo-electron tomography to directly image the nanoscale architecture of bacterial tools deployed for host manipulation and germline transmission. We discovered that Wolbachia assembles multiple structures at the host-endosymbiont interface including a filamentous ladder-like framework hypothesized to serve as a specialized motility mechanism that enables bacterial translocation to specific host cell compartments during embryogenesis and somatic tissue dissemination. In addition, we present the first in situ structure of the Rickettsiales vir homolog type IV secretion system (rvh T4SS). We provide evidence that the rvh T4SS nanomachine exhibits architectural similarities to the pED208-encoded T4SS apparatus including the biogenesis of rigid conjugative pili extending hundreds of nanometers beyond the bacterial cell surface. Coupled with integrative structural modeling, we demonstrate that in contrast to canonical T4SS architectures, the α-proteobacterial T4SS outer membrane complex assembles a periplasmic baseplate structure predicted to comprise VirB9 oligomers complexed with cognate VirB10 subunits that form extended antennae projections surrounding the translocation channel pore. Collectively, these studies provide an unprecedented view into Wolbachia structural cell biology and unveil the molecular blueprints for architectural paradigms that reinforce ancient host-microbe symbioses.},
}

@article {pmid40946610,
year = {2025},
author = {Kochman, NR and Fine, M},
title = {Gulf of Aqaba as a thermal refuge: Insights from four years of intensifying marine heatwaves.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180463},
doi = {10.1016/j.scitotenv.2025.180463},
pmid = {40946610},
issn = {1879-1026},
abstract = {Marine heatwaves (MHWs) are intensifying, posing an increasing threat to coral reefs globally. Despite warming faster than the global average, the Gulf of Aqaba (GoA, Northern Red Sea) has been regarded as a climate refuge for corals. In this study, we analyzed coral-algae symbiosis integrity based on algal densities, chlorophyll content, and host and symbiont energy reserves (proteins, carbohydrates, lipids) of tagged colonies of Stylophora pistillata and Pocillopora damicornis throughout four consecutive summers characterized by moderate (2022), strong (2021, 2023), and severe (2024) MHWs. The 2024 MHW, lasting 113 days, was exceptional, with sea surface temperatures reaching 32.6 °C, 3.4 °C above the long-term climatology, and accumulating 30 Degree Heating Weeks, the highest recorded globally during 2024. Nonetheless, S. pistillata and P. damicornis persisted without bleaching, while maintaining stable host energy reserves and higher symbiont carbohydrates in 2024 compared to previous summers. To assess potential species-specific responses, we additionally monitored Seriatopora hystrix, Porites spp., and Cyphastrea spp. colonies before, during, and after the severe 2024 MHW. All monitored colonies endured the unprecedented thermal stress without bleaching or photosynthetic impairment. Porites spp. displayed metabolic tolerance with stable values throughout the event. Only Cyphastrea spp. showed significant symbiont reduction (-55 %) during peak stress, recovering by January 2025. As climate change places 44 % of reef-building corals at risk of extinction, our findings highlight the resilience of GoA corals. However, emerging shallow bleaching suggests that this refuge may be approaching its limit, underscoring the urgent need for regional conservation efforts.},
}

@article {pmid40945623,
year = {2025},
author = {Chen, WY and Qin, YS and Zhang, TF and Zou, J and Yang, J and Chen, ZY},
title = {A chromosome-level genome assembly of Termitomyces fuliginosus using Oxford Nanopore and Hi-C sequencing.},
journal = {Genomics},
volume = {},
number = {},
pages = {111110},
doi = {10.1016/j.ygeno.2025.111110},
pmid = {40945623},
issn = {1089-8646},
abstract = {Termitomyces fuliginosus is a tasty edible mushroom with both nutritional and medicinal values, consumed by native people throughout Asia. However, studies about this mushroom are limited due to lack of fine genomic information, such as the molecular mechanisms underlying development, symbiosis with termites, and plant biomass degradation. In this study, we reported a chromosome-level reference genome of T. fuliginosus assembled using Oxford Nanopore technologies (ONT) and Hi-C technologies. In total, the clean data obtained from ONT and Hi-C sequencing amounted to 10.42 Gb and 21.75 Gb, respectively. The assembled genome consisted of 13 chromosomes with a total length of 65.66 Mb. Completeness evaluations showed that this assembled genome had high quality, with a complete BUSCO score of 91.6 %. In total, 10,319 protein-coding genes were identified, and each gene received at least one functional annotation hit across the queried databases. Based on single-copy orthologous genes, phylogenetic analysis revealed that T. fuliginosus shared a close evolutionary relationship with Termitomyces cryptogamus, Arthromyces matolae, Tricholoma furcatifolium, Tephrocybe rancida, Lyophyllum atratum, and Tricholoma matsutake. A total of 303 carbohydrate-active enzymes (CAZyme) genes were identified in the T. fuliginosus genome, enabling a better understanding of the carbohydrate degradation capabilities for T. fuliginosus. This chromosome-level genome of T. fuliginosus provides valuable reference data for utilizing the medicinal and nutritional value of this mushroom, such as accurate genomic sequences without gaps, genomic analysis of functional genes, and visualization of chromosomal structural variations.},
}

@article {pmid40945362,
year = {2025},
author = {Bosco, C and Raspati, GS and Maurin, N and Helness, H},
title = {A systematic literature review on resource recovery toward symbiotic circular economy solutions in the water sector.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127298},
doi = {10.1016/j.jenvman.2025.127298},
pmid = {40945362},
issn = {1095-8630},
abstract = {Population growth, climate change, and unsustainable water use have prompted the exploration of alternative solutions for sustainable water management. While significant advancements have been made in resource recovery technologies from wastewater, the large-scale implementation of these systems and associated impact on the environment and society are still far from full realization. This paper reviews the scientific state-of-the art on resource recovery in the water sector with respect to the four pillars of symbiotic circular economy solutions, consisting of technological processes, final applications, business models, and stakeholder involvement. A systematic and transparent literature review has been carried out, showing that a variety of technologies for recovering water, materials, energy, and nutrients have been proposed and tested, but widespread application is constrained by multiple barriers. These include the technical limitations of existing recovery processes, financial obstacles, and the difficulties associated with integrating technologies into existing value chains. This work emphasizes the need for additional research on novel approaches to promote alternative business models and bottom-up involvement of stakeholders, from public and private organisations to local communities, in the planning and implementation of resource recovery systems in the water sector.},
}

@article {pmid40945100,
year = {2025},
author = {Caley, A and Marzinelli, EM and Mayer-Pinto, M},
title = {Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107536},
doi = {10.1016/j.marenvres.2025.107536},
pmid = {40945100},
issn = {1879-0291},
abstract = {Multiple stressors such as Artificial Light at Night (ALAN) and warming are increasingly common in marine systems and can interact in complex ways. Microbial communities play critical roles in the functioning of coastal habitat-forming species such as seaweeds, however the effects of ALAN on seaweed-associated microbial communities remain unknown. We tested the independent and combined effects of ALAN and warming on microbial communities associated with the habitat-forming seaweeds Ecklonia radiata and Sargassum sp. In Ecklonia, ALAN increased the relative abundance of two potentially light-responsive taxa: Dokdonia sp000212355 and an unidentified ASV from Pseudomonadales, whereas warming had the opposite effect. Warming increased microbial community dispersion in Ecklonia and resulted in non-significant increases in relative abundance of putative pathogenic and agarolytic taxa (microbes capable of degrading algal polysaccharides). However, further analyses using metagenomics are needed to confirm functional roles. In contrast, neither ALAN nor warming affected dominant taxa associated with Sargassum. Contrary to expectations, cyanobacteria relative abundance was unaffected by ALAN in either seaweed host, despite their photosynthetic capacity. We found limited evidence for interactive effects of ALAN and warming, and community composition remained unchanged in both seaweed species. Our findings highlight the importance of considering species-specific microbial responses to ALAN and warming, with implications for coastal management.},
}

@article {pmid40944660,
year = {2025},
author = {Rondilla, RR and Edrada-Ebel, R},
title = {Recent biotechnological advances in bioprospecting secondary metabolites from endolichenic fungi for drug discovery applications.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/1040841X.2025.2556931},
pmid = {40944660},
issn = {1549-7828},
abstract = {Endolichenic fungi (ELF) are symbiotic organisms residing in lichens. Since the initial report of its application in natural products and drug discovery, they have emerged as unique valuable sources of compounds with a wide range of structural diversity and biological activities. In this review, we critically examine current strategies to expand ELF metabolite diversity, with emphasis on the One Strain, Many Compounds (OSMAC) approach and metabolomics-guided profiling. We highlight how co-culture systems, epigenetic modifiers, and advanced data acquisition platforms can open new avenues for chemical space exploration. Genomic and transcriptomic studies, though still limited in ELF, reveal untapped biosynthetic potential and point toward integrative omics pipelines. Recent computational and artificial intelligence tools further accelerate genome-metabolome mining, structural elucidation, and prediction of bioactivity. We propose a forward-looking framework that combines OSMAC, integrative omics, and AI to maximize the natural product bioprospecting potential of ELF, while also uncovering their ecological roles within the lichen holobiome.},
}

@article {pmid40944224,
year = {2025},
author = {Álvarez-Herms, J and Burtscher, M and Corbi, F and González, A and Odriozola, A},
title = {A Narrative Hypothesis: The Important Role of Gut Microbiota in the Modulation of Effort Tolerance in Endurance Athletes.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172836},
pmid = {40944224},
issn = {2072-6643},
abstract = {Background: Regulating sensations of fatigue and discomfort while performing maximal endurance exercise becomes essential for making informed decisions about persistence and/or failure during intense exercise. Athletes with a higher effort capacity have competitive advantages over those with a lower one. The microbiota-brain axis is a considered the sixth sense and a modulator of the host's emotional stability and physical well-being. Objectives: This narrative review aims to explore and evaluate the potential mechanisms involved in regulating perceptions during endurance exercise, with a focus on the possible relationship between the gut microbiota balance and the neural system as an adaptive response to high fatigue chronic exposure. Methods: Electronic databases (PubMed, Web of Science, Google Scholar, and Scopus) were used to identify studies and hypotheses that had documented predefined search terms related to endurance exercise, gut microbiota, the central nervous system, pain, discomfort, fatigue, and tolerance to effort. Results: This narrative review shifts the focus concerning the symbiotic relationship between the gut microbiota, the vagus nerve, the central/enteric nervous system, and the regulation of afferences from different organs and systems to manage discomfort and fatigue perceptions during maximal physical effort. Consequently, the chronicity supporting fatigued exercise and nutritional stimuli could specifically adapt the microbiota-brain connection through chronic efferences and afferences. The present hypothesis could represent a new focus to be considered, analysing individual differences in tolerating fatigue and discomfort in athletes supporting conditions of intense endurance exercise. Conclusions: A growing body of evidence suggests that the gut microbiota has rapid adaptations to afferences from the brain axis, with a possible relationship to the management of fatigue, pain, and discomfort. Therefore, the host-microbiota relationship could determine predisposition to endurance performance by increasing thresholds of sensitive afferences perceived and tolerated. A richer and more diverse GM of athletes in comparison with sedentary subjects can improve the bacteria-producing metabolites connected to brain activity related with fatigue. The increase in fatigue thresholds directly improves exercise performance, and the gut-brain axis may contribute through the equilibrium of metabolites produced for the microbiota.},
}

@article {pmid40943619,
year = {2025},
author = {Vladimirova, ME and Roumiantseva, ML and Saksaganskaia, AS and Kozlova, AP and Muntyan, VS and Gaponov, SP},
title = {Dark Matter Carried by Sinorhizobium meliloti phiLM21-like Prophages.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178704},
pmid = {40943619},
issn = {1422-0067},
support = {Agreement of May 29, 2025 No. 075-15-2025-472//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {A comprehensive comparative analysis was conducted on the nucleotide and amino acid sequences of intact phiLM21-like prophages (phiLM21-LPhs), which currently represent the most prevalent prophages in Sinorhizobium meliloti-a symbiotic partner of Fabaceae plants. Remarkably, the nucleotide sequences of 25 phiLM21-LPhs, identified across 36 geographically dispersed S. meliloti strains, covered no more than 34% of the phiLM21 phage genome. All prophages were integrated into specific isoacceptor tRNA genes and carried a tyrosine-type integrase gene; however, this integration did not exhibit features of tRNA-dependent lysogeny. Only one-fifth of phiLM21-LPhs encoded the minimal set of regulators for lysogenic/lytic cycle transitions, while the remainder contained either uncharacterized regulatory elements or appeared to be undergoing genomic "anchoring" within the host bacterium. The phiLM21-LPhs harbored open reading frames (ORFs) of diverse origins (phage-derived, bacterial, and unknown), yet over half of these ORFs had undeterminable functions, representing genetic "dark matter". The observed diversification of intact phiLM21-like prophages likely stems from recombination events involving both virulent/temperate phages and phylogenetically remote bacterial taxa. The evolutionary and biological significance of the substantial genetic "dark matter" within these prophages in soil saprophytic bacteria remains an unresolved question.},
}

@article {pmid40943531,
year = {2025},
author = {Hao, S and Hua, Z and Yuan, Y},
title = {Stage-Specific Lipidomes of Gastrodia elata Extracellular Vesicles Modulate Fungal Symbiosis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178611},
pmid = {40943531},
issn = {1422-0067},
support = {SQ2024YFC3500027//National Key Research and Development Program of China/ ; 82325049//National Natural Science Foundation of China/ ; CI2023D001/CI2023E002-04//Science and Technology Innovation Project of CACMS/ ; },
abstract = {The mycoheterotrophic orchid Gastrodia elata relies entirely on symbiosis with Armillaria for nutrient acquisition during tuber development. The signaling mechanisms underlying this interaction have long been a research focus, and several pathways, such as phytohormone-mediated signaling, have been reported. However, the role of plant-derived extracellular vesicles (PDEVs) in G. elata-Armillaria communication remains unexplored. In this study, we conducted a comprehensive lipidomic analysis of G. elata-derived extracellular vesicles (GDEVs) isolated from juvenile, immature (active symbiosis), and mature tubers. By employing high-resolution mass spectrometry and advanced statistical methods, we established a detailed EV lipidome profile for G. elata, identifying 996 lipid species spanning eight major classes. Distinct lipidomic remodeling was observed throughout tuber maturation. Notably, as the immature stage corresponds to the period of peak symbiotic activity, targeted lipidome comparisons enabled the identification of core lipid markers, particularly Glc-sitosterols and the polyketide 7,8-dehydroastaxanthin, which are highly enriched during active symbiosis and potentially associated with inter-kingdom communication. These findings suggest that developmentally regulated lipid transport via EVs plays a critical role in mediating G. elata-Armillaria interaction. Our work not only illuminates the contribution of vesicle lipids to plant-fungal interaction but also provides a methodological foundation for investigating EV-mediated signaling in non-model plant-microbe systems.},
}

@article {pmid40941956,
year = {2025},
author = {Cántaro-Segura, H and Zúñiga-Dávila, D},
title = {Exogenous Application of ENOD40 and CEP1 Peptides Boosts Symbiotic Signaling Gene Expression and Productivity in Common Bean.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172786},
pmid = {40941956},
issn = {2223-7747},
support = {177//Universidad Nacional Agraria La Molina/ ; },
abstract = {Small signaling peptides play crucial roles in the regulation of legume-rhizobia symbiosis, yet their potential as exogenous biostimulants remains largely unexplored. In this study, we evaluated the effects of foliar application of the synthetic peptides ENOD40 and CEP1 on common bean (Phaseolus vulgaris) under both greenhouse and field conditions. Using a factorial design, we examined gene expression patterns, nodulation parameters, and yield-related traits in response to peptide treatments alone or in combination with Rhizobium. Results showed that ENOD40 and CEP1 significantly enhanced the transcription of key symbiotic signaling genes (PvENOD40, PvSYMRK, PvCCaMK, PvCYCLOPS, PvVAPYRIN) and modulated defense-related genes (PvAOS, PvICS), with the strongest effects observed at concentrations of 10[-7] M and 10[-8] M. In greenhouse assays, peptide-treated plants exhibited increased root and shoot biomass, nodule number, and seed yield. Field trials confirmed these responses, with CEP1 10[-7] M + Rhizobium treatment achieving the highest grain yield (3322 kg ha[-1]). Our findings provide the first evidence that ENOD40 and CEP1 peptides can function as foliar-applied biostimulants to enhance nodulation efficiency and improve yield in legumes. This approach offers a promising and sustainable strategy to reduce chemical nitrogen inputs and support biological nitrogen fixation in agricultural systems.},
}

@article {pmid40941938,
year = {2025},
author = {Rahbari, A and Esmaielpour, B and Azarmi, R and Fatemi, H and Lajayer, HM and Panahirad, S and Gohari, G and Vita, F},
title = {Symbiotic Fungus Serendipita indica as a Natural Bioenhancer Against Cadmium Toxicity in Chinese Cabbage.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172773},
pmid = {40941938},
issn = {2223-7747},
abstract = {Heavy metal toxicity, particularly cadmium (Cd), poses a growing threat to agriculture and human health due to its persistence and high solubility, which facilitates its entry into the food chain. Among the strategies proposed to reduce Cd toxicity in plants and the environment, the use of beneficial microorganisms, such as endophytic fungi, has gained attention due to its effectiveness and eco-friendliness. This study investigates the potential of the root-colonizing fungus Serendipita indica (formerly Piriformospora indica) to mitigate cadmium (Cd) stress in Chinese cabbage (Brassica rapa L. subsp. Pekinensis) grown hydroponically under varying Cd concentrations (0, 1, 3, and 4 mM). Several parameters were assessed, including morphological traits, physiological and biochemical responses, and changes in leaf composition. Exposure to Cd significantly reduced plant growth, increased membrane electrolyte leakage, and decreased relative water content and root colonization, while enhancing antioxidant enzyme activities and the accumulation of phenolics, flavonoids, proline, glycine betaine, and carbohydrates. Notably, plants treated with S. indica showed improved tolerance to Cd stress, indicating the potential of the fungus. These findings suggest that S. indica can enhance plant resilience in Cd-contaminated environments and may offer a promising biological strategy for sustainable crop production under heavy metal stress.},
}

@article {pmid40941937,
year = {2025},
author = {Li, J and Wang, Y and Xu, Z and Wu, C and Zhu, Z and Lyu, X and Li, J and Zhang, X and Wang, Y and Luo, Y and Li, W},
title = {Effects of Roxithromycin Exposure on the Nitrogen Metabolism and Environmental Bacterial Recruitment of Chlorella pyrenoidosa.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172774},
pmid = {40941937},
issn = {2223-7747},
support = {32171628, U24A20639//National Natural Science Foundation of China/ ; BK20241096//Natural Science Foundation of Jiangsu Province/ ; 24KJD180001, 24KJB210003//NaturalScience Research of Jiangsu Higher Education Institutions of China/ ; SJCX25_2168//Postgraduate Research & Practice Innovation Program of Jiangsu Province, China/ ; },
abstract = {The ecotoxicity induced by macrolides has attracted widespread attention, but their impacts on the nitrogen metabolism and symbiotic environmental bacteria of microalgae remain unclear. This study examined the effects of roxithromycin (ROX) on the growth, chlorophyll levels, and nitrogen metabolism of Chlorella pyrenoidosa; investigated the changes in the composition and functions of environmental bacterial communities; and finally, analyzed the relationship between microalgae and environmental bacteria. The results indicated that all concentrations of ROX (0.1, 0.25, and 1 mg/L) inhibited microalgae growth, but the inhibition rates gradually decreased after a certain exposure period. For instance, the inhibition rate in the 1 mg/L treatment group reached the highest value of 43.43% at 7 d, which then decreased to 18.93% at 21 d. Although the total chlorophyll content was slightly inhibited by 1 mg/L ROX, the Chl-a/Chl-b value increased between 3 and 21 d. The nitrate reductase activities in the three treatments were inhibited at 3 d, but gradually returned to normal levels and even exceeded that of the control group at 21 d. Under ROX treatment, the consumption of NO3[-] by microalgae corresponded to the nitrate reductase activity, with slower consumption in the early stage and no obvious difference from the control group in the later stage. Overall, the diversity of environmental bacteria did not undergo significant changes, but the abundance of some specific bacteria increased, such as nitrogen-fixing bacteria (unclassified-f-Rhizobiaceae and Mesorhizobium) and organic contaminant-degrading bacteria (Limnobacter, Sphingopyxis, and Aquimonas). The 0.25 and 1 mg/L ROX treatments significantly enhanced the carbohydrate metabolism, cofactor and vitamin metabolism, amino acid metabolism, and energy metabolism of the environmental bacteria, but significantly downregulated nitrogen denitrification. This study provides new insights into the environmental bacteria-driven recovery mechanism of microalgae under antibiotic stress.},
}

@article {pmid40941930,
year = {2025},
author = {Vásquez, HV and Valqui, L and Valqui-Valqui, L and Bobadilla, LG and Reyna, M and Maravi, C and Pajares, N and Altamirano-Tantalean, MA},
title = {Influence of Nitrogen Fertilization and Cutting Dynamics on the Yield and Nutritional Composition of White Clover (Trifolium repens L.).},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172765},
pmid = {40941930},
issn = {2223-7747},
support = {No. 127-2020-FONDECYT//National Program for Scientific Research and Advanced Studies (PROCIENCIA)/ ; 2253484//Creation of an Agrostology Laboratory Service at the Toribio Rodríguez de Mendoza National University/ ; s/n//National University Toribio Rodríguez de Mendoza/ ; },
abstract = {White clover (Trifolium repens L.) is known for its ability to fix nitrogen biologically, its high nutritional value, and its adaptability to livestock systems. However, excessive fertilization with synthetic nitrogen alters its symbiosis with Rhizobium and reduces the protein content of the forage. The objective of this study was to evaluate the interaction between nitrogen fertilization (0 and 60 kg N ha[-1]), cutting time, and post-cutting evaluation on the morphology, yield, and nutritional composition of white clover. A completely randomized block experimental design with three factors, distributed in three blocks, was used. Within each block, three replicates of each treatment were assigned (six interactions), giving a total of 54 experimental units. The data were analyzed using a three-way analysis of variance and Tukey's multiple comparison test. Exponential models and generalized additive models (GAMs) were applied to the morphology and yield data to identify the best fit. The treatment with 60 kg N ha[-1] and cutting at 30 days showed significant increases in plant height (47.42%), fresh weight (59.61%), dry weight (98.41%), and leaf width (27.55%) compared to the control. It also produced the highest protein content (28.44%) compared to the other treatments with fertilization, without negatively affecting digestibility. The GAMs best fit most morphological and yield parameters (except leaf height and width). All fertilized treatments had higher fresh and dry weight yields. In conclusion, applying 60 kg N ha[-1] after cutting at 30 days, followed by harvesting between 54 and 60 days, improved both the quality and yield of white clover, which favored sustainable pasture management and reduced excessive nitrogen use.},
}

@article {pmid40941856,
year = {2025},
author = {Yurkov, AP and Puzanskiy, RK and Kryukov, AA and Kudriashova, TR and Kovalchuk, AI and Gorenkova, AI and Bogdanova, EM and Laktionov, YV and Romanyuk, DA and Yemelyanov, VV and Shavarda, AL and Shishova, MF},
title = {The Effect of Arbuscular Mycorrhizal Fungus and Phosphorus Treatment on Root Metabolome of Medicago lupulina During Key Stages of Development.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172685},
pmid = {40941856},
issn = {2223-7747},
support = {22-16-00064-π//The Russian Science Foundation/ ; },
abstract = {The arbuscular mycorrhizal fungi (AMF) effect on the plant metabolome is an actual question of plant biology. Its alteration during host plant development and at different phosphorus supplies is of special interest. The aim of this study was to evaluate the effect of Rhizophagus irregularis (Błaszk., Wubet, Renker & Buscot) C. Walker & A. Schüßler inoculation and/or phosphorus treatment on the root metabolome of Medicago lupulina L. subsp. vulgaris Koch at the first true leaf, second leaf, third leaf development stages, the lateral branching initiation, the flowering and the mature fruit stages. The assessment of metabolic profiles was performed using GC-MS. In total, 327 metabolites were annotated: among them 20 carboxylic acids, 26 amino acids, 14 fatty acids and 58 sugars. The efficient AM was characterized by the upregulation of the metabolism of proteins, carbohydrates and lipids, as well as an increase in the content of phosphates. The tricarboxylic acid abundance was generally lower during mycorrhization. Fourteen metabolic markers of the efficient AM symbiosis were identified. The lateral branching initiation stage was shown to have key importance. Long-lasting metabolomic profiling indicated variances in mycorrhization and Pi supply effects at different key stages of host plant development.},
}

@article {pmid40941841,
year = {2025},
author = {Bravo, TEP and Teixeira, IR and Teixeira, GCDS and Cunha, NMB and Rocha, EC and Comachio, LB and Alves, GPDC},
title = {Optimizing Common Bean Symbiosis via Stage-Specific Reinoculation and Co-Inoculation.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172676},
pmid = {40941841},
issn = {2223-7747},
support = {PRÓ-PROGRAMAS No. 01/2023;//Universidade Estadual de Goiás/ ; },
abstract = {The common bean relies on biological nitrogen fixation to meet part of its nitrogen requirements. This study aimed to evaluate the effect of reinoculation with Rhizobium tropici, alone or combined with Azospirillum brasilense, at different phenological stages. The experiments were conducted in the winter of 2023 and the rainy season of 2023/24, and significant differences were observed between seasons, mainly due to temperature and water stress, which impacted nodulation, plant growth and grain yield. However, appropriate water management mitigated these limitations, allowing reinoculation combined with co-inoculation at the V4 stage to improve nodular and morphophysiological traits, ensuring adequate nutrition through biological nitrogen fixation. This strategy promoted nodulation and plant development, resulting in an 8.5% increase in yield compared to nitrogen fertilization (80 kg ha[-1]), reaching 2197.87 kg ha[-1]. These results suggest that reinoculation with co-inoculation at the V4 stage can enhance biological nitrogen fixation, reduce dependence on synthetic fertilizers and serve as a sustainable and economically viable alternative.},
}

@article {pmid40941791,
year = {2025},
author = {Bursakov, SA and Karlov, GI and Kroupin, PY and Divashuk, MG},
title = {Microorganisms as Potential Accelerators of Speed Breeding: Mechanisms and Knowledge Gaps.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172628},
pmid = {40941791},
issn = {2223-7747},
support = {075-15-2025-480//Ministry of science and higher education of the Russian Federation/ ; },
abstract = {The rapid and widespread development of technology is in line with global trends of population growth and increasing demand for food. Significant breakthroughs in science have not yet fully met the needs of agriculture for increased food production and higher yields. The aim of this work is to discuss the current advancements in the application of beneficial microorganisms for crop cultivation and their integration into speed breeding technology to create optimal growing conditions and achieve the ultimate goal of developing new plant varieties. New breeding techniques, such as speed breeding-now a critical component of the breeding process-allow multiple plant generations to be produced in a much shorter time, facilitating the development of new plant varieties. By reducing the time required to obtain new generations, breeders and geneticists can optimize their efforts to obtain the required crop genotypes for both agriculture and industry. This helps to meet the demand for food, animal feed and plant raw materials for industrial use. One potential aspect of speed breeding technology is the incorporation of effective beneficial microorganisms that inhabit both the above-ground and below-ground parts of plants. These microorganisms have the potential to enhance the speed breeding method. Microorganisms can stimulate growth and development, promote overall fitness and rapid maturation, prevent disease, and impart stress resistance in speed breeding plants. Utilizing the positive effects of beneficial microorganisms offers a pathway to enhance speed breeding technology, an approach not yet explored in the literature. The controlled practical use of microorganisms under speed breeding conditions should contribute to producing programmable results. The use of beneficial microorganisms in speed breeding technology is considered an indispensable part of future precision agriculture. Drawing attention to their practical and effective utilization is an urgent task in modern research.},
}

@article {pmid40940224,
year = {2025},
author = {Arai, H and Harumoto, T and Katsuma, S and Nagamine, K and Kageyama, D},
title = {Striking diversity of male-killing symbionts and their mechanisms.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.08.003},
pmid = {40940224},
issn = {0168-9525},
abstract = {Symbiosis is a fundamental characteristic of eukaryotic biology. Arthropods, including insects, often harbor maternally inherited endosymbiotic microbes, some of which have evolved the ability to selectively kill male hosts - a phenomenon known as 'male killing.' The evolutionary history and mechanisms of symbiont-induced male killing have remained poorly understood. However, recent studies have revealed a remarkable diversity of male-killing strategies and their associated causative genes in diverse bacteria and viruses that target different aspects of the host reproductive system. Some insects have evolved various suppressor genes to counteract male-killing actions. This review synthesizes the current knowledge on the evolution and mechanisms underlying microbe-induced male killing and explores their broader implications for the ecology and evolution of eukaryotic life forms.},
}

@article {pmid40939656,
year = {2025},
author = {Ren, Z and Sun, P and Li, H and Wei, Y and Kraslawski, A and An, X and Sun, L},
title = {Novel photocatalytic bacteria-algae coupling system mediated by g-C3N4 nanoparticles: Effects of microbial ratio on performance and microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133301},
doi = {10.1016/j.biortech.2025.133301},
pmid = {40939656},
issn = {1873-2976},
abstract = {This study explored symbiotic interactions within a graphitic carbon nitride (g-C3N4)-enhanced bacterial-algal system for advanced wastewater treatment by examining the effects of varying bacterial-algal ratios (10:1, 5:1, and 1:1) on nutrient removal, microbial aggregation, and community dynamics in sequencing batch reactors. The 1:1 ratio (R3) exhibited optimal performance, achieving highest chemical oxygen demand removal (98.7 %) and ammonium nitrogen removal (92.4 %), alongside increased algal biomass. R3 enhanced microbial aggregation via elevated extracellular polymeric substances (EPS, 80.2 mg/g SS), reduced electrostatic repulsion. Microbial profiling revealed higher abundances of Proteobacteria (37.6 %) and Cyanobacteria (9.1 %), synergistically enabling nitrogen assimilation and integration of photocatalytic and biological degradation pathways. The balanced ratio improved dissolved oxygen regulation via algal photosynthesis, while EPS helped mitigate g-C3N4-induced oxidative stress. These findings provide mechanistic insights for the strategic optimization of bacterial-algal consortia in photocatalytically enhanced wastewater treatment systems, with implications for the development of sustainable and energy-efficient water remediation technologies.},
}

@article {pmid40938452,
year = {2025},
author = {Inès, D and Pichereaux, C and Wendehenne, D and Courty, PE and Rosnoblet, C},
title = {Rhizophagus irregularis DAOM197198 modulates the root ubiquitinome of Medicago truncatula in the establishment and functioning of arbuscular mycorrhizal symbiosis.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {54},
pmid = {40938452},
issn = {1432-1890},
support = {456 RA21031.AEC.IS//I-SITE UBFC project STRESSPROT/ ; 456 RA21031.AEC.IS//I-SITE UBFC project STRESSPROT/ ; 456 RA21031.AEC.IS//I-SITE UBFC project STRESSPROT/ ; 456 RA21031.AEC.IS//I-SITE UBFC project STRESSPROT/ ; 457 UB18052.AGR.AN//Research National Agency project ALGAE-NOS/ ; 457 UB18052.AGR.AN//Research National Agency project ALGAE-NOS/ ; 457 UB18052.AGR.AN//Research National Agency project ALGAE-NOS/ ; 457 UB18052.AGR.AN//Research National Agency project ALGAE-NOS/ ; ANR-10-INBS-08//ProFI, Proteomics French Infrastructure project/ ; },
abstract = {The regulation of cellular protein homeostasis involves the ubiquitin-proteasome system (UPS) by selectively targeting misfolded or end-of-life proteins. The involvement of the UPS in biotic stresses has been studied mainly in plant-pathogen interactions and poorly in plant-mutualistic interactions. Here, we studied through proteomic approaches (western blot, pull-down of polyubiquinated proteins and nano-LC-MS-MS analysis), the involvement of the UPS during the establishment of the mutualistic interaction between the arbuscular mycorrhizal fungus Rhizophagus irregularis DAOM197198 and the roots of Medicago truncatula, as well as in the established symbiosis. Roots of M. truncatula seedlings were harvested 0 h, 3 h, 6 h, 9 h, 12 h, 24 h and 15 days post-inoculation. We characterized a short-time and a-long-time response of the root ubiquitinome. Some proteins as such as flotilins or involved in the translational machinery were less-ubiquitinated, suggesting the facilitation of the de novo synthesis of proteins required to the establishment of arbuscular mycorrhizal symbiosis. In contrast, other proteins as transporters involved in plant nutrition through the direct pathway (i.e., MtPT5) and some enzymes involved in the lipid biosynthesis pathways were more-ubiquitinated, highlighting their putative degradation. In addition, Cdc48 protein accumulates in roots from 9 to 24 h post-inoculation, suggesting a role of Cdc48 in the transitory immune response during plant-fungal interactions. The activity of the UPS is consequently central in the establishment and functioning of arbuscular mycorrhizal symbiosis by modulating protein ubiquitination.},
}

@article {pmid40938124,
year = {2025},
author = {Bernabéu-Roda, LM and Rivera-Hernández, G and Cuéllar, V and Núñez, R and Moreno-Ocampo, Á and Sohlenkamp, C and Geiger, O and Soto, MJ and López-Lara, IM},
title = {Identification of aSinorhizobium meliloti YbgC-like thioesterase that contributes to the production of the infochemical 2-tridecanone.},
journal = {The Biochemical journal},
volume = {},
number = {},
pages = {},
doi = {10.1042/BCJ20253120},
pmid = {40938124},
issn = {1470-8728},
abstract = {Sinorhizobium meliloti is a soil bacterium that can establish beneficial symbiosis with legume plants. The fadD gene encodes a long-chain fatty acyl-coenzyme A (CoA) synthetase. Inactivation of FadD in S. meliloti leads to a pleiotropic phenotype, including the overproduction of several volatile methylketones (MKs). One of them, 2-tridecanone (2-TDC), was found to act as an infochemical that affects important bacterial traits and hampers plant-bacteria interactions. Knowledge about bacterial genes involved in MK production is limited. In wild tomato species, MK synthesis requires intermediates of fatty acid biosynthesis and the activity of the methylketone synthase 2 (MKS2), a thioesterase belonging to the hot dog-fold family. In this study, we have identified SMc03960, a conserved hypothetical protein with homology to bacterial YbgC-like thioesterases, as an ortholog of MKS2 in S. meliloti. Heterologous expression of smc03960 in Escherichia coli results in the formation of several MKs, including 2-TDC, and causes the accumulation of free fatty acids. Purified His-SMc03960 showed thioesterase activity for different acyl groups linked either to acyl carrier protein (ACP) or to CoA with preference for C14-long substrates. Moreover, formation of 2-TDC in vitro was achieved by using His-SMc03960 and 3-oxo-myristoyl-ACP. Although deletion of smc03960 in the wild type or in the fadD mutant does not significantly alter the amount of MKs released by S. meliloti, overexpression of the gene results in increased production of 2-TDC in these two strains. Overall, our data demonstrate that SMc03960 is an acyl-ACP/acyl-CoA thioesterase with broad substrate specificity that contributes to 2-TDC formation.},
}

@article {pmid40937477,
year = {2025},
author = {Zhong, W and Lin, Z and Schmidt, EW and Agarwal, V},
title = {Discovery, biosynthesis, and bioactivities of peptidic natural products from marine sponges and sponge-associated bacteria.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00048c},
pmid = {40937477},
issn = {1460-4752},
abstract = {Covering 2010 to 2025Sponges are benthic, sessile invertebrate metazoans that are some of the most prolific sources of natural products in the marine environment. Sponge-derived natural products are often endowed with favorable pharmaceutical bioactivities, and paired with their structural complexity, have long served as title compounds for chemical syntheses. Sponges are holobionts, in that the sponge host is associated with symbiotic and commensal microbiome. Natural products isolated from sponges can be produced by the sponge host, or the associated microbiome. Recent genomic studies have shed light on the sponge eukaryotic host as the true producer of several classes of sponge-derived peptidic natural products. In this review spanning years 2010-2025, we describe peptidic natural products isolated from the sponge hosts and the associated microbiome, detail their biosynthetic processes where known, and offer forward looking insights into future innovation in discovery and biosynthesis of peptidic natural products from marine sponges.},
}

@article {pmid40936089,
year = {2025},
author = {Sun, Q and Wang, J and Zhang, H and Yao, L and Si, E and Li, B and Meng, Y and Wang, C and Yang, K and Shang, X and Xie, X and Wang, H and Ma, X},
title = {The effect of arbuscular mycorrhizal fungi on the growth of wheat seedlings with contrasting phosphorus use efficiencies under low phosphorus stress.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1201},
pmid = {40936089},
issn = {1471-2229},
support = {25ZYJA002//the Central guidance for local scientific and technological development funding projects/ ; 25ZYJA002//the Central guidance for local scientific and technological development funding projects/ ; 24JRRA637//Key Project of Natural Science Foundation of Gansu Province/ ; 24JRRA637//Key Project of Natural Science Foundation of Gansu Province/ ; 24JRRA637//Key Project of Natural Science Foundation of Gansu Province/ ; ZYGG-2025-12-3//the Modern Cold and Drought Characteristic Agricultural Seed Industry Research Project/ ; ZYGG-2025-3//the Modern Cold and Drought Characteristic Agricultural Seed Industry Research Project/ ; 24CXNA038//the Science and Technology Program of Gansu Province/ ; 24CXNA038//the Science and Technology Program of Gansu Province/ ; GSCS-2021-05//the State Key Laboratory of Aridland crop science Open Fund/ ; GSCS-2021-05//the State Key Laboratory of Aridland crop science Open Fund/ ; 24JRRA840//the Gansu Province Science and Technology Joint Plan Fund Project/ ; 24JRRA840//the Gansu Province Science and Technology Joint Plan Fund Project/ ; 24JRRA840//the Gansu Province Science and Technology Joint Plan Fund Project/ ; },
abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) can stimulate root development in plants and enhance their ability to adapt to stress conditions. This study investigated the effects of arbuscular mycorrhizal fungi (AMF) inoculation on the growth, hormone dynamics, and phosphorus (P) metabolism of two wheat cultivars with differing phosphorus utilization efficiencies under both normal and low phosphorus concentration conditions. The research focused on the symbiotic interaction between AMF and these wheat varieties to elucidate their responses to varying phosphorus availability.

RESULT: The experiment showed that phosphorus inefficient wheat SW14 inoculated with AMF for 30 days under low phosphorus stress showed significant enhancement in plant height, biomass, leaf width, stem thickness, root surface area, and vegetative phosphorus content, while total root length and primary root length were reduced, This change in root length was attributed to the fact that the root system undergoes elongation and growth to adapt to the adversity under low phosphorus stress in crops, and inoculation with AMF effectively alleviated the extent of this low phosphorus stress. while IAA, SL, cellulose and lignin hormone levels and APC enzyme activities were significantly elevated, and stem structure was significantly optimized; whereas, the phosphorus-efficient variety, SW2, did not show significant improvement due to its own unique tolerance to low phosphorus stress (Table 2). Transcriptomic profiling identified 2,500 differentially expressed genes (DEGs: 983↑/1,517↓), enriched in ABC transporters (ko02010), Plant hormone signal transduction (ko04075), and MAPK signaling pathway - plant (ko04016), Cutin, suberin and wax biosynthesis(ko00073). WGCNA further resolved that AMF responded to low phosphorus stress by up-regulating the expression of cellulose, lignin, APC synthesis, and IAA/SL-related genes in SW14, with the most relevant phenotypes shown to correlate to primary root length, total root length, root dry weight and stem diameter.

CONCLUSION: AMF inoculation significantly enhanced growth and dry matter accumulation in the low-phosphorus-use-efficiency wheat variety SW14 under phosphorus-deficient stress. This treatment concurrently stimulated IAA, SL, and APC activities, resulting in increased phosphorus uptake/accumulation, notable accumulation of cellulose and lignin, and consequently significantly improved stem strength. Although AMF inoculation improved growth in the high-phosphorus-use-efficiency wheat variety SW2, these enhancements failed to reach statistical significance.},
}

@article {pmid40934553,
year = {2025},
author = {Zonneveld, KL and Bustos-Diaz, ED and Francisco, BG and Angelica, CJ},
title = {The cycad coralloid root: is there evidence for plant-microbe coevolution?.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102660},
doi = {10.1016/j.mib.2025.102660},
pmid = {40934553},
issn = {1879-0364},
abstract = {Cycads are survivors, ancient plants originating in the Carboniferous. We hypothesize that cycad resilience and recent diversification could be partially explained by their specialized coral-like (coralloid) roots and their microbiome and that these symbiotic partners are co-evolving. The coralloid root is unique in gymnosperms and rare in vascular plants. Coralloid roots and their associated microbes have been studied since the late 19th century, but a deeper understanding of their taxonomy and function has taken place only recently. And yet, we are at the 'tip of the root' as there are many open questions regarding this specialized organ and its evolutionary history. This review provides an overview of cycad coralloid roots and their microbiome, the technical limitations of their study to date, and the exciting questions that remain to be answered.},
}

@article {pmid40934431,
year = {2025},
author = {Wang, Y and Liu, M},
title = {Relational vulnerability and technological mediation: The ethics of intelligent eldercare.},
journal = {Nursing ethics},
volume = {},
number = {},
pages = {9697330251374394},
doi = {10.1177/09697330251374394},
pmid = {40934431},
issn = {1477-0989},
abstract = {In current China, the 9073 elderly care system is accelerating the process of intelligentization. The fundamental tension between conventional filial piety ethics and technological rationality is evident in the numerous ethical debates triggered by intelligent older people's care services, despite their convenience. This study proposes an analytical paradigm called relational vulnerability, which creatively combines the philosophy of technology with Confucian relational ethics. Through the use of intricate mechanisms, this framework seeks to shed light on how technological mediation alters intergenerational ethics. According to research, intelligent services that improve physical care for older people while weakening emotional ties have a paradoxical effect that creates new kinds of alienation, such as the measurement of filial duty and the breakdown of ritual-embodied behaviors. By incorporating cultural calibration into the development of human-machine symbiosis, this study addresses this issue by proposing the design concepts of "differential regulation" and "embodiment retention." This counteracts the interpretive shortcomings of the Western autonomy-based ethical paradigm in the context of Chinese older people care, creating new avenues for the application of Confucian bioethics in the age of technology and offering fresh perspectives on moral dilemmas in intelligent older people care.},
}

@article {pmid40931017,
year = {2025},
author = {Montoya, QV and Gerardo, NM and Martiarena, MJS and Solís-Lemus, C and Kriebel, R and Schultz, TR and Sosa-Calvo, J and Rodrigues, A},
title = {Digging into the evolutionary history of the fungus-growing-ant symbiont, Escovopsis (Hypocreaceae).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1340},
pmid = {40931017},
issn = {2399-3642},
support = {305269/2018-6//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; },
mesh = {Animals ; *Symbiosis ; *Ants/microbiology/physiology ; *Hypocreales/physiology/genetics/classification ; *Biological Evolution ; Phylogeny ; },
abstract = {Symbiotic relationships shape the evolution of organisms. Fungi in the genus Escovopsis share an evolutionary history with the fungus-growing "attine" ant system and are only found in association with these social insects. Despite this close relationship, there are key aspects of Escovopsis evolution that remain poorly understood. To gain further insight into the evolutionary history of these unique fungi, we delve deeper into Escovopsis' origin and distribution, considering the largest sampling, so far, across the Americas. Furthermore, we investigate Escovopsis' trait evolution, and relationship with attine ants. We demonstrate that, while the genus originated approximately 56.9 Mya, it only became associated with 'higher attine' ants in the last 38 My. Our results, however, indicate that it is likely that the ancestor of Escovopsis lived in symbiosis with early-diverging fungus-growing ants. Since then, the fungi have evolved morphological and physiological adaptations that have increased their reproductive efficiency, possibly to overcome barriers mounted by the ants and their other associated microbes. Taken together, these results provide new clues as to how Escovopsis has evolved within the context of this complex symbiosis and shed light on the evolutionary history of the fungus-growing ant system.},
}

Animals
*Symbiosis
*Ants/microbiology/physiology
*Hypocreales/physiology/genetics/classification
*Biological Evolution
Phylogeny

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40928961,
year = {2025},
author = {Huang, X and Li, C and Zhang, K and Li, K and Xie, J and Quan, M and Sun, Y and Hu, Y and Xia, L and Hu, S},
title = {Engineering and Functional Expression of the Type III Secretion System in Xenorhabdus: Enhancing Insecticidal Efficacy and Expanding T3SE Libraries.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08269},
pmid = {40928961},
issn = {1520-5118},
abstract = {Entomopathogenic nematode symbiotic bacteria (EPNB) enhance nematode insecticidal capacity through symbiosis. This study cloned the complete 32-kb type III secretion system (T3SS) gene cluster from Photorhabdus luminescens TT01 using Red/ET recombineering and functionally expressed it in T3SS-deficient Xenorhabdus stockiae HN_xs01. Heterologous T3SS expression significantly enhanced HN_xs01 adhesion and invasion capabilities in CF-203 cells. In Helicoverpa armigera models, the engineered strain induced severe intestinal damage by suppressing antimicrobial peptide expression and demonstrated improved colonization and biocontrol efficacy (LC50 decreased by 3.7-fold). Crucially, the TT01 derived T3SS mediated delivery of XopA─a novel effector exhibiting YopJ-family homology and characteristic T3SS effector features─into host cells. These findings establish the synthetic biology-driven potential of T3SS and its effectors for biological control applications while providing a mechanistic framework for future research.},
}

@article {pmid40928749,
year = {2025},
author = {Fox, PT},
title = {Thirty years of SPM-BrainMap synergy: making and mining coordinate-based literature.},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
volume = {35},
number = {8},
pages = {},
doi = {10.1093/cercor/bhaf240},
pmid = {40928749},
issn = {1460-2199},
support = {AG082661//United States National Institutes of Health/ ; AG066456//United States National Institutes of Health/ ; AG076581//United States National Institutes of Health/ ; MH074457//United States National Institutes of Health/ ; },
mesh = {Humans ; *Brain/physiology/diagnostic imaging ; *Brain Mapping/methods/history ; Magnetic Resonance Imaging/methods ; *Data Mining ; Databases, Factual ; },
abstract = {Statistical Parametric Mapping (SPM) adheres to rigorous methodological standards, including: spatial normalization, inter-subject averaging, voxel-wise contrasts, and coordinate reporting. This rigor ensures that a thematically diverse literature is amenable to meta-analysis. BrainMap is a community database (www.brainmap.org; www.portal.brainmap.org) launched contemporaneously with SPM with the goal of efficiently sharing the results and methods of the literature compliant with SPM standards. The SPM-BrainMap symbiosis has motivated the development of coordinate-based meta-analytic methods and a substantial literature of secondary analyses. Collectively this corpus constitutes system-level probabilistic maps and models of the human brain, which details its functional organization, network architecture, and alterations by disease.},
}

Humans
*Brain/physiology/diagnostic imaging
*Brain Mapping/methods/history
Magnetic Resonance Imaging/methods
*Data Mining
Databases, Factual

@article {pmid40928528,
year = {2025},
author = {Zhang, X and Chen, L and Li, X and Zhang, L and Deveau, A and Martin, F and Zhang, X},
title = {Ectomycorrhizal symbiosis with Tuber spp. Enhances host performances in Pinus and Carya and induces host-specific patterns in defense-related regulation in the leaf transcriptomes.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {53},
pmid = {40928528},
issn = {1432-1890},
support = {2021YFYZ0026, 2024YFHZ0165//Science and Technology Support Project in Sichuan Province/ ; SCCXTD-2024-07//Sichuan Mushroom Innovation Team/ ; },
mesh = {*Mycorrhizae/physiology ; *Symbiosis ; *Pinus/microbiology/genetics/physiology/growth & development ; *Plant Leaves/microbiology/genetics/metabolism ; *Transcriptome ; *Plant Tubers/microbiology ; *Ascomycota/physiology ; Gene Expression Regulation, Plant ; },
abstract = {Ectomycorrhizal fungi (EMF) colonize roots to establish symbiotic associations with plants. Sporocarps of the EMF Tuber spp. are considered as a delicacy in numerous countries and is a kind of EMF of great economic and social importance. Elucidating host responses to Tuber colonization would facilitate the exploration of symbiotic interactions and contribute to truffle cultivation. Tuber indicum and T. panzhihuanense, two primary commercial truffle species in China, were selected to colonize Pinus armandii and Carya illinoinensis in a two-and-a-half-year symbiosis experiment. Host performances, including growth, nutrient uptake, and physiological characteristics, were dynamically monitored. The molecular response of host leaf to Tuber symbiosis was further analyzed using RNA-seq. Tuber indicum and T. panzhihuanense exhibited superior colonization of P. armandii compared to that of C. illinoinensis. Both Tuber species enhanced the performance of the two hosts by increasing their height, stem circumference, and biomass. Phosphorus levels and activities of peroxidase and catalase in hosts were observed to increase during Tuber symbiosis. The results confirmed that Tuber colonization led to significant alterations in leaf transcriptomic profiles of the two trees. Tuber indicum and T. panzhihuanense both elicited defense-related regulation in host leaves, such as secondary metabolism, cell wall biogenesis, plant hormone signal transduction, and plant-pathogen interaction, with distinct patterns in P. armandii and C. illinoinensis. Our study provides an evaluation of host performance during truffle symbiosis and highlights the diverse patterns of Tuber-induced systematic defense regulation in hosts, offering insights into the specific symbiotic traits of Tuber-host pairs.},
}

*Mycorrhizae/physiology
*Symbiosis
*Pinus/microbiology/genetics/physiology/growth & development
*Plant Leaves/microbiology/genetics/metabolism
*Transcriptome
*Plant Tubers/microbiology
*Ascomycota/physiology
Gene Expression Regulation, Plant

@article {pmid40927988,
year = {2025},
author = {Veresoglou, SD},
title = {Mycorrhizal ecology: In the land of the one-eyed king.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf399},
pmid = {40927988},
issn = {1460-2431},
abstract = {Unlike most of the other disciplines in microbial ecology, a substantial fraction of the theory on mycorrhizal ecology originates from times when assaying microbes was laborious and inefficient. Most of those hypotheses target, as a result, the plant partner of the symbiosis, or at best treat the two mycorrhizal partners as a unified organism, a holobiont. I here address the legacy of this era of mycorrhizal ecology, as a means of systematizing our understanding of the discipline, but also identifying gaps of knowledge. First, I pair and review hypotheses that align with the holobiont concept with complementary hypotheses that explicitly consider the fitness of the mycorrhizal fungus. Second, I generate a hierarchy of hypotheses in mycorrhizal ecology to showcase the high potential for classifying theory that the distinction between hypotheses considering mycorrhiza as either a holobiont or an association of two individual partners maintains. Third, I identify settings that might dictate when to better abstract mycorrhizas into holobionts and when to consider all their partners individually to foster research progress. I conclude the review with suggestions on how to further unify expectations in mycorrhizal ecology.},
}

@article {pmid40927683,
year = {2025},
author = {Boyno, G and Danesh, YR and Çevik, R and Teniz, N and Demir, S and Calayır, O and Farda, B and Mignini, A and Mitra, D and Pellegrini, M and Porcel, R and Mulet, JM},
title = {Plant-fungus synergy against soil salinity: The cellular and molecular role of arbuscular mycorrhizal fungi.},
journal = {iScience},
volume = {28},
number = {9},
pages = {113384},
pmid = {40927683},
issn = {2589-0042},
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in disease control by establishing symbiotic relationships with plant roots. AMF improve salinity tolerance in plants by regulating the Na[+]/K[+] ratio through selective ion transport and mediate osmotic regulation by inducing the accumulation of osmotic-compatible solutes such as glycine betaine and proline to enable plant cells to maintain water content and the metabolic balance. AMF can also activate antioxidant defense responses by stimulating enzymes that protect plant cells from harmful oxidation and pathological infections. Plant salinity tolerance induced by AMF depends on abscisic acid (ABA)-dependent signaling mechanisms, calcium-calmodulin-dependent pathways, and reactive oxygen species (ROS)-modulated mitogen-activated protein kinase (MAPK) cascades. Therefore, future research should focus on optimizing the production and field efficacy of AMF-based inoculants, including their combined use with microbial biostimulants, to support the implementation of sustainable agricultural practices.},
}

@article {pmid40926683,
year = {2025},
author = {Guo, G and Zhao, C and Xu, W and Lu, B and Zhao, Y and Wang, Z},
title = {Treatment of Aquaculture Wastewater by Utilizing Single and Symbiotic Systems of Microalgae-Based Technology and Strigolactone Induction.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {9},
pages = {e70174},
doi = {10.1002/wer.70174},
pmid = {40926683},
issn = {1554-7531},
support = {212102110105//Henan Science and Technology Research Project of Research and utilization of key microorganisms for nitrogen transformation during composting of pond sediment/ ; HARS-22-16-Z1//Special Fund for Henan Agriculture Research System/ ; 31971514//National Natural Science Foundation of China/ ; 31670511//National Natural Science Foundation of China/ ; 2023ss04//Science and Technology Program of Suzhou/ ; },
mesh = {*Microalgae/physiology/metabolism ; *Aquaculture ; *Wastewater/chemistry ; *Lactones/metabolism ; Symbiosis ; *Waste Disposal, Fluid/methods ; *Heterocyclic Compounds, 3-Ring/metabolism ; *Chlorella vulgaris/metabolism ; },
abstract = {This study investigated the efficacy of two microalgae treatment systems (Chlorella vulgaris monoculture and a Chlorella vulgaris-S395-2-Clonostachys rosea symbiotic system) in treating aquaculture wastewater, under varying concentrations of synthetic strigolactone analog (GR24). By exposing the systems to four GR24 doses (0, 10[-11], 10[-9], and 10[-7] M), we examined the impact on biomass growth, photosynthesis, and wastewater treatment. Elevated GR24 concentrations bolstered metabolism and photosynthesis in the systems, fostering rapid symbiont growth and enhanced treatment efficiency. Notably, the coculture system outperformed the monoculture in terms of photosynthetic rate, daily biomass accumulation, and nutrient reduction in aquaculture wastewater (p < 0.05). Optimally, at 10[-9] M GR24, the symbiotic system achieved remarkable average removal rates of COD (78.54 ± 6.11%), TN (81.69 ± 7.02%), and TP (82.67 ± 7.58%) from aquaculture wastewater. Additionally, a comparative analysis revealed the system's exceptional capacity to reduce oxytetracycline hydrochloride (OTC) levels, achieving a notable 98.72% removal rate. The outcomes significantly advance bioenhancement approaches and inform the design of efficient algal-bacterial-fungal symbiotic processes for treating antibiotic-contaminated wastewater.},
}

*Microalgae/physiology/metabolism
*Aquaculture
*Wastewater/chemistry
*Lactones/metabolism
Symbiosis
*Waste Disposal, Fluid/methods
*Heterocyclic Compounds, 3-Ring/metabolism
*Chlorella vulgaris/metabolism

@article {pmid40926201,
year = {2025},
author = {Bakrani, Z and Ehsanzadeh, P},
title = {Mycorrhizal inoculation mitigates drought stress in borage (Borago officinalis L.): Evidence from biochemical, physiological, and growth responses.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1198},
pmid = {40926201},
issn = {1471-2229},
}

@article {pmid40925330,
year = {2025},
author = {Udvardi, M and Mens, C},
title = {Symbiosis: A SWEET deal for nodules.},
journal = {Current biology : CB},
volume = {35},
number = {17},
pages = {R830-R832},
doi = {10.1016/j.cub.2025.07.069},
pmid = {40925330},
issn = {1879-0445},
mesh = {*Symbiosis/physiology ; *Root Nodules, Plant/microbiology/metabolism/physiology ; *Glycine max/microbiology/physiology/metabolism ; Nitrogen Fixation ; *Sucrose/metabolism ; Plant Root Nodulation ; Plant Proteins/metabolism/genetics ; Plant Roots/microbiology/metabolism ; },
abstract = {A new study shows that sucrose allocation within soybean roots by the sucrose transporter GmSWEET3c promotes rhizobial infection, nodulation, and symbiotic nitrogen fixation.},
}

*Symbiosis/physiology
*Root Nodules, Plant/microbiology/metabolism/physiology
*Glycine max/microbiology/physiology/metabolism
Nitrogen Fixation
*Sucrose/metabolism
Plant Root Nodulation
Plant Proteins/metabolism/genetics
Plant Roots/microbiology/metabolism

@article {pmid40925006,
year = {2025},
author = {Hu, Y and Moreau, CS},
title = {Nutritional Symbiosis Between Ants and Their Symbiotic Microbes.},
journal = {Annual review of entomology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-ento-121423-013513},
pmid = {40925006},
issn = {1545-4487},
abstract = {Nutritional symbioses with microorganisms have profoundly shaped the evolutionary success of ants, enabling them to overcome dietary limitations and thrive across diverse ecological niches and trophic levels. These interactions are particularly crucial for ants with specialized diets, where microbial symbionts compensate for dietary imbalances by contributing to nitrogen metabolism, vitamin supplementation, and the catabolism of plant fibers and proteins. This review synthesizes recent advances in our understanding of ant-microbe symbioses, focusing on diversity, functional roles in host nutrition, and mechanisms of transmission of symbiotic microorganisms. Despite progress, most research has concentrated on a few ant genera, and further exploration of microbial roles in different ant morphs and life stages and across various ant species is needed. Expanding research to include a broader array of ant lineages and integrating genomic data with additional experimental data will provide deeper insights into the metabolic strategies that facilitate ant success across diverse ecological habitats.},
}

@article {pmid40924927,
year = {2025},
author = {Colombo, M},
title = {Cognitive Symbionts. Expanding the Scope of Cognitive Science With Fungi.},
journal = {Topics in cognitive science},
volume = {},
number = {},
pages = {},
doi = {10.1111/tops.70024},
pmid = {40924927},
issn = {1756-8765},
abstract = {It has been argued that fungi have cognitive capacities, and even conscious experiences. While these arguments risk ushering in unproductive disputes about how words like "mind," "cognitive," "sentient," and "conscious" should be used, paying close attention to key properties of fungal life can also be uncontroversially productive for cognitive science. Attention to fungal life can, for example, inspire new, potentially fruitful directions of research in cognitive science. Here, I introduce a concept of cognitive symbiosis whose significance for cognitive science becomes salient when we consider the centrality of symbioses in the life of fungi. Like fungi, virtually all cognitive systems live in close association with other kinds of cognitive systems, and this living together can have substantive psychological consequences. Expanding the scope of cognitive science to study a wide variety of cognitive symbioses underwrites the importance of biology and evolution in understanding minds.},
}

@article {pmid40924749,
year = {2025},
author = {Amoros, J and Buysse, M and Floriano, AM and Moumen, B and Vavre, F and Bouchon, D and Duron, O},
title = {Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts.},
journal = {PLoS genetics},
volume = {21},
number = {9},
pages = {e1011856},
doi = {10.1371/journal.pgen.1011856},
pmid = {40924749},
issn = {1553-7404},
abstract = {Cytoplasmic Incompatibility (CI) causes embryonic lethality in arthropods, resulting in a significant reduction in reproductive success. In most cases, this reproductive failure is driven by Wolbachia endosymbionts through their cifA/cifB gene pair, whose products disrupts arthropod DNA replication during embryogenesis. While a cif pair has been considered a hallmark of Wolbachia, its presence and functional significance in other bacterial lineages remains poorly investigated. Here, we conducted a comprehensive survey of 762 genomes spanning non-Wolbachia endosymbionts and their close relatives, revealing that the cif pair is far more widespread than previously recognized. We identified cif loci in 8.4% of the surveyed genomes, with a striking incidence of 17.4% in facultative symbionts. Beyond Wolbachia, cif pair occurs across eight bacterial genera spanning α-Proteobacteria, γ-Proteobacteria, Mollicutes, and Bacteroidota. Notably, cif pair has been identified in several intracellular pathogens of mammals showing high rate of transovarial transmission in their arthropod hosts, suggesting a potential role of cif pair and CI in vector-borne disease dynamics. Structural analyses further reveal that the PD(D/E)-XK nucleases and AAA-ATPase-like motifs are consistently conserved across cif pairs in all bacterial taxa. Moreover, cif pairs are frequently integrated within diverse mobile genetic elements, from transposons to large intact WO prophages in Wolbachia and RAGEs in Rickettsiaceae. Phylogenetic analyses reveal recent and potentially ongoing horizontal transfers of cif pair between distantly related bacterial lineages, a process potentially facilitated by mobile genetic elements. Indeed, the PDDEXK2 transposase exhibits a phylogenetic pattern consistent with the co-transmission of cif genes, suggesting that it may facilitate horizontal transfers of cif across bacterial lineages. Furthermore, the detection of endosymbionts harboring cif pair in arthropod groups where Wolbachia is scarce, such as ticks, suggests that CI may be more widespread than previously known, with significant implications for arthropod symbiosis, reproductive manipulation, and future biocontrol strategies.},
}

@article {pmid40924454,
year = {2025},
author = {Finegan, C and Kates, HR and Guralnick, RP and Soltis, PS and Resende, MFR and Ané, JM and Kirst, M and Folk, RA and Soltis, DE},
title = {Convergent evolution of NFP-facilitated root nodule symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2424902122},
doi = {10.1073/pnas.2424902122},
pmid = {40924454},
issn = {1091-6490},
support = {DE-SC0018247//US Department of Energy/ ; },
mesh = {*Symbiosis/genetics/physiology ; Phylogeny ; *Root Nodules, Plant/microbiology/genetics ; *Medicago truncatula/genetics/microbiology ; *Evolution, Molecular ; *Plant Proteins/genetics/metabolism ; Nitrogen Fixation ; Lipopolysaccharides/metabolism ; Biological Evolution ; },
abstract = {The origin and phylogenetic distribution of symbiotic associations between nodulating angiosperms and nitrogen-fixing bacteria have long intrigued biologists. Recent comparative evolutionary analyses have yielded alternative hypotheses: a multistep pathway of independent gains and losses of root nodule symbiosis vs. a single gain followed by numerous losses. A detailed reconstruction of the history of genes involved in signaling between nitrogen-fixing bacteria and potential hosts, particularly lipo-chitooligosaccharide (LCO) signaling, is needed to distinguish between these hypotheses. LCO recognition by plants involves the Nod Factor Perception (NFP) gene family; in the legume model Medicago truncatula (Fabales), MtNFP is essential for establishing rhizobial symbiosis. Here, we document convergent evolution of NFP, indicating multiple origins of LCO-driven symbiosis. In contrast to previous models that explain the recruitment of NFP via a single duplication in the ancestor of the nitrogen-fixing clade, our phylogenomic and synteny results suggest this duplication does not span the entire clade. Tandem duplication in a common ancestor of Cucurbitales and Rosales resulted in the NFP1 and NFP2 groups. In contrast, the phylogenetically closest paralog of MtNFP is MtLYR1, located on a different chromosome within a large syntenic block. All available data indicate that a large-scale duplication resulted in MtNFP and MtLYR1, likely corresponding to a whole-genome duplication in an ancestor of subfamily Papilionoideae of Fabaceae. We show that MtNFP and the NFP2-like group are not orthologous, indicating multiple independent gains of NFP-based LCO signaling. This molecular convergence provides a possible mechanism for multiple gains of root nodule symbiosis across the nitrogen-fixing clade.},
}

*Symbiosis/genetics/physiology
Phylogeny
*Root Nodules, Plant/microbiology/genetics
*Medicago truncatula/genetics/microbiology
*Evolution, Molecular
*Plant Proteins/genetics/metabolism
Nitrogen Fixation
Lipopolysaccharides/metabolism
Biological Evolution

@article {pmid40922700,
year = {2025},
author = {Wang, S and Wang, X and Adeniji, OD and Batchelor, WD and Wang, Y and Blersch, D and Higgins, BT and Liles, MR and Luo, W and Chen, CY and Feng, Y and Wang, Y},
title = {Targeted Genome Editing of the ACC Deaminase Gene in Bradyrhizobium: Toward Enhanced Plant Growth and Stress Tolerance.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70064},
pmid = {40922700},
issn = {1097-0290},
support = {//This study was supported by the National Peanut Board award (APPA-RIA16-PID 488 BID 1664)./ ; },
abstract = {Ensuring sufficient crop yields in an era of rapid population growth and limited arable land requires innovative strategies to enhance plant resilience and sustain, or even improve, growth and productivity despite environmental stress. Besides symbiotic nitrogen fixation, rhizobia may play a central role in sustainable agriculture by alleviating the detrimental effects of ethylene-a key stress hormone in plants-especially under conditions like drought through the deamination of 1-aminocyclopropane-1-carboxylic acid (ACC). In this study, we focused on genetically engineering a new Bradyrhizobium sp. isolate (Strain 9) from peanut root nodules to enhance its ACC deaminase activity. First, we developed a sacB-based genome-engineering tool and used it to knock out the ACC deaminase gene (acdS), confirming that its disruption severely diminished the strain's capacity to degrade ACC. Subsequently, we constructed an acdS-overexpressing strain by integrating a strong promoter and an optimized ribosome binding site upstream of acdS, achieving a five-fold increase in ACC deaminase activity relative to the wild-type. Peanut inoculation experiments demonstrated that both the acdS knockout and overexpression mutants effectively nodulated roots without impairing plant growth and nitrogen fixation, indicating that these modifications did not compromise symbiosis. Overall, this study highlights the utility of sacB-mediated counter-selection for precise genome editing in Bradyrhizobium and underscores the potential of enhanced ACC deaminase activity to improve plant growth under stress conditions. These findings pave the way for developing next-generation bioinoculants with superior ethylene mitigation capabilities, contributing to more productive and sustainable crop systems.},
}

@article {pmid40920925,
year = {2025},
author = {Marks, JC and Zampini, MC and Fitzpatrick, R and Kariunga, SH and Sitati, A and Samo, TJ and Weber, PK and Thomas, S and Hungate, BA and Ramon, CE and Wulf, M and Leshyk, VO and Schwartz, E and Pett-Ridge, J and Power, ME},
title = {Ecosystem consequences of a nitrogen-fixing proto-organelle.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2503108122},
doi = {10.1073/pnas.2503108122},
pmid = {40920925},
issn = {1091-6490},
support = {2125088//NSF (NSF)/ ; DE-AC52-07NA27344//US Department of Energy/ ; },
mesh = {*Nitrogen Fixation/physiology ; *Ecosystem ; *Symbiosis/physiology ; Nitrogen/metabolism ; Animals ; Food Chain ; Rivers ; *Diatoms/metabolism/physiology ; Carbon/metabolism ; Seasons ; Cyanobacteria/metabolism/physiology ; Nitrogen Isotopes ; Carbon Isotopes ; },
abstract = {Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.},
}

*Nitrogen Fixation/physiology
*Ecosystem
*Symbiosis/physiology
Nitrogen/metabolism
Animals
Food Chain
Rivers
*Diatoms/metabolism/physiology
Carbon/metabolism
Seasons
Cyanobacteria/metabolism/physiology
Nitrogen Isotopes
Carbon Isotopes

@article {pmid40919919,
year = {2025},
author = {Luo, Y and Srinivas, A and Guidry, C and Bull, C and Haney, CH and Hamilton, C},
title = {GacA regulates symbiosis and mediates lifestyle transitions in Pseudomonas.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0027725},
doi = {10.1128/msphere.00277-25},
pmid = {40919919},
issn = {2379-5042},
abstract = {Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the brassicacearum/corrugata/mediterranea (BCM) subclade of Pseudomonas fluorescens, including Pseudomonas species N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. Pseudomonas sp. N2E2 is a plant commensal and contains genes encoding biosynthetic enzymes for the antifungal compound 2,4-diacetylphloroglucinol (DAPG). In contrast, Pseudomonas sp. N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)- and syringopeptin (SYP)-like toxins from the plant pathogen Pseudomonas syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant-pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle. Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.IMPORTANCEEmerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer (HGT) aids in the acquisition of novel genes that facilitate adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT. These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. This work provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.},
}

@article {pmid40919716,
year = {2025},
author = {Xie, T and Lv, J and Wang, L and Wu, H and Chen, Y and Chen, R and Pan, H},
title = {Uninfected cell-specific enzymes coordinate carbon supply and nitrogen assimilation in Medicago truncatula nodules.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70560},
pmid = {40919716},
issn = {1469-8137},
support = {2024JJ2014; 2025ZYJ003//Natural Science Foundation of Hunan Province/ ; 32441035//National Natural Science Foundation of China/ ; 32470255//National Natural Science Foundation of China/ ; },
abstract = {In legume root nodules, rhizobia invade host cells to form symbiosomes that drive atmospheric nitrogen fixation. Although the metabolic roles of infected cells (ICs) are well established, the contributions of adjacent uninfected cells (UCs) have remained largely unexplored. Here, through forward genetics methods, we identify DEBINO4, a phosphoenolpyruvate carboxylase (PEPC) uniquely expressed in UCs, as a pivotal regulator of carbon metabolism essential for sustaining symbiosome function and nitrogen assimilation. DEBINO4-deficient mutants display premature nodule senescence characterized by nonviable symbiosomes in the fixation zone and disrupted carbon and nitrogen metabolic profiles. The nodule-specific PEPC kinases (PPCKs), which are probably involved in DEBINO4 activation, are required to preserve symbiosome integrity, while Glutamine Synthetase 1a (GS1a), also restricted to UCs, is critical for ammonium assimilation and maintaining differentiated symbiosomes. Comprehensive analysis of metabolism-related genes further reveals that UCs execute specialized, stage-specific functions during nitrogen fixation. Collectively, our findings underscore the importance of cell-type-specific metabolic networks in orchestrating successful symbiosis and provide a framework for understanding how distinct nodule cell populations coordinate carbon and nitrogen metabolism to support efficient nitrogen fixation.},
}

@article {pmid40919702,
year = {2025},
author = {Zhang, L and Tian, Y and Li, L and Zhan, W and Sun, H and Ren, N and Tang, Z and Ngo, HH},
title = {Movement Mechanisms Harness Lévy Flight for Energy-Efficient Wastewater Treatment in Microalgae-Bacteria Systems.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04676},
doi = {10.1002/advs.202504676},
pmid = {40919702},
issn = {2198-3844},
support = {52341001//National Natural Science Foundation of China/ ; 2022M710953//Postdoctoral Research Foundation of China/ ; 2022ZX02C16//Heilongjiang Key R&D Programme/ ; ES202424//The Open Project of State Key Laboratory of Urban Water Resources and Environment/ ; },
abstract = {Microalgae-bacteria symbiosis system is significant for sustainable and low-carbon wastewater treatment, with self-aggregation being key to its stable operation and effective pollutant removal. Cellular motility is the main driving force behind self-aggregation, crucial for symbiosis stability, but the characteristics and patterns involved still remain largely unexplored. Here, cellular movement dynamics into the microalgae-activated sludge model (ASM3) is incorporated, enabling synchronized simulation of metabolic activities and movement behaviors through physical and biochemical interactions in bioreactor systems. These findings indicate that microalgae induce bacterial movement towards Lévy flights, thereby increasing the bacterial encounter rate by 12.20%, augmenting signaling molecule concentration and biomass by 20.0% and 27.3%, respectively, which in turn strengthens the bacteria self-aggregation effect. Through practical reactor operations with metagenomic analysis, the efficacy of this model in elucidating self-aggregation is further corroborated, improving system stability and pollutant removal efficiency. An optimized microalgae-bacteria system reduces energy costs associated with cellular aggregation processes, economizing on the cost of chemotaxis-related proteins. This study not only elucidate the unique role of Lévy flight in self-aggregation, enhancing the understanding of microalgae-bacteria symbiosis, but also establish response mechanisms between motility patterns and operation dynamics. This allows for targeted regulation across various biosystems, ensuring cost-effective wastewater treatment and proactive prediction.},
}

@article {pmid40917997,
year = {2025},
author = {Meng, G and Li, J and Cao, Y and Li, F and Liu, M and Li, R and Dong, C},
title = {Haplotype-resolved genomes of Phlebopus portentosus reveal nuclear differentiation, TE-mediated variation, and saprotrophic potential.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e161411},
pmid = {40917997},
issn = {2210-6340},
abstract = {Phlebopus portentosus is a widely consumed edible mushroom and the only Boletales species currently cultivated on an industrial scale. Despite its economic importance, its trophic strategy and genomic adaptations remain elusive. Here, we presented high-quality, chromosome-level genome assemblies for two sexually compatible monokaryons (PP78 and PP85) of P. portentosus. Comparative genomic analysis revealed a genome size difference of 1.17 Mb (30.87 vs. 32.04 Mb), primarily attributed to transposable element (TE) expansion in strain PP85. Genome structural variations were largely driven by TEs, particularly LTR retrotransposons. DNA transposons were also involved in structural rearrangement of secondary metabolite biosynthetic gene clusters, impacting their organization and transcriptional profiles. Functional annotation identified 187 PP78-specific and 236 PP85-specific genes, with the latter enriched in TE-related and putative virulence factors. P. portentosus displays genomic signatures of both ECM symbiosis (reduced lignocellulose-degrading enzymes) and saprotroph (expanded glycoside hydrolase 31 and sugar transporters), supporting a facultative ECM lifestyle. The expansion of non-ribosomal peptide synthetase and polyketide synthase pathways, alongside contraction of terpenoid clusters typical of ECM fungi, further indicated its adaptation to saprotroph. These findings highlight the role of TEs in driving genome plasticity, metabolic diversity, and nuclear divergence in P. portentosus, providing valuable genomic resources for this species.},
}

@article {pmid40917749,
year = {2025},
author = {Fu, L and Wang, M and Li, D and Ma, S and Zhang, F and Zheng, L},
title = {Microbial metabolites short chain fatty acids, tight junction, gap junction, and reproduction: a review.},
journal = {Frontiers in cell and developmental biology},
volume = {13},
number = {},
pages = {1624415},
pmid = {40917749},
issn = {2296-634X},
abstract = {The gut microbiota, comprising trillions of bacteria, fungi, and viruses, exists in symbiosis with the host. As the largest microbial ecosystem in the human body. The gut microbiota not only shapes the homeostasis of the intestinal microenvironment through gut-derived metabolites but also exerts regulatory effects on the functions of diverse tissues and organs throughout the body via the intricate "gut-distal organ axis" mechanism. Short chain fatty acids, such as acetic acid, propionic acid and butyric acid are high abundance intestinal metabolites, not only influence the intestinal barrier by regulating tight junction proteins, but also affect intestinal peristalsis by regulating gap junction proteins. These microbial metabolites may also play a important role in the formation and maintenance of the key barriers of the reproductive system, such as the ovarian blood follicle barrier, the testicular blood-testis barrier, and the endometrial epithelial barrier. In reproductive system, Gap junction-mediated intercellular communication, facilitated by connexins, proves essential in germ cell maturation, embryo implantation, and spermatogenesis. The dysregulation of these microbial metabolites leading to abnormal tight junction and gap junction protein functions provides novel perspectives for understanding the pathogenesis of reproductive disorders such as polycystic ovary syndrome and premature ovarian failure. This review systematically elucidates the molecular networks through which short-chain fatty acids regulate tight and gap junction proteins, highlighting their potential roles in reproductive physiology.},
}

@article {pmid40916562,
year = {2025},
author = {Sharoni, T and Jaimes-Becerra, A and Lewandowska, M and Aharoni, R and Voolstra, CR and Fine, M and Moran, Y},
title = {Heat Stress Drives Rapid Viral and Antiviral Innate Immunity Activation in Hexacorallia.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70098},
doi = {10.1111/mec.70098},
pmid = {40916562},
issn = {1365-294X},
support = {863809//H2020 European Research Council/ ; },
abstract = {The class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. Here the model sea anemone Nematostella vectensis is used to explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor genes involved in antiviral responses. Under heat stress, the reporter genes showed significant upregulation. Further, transcriptomes from N. vectensis, Exaiptasia diaphana and the stony coral Stylophora pistillata were analysed to reveal stress-induced activation of a set of bona fide immune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in both Nematostella and Stylophora, depending on geographic origin. In Exaiptasia, the presence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves contribute to this immune response under stress, we subjected N. vectensis to heat stress and measured the transcription dynamics of resident viruses as well as selected antiviral genes. While the antiviral genes responded within hours of heat stress, viral gene expression was already upregulated within 30 min, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the interplay between environmental stress, viruses, immune responses and symbiotic states in Hexacorallia.},
}

@article {pmid40915801,
year = {2025},
author = {Xue, H and Qiao, X and Du, L and Wang, L and Zhang, K and Li, D and Ji, J and Cui, J and Zhu, X and Luo, J and Gao, X},
title = {Host-microbe synergy in pesticide resilience: Rhodococcus-driven fitness compensation in chlorpyrifos-stressed Binodoxys communis.},
journal = {Pesticide biochemistry and physiology},
volume = {214},
number = {},
pages = {106609},
doi = {10.1016/j.pestbp.2025.106609},
pmid = {40915801},
issn = {1095-9939},
mesh = {*Chlorpyrifos/pharmacology/toxicity ; Animals ; *Rhodococcus/physiology/drug effects ; *Insecticides/pharmacology/toxicity ; *Aphids/drug effects ; *Host Microbial Interactions/drug effects ; Symbiosis ; },
abstract = {Chlorpyrifos (CPF), a widely used organophosphate insecticide in cotton cultivation for controlling Aphis gossypii, has Binodoxys communis as the primary parasitic natural enemy of A. gossypii. This study evaluated the impact of two sub-lethal CPF concentrations (LC10 and LC30) on key biological parameters across two generations, transcriptomic responses, and symbiotic bacterial communities in B. communis. CPF exposure significantly reduced F1 generation survival by 39.89 % (LC10) and F2 generation survival by 33.31 % (LC30). Emergence rates were markedly decreased in both F1 (33.43 %) and F2 (19.86 %) generations under LC10 exposure. Furthermore, LC10 treatment significantly prolonged the F1 pre-pupal stage by 31.58 %. Short-term (1 h) CPF exposure markedly suppressed the expression of genes involved in energy metabolism, lipid metabolism, and PPAR signaling pathways. Notably, CPF exposure (both 1 h and 3 days) resulted in a significant increase in the relative abundance of Rhodococcus, suggesting a potential role of this bacterium in enhancing B. communis fitness under insecticide stress. Our findings not only inform the judicious application of CPF, but also identify molecular targets associated with energy and nutrient metabolism, while laying the groundwork for harnessing bacteria to enhance pesticide resistance in parasitoid wasps.},
}

*Chlorpyrifos/pharmacology/toxicity
Animals
*Rhodococcus/physiology/drug effects
*Insecticides/pharmacology/toxicity
*Aphids/drug effects
*Host Microbial Interactions/drug effects
Symbiosis

@article {pmid40894694,
year = {2025},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40894694},
issn = {2692-8205},
support = {P41 GM103399/GM/NIGMS NIH HHS/United States ; P41 GM136463/GM/NIGMS NIH HHS/United States ; P41 RR002301/RR/NCRR NIH HHS/United States ; T32 GM008349/GM/NIGMS NIH HHS/United States ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season.},
}

@article {pmid40919466,
year = {2025},
author = {Lian, J and Zou, D and Trebuch, LM and Duan, C and Li, M},
title = {Exploring the interactions between algae and archaea.},
journal = {Marine life science & technology},
volume = {7},
number = {3},
pages = {450-465},
pmid = {40919466},
issn = {2662-1746},
abstract = {Algae and archaea co-exist in diverse aquatic ecosystems and play a significant role in ecological functions and biogeochemical cycles. Compared to well-studied algal-bacterial interactions, there is a lack of information on algal-archaeal interactions and how their interactions affect their physiological fitness and nutrient cycles in either artificial cultivation systems or natural environments. The vast archaeal biodiversity, as indicated by genomic sequencing and computational approaches, has stimulated great interest in exploring uncultivated archaea to expand our knowledge of algae-archaea symbiosis. In this review, we summarize the latest studies on the diversity of algae-associated archaea and their (putative) symbiotic interactions, highlight the effects of algal-archaeal interactions on biogeochemical cycles and extend such knowledge to facilitate novel archaeal isolation and a broad range of algae-based biotechnological applications.},
}

@article {pmid40915677,
year = {2025},
author = {Costa, FF and Lustosa, BPR and Perico, CP and Belmonte-Lopes, R and Carvalho, JLVR and Razzolini, EL and Santos, GDD and Lima, BJFS and Souza-Motta, CM and Raittz, RT and Song, Y and Selbmann, L and de Hoog, GS and Meis, J and Vicente, VA},
title = {In silico search reveals the association of lichens with black yeast-like fungi in the order Chaetothyriales.},
journal = {Fungal biology},
volume = {129},
number = {6},
pages = {101618},
doi = {10.1016/j.funbio.2025.101618},
pmid = {40915677},
issn = {1878-6146},
mesh = {*Lichens/microbiology/classification ; *Ascomycota/genetics/classification/isolation & purification/physiology ; Metagenomics ; Symbiosis ; Phylogeny ; Computer Simulation ; Metagenome ; },
abstract = {Lichens exemplify a unique symbiotic relationship between fungi and algae or cyanobacteria, where fungi (mycobionts) provide structural support, while algae or cyanobacteria (photobionts) provide nutrients. Recent discoveries in the order Chaetothyriales have led to the description of several lichenicolous species, underscoring an intricate relationship of some black yeast-like fungi with lichens. The present study aims to investigate public metagenomic data of lichens available in the SRA database, covering a total of 2888 samples. The analysis incorporated 122 molecular marker sequences (barcodes and padlock probes) previously documented in the literature for species classified within Chaetothyriales. Additionally, 11 novel barcodes for species recently identified in lichens of the genera Cladophialophora and Paracladophialophora are described. The selected metagenomes were then compared with molecular marker sequences using local BLASTn (v2.6.0+), considering only alignments with a coverage cut-off and 100 % identity (perfect match). Reads from each sample were retrieved from the SRA as a multifasta file and analyzed with the SWeeP method for vector-based, alignment-free sequence analysis. The analysis identified fungi that are known as environmental inhabitants and, occasionally, opportunistic pathogens of vertebrates, including species in the genera Cladophialophora, Cyphellophora, and Exophiala. These species were distributed across 11 BioProjects from various locations around the world. The findings of this study corroborate extant knowledge concerning fungal colonization in diverse extremophilic environments, including deserts, tundra, and rocky surfaces.},
}

*Lichens/microbiology/classification
*Ascomycota/genetics/classification/isolation & purification/physiology
Metagenomics
Symbiosis
Phylogeny
Computer Simulation
Metagenome

@article {pmid40915132,
year = {2025},
author = {Shu, P and Zhao, L and Wen, X and Wei, Z and Yuan, C and Liu, H and Zhang, X and Long, X and He, Q and Li, W},
title = {Iron oxide-mediated enhancement of extracellular electron transfer and symbiosis in consortium of electroactive bacteria and microalgae for wastewater treatment.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124516},
doi = {10.1016/j.watres.2025.124516},
pmid = {40915132},
issn = {1879-2448},
abstract = {This study explores the role of α-Fe2O3 in improving extracellular electron transfer (EET) and symbiotic interactions between electroactive Shewanella oneidensis MR-1, its gene-deficient mutants (ΔmtrC, ΔomcA, and ΔcymA), and microalgae (Chlorella vulgaris). The iron oxide facilitates the efficient transfer of electrons generated by MR-1 to microalgal photosystem via the pathway of CymA-MtrC-OmcA to α-Fe2O3. This process enhances the removals of TOC, TN, and NH4[+]-N in the MR-1 bacterial-algal consortium by 9.99%, 12.32%, and 52.25% respectively via OmcA regulation while boosting phosphorus removal by 16.27% through CymA regulation. The consortium exhibits 26.76% lower CO2 emission and 62.93% higher biomass productivity. When integrated into microbial fuel cells with ΔcymA mutants, α-Fe2O3 elevates open-circuit voltage by 283.33%, confirming its ability to compensate for electron deficiencies caused by CymA defects. α-Fe2O3 enhances energy metabolisms (TCA cycle, quinone pool, and photosynthesis) to modulate the key metabolites including starch/sucrose, glycolysis, amino acids, lipids, and quorum sensing. These adaptations strengthen the symbiotic interactions and utilization of MR-1 bacterial-algal consortium for carbon and nutrients. Reactor experiments validate that α-Fe2O3 integration with the consortium achieves 93.43% COD removal and 55.99% NH4[+]-N removal, while reducing N2O emissions by 61.37%. The results reveal the interplay between OmcA, CymA, and iron oxides in optimizing bacterial-algal consortia and underscore the molecular mechanisms underlying iron oxide-enhanced EET for developing low-carbon, resource-efficient wastewater treatment.},
}

@article {pmid40915025,
year = {2025},
author = {Ortiz, J and Sanhueza, C and Romero-Munar, A and Sierra, S and Palma, F and Aroca, R and de la Peña, TC and López-Gómez, M and Bascuñán-Godoy, L and Del-Saz, NF},
title = {Nitrogen source and availability associate to mitochondrial respiratory pathways and symbiotic function in Lotus japonicus.},
journal = {Journal of plant physiology},
volume = {314},
number = {},
pages = {154606},
doi = {10.1016/j.jplph.2025.154606},
pmid = {40915025},
issn = {1618-1328},
abstract = {Legumes form symbioses with nitrogen-fixing bacteria, well studied metabolically but less so in terms of respiration. Symbiotic nitrogen fixation demands high respiratory ATP and carbon skeletons, linking nitrogen assimilation and both NADH- and ATP-dependent process to mitochondrial respiration. The plant mitochondrial electron transport chain contains two terminal oxidases that differentially fractionate against [18]O, providing estimations in vivo of the energy efficiency of respiration. The regulation of N2 fixation by plant respiratory parameters remains unknown. To investigate the regulatory interactions of these two metabolic processes, we tested the effect of different plant N status and sources on respiratory parameters and nutrition in Lotus japonicus. Plants were grown with two levels of KNO3 fertilization (5 mM and 25 mM) and with the N2 fixing symbiotic bacteria Mesorhizobium loti, which induced the formation of root nodules (NP). Additionally, we characterized roots containing non-fixing nodules by growing plants that display spontaneous nodule formation (snf) (SNF). We evaluated the natural abundances of [13]C and [15]N, and [18]O discrimination during respiration in leaves and roots using isotope-ratio mass spectrometry. NADH and nutrient content were measured using ultra-performance liquid chromatography and inductively coupled plasma spectrometry. We observed that cytochrome c oxidase activity was higher in nodulated roots capable of nitrogen fixation than in plants fertilized with high availability of nitrate, and that nitrogen status strongly associates to respiratory parameters. These findings highlight the role of cytochrome c oxidase in meeting the carbon and energy demands of symbiotic nitrogen fixation.},
}

@article {pmid40914954,
year = {2025},
author = {Gao, Y and Wu, Y and Chang, P and Li, P and Hu, S and Liu, L},
title = {Mycorrhizal Network and Symbiotic N-Fixer Jointly Enhance the Interplant Nitrogen Sharing.},
journal = {Ecology letters},
volume = {28},
number = {9},
pages = {e70204},
doi = {10.1111/ele.70204},
pmid = {40914954},
issn = {1461-0248},
support = {2022YFF1301701//National Key Research and Development Program of China/ ; 32125025//National Natural Science Foundation of China/ ; 32330066//National Natural Science Foundation of China/ ; },
mesh = {*Symbiosis ; *Mycorrhizae/physiology ; *Nitrogen/metabolism ; *Nitrogen Fixation ; *Nitrogen-Fixing Bacteria/physiology/metabolism ; },
abstract = {Symbioses with mycorrhizal fungi and nitrogen-fixing bacteria (NFB) enhance nitrogen (N) acquisition in host plants and may promote N transfer to neighbouring plants through mycorrhizal networks (MN). Nevertheless, the extent and mechanisms of this transfer remain unclear. On the basis of a synthesis of [15]N labeling studies, we show that MN and NFB synergistically enhanced interplant N sharing. In the presence of MN, N transfer from N-fixing donors to non-N-fixing receivers increased by an average of 9.7-fold, accounting for 5.61% of the total N in receiver plants. Moreover, greater amounts of N were transferred from N-fixing plants towards their phylogenetically distant plants. Source-sink gradients driven by differences in N content between neighbouring plants further promoted N transfer. Together, our findings highlight the ecological significance of an expanded MN framework in explaining interplant N sharing and provide new insights into how symbiotic guild interactions promote species coexistence and biodiversity maintenance.},
}

*Symbiosis
*Mycorrhizae/physiology
*Nitrogen/metabolism
*Nitrogen Fixation
*Nitrogen-Fixing Bacteria/physiology/metabolism

@article {pmid40914099,
year = {2025},
author = {Havlik, MN and Geraldi, NR and Hopkins, LW and Hubert, J and Chapuis, L and Gaffney, LP and Wilson, RP and Simpson, SD and Juanes, FJ and Duarte, CM},
title = {Boat noise alters behaviour of two coral reef macroinvertebrates, Lambis lambis and Tridacna maxima.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 1},
pages = {118650},
doi = {10.1016/j.marpolbul.2025.118650},
pmid = {40914099},
issn = {1879-3363},
abstract = {Boat noise has been shown to distract and cause harm to many marine organisms. Most of the study effort has focused on fish & marine mammals, even though invertebrates represent over 92 % of all marine life. The few studies conducted on invertebrates have demonstrated clear negative effects of anthropogenic noise pollution. The small giant clam Tridacna maxima and the spider conch Lambis lambis are two invertebrate species which play key roles in coral reef ecosystems, and are little studied for the effects of noise disturbance. T. maxima functions as prey for many fish species, contributes up to 9 % of the reef's calcium carbonate budget, and plays a role in nutrient cycling. The herbivorous strombid L. lambis can occur in large numbers on reef flats and is prey for other snails and several elasmobranchs. Using two case study reefs, we show that both boat noise and biotic sounds are prominent sound sources in Red Sea reef habitats. In-situ controlled exposure experiments were conducted on two shallow central Red Sea reefs, where Daily Diary smart tags were used to measure the reactions of T. maxima and L. lambis during underwater playback of boat noise and ambient reef sound. Both macroinvertebrates exhibited behavioral changes during the boat noise treatment. Our results suggest that L. lambis and T. maxima individuals may spend energy averting the invisible "threat" of boat noise, rather than feeding or staying open for symbiotic algae to perform photosynthesis, in the case of T. maxima. As boat noise is prevalent on Red Sea reefs, invertebrates may be affected on a large scale in the Red Sea.},
}

@article {pmid40913714,
year = {2025},
author = {Lopes, MR and Direito, R and Guiguer, EL and Catharin, VCS and Zutin, TLM and Rubira, CJ and Catharin, VMCS and Sloan, KP and Sloan, LA and Junior, JLY and Laurindo, LF and Barbalho, SM and de Alvares Goulart, R},
title = {Bridging the Gut Microbiota and the Brain, Kidney, and Cardiovascular Health: The Role of Probiotics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40913714},
issn = {1867-1314},
abstract = {The symbiosis between intestinal bacteria and the human body's physiological processes can modulate health. The intestinal microbiota is linked to the development of neurotrophic factors; therefore, it is increasingly related to the modulation of nervous system pathologies. Moreover, microbiota can interfere with inflammation and oxidative stress, which are closely linked to cardiovascular risk factors and several other inflammatory conditions, such as kidney and neurodegenerative diseases. Probiotics are live microorganisms that help regulate and maintain healthy microbiota; thus, they can help prevent these diseases. Due to these reasons, this review aimed to evaluate the effects of probiotics on the gut, kidneys, brain, and heart homeostasis. Clinical trials showed several positive results with the treatment. In the brain, probiotics reduce depressive symptoms (decreases in HAMA, GAD-7, and BDI-II scales), improving patients' sleep quality and fatigue, enhancing cognitive subscales while slowing brain atrophy, and reducing IL-6 levels in the central areas, also modulating REM delta power to reduce high-frequency brain waves. Probiotics can also reduce cardiovascular risk factors, such as inflammation. Probiotics can also benefit the heart by decreasing TMAO, LDL-c, TG, CRP, MDA, TNF-α, IL-6, and urea levels, improving dyslipidemia and toxin profiles. Probiotics also increase HDL-c, ApoE, and insulin sensitivity, decreasing BMI, body fat, and the risk of developing chronic hyperglycemia while increasing lean mass. Besides, probiotic supplementation helped reduce toxic uremic toxins (serum urea) and sodium levels, bringing benefits to the kidneys, and improve energy/amino acid metabolism. Probiotics can also modulate and enhance kidney function due to decreased pro-inflammatory TGFβ-1 and TNF-α levels and RUNX2. Furthermore, enhanced gastrointestinal motility and diversity have been reported using specific bacteria. Although probiotics can bring several health benefits, there are still challenges regarding these supplements, such as dose, frequency, and pharmaceutical formula. Therefore, new studies are welcome to deepen the understanding of these microorganisms.},
}

@article {pmid40913463,
year = {2025},
author = {Mostafa, KM and Cheng, YH and Chu, LW and Nguyen, PT and Liu, CJ and Liao, CW and Posch, T and Leu, JY},
title = {Environment-dependent mutualism-parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf203},
pmid = {40913463},
issn = {1751-7370},
abstract = {Mutualistic endosymbiosis is a cornerstone of evolutionary innovation, enabling organisms to exploit diverse niches unavailable to individual species. However, our knowledge about the early evolutionary stage of this relationship remains limited. The association between the ciliate Tetrahymena utriculariae and its algal endosymbiont Micractinium tetrahymenae indicates an incipient stage of photoendosymbiosis. Although T. utriculariae cells rely on endosymbiotic algae to grow in low-oxygen conditions, they gradually lose the endosymbionts in oxic conditions. In this study, comparative phylogenomics revealed accelerated evolution in mitochondrial DNA and nucleus-encoded mitochondrial genes in T. utriculariae. Symbiotic cells displayed elongated mitochondria that interacted intimately with endosymbionts. Inhibition of mitochondrial fatty acid oxidation reduced host fitness but increased the endosymbiont population. Time-series transcriptomics revealed physiological fine-tuning of the host across day-night cycles, highlighting symbiosis-associated regulatory adjustments. Endosymbiotic algae downregulated photosynthesis-related genes compared with free-living cells, which correlated with reduced chlorophyll content, suggesting a shift toward host resource exploitation to compensate for diminished photosynthetic capacity. Under oxic conditions, symbiotic T. utriculariae cells exhibited lower fitness than aposymbiotic cells. Our results demonstrate that incipient endosymbioses employ mitochondrial remodeling and endosymbiont metabolic reprogramming to actively regulate transitions between mutualistic and parasitic states, revealing how symbiotic partnerships navigate environmental pressures during their incipient stage of evolutionary establishment.},
}

@article {pmid40913088,
year = {2025},
author = {Chandola, U and Manirakiza, E and Maillard, M and Lavier Aydat, LJ and Camuel, A and Trottier, C and Tanaka, A and Chaumier, T and Giraud, E and Tirichine, L},
title = {A Bradyrhizobium isolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40913088},
issn = {2058-5276},
abstract = {Biological nitrogen fixation converts atmospheric nitrogen into ammonia, essential to the global nitrogen cycle. While cyanobacterial diazotrophs are well characterized, recent studies have revealed a broad distribution of non-cyanobacterial diazotrophs (NCDs) in marine environments, although their study is limited by poor cultivability. Here we report a previously uncharacterized Bradyrhizobium isolated from the marine diatom Phaeodactylum tricornutum. Phylogenomic analysis places the strain within photosynthetic Bradyrhizobium, suggesting evolutionary adaptations to marine and terrestrial niches. Average nucleotide identity supports its classification as a previously undescribed species. Remarkably, inoculation experiments showed that the isolate induced nitrogen-fixing nodules in the Aeschynomene indica legume, pointing to symbiotic capabilities across ecological boundaries. Pangenome analysis and metabolic predictions indicate that this isolate shares more features with terrestrial photosynthetic Bradyrhizobium than with marine NCDs. Overall, these findings suggest that symbiotic interactions could evolve across different ecological niches, and raise questions about the evolution of nitrogen fixation and microbe-host interactions.},
}

@article {pmid40911574,
year = {2025},
author = {Chang, ACG and Amaral, MWW and Greenwood, M and Ikudaisi, C and Li, J and Hamsher, SE and Miller, S and Kociolek, P},
title = {Evolutionary dynamics in plastomes and mitogenomes of diatoms.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331749},
doi = {10.1371/journal.pone.0331749},
pmid = {40911574},
issn = {1932-6203},
mesh = {*Diatoms/genetics/classification ; *Genome, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; Pseudogenes ; },
abstract = {Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling, contributing significantly to photosynthesis and serving as fundamental components in aquatic ecosystems. Recent advancements in genomic sequencing have shed light on their evolutionary dynamics, revealing evolutionary complex genomes influenced by symbiotic relationships and horizontal gene transfer events. By analyzing publicly available sequences for 120 plastomes and 70 mitogenomes, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. Gene losses and pseudogenes were more frequently observed in plastomes compared with mitogenomes. Overall, gene losses were particularly abundant in the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp. Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC, ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost repeatedly across several diatom taxa. Analysis of nucleotide substitution rates indicated that, in general, mitogenomes were evolving at a more rapid rate compared to plastomes. This is contrary to what was observed in synteny analyses, where plastomes exhibited more structural rearrangements than mitogenomes, with the exception of the genus Coscinodiscus and one group of species within Thalassiosira.},
}

*Diatoms/genetics/classification
*Genome, Mitochondrial/genetics
*Evolution, Molecular
Phylogeny
Pseudogenes

@article {pmid40911442,
year = {2025},
author = {Tang, J and Yang, S and Li, S and Yue, X and Jin, T and Yang, X and Zhang, K and Yang, Q and Liu, T and Zhao, S and Gai, J and Li, Y},
title = {Editing a gibberellin receptor gene improves yield and nitrogen fixation in soybean.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70026},
pmid = {40911442},
issn = {1744-7909},
support = {32372192//National Natural Science Foundation of China/ ; JBGS-2021-014//Core Technology Development for Breeding Program of Jiangsu Province/ ; BM2024005//Jiangsu Key Laboratory of Soybean Biotechnology and Intelligent Breeding/ ; },
abstract = {Soybean is an important source of oil, protein, and feed. However, its yield is far below that of major cereal crops. The green revolution increased the yield of cereal crops partially through high-density planting of lodging-resistant semi-dwarf varieties, but required more nitrogen fertilizers, posing an environmental threat. Genes that can improve nitrogen use efficiency need to be integrated into semi-dwarf varieties to avoid the overuse of fertilizers without the loss of dwarfism. Unlike cereal crops, soybean can assimilate atmospheric nitrogen through symbiotic bacteria. Here, we created new alleles of GmGID1-2 (Glycine max GIBBERELLIN INSENSITIVE DWARF 1-2) using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) editing, which improved soybean architecture, yield, seed oil content, and nitrogen fixation, by regulation of important pathways and known genes related to branching, lipid metabolism, and nodule symbiosis. GmGID1-2 knockout reduced plant height, and increased stem diameter and strength, number of branches, nodes on the primary stem, pods, and seeds per plant, leading to an increase in seed weight per plant and yield in soybean. The nodule number, nodule weight, nitrogenase activity, and nitrogen content were also improved in GmGID1-2 knockout soybean lines, which is novel compared with the semi-dwarf genes in cereal crops. No loss-of-function allele for GmGID1-2 was identified in soybean germplasm and the edited GmGID1-2s are superior to the natural alleles, suggesting the GmGID1-2 knockout mutants generated in this study are valuable genetic resources to further improve soybean yield and seed oil content in future breeding programs. This study illustrates the pleiotropic functions of the GID1 knockout alleles with positive effects on plant architecture, yield, and nitrogen fixation in soybean, which provides a promising strategy toward sustainable agriculture.},
}

@article {pmid40911291,
year = {2025},
author = {Zhang, G and Yue, Y and Tu, L and Liu, Q and Zhang, Q and Shang, K},
title = {Responses of microbial communities during oilseed plant-based phytoremediation of heavy metal contaminated soils.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf226},
pmid = {40911291},
issn = {1365-2672},
abstract = {AIMS: Phytoremediation is an effective method of remediating soils contaminated with heavy metals. However, it has some limitations in practical applications with regard to rare plant species, poor environmental adaptability, and long growth cycles. The dynamic response mechanisms of soil microbial communities during phytoremediation are still unclear, which restricts the optimization and promotion of this approach.

METHODS AND RESULTS: No ethical approval was required for this study. In this study, soil bacterial, fungal, and archaeal communities during the remediation of Cu-, Pb-, and Zn-contaminated soils with five industrial oilseed plants (Xanthium strumarium (XS), Bidens pilosa (BP), Kosteletzkya virginica (KV), Sesbania cannabina (SC), and Commelina communis (CC)) were analyzed using metagenome sequencing. Compared with soil contaminated with heavy metals, remediation through five industrial oilseed plants significantly reduced the content of heavy metals in the soil, with soil Cu, Pb, and Zn decreasing by 44.01%, 46.32%, and 27.62%, respectively, and WSCu, WSPb, and WSZn content decreasing by 28.23%, 50.68%, and 75.26%, respectively. Microbial diversity analysis showed that phytoremediation significantly affected the soil microbial communities, with a significant decrease in archaeal diversity. Variation partitioning analysis and Mantel tests revealed that heavy metals and soil physicochemical properties significantly affected microbial communities, and heavy metals exerted stronger effects on archaeal communities. Meanwhile, soil contaminated with heavy metals was mainly dominated by fungal-fungal interactions, whereas phytoremediation increased the complexity of microbial symbiotic networks.

CONCLUSION: Collectively, these results provide fundamental insights into the microbial community structure during phytoremediation of heavy metal contaminated soil, which may aid in the bioregulation of phytoremediation.},
}

@article {pmid40911260,
year = {2025},
author = {Irum, S and Cilkiz, M and Al-Kubaisi, N and Elshikh, MS and Iqbal, R},
title = {Genome-wide characterization and expression analysis of the chitinase gene family in chickpea (Cicer arietinum L.) for fungal stress resistance.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {871},
pmid = {40911260},
issn = {1573-4978},
mesh = {*Cicer/genetics/microbiology/enzymology ; *Chitinases/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant/genetics ; *Disease Resistance/genetics ; Stress, Physiological/genetics ; Fusarium/pathogenicity ; Plant Diseases/microbiology/genetics ; Multigene Family ; Plant Proteins/genetics/metabolism ; Gene Expression Profiling/methods ; Genome, Plant ; },
abstract = {Chitinases, enzymes responsible for hydrolyzing chitin, a significant component of fungal cell walls, play a crucial role in plant defense mechanisms, growth, symbiotic relationships, and stress resistance. In this study, we identified 27 chitinase genes in chickpeas (CaChi) and classified them into five classes based on phylogenetic analysis. Overall, chitinase genes are clustered on eight chromosomes. Among these chromosomes (Chr), Chr-2 displayed the maximum number of genes. Meanwhile, promoter analysis revealed that cis-elements are involved in responses to phytohormones, biotic stress, plant growth, and development. Tissue-based expression analysis indicated that CaChi genes are predominantly expressed in the seedling and floral parts. Furthermore, qRT-PCR analysis revealed that CaChi genes play diverse roles in plant-environment interactions. Notably, several CaChi members were strongly induced by Fusarium oxysporum f. sp. and fourteen genes (CaChi20, CaChi25, CaChi11, CaChi3, CaChi16, CaChi14, CaChi1, CaChi4, CaChi5, CaChi8, CaChi9, CaChi21, CaChi18, CaChi13) exhibited elevated expression levels after post-inoculation, depicting a significant function of Chi genes in chickpea resistance to Fusarium wilt. These findings enhance understanding of the chitinase family in chickpea crops and clarify the functions of chickpea chitinase in response to fungal stress.},
}

*Cicer/genetics/microbiology/enzymology
*Chitinases/genetics/metabolism
Phylogeny
Gene Expression Regulation, Plant/genetics
*Disease Resistance/genetics
Stress, Physiological/genetics
Fusarium/pathogenicity
Plant Diseases/microbiology/genetics
Multigene Family
Plant Proteins/genetics/metabolism
Gene Expression Profiling/methods
Genome, Plant

@article {pmid40910153,
year = {2025},
author = {Chen, M and Raisin, A and Judkins, N and Allard, PM and Défossez, E and Stumpe, M and Yruela, I and Becana, M and Reinhardt, D},
title = {Inhibition of rhizobial cheaters by the host Medicago truncatula involves repression of symbiotic functions and induction of defense.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70494},
pmid = {40910153},
issn = {1469-8137},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia, Tecnología e Innovación/ ; 310030_200367//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; E35_23R//Gobierno de Aragón/ ; },
abstract = {In symbiotic plant-microbe interactions, the host invests considerable amounts of resources in the microbial partner. If the microbe does not reciprocate with a comparable symbiotic benefit, it is regarded as a cheater. The host responds to cheaters with negative feedback mechanisms (sanctions) to prevent fitness deficits resulting from being exploited. We study sanctioning in the symbiosis between Medicago truncatula and the nitrogen-fixing rhizobium Sinorhizobium meliloti. We manipulated the exchange of resources between the partners in three ways: by using mutant rhizobia defective in nitrogenase; replacing nitrogen in the atmosphere with argon gas; and supplying rich nitrogen fertilizer to the host. We follow the consequences of simulated cheating by examining the metabolome and proteome of both partners. We find that sanctioning occurs at multiple levels. In particular, we observe repression of essential symbiotic functions and changes in central metabolism that are likely to be relevant for microbial fitness and that could therefore contribute to sanctioning. In addition, sanctioning triggers a broad panel of defense markers. A thorough understanding of the multilevel phenomenon of sanctioning will be essential for its genetic dissection and for the breeding of elite legume crops with efficient symbiosis.},
}

@article {pmid40909766,
year = {2025},
author = {Bruzzese, DJ and Gstöttenmayer, F and Weiss, BL and Khalil, H and Mach, R 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 = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7295611/v1},
pmid = {40909766},
issn = {2693-5015},
abstract = {Tsetse (Glossina spp.) are vectors of African trypanosomes, the causative agents of Human and African Animal trypanosomiases, diseases that remain significant medical and socioeconomic challenges in sub-Saharan Africa. In addition to trypanosomes, tsetse harbor both obligate and facultative symbiotic bacteria that can influence vector competence and reproductive biology. One such facultative symbiont, Spiroplasma glossinidia , infects several tsetse species within the Palpalis subgroup. In Glossina fuscipes fuscipes (Gff), the Spiroplasma glossinidia strain s Gff induces a trypanosome-refractory phenotype and negatively impacts reproductive fitness by reducing female fecundity. However, the mechanisms behind these Spiroplasma -derived phenotypes remain poorly understood. Here, we report successful in vitro cultivation of s Gff and present complete genomes from three sources: in vitro cultured s Gff and s Gff isolated from both laboratory-maintained and wild-caught (Uganda) Gff flies. Comparative genomic analyses revealed a high degree of similarity in gene content and synteny among these s Gff samples, confirming that they represent isolates of the same strain. Phylogenomic analyses placed s Gff within the Spiroplasma poulsonii clade. The s Gff genome is highly dynamic, containing numerous mobile genetic elements. Additionally, in silico annotations indicate that s Gff relies on its host for both lipids and carbohydrates and produces several toxins, all of which could be implicated in the observed trypanosome refractory phenotype. Finally, comparative transcriptomic analysis of s Gff from host hemolymph versus in vitro culture provided insights into potential factors relevant to host-symbiont interactions. Our findings provide a foundation for understanding the nutritional dialogue between s Gff and its host and identify symbiotic products that may contribute to trypanosome resistance. Furthermore, the establishment of an in vitro culture system for s Gff represents a significant resource for future functional studies with potential implications for vector control.},
}

@article {pmid40908936,
year = {2025},
author = {Oguchi, K and Munakata, M and Hiruta, C and Kakui, K},
title = {Intracellular Localization of the Bacterial Endosymbiont Cardinium in the Ostracod Heterocypris spadix.},
journal = {Zoological science},
volume = {42},
number = {4},
pages = {},
doi = {10.2108/zs250018},
pmid = {40908936},
issn = {0289-0003},
mesh = {Animals ; *Symbiosis ; *Crustacea/microbiology ; Female ; *Bacteroidetes/physiology ; },
abstract = {Symbiosis is a key driver of evolution in life-history traits and reproductive strategies. Some symbiotic microorganisms manipulate host reproduction to enhance their own transmission, a phenomenon well studied in insects but less understood in crustaceans. Among these microorganisms, Cardinium manipulates host reproductive systems, such as parthenogenesis, cytoplasmic incompatibility, and male killing in arthropods. However, its role in ostracods, small bivalve-shelled crustaceans, remains unclear. Some ostracod species reproduce via parthenogenesis, and high Cardinium infection rates in these lineages suggest a potential link between the symbiont and asexual reproduction. To investigate this relationship, we examined Cardinium localization in the parthenogenetic ostracod Heterocypris spadix from Japan. Using tissue clearing and fluorescence in situ hybridization (FISH), we visualized Cardinium within the ovaries. FISH observations revealed a widespread infection across the germarium, nurse cells, and oocytes. In early-stage oocytes, bacteria were evenly dispersed throughout the cytoplasm, whereas in more-developed oocytes, they clustered around the nucleus. Additionally, Cardinium was also detected in the hepatopancreas, indicating infection of both the reproductive and digestive systems. The presence of Cardinium in host reproductive structures, particularly the germarium, nurse cells, and developing oocytes, suggests its role in reproductive manipulation. To our knowledge, this study provides the first detailed localization of Cardinium in ostracods, reinforcing its potential influence on reproduction. Future research using antibiotics and genomic analysis will be crucial to confirm Cardinium's role in parthenogenesis induction.},
}

Animals
*Symbiosis
*Crustacea/microbiology
Female
*Bacteroidetes/physiology

@article {pmid40908830,
year = {2025},
author = {Yamlahi, YE and Remmal, I and Maurady, A and Britel, MR and Bakali, AH and Mokhtar, NB and Galiatsatos, I and Stathopoulou, P and Tsiamis, G},
title = {Characterization of the olive fly (Bactrocera oleae) microbiome across diverse geographic regions of Morocco.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70126},
pmid = {40908830},
issn = {1744-7917},
support = {22662//International Atomic Energy Agency/ ; },
abstract = {The olive fruit fly (Bactrocera oleae) is a significant pest threatening olive production worldwide. Bactrocera oleae relies on symbiotic bacteria for nutrition, development, and adaptation to its environment. Among these, Candidatus Erwinia dacicola is the most dominant symbiont and plays a key role in the fly's physiology and ecological adaptation. Understanding the dynamics between B. oleae, Ca. E. dacicola, and other components of the B. oleae microbiome is essential for developing effective targeted area-wide pest management strategies. This study aims to leverage full 16S rRNA gene sequencing to enhance the characterization of microbiome diversity in wild B. oleae populations from different regions in Morocco: Ouezzane, Rabat, Tanger, Errachidia, and Beni-Mellal. The results revealed distinct microbiome compositions influenced by geographic locations, with Candidatus Erwinia dacicola as the dominant symbiont, followed by Erwinia persicina as a secondary contributor. Other bacterial taxa, including Asaia bogorensis, were also identified, highlighting the functional diversity within the olive fly microbiome. These findings provide insights into the microbial ecology of B. oleae, contributing to the development and enhancement of sustainable pest control strategies.},
}

@article {pmid40908814,
year = {2025},
author = {Afonso, GVF and Johnson, GD and Collins, R and Pastana, MNL},
title = {Associations between fishes (Actinopterygii: Teleostei) and anthozoans (Anthozoa: Hexacorallia) in epipelagic waters based on in situ records.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70214},
pmid = {40908814},
issn = {1095-8649},
abstract = {We formally describe the association of fishes and anthozoans in epipelagic waters, extending this relationship to beyond the benthos. In situ observations and photographs of Aluterus schoepfii, Ariomma regulus, Caranx cf. latus and Brama spp. swimming alongside or holding larval tube anemones (Cerianthidae and Arachnactidae) and larval zoanthids (Sphenopidae) were made during blackwater SCUBA dives off Palm Beach, Florida, USA, and off Punaauia, Tahiti, French Polynesia. We report and illustrate the behaviour of these interactions, and suggest an advantage for the anthozoans.},
}

@article {pmid40908282,
year = {2025},
author = {Nishida, H and Itakura, M and Win, KT and Li, F and Kakizaki, K and Suzuki, A and Ohkubo, S and Duc, LV and Sugawara, M and Takahashi, K and Shenton, M and Masuda, S and Shibata, A and Shirasu, K and Fujisawa, Y and Tsubokura, M and Akiyama, H and Shimoda, Y and Minamisawa, K and Imaizumi-Anraku, H},
title = {Genetic design of soybean hosts and bradyrhizobial endosymbionts reduces N2O emissions from soybean rhizosphere.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8023},
pmid = {40908282},
issn = {2041-1723},
support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; },
mesh = {*Glycine max/genetics/microbiology/metabolism ; *Symbiosis/genetics ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Bradyrhizobium/genetics/physiology ; Nitrogen Fixation ; Soil Microbiology ; Rhizobium/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Soybeans fix atmospheric N2 through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N2O)-reducing (N2OR) activities, can be leveraged to reduce N2O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N2OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N2OR activity predominantly infect. Our optimize symbiotic system substantially reduces N2O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices.},
}

*Glycine max/genetics/microbiology/metabolism
*Symbiosis/genetics
*Nitrous Oxide/metabolism
*Rhizosphere
*Bradyrhizobium/genetics/physiology
Nitrogen Fixation
Soil Microbiology
Rhizobium/genetics
Bacterial Proteins/genetics/metabolism

@article {pmid40906400,
year = {2025},
author = {Zeng, Q and Wang, Z and Shen, Z and Li, W and Luo, K and Qin, Q and Li, S and Gu, Q},
title = {Microbiome Diversity and Dynamics in Lotus-Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081092},
pmid = {40906400},
issn = {2079-7737},
support = {2023YFD2400902//National Key Research and Development Program of China/ ; 2023YFD2401605//National Key Research and Development Plan Program/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; },
abstract = {The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.},
}

@article {pmid40906396,
year = {2025},
author = {Makwarela, TG and Seoraj-Pillai, N and Nangammbi, TC},
title = {Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081086},
pmid = {40906396},
issn = {2079-7737},
abstract = {Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host's genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk-microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science.},
}

@article {pmid40906361,
year = {2025},
author = {Alcantar-Orozco, EJ and Hernández-Elizárraga, VH and Vega-Tamayo, JE and Ibarra-Alvarado, C and Caballero-Pérez, J and Rodríguez de San Miguel, E and Rojas-Molina, A},
title = {Comparative Proteomic Analysis of Non-Bleached and Bleached Fragments of the Hydrocoral Millepora complanata Reveals Stress Response Signatures Following the 2015-2016 ENSO Event in the Mexican Caribbean.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081042},
pmid = {40906361},
issn = {2079-7737},
abstract = {The hydrocoral Millepora complanata (fire coral) plays a critical role in reef structure and relies on a symbiotic relationship with Symbiodiniaceae algae. Environmental stressors derived from climate change, such as UV radiation and elevated temperatures, disrupt this symbiosis, leading to bleaching and threatening reef survival. To gain insight into the thermal stress response of this reef-building hydrocoral, this study investigates the proteomic response of M. complanata to bleaching during the 2015-2016 El Niño event. Fragments from non-bleached and bleached colonies of the hydrocoral M. complanata were collected from a coral reef in the Mexican Caribbean, and proteomic extracts were analyzed using nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). Uni- and multivariate analyses were applied to identify significant differences in protein abundance. A total of 52 proteins showed differential abundance, including 24 that showed increased expression and 28 whose expression decreased in bleached fragments. Differentially abundant proteins were associated with amino acid biosynthesis, carbohydrate metabolism, cytoskeleton organization, DNA repair, extracellular matrix composition, redox homeostasis, and protein modification. These molecular alterations reflect critical physiological adaptations that may influence stress sensitivity or tolerance in hydrocorals. The findings indicate that heat stress induces molecular responses involving protein refolding, enhanced vesicular transport, cytoskeletal reorganization, and modulation of redox activity. This contributes to a deeper understanding of the molecular mechanisms underlying bleaching in reef-building hydrozoans and broadens current knowledge beyond the more extensively studied anthozoan corals.},
}

@article {pmid40906247,
year = {2025},
author = {Mohamed, HI and Ullah, I and Toor, MD and Tanveer, NA and Din, MMU and Basit, A and Sultan, Y and Muhammad, M and Rehman, MU},
title = {Heavy metals toxicity in plants: understanding mechanisms and developing coping strategies for remediation: a review.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {95},
pmid = {40906247},
issn = {2197-4365},
abstract = {Heavy metal (HM) contamination is an increasing environmental and agricultural concern due to the persistence, toxicity, and bioaccumulative nature of metals such as cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As). These pollutants are primarily introduced through industrial effluents, mining, and agrochemicals, negatively impacting soil health, crop productivity, and food safety, ultimately posing serious risks to both ecosystems and human health. Conventional remediation methods can be costly, labor-intensive, and environmentally disruptive. Heavy metals like Cd, Pb, Hg, and As disrupt cellular homeostasis, inhibit photosynthesis, generate oxidative stress, and interfere with nutrient uptake, leading to significant yield losses in plants. In response to these stresses, plants utilize complex molecular mechanisms for tolerance, including the activation of antioxidant enzymes, upregulation of metal transporters, production of metal-chelating molecules, and modulation of stress-responsive genes and transcription factors. In contrast, bioremediation offers a sustainable and eco-friendly alternative by leveraging the detoxification capabilities of plants, microbes, and their symbiotic interactions. Techniques such as phytoremediation, microbial-assisted remediation, and integrated strategies involving biochar and organic amendments have demonstrated promising results in restoring heavy metal-contaminated soils. Recent advancements in molecular biology and synthetic biology have further improved the efficiency of bioremediation through the genetic engineering of hyperaccumulator plant species and metal-resistant microbes. This review examines the toxic effects of heavy metals on plants and highlights innovative, nature-based remediation strategies, emphasizing their potential for scalable and sustainable environmental cleanup.},
}

@article {pmid40906125,
year = {2025},
author = {Basit, A and Haq, IU and Hyder, M and Humza, M and Younas, M and Akhtar, MR and Ghafar, MA and Liu, TX and Hou, Y},
title = {Microbial Symbiosis in Lepidoptera: Analyzing the Gut Microbiota for Sustainable Pest Management.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080937},
pmid = {40906125},
issn = {2079-7737},
support = {National Natural Science Foundation of China (U22A20489; 32361143791).//National Natural Science Foundation of China (U22A20489; 32361143791)./ ; },
abstract = {Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms-including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia-that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future.},
}

@article {pmid40906110,
year = {2025},
author = {Meesil, W and Ardpairin, J and Sharkey, LKR and Pidot, SJ and Vitta, A and Thanwisai, A},
title = {Whole-Genome Sequencing and Biosynthetic Gene Cluster Analysis of Novel Entomopathogenic Bacteria Xenorhabdus thailandensis ALN 7.1 and ALN 11.5.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080905},
pmid = {40906110},
issn = {2079-7737},
support = {PHD / 0084/2561//Royal Golden Jubilee Ph.D. Program/ ; R2566B043//Naresuan University (NU) and the National Science, Research and Innovation Fund (NSRF)/ ; R2567C003//Global and Frontier Research University Fund, Naresuan University/ ; },
abstract = {Xenorhabdus species are entomopathogenic bacteria that live in symbiosis with Steinernema nematodes and produce a wide range of bioactive secondary metabolites. This study aimed to characterize the complete genomes and biosynthetic potential of two novel Xenorhabdus isolates, ALN7.1 and ALN11.5, recovered from Steinernema lamjungense collected in Northern Thailand. High-quality genome assemblies were generated, and phylogenomic comparisons confirmed that both isolates belonged to the recently described species Xenorhabdus thailandensis. The assembled genomes were approximately 4.02 Mb in size, each comprising a single circular chromosome with a GC content of 44.6% and encoding ~3800 protein-coding sequences, consistent with the features observed in other members of the genus. Biosynthetic gene cluster (BGCs) prediction using antiSMASH identified 19 BGCs in ALN7.1 and 18 in ALN11.5, including known clusters for holomycin, pyrrolizixenamide, hydrogen cyanide, and gamexpeptide C, along with several uncharacterized clusters, suggesting unexplored metabolic potential. Comparative analyses highlighted conserved yet strain-specific BGC profiles, indicating possible diversification within the species. These results provide genomic insights into X. thailandensis ALN7.1 and ALN11.5 and support their potential as valuable sources for the discovery of novel natural products and for future biotechnological applications.},
}