@article {pmid41198545,
year = {2025},
author = {Stefano, GB},
title = {Adaptability Beyond Darwin: Microbial Evolution, Mitochondria, and the Thermodynamic Frontiers of Survival.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {30},
number = {10},
pages = {45962},
doi = {10.31083/FBL45962},
pmid = {41198545},
issn = {2768-6698},
mesh = {*Mitochondria/physiology/metabolism ; *Biological Evolution ; Thermodynamics ; Humans ; *Adaptation, Physiological ; Bacteria/genetics ; Animals ; },
abstract = {Charles Darwin hypothesized that evolution is based on adaptations to a changing environment, and that organisms that developed even slightly favorable variations would ultimately be most likely to survive. This concept is clearly reflected in the life cycles of pathogenic species. While modern antibiotics, antiviral agents, and vaccines can successfully eliminate many pathogens and prevent infections, only susceptible strains are affected. Bacteria and viruses that can adapt and develop resistance mechanisms will survive and thrive in the absence of ongoing competition. We build on this framework by considering the evolutionary impact of microbial-mediated adaptations experienced by the host. For example, intracellular mitochondria, largely believed to be descendants of symbiotic ancestral bacteria, can be specifically targeted by viral pathogens. Taken one step further, we hypothesize that Darwinian theory may also apply to atoms and molecules, which are not "alive" by any conventional definition, but interact with one another and self-assemble according to the principles of thermodynamics that promote stability in defined environments. Building on these foundations, our hypotheses and conceptual framework will facilitate further exploration into the evolution of microbial mechanisms that modulate behavior, shape the development of the immune system, and promote host evolution.},
}

*Mitochondria/physiology/metabolism
*Biological Evolution
Thermodynamics
Humans
*Adaptation, Physiological
Bacteria/genetics
Animals

@article {pmid41197509,
year = {2025},
author = {Li, Q and Zhang, T and Zhao, X and Zhang, H and Guo, M and Meng, X and Hou, N and Hao, Q and Li, L},
title = {Driving synergistic Fe-N-Plastic co-metabolism and functional microbial symbiosis via nZVI@RA for enhanced decontamination in constructed wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140342},
doi = {10.1016/j.jhazmat.2025.140342},
pmid = {41197509},
issn = {1873-3336},
abstract = {Nanoplastics (NPs) significant challenges to nitrogen removal in constructed wetlands (CWs). Although nano-zero valent iron (nZVI)-based composites have shown potential in enhancing pollutant removal, the integrated mechanisms governing iron, nitrogen, and plastic metabolism, as well as their influence on the microbial network remain poorly understood. Here, we developed recycled aggregates-supported nZVI (nZVI@RA) and systematically investigated its impact on microbial nitrogen metabolism and plastic degradation within CWs. The results revealed that nZVI@RA profoundly reshaped the microbial symbiotic network, promoting Exiguobacterium and Bacillus as dominant genera and facilitating synergistic interactions. Mechanistically, nZVI@RA enhanced iron metabolism and electron transfer, leading to the upregulation of key genes and enzymes involved in nitrogen transformation (e.g., amoABC and nirKS) and NP degradation (e.g., styA and styC). These processes, coupled with superior adsorption capacity, improved removal efficiencies of COD (64.57 ± 3.57 %), TN (70.79 ± 4.19 %), and NPs (92.46 ± 3.66 %). Structural equation modeling revealed strong correlations between iron metabolism, microbial activity (0.82), nitrogen metabolism (0.51), and plastic degradation (0.40) in the nZVI@RA system, underscoring the central role of iron cycling. This study elucidates the critical function of nZVI@RA in orchestrating microbial interactions and optimizing pollutant removal, providing a foundation for advanced CW design.},
}

@article {pmid41197331,
year = {2025},
author = {Fan, K and Wu, Y and Qin, Y and He, H and Lv, L and Li, G and Liu, J and Qin, R and Liu, H},
title = {Functional characterization of GmSRS14 in regulating root nodule development of soybean.},
journal = {Journal of plant physiology},
volume = {315},
number = {},
pages = {154649},
doi = {10.1016/j.jplph.2025.154649},
pmid = {41197331},
issn = {1618-1328},
abstract = {SHORT INTERNODES (SHI)-related sequence (SRS) proteins are plant-specific transcription factors that modulate hormone biosynthesis and signalling. Their contribution to legume-rhizobium symbiosis, however, remains largely unexplored. Phylogenetic and collinearity analyses of legume SRS genes classified 12 subclasses and revealed soybean's evolutionary relationships, including large-scale gene duplication. GmSRS14 was specifically highly expressed in root nodules and localised in the nucleus only. Exogenous IAA modulates its expression at low concentrations (1 μM), while high concentrations (100 μM) decrease nodule expression. All ABA concentrations tested (10, 20 and 50 μM) inhibited nodule growth, nitrogenase activity and GmSRS14 expression. Functional validation via hairy root transformation demonstrated GmSRS14 overexpression (GmSRS14-OE) increased nodule number, weight, and nitrogenase activity, while GmSRS14 silencing (GmSRS14-RNAi) suppressed nodulation. This study provides a new idea for breeding soybean varieties with high efficiency of nitrogen fixation.},
}

@article {pmid41196415,
year = {2025},
author = {He, Y and Yang, T and Mi, J and He, S and Yang, Z and Lu, S and Yue, K and Huang, Y and Song, L and Xiao, Y and Ren, Z},
title = {B.uniformis IM01-derived IAA alleviates asthma via AhR/NLRP3 pathways in mice.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {388},
pmid = {41196415},
issn = {1420-9071},
support = {2023YFC0871200//the National Key R&D Program of China/ ; 33054//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; 29172//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *Asthma/pathology/metabolism/immunology/drug therapy ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Indoleacetic Acids/metabolism/pharmacology ; Mice ; *Signal Transduction/drug effects ; Disease Models, Animal ; NF-kappa B/metabolism ; Mice, Inbred BALB C ; T-Lymphocytes, Regulatory/immunology ; Female ; Lung/pathology ; Interleukin-22 ; Tryptophan/metabolism ; Th2 Cells/immunology ; Interleukins/metabolism ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; },
abstract = {Symbiotic flora exhibits a strong association with the pathogenesis of allergic disorders. Certain Bacteroides species have demonstrated potential in ameliorating allergic conditions. However, the specific role of Bacteroides uniformis in allergic asthma and its underlying mechanisms remain incompletely understood. This study demonstrates that oral administration of B.uniformis IM01 significantly enhanced the production of indole-3-acetic acid (IAA), suppressed airway inflammatory cell airway infiltration and aberrant T helper 2 (Th2) immune responses, and improved the epithelial barrier function in a murine model of asthma. Mechanistically, B.uniformis IM01 upregulated tryptophan metabolism, elevating IAA levels in both colon and serum, which activated the aryl hydrocarbon receptor (AhR) and induced interleukin-22 (IL-22) production. Activated AhR may inhibit NF-κB/NLRP3 signaling pathway and facilitate the splenic differentiation of Foxp3[+] regulatory T cells (Tregs), thus attenuating lung barrier dysfunction and improving allergic asthma symptoms. In summary, our results revealed that B.uniformis IM01 upregulated production of IAA to activate AhR leading to inhibited NF-κB/NLRP3-mediated immune responses, and ameliorated allergic asthma through the gut-lung axis.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*Asthma/pathology/metabolism/immunology/drug therapy
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Indoleacetic Acids/metabolism/pharmacology
Mice
*Signal Transduction/drug effects
Disease Models, Animal
NF-kappa B/metabolism
Mice, Inbred BALB C
T-Lymphocytes, Regulatory/immunology
Female
Lung/pathology
Interleukin-22
Tryptophan/metabolism
Th2 Cells/immunology
Interleukins/metabolism
*Basic Helix-Loop-Helix Transcription Factors/metabolism

@article {pmid41195911,
year = {2025},
author = {Pai, YC and Huang, CY and Lin, LY and Li, YH and Yu, LC},
title = {Infectious Carcinogens Derived from Intestinal Microflora: Mechanisms of Microbial Transitions from Eubionts to Pathobionts.},
journal = {Journal of physiological investigation},
volume = {},
number = {},
pages = {},
doi = {10.4103/ejpi.EJPI-D-25-00045},
pmid = {41195911},
issn = {2950-6344},
abstract = {A diverse community of microorganisms inhabits the gastrointestinal tract in a physiological state. While a symbiotic relationship exists between commensal bacteria and the healthy host, an imbalanced microbial population (dysbiosis) is associated with the development of colitis-associated colorectal cancers. The decline of beneficial microbes (eubionts) and the expansion of commensal-derived opportunistic pathogens (pathobionts) are widely recognized as key factors in the microbial etiology of various diseases. In particular, certain bacteria with emerging virulence elements are present in the gut microbiome and have been implicated as contributors to the development of colon cancer, such as Escherichia coli, Bacteroides fragilis, and Fusobacterium nucleatum. Bacterial virulent factors, including lipopolysaccharide, fimbriae and adhesins, and toxins, promote oncogenesis through direct or indirect mechanisms. These microbial products modify host cellular functions, resulting in DNA damage, increased epithelial proliferation, and intensified inflammation, all of which ultimately contribute to tumor formation. Although the existence of pathobionts is generally accepted nowadays, an open question remains regarding why bacteria shift from harmless commensals to disease-causing pathobionts. Accumulating evidence suggests that host epithelial functions influence the composition of the intestinal microbiota by regulating oxygen availability in the lumen, providing antimicrobial defense, activating innate immune responses, synthesizing mucin glycoproteins, and establishing a physical barrier through the organization of microvilli. This review examines the various aspects of mucosal drivers that shape microbiota and provides evidence that intraepithelial stress plays a significant role in configuring colitogenic and tumorigenic microflora. Understanding the mechanisms by which microbes transition from eubionts to pathobionts that promote cancer progression is crucial for developing bacterial precision medicine. Identifying the roles of intestinal pathobionts and the critical time point for host-microbe interactions in tumorigenesis could lead to the development of new strategies for prevention and therapy.},
}

@article {pmid41195882,
year = {2025},
author = {Lin, M and de Kruijff, M and Poulsen, M and Beemelmanns, C},
title = {Genome-Mining Based Discovery of Pyrrolomycin K and L from the Termite-Associated Micromonospora sp. RB23.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01051},
pmid = {41195882},
issn = {1520-6025},
abstract = {Natural products derived from symbiotic microbes remain a rich source of structurally diverse and bioactive molecules. In this study, we report de novo genome sequencing of the termite-associated isolate Micromonospora sp. RB23. Genome mining uncovered a type I polyketide synthase (T1PKS) biosynthetic gene cluster encoding five halogenases, predicted to produce pyrrolomycin-like antimicrobial compounds. Mass-spectrometry-based molecular networking facilitated the identification and isolation of N-methylated pyrrolomycin K and mycothiol-adduct, pyrrolomycin L. Structure elucidation was accomplished based on liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) alongside 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. Based on the evaluated of antimicrobial activity, we propose that N-methylation and mycothiol-based conjugation in pyrrolomycins are possible detoxification mechanisms that play a role in enhancing self-tolerance.},
}

@article {pmid41195197,
year = {2025},
author = {Wang, X and Long, L},
title = {The innovation paradox in human-AI symbiosis: ambidextrous effects of AI technology adoption on innovative behavior.},
journal = {Frontiers in artificial intelligence},
volume = {8},
number = {},
pages = {1635246},
pmid = {41195197},
issn = {2624-8212},
abstract = {INTRODUCTION: AI is radically changing workplace ecosystems in the midst of the Fourth Industrial Revolution, making human-machine collaboration a need for organizations. The ambidextrous processes by which AI simultaneously encourages and constrains inventive behaviors need systematic examination, even though employee innovation is still essential for maintaining competitive advantage. In order to understand the paradoxical consequences of AI, this study builds a dual-path moderated mediation model based on the Job Demands-Resources (JD-R) paradigm.

METHODS: Using a two-wave longitudinal design with a 3-month interval and multi-source data from 250 experts in China, we combined survey measurements with quasi-experimental manipulations. The following findings were obtained using structural equation modeling (SEM) and bootstrapping.

RESULTS: (1) AI technology adoption is a job resource that increases Felt Obligation for Constructive Change (FOCC), but it also acts as a job demand that inhibits innovation by creating a sense of job insecurity; (2) task crafting is a crucial boundary condition that amplifies the positive mediation path while attenuating the negative pathway.

DISCUSSION: Based on the aforementioned findings, this study highlights the importance of considering employees' psychological states and behavioral changes while fostering technological innovation, exposing the intricacy of artificial intelligence technology in HRM from both a subjective and objective standpoint. Job insecurity is a possible drawback of technology use, hence businesses should take appropriate steps to lessen employee uneasiness while using new technologies. Felt Obligation for Constructive Change, on the other hand, is a crucial strategy for encouraging creative behavior. To do this, managers must investigate and enhance employees' intrinsic motivation for their everyday tasks and foster a culture of creativity. Task crafting, as an effective self-management and driving factor, is also very important to reduce the negative effects of technology adoption and increase its positive effects. For this reason, businesses should support and encourage employees to improve their autonomy and flexibility, iterate on their work methods, and stimulate their ability to innovate. This will not only help employees develop their own skills but also give businesses a competitive edge and continuous innovation motivation.},
}

@article {pmid41194726,
year = {2025},
author = {Wang, C and Peng, YL and Liu, XY and Cao, TT and Shi, M and Wang, ZK and Li, Q and Song, XZ},
title = {Effects of phosphorus addition on phosphorus acquisition strategies in Phyllostachys edulis rhizome roots.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {10},
pages = {3061-3068},
doi = {10.13287/j.1001-9332.202510.004},
pmid = {41194726},
issn = {1001-9332},
mesh = {*Phosphorus/metabolism/pharmacology ; *Rhizome/metabolism ; Mycorrhizae/physiology ; *Poaceae/metabolism/growth & development ; *Plant Roots/metabolism ; Symbiosis ; },
abstract = {To elucidate the root phosphorus (P) acquisition strategies of Phyllostachys edulis to maintain high productivity under P deficiency, we conducted an in situ P addition experiment (0, 50, 100 kg P·hm[-2]·a[-1] defined as CK, low-P (LP), and high-P (HP) addition). We investigated the regulatory effects of P addition on morphological and physiological traits of rhizome root, root exudates, and mycorrhizal symbiosis characteristics. The results showed that P addition significantly increased specific root surface area (LP:19.1%; HP:23.4%), root nitrogen (LP:42.6%; HP:37.7%) and P contents (LP:83.8%; HP:115.3%), but significantly decreased phosphatase activity (LP:22.2%; HP:30.4%) and arbuscular mycorrhizal fungi (AMF) infection rate (LP:24.1%; HP:25.3%). There were no significant differences between low-P and high-P treatments for these impacts. P addition significantly increased rhizosphere soil pH, citrate-P, enzyme-P, HCl-P and microbial biomass carbon, nitrogen and P in the rhizosphere soil. Notably, citrate-P, enzyme-P, and HCl-P contents in HP treatment were significantly higher than those in LP treatment. There were significant correlations between rhizosphere soil P fractions and specific root surface area, phosphatase activity, as well as AMF infection rate, indicating that rhizosphere soil P fractions were important drivers of P acquisition pathways in rhizome roots. Under P addition, rhizome roots shifted from a conservative pathway relying on "root exudation and mycorrhizal symbiosis" to an acquisitive pathway characte-rized by "high surface area".},
}

*Phosphorus/metabolism/pharmacology
*Rhizome/metabolism
Mycorrhizae/physiology
*Poaceae/metabolism/growth & development
*Plant Roots/metabolism
Symbiosis

@article {pmid41194578,
year = {2025},
author = {Kalem, M and Ozgan Kurt, A and Goktepeli, G and Onen, V and Ahmetli, G and Yel, E},
title = {Thermochemical treatment of waste polypropylene (PP) using marble sludge as catalyst-II: Evaluation of chemicals recovery potential from pyrolytic fluids.},
journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X251385853},
doi = {10.1177/0734242X251385853},
pmid = {41194578},
issn = {1096-3669},
abstract = {In this study, waste polypropylene (PP) was pyrolysed together with marble processing industry effluents physicochemical treatment sludge (named as K1) catalyst, and the valuable component recovery and usage potential from resulting liquid and gaseous products were investigated. In the fixed bed pyrolysis reactor under inert conditions with N2 gas, the studied experimental variables were temperature and mixing ratio. The resultant liquid and gaseous fractions were characterized via GC-MS, Fourier transform infrared, thermogravimetric analysis and calorific value analyses. Liquid products contain predominantly paraffinic and olefinic, but minor aromatic hydrocarbons (HCs) and also minor amounts of oxygenated compounds with 20-30% K1 catalyst. Heating values of the liquid products were around 10 kcal.g[-1]. The gas products predominantly contain alkanes, alkenes and aromatic HC compounds with economic value such as benzene isotridecanol, heptanol, ketone and terpene. Ca and Mg carbonate structure of K1 catalyst increased the compound diversity in the pyrolysis gas, especially in the aliphatic groups. The detected low C number alkane compounds were pentane, heptane, cyclohexane and high C number long-chain n-alkane aliphatic compounds were docosane, hexacosane and hexatriacontane. The recoverable compounds are economically and environmentally important as they can be used in many industries such as cleaning, cosmetics, pharmacology and petrochemistry as feedstock. The proposed pyrolysis provided symbiotic solution to these two types of wastes and the resultant products of this application have potential for energy and compound recovery. Recovery methods can be further studied.},
}

@article {pmid41193803,
year = {2025},
author = {Tsitsikli, M and Simonsen, B and Luu, TB and Larsen, MM and Andersen, CG and Gysel, K and Lironi, D and Krönauer, C and Rübsam, H and Hansen, SB and Bærentsen, R and Wulff, JL and Johansen, SH and Sezer, G and Stougaard, J and Andersen, KR and Radutoiu, S},
title = {Two residues reprogram immunity receptors for nitrogen-fixing symbiosis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41193803},
issn = {1476-4687},
abstract = {Receptor signalling determines cellular responses and is crucial for defining specific biological outcomes. In legume root cells, highly similar and structurally conserved chitin and Nod factor receptor kinases activate immune or symbiotic pathways, respectively, when chitinous ligands are perceived[1]. Here we show that specific amino acid residues in the intracellular part of the Nod factor receptor NFR1 control signalling specificity and enable the distinction of immune and symbiotic responses. Functional investigation of CERK6, NFR1 and receptor variants thereof revealed a conserved motif that we term Symbiosis Determinant 1 in the juxtamembrane region of the kinase domain, which is key for symbiotic signalling. We show that two residues in Symbiosis Determinant 1 are indispensable hallmarks of NFR1-type receptors and are sufficient to convert Lotus CERK6 and barley RLK4 kinase outputs to enable symbiotic signalling in Lotus japonicus.},
}

@article {pmid41193506,
year = {2025},
author = {Voß, L and Keller, I and Schröder, R and Mehner-Breitfeld, D and Specht, A and Dräger, G and Rinne, J and Franke, J and Medina-Escobar, N and Herde, M and Brüser, T and Neuhaus, HE and Witte, CP},
title = {A plastid carbohydrate carrier mediates ribose recycling from nucleotide catabolism and glucose export from starch degradation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9747},
pmid = {41193506},
issn = {2041-1723},
support = {452173586//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 423879281//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC175, project B03//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Plastids/metabolism ; Arabidopsis/metabolism/genetics ; *Starch/metabolism ; *Glucose/metabolism ; *Ribose/metabolism ; *Nucleotides/metabolism ; Phaseolus/metabolism/genetics ; *Arabidopsis Proteins/metabolism/genetics ; Glycine max/metabolism/genetics ; Root Nodules, Plant/metabolism ; Mutation ; Fructose/metabolism ; Nitrogen Fixation ; Cytosol/metabolism ; Escherichia coli/metabolism/genetics ; Biological Transport ; Carbohydrate Metabolism ; },
abstract = {In plants, nucleotide degradation releases ribose in the cytosol. An unidentified transporter then brings the ribose into the plastids for phosphorylation. This process of ribose recycling is particularly prominent in root nodules of soybean (Glycine max) and common bean (Phaseolus vulgaris) during symbiotic nitrogen fixation. In this biological context, we identified a plastid ribose transporter, which is an ortholog of the putative plastid glucose transporter (pGlcT) of Arabidopsis thaliana. We show that Arabidopsis mutants of At-pGlcT, but not of the related At-pGlcT2, accumulate ribose and fructose constitutively, whereas glucose accumulates only at night. Uridine feeding experiments leading to cytosolic ribose release indicated that At-pGlcT transports ribose from the cytosol into the plastids. Uptake assays with complemented Escherichia coli sugar transport mutants directly demonstrated that At-pGlcT transports ribose, glucose, and fructose. Ribose and fructose accumulation were also observed in CRISPR-induced bean nodule mutants of Pv-pGlcT. Additionally, our data show that ribose recycling is important for producing allantoin, a nitrogen fixation product used for nitrogen export from nodules to shoots. We conclude that pGlcT is a plastid facilitator for the import of ribose from nucleotide catabolism, for the export of glucose from nocturnal starch breakdown, and for cytosol-plastid fructose exchange in vivo.},
}

*Plastids/metabolism
Arabidopsis/metabolism/genetics
*Starch/metabolism
*Glucose/metabolism
*Ribose/metabolism
*Nucleotides/metabolism
Phaseolus/metabolism/genetics
*Arabidopsis Proteins/metabolism/genetics
Glycine max/metabolism/genetics
Root Nodules, Plant/metabolism
Mutation
Fructose/metabolism
Nitrogen Fixation
Cytosol/metabolism
Escherichia coli/metabolism/genetics
Biological Transport
Carbohydrate Metabolism

@article {pmid41192520,
year = {2025},
author = {Sehrawat, A and Corpas, FJ},
title = {Pivotal role of Nitric oxide in regulating beneficial plant-microbe interactions under both physiological and stress conditions.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112851},
doi = {10.1016/j.plantsci.2025.112851},
pmid = {41192520},
issn = {1873-2259},
abstract = {Plant-microbe interactions involve a complex communication network, where microbes can serve as either beneficial partners or harmful pathogens. Nitric oxide (NO) is a crucial signaling molecule that regulates plant growth and development, while enhancing tolerance to both biotic and abiotic stresses. It does this by interacting directly with reactive oxygen species (ROS) and regulating antioxidant enzyme activity through post-translational modifications (PTMs), such as S-nitrosation and nitration. Additionally, NO affects transcription factors that regulate gene expression and modulates phytohormone signaling, which helps alleviate oxidative stress. NO plays a pivotal role in symbiotic relationships between plant roots and microbes. In legumes, it is essential for rhizobial recognition, root hair curling, infection thread formation, nodule initiation, development, and senescence. Similarly, NO supports positive interactions with mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR), which enhance nutrient availability, particularly nitrogen and phosphorus, and improve plant resilience under stress. At the molecular level, NO regulates symbiosis-related gene expression and modifies proteins through PTMs such as S-nitrosation of nitrogenase and tyrosine nitration of glutamine synthetase and leghemoglobin, while maintaining cellular redox balance. This review provides an updated and comprehensive overview of NO signaling in beneficial plant-microbe interactions under both physiological and stress conditions. It further analyzes the specific sources, regulatory mechanisms, and molecular targets of NO, which remain poorly understood. In addition, it highlights the application of omics-based approaches to unravel these processes, offering insights that could guide the development of new strategies to enhance crop productivity through the targeted exploitation of symbiotic associations.},
}

@article {pmid41192114,
year = {2025},
author = {Chen, B and Wang, H and Yang, Y and Wang, W and Zuo, M and Zhou, J and Tang, S and Zhai, R and Liu, S and Ai, Y and Guo, Z and Liu, R},
title = {Microbial metabolite tigloside alleviates osteoarthritis by repolarizing macrophages from M1 to M2 phenotype through Trafd1 destabilization and Trafd1-mediated NF-κB/STAT6 signaling pathways.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115747},
doi = {10.1016/j.intimp.2025.115747},
pmid = {41192114},
issn = {1878-1705},
abstract = {Osteoarthritis (OA) is the most prevalent joint disease among the middle-aged and elderly individuals, primarily characterized by synovitis and cartilage damage. Although non-steroidal anti-inflammatory drugs (NSAIDs) are widely used to manage OA, they fail to fundamentally prevent or alleviate cartilage damage and can cause severe gastrointestinal or cardiovascular side effects. Therefore, developing OA drugs that address both symptoms and underlying causes is of significant importance. Our study found that tigloside (TIG), a main metabolite derived from symbiotic actinomyces, could repolarize macrophages from pro-inflammatory M1 type to anti-inflammatory M2 type, suppress the release of multiple inflammatory factors and facilitate the secretion of the anti-inflammatory cytokine IL-10, thereby creating a favorable microenvironment for chondrocyte regeneration and extracellular matrix (ECM), and alleviating pain, synovitis and OA cartilage damage. Mechanistically, TIG competes with the signaling adaptor molecule Traf1 to bind at the middle region (aa 104-414) of Trafd1, disrupting the interaction between Trafd1 and Traf1. This disruption promotes the degradation of Trafd1 and Traf1 via proteasome-ubiquitination pathway, leading to a reduction in their protein levels. Consequently, the downregulation of Trafd1 further inhibits NF-κB signaling and M1 polarization while promoting STAT6 pathway and M2 polarization, resulting in the repolarization of macrophages from M1 to M2 type and the amelioration of OA. Importantly, these findings were further validated in human macrophages derived from OA patients. In summary, this study highlights the potential of TIG as a disease-modifying drug for OA, and identifies Trafd1 as a novel therapeutic target for OA treatment.},
}

@article {pmid41192042,
year = {2025},
author = {Wu, J and Yin, H and Li, Y and Zhao, L and Guo, H and Xu, C and Shang, J and Fu, X and Ma, F and Song, R},
title = {Dynamic drivers of PAHs transformation in the spatial and temporal continuum of the rhizosphere: An analysis of plant-microbe synergistic mechanism.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128380},
doi = {10.1016/j.micres.2025.128380},
pmid = {41192042},
issn = {1618-0623},
abstract = {The migration and transformation of polycyclic aromatic hydrocarbons (PAHs) in soil systems are inherently constrained by their low solubility, strong sorption affinity to soil particles, and limited bioavailability for biological uptake and degradation. As a critical ecological interface mediating plant-microbe interactions, the rhizosphere plays a pivotal role in facilitating PAHs mobilization and transformation processes. This review systematically examines the spatiotemporal dynamics of PAHs migration and transformation within rhizosphere systems under plant-microbe collaborative regulation, characterized by sequential temporal phases (initial desorption-solubilization, intermediate absorption-accumulation, and terminal degradation-transformation) and spatial stratification (rhizosphere soil-liquid interface, root surface microenvironment, and internal root tissues). We particularly emphasize the synergistic plant-microbe interactions that drive PAHs desorption, solubilization, phytoaccumulation, and biodegradation. Furthermore, we elucidate four potential mechanistic pathways: AHL analogs in root exudates activate bacterial quorum sensing systems to stimulate surfactant production and PAHs-degrading enzyme synthesis; Microbial-derived IAA enhances H[+] -ATPase activity in plants, facilitating PAHs/H[+] co-transport mechanisms; Coordinated AHL-IAA signaling promotes Ca[2+] uptake and upregulates root nodule symbiosis-related gene expression; ROS in root exudates activate bacterial c-di-GMP signaling pathways to enhance microbial colonization and PAHs-degrading enzyme production. We also analyze the practical limitations affecting rhizoremediation efficacy, including climatic conditions, soil heterogeneity, and variations in pollutant types, and propose corresponding future research directions toward the end of the article. This comprehensive analysis establishes a theoretical framework for understanding the mechanistic basis of plant-microbe synergism in rhizospheric PAHs remediation, offering a foundation for advancing rhizosphere engineering and phytoremediation strategies.},
}

@article {pmid41191165,
year = {2025},
author = {Steffen, GPK and Steffen, RB and Schú, AL and da Silva Sousa, TC and da Costa, LC and de São José, JFB},
title = {Impact of urea and Azospirillum brasilense on soybean nodulation and early growth.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {11},
pages = {437},
pmid = {41191165},
issn = {1573-0972},
mesh = {*Glycine max/growth & development/microbiology/drug effects ; *Azospirillum brasilense/physiology/growth & development/metabolism ; Bradyrhizobium/growth & development/physiology/metabolism ; *Urea/metabolism ; *Plant Root Nodulation ; Root Nodules, Plant/microbiology/growth & development ; Symbiosis ; Nitrogen Fixation ; Leghemoglobin/analysis ; Nitrogen/metabolism ; Soil Microbiology ; Plant Roots/growth & development/microbiology ; Chlorophyll/analysis ; Fertilizers ; },
abstract = {The effects of isolated and combined inoculation with Bradyrhizobium japonicum (SEMIA 3079 and 5080) and Azospirillum brasilense (Ab-V5), with and without nitrogen fertilization, on nodulation and early soybean growth were evaluated in a greenhouse under controlled temperature and irrigation conditions, using non-sterilized soil. The experimental design included five treatments: (1) urea (200 kg ha[-1]); (2) B. japonicum; (3) A. brasilense; (4) co-inoculation (B. japonicum + A. brasilense); and (5) B. japonicum + 100 kg ha[-1] of urea. Evaluations were carried out 50 days after sowing and included plant height, shoot and root dry mass, number and fresh mass of nitrogen-fixing nodules, Falker chlorophyll index, and leghemoglobin content. Co-inoculation increased the number of nodules by 26.13% compared to B. japonicum alone (88 → 111 nodules), while A. brasilense alone also promoted nodulation (113.3 nodules), indicating synergy with native soil rhizobia. Higher leghemoglobin levels were observed in nodules under co-inoculation, suggesting enhanced symbiotic functionality, whereas urea application reduced this indicator. Nitrogen fertilization strongly suppressed symbiosis (-75.77% in nodule number and - 83.36% in nodule fresh mass; B. japonicum + N vs. B. japonicum), confirming the inhibitory effect of mineral nitrogen on biological nitrogen fixation (BNF). It is concluded that co-inoculation with B. japonicum (SEMIA 3079 and 5080) and A. brasilense (Ab-V5) enhances nodule functionality and BNF in non-sterile soil conditions, providing a biological basis for reducing reliance on mineral nitrogen in soybean production systems.},
}

*Glycine max/growth & development/microbiology/drug effects
*Azospirillum brasilense/physiology/growth & development/metabolism
Bradyrhizobium/growth & development/physiology/metabolism
*Urea/metabolism
*Plant Root Nodulation
Root Nodules, Plant/microbiology/growth & development
Symbiosis
Nitrogen Fixation
Leghemoglobin/analysis
Nitrogen/metabolism
Soil Microbiology
Plant Roots/growth & development/microbiology
Chlorophyll/analysis
Fertilizers

@article {pmid41190647,
year = {2025},
author = {Bromfield, ESP and Cloutier, S},
title = {Analysis of the complete genome sequence of Bradyrhizobium diazoefficiens 172S4, a highly efficient nitrogen-fixing symbiont of soybeans, reveals large-scale genomic inversion.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0088925},
doi = {10.1128/mra.00889-25},
pmid = {41190647},
issn = {2576-098X},
abstract = {We announce the complete genome sequence of Bradyrhizobium diazoefficiens 172S4, a highly efficient nitrogen-fixing symbiont isolated from a soybean root nodule. The chromosome (~9.1 Mb) exhibits a large inversion (~5.3 Mb) and encodes genes for symbiosis, nitrogen fixation, N2O reduction, and hydrogen uptake, highlighting the potential of 172S4 for sustainable agriculture.},
}

@article {pmid41189400,
year = {2025},
author = {Gao, L and Liu, J and Xing, C and Qiu, X and Xia, J and Zhao, C and Dou, X and Feng, C},
title = {Conformation-Matched Symbiotic Noncovalent Sites Facilitated Supramolecular Nanotwists Featuring both P and M Sub-Helical Domains.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e16712},
doi = {10.1002/anie.202516712},
pmid = {41189400},
issn = {1521-3773},
support = {2024YFB3814600//National Key Research and Development Program/ ; 52533014//National Natural Science Foundation of China/ ; 52403193//National Natural Science Foundation of China/ ; 52373147//National Natural Science Foundation of China/ ; 52403161//National Natural Science Foundation of China/ ; 25CL2900600//Science and Technology Commission of Shanghai Municipality/ ; GZB20240420//CPSF/ ; 2024M751970//Chinese Postdoctoral Science Foundation/ ; 2024M762008//Chinese Postdoctoral Science Foundation/ ; },
abstract = {Living system can use homochiral blocks to simultaneously fabricate diverse structures with opposite chirality (e.g., right-handed α-helices and left-handed polyproline-II helices) for maintaining three-dimensional conformations and functions of biostructures, but realizing this process in artificial systems remains exceptional challenge due to difficulty in constructing precise noncovalent pattern for diverse chirality transfer. Herein, we report a strategy to fabricate helical nanofibers featuring P and M sub-domains by delicately introducing symbiotic noncovalent sites in the terminal of l-phenylalanine derivatives (LCN). Benefiting from the conformation match of LCN, two symbiotic sites (C≡N, Ar─Hortho) in terminal cyanophenyl group can synergistically form noncovalent with different sites (C≡N⋯Hmeta─Ar; Ar─Hortho⋯N≡C), resulting in a precise noncovalent network. Furthermore, these two noncovalent facilitate the simultaneous formation of M-type and P-type domains due to their opposite spatial direction. Similar phenomenon is also observed from symbiotic sites in another terminal hydroxy group (O, H), further confirming an unusual chirality transfer where molecular homochirality propagates to supramolecular domains with opposite handedness. Besides, these helical domains can further cooperatively organize into higher-order P-type helices, in which fiber longitudinal axes aligns with the screw axes of noncovalent-defined helices. This study accelerates the understanding of diverse chirality transfer based on homochirality in nature and takes into a realm of constructing helical nanostructures with diverse sub-helices by homochiral blocks.},
}

@article {pmid41189012,
year = {2025},
author = {Ding, Z and Li, J and Bai, L},
title = {Ecological Modules Link Soil Aggregate Stability, Chemical Properties and Fungal Communities Under Plant Species-Based Revegetation.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70228},
doi = {10.1111/1758-2229.70228},
pmid = {41189012},
issn = {1758-2229},
support = {LJKMZ20221053//The Educational Department of Liaoning Province/ ; X2021012//Shenyang Agricultural University/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/classification/genetics/isolation & purification ; *Mycobiome ; *Plants/microbiology/classification ; Grassland ; Ecosystem ; },
abstract = {The establishment of native grassland species is widely implemented on abandoned land as a strategy to restore degraded soils. However, its effects on soil properties are highly species-specific, as plant-driven physicochemical changes subsequently reshape microbial community structure. The linkages between soil physicochemical properties and microbial communities following native grassland establishment remain poorly understood. To address this knowledge gap, we examined the effects of 11 native grassland species on soil physicochemical properties and fungal community structure. Using co-occurrence network analysis, we elucidate how plants drive fungal community reorganisation through soil-mediated trophic pathways. The results showed that soil aggregate stability, chemical properties, and fungal communities differed significantly among the 11 species. Soil chemical properties, such as pH and EC, correlated with symbiotic fungi dominated modules; both soil aggregate stability and chemical properties were linked to pathogenic fungi dominated modules, while saprophytic fungi dominated modules displayed no linkage to either soil aggregate stability or chemical properties. These findings establish that fungal trophic modes govern species-dependent restoration outcomes via modular soil-microbe linkages, thereby offering predictive frameworks for species-specific management of abandoned soils.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/classification/genetics/isolation & purification
*Mycobiome
*Plants/microbiology/classification
Grassland
Ecosystem

@article {pmid41188658,
year = {2025},
author = {Nysanth, NS and Yadav, V and Gambhir, S and Pooniya, V and Sagar, D and Lama, A and Pal, KK and Swarnalakshmi, K},
title = {Endophytic Bacillus strains enhance chickpea growth and performance under controlled and field conditions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {186},
pmid = {41188658},
issn = {1572-9699},
support = {ICAR-Extramural project [12-174] and ICAR-AINP [21-30]//Indian Council of Agricultural Research/ ; },
abstract = {Endophytic Bacillus species are known to improve legume symbiosis and plant performance through an array of mechanisms. This study evaluated the potential of endophytic Bacillus strains (B. firmus, B. subtilis, and B. tequilensis) to promote growth and productivity of chickpea (Cicer arietinum L) grown under rainfed conditions. Among the Bacillus strains evaluated for in vitro plant growth-promoting traits, B. firmus exhibited the highest potential for phosphate solubilization (pH drop to 5.0) and indole-3-acetic acid (IAA) production (28.9 PPM). Seed biopriming with Bacillus strains enhanced antioxidant accumulation in chickpea seedlings, with B. subtilis markedly boosting key antioxidant enzymes, while B. tequilensis and B. firmus exerted distinct tissue-specific effects, as revealed by principal component analysis (PCA). At the critical threshold of 20% polyethylene glycol (PEG 6000), which inhibit chickpea seed germination, B. firmus and B. tequilensis maintained viability and biopriming chickpea seeds with these strains restored germination (25% and 41.7%, respectively), whereas UnInoculated and B. subtilis bioprimed seeds failed to germinate. In a controlled pot study, B. firmus inoculation enhanced chickpea biomass, increasing root and shoot growth by 37.4% and 27.7%, respectively, over the UnInoculated control. Field study showed that co-inoculation of B. firmus with Mesorhizobium ciceri enhanced leghemoglobin content (79.6%), nodule biomass (69.0%), nutrient uptake (N: 13.8%, P: 20.3%), plant biomass (14%) and seed yield (8%) over the absolute control. Ordination analysis clearly indicated that co-inoculation of M. ciceri with B. firmus had the strongest effect on chickpea performance under field conditions. Our findings establish B. firmus as a promising bioinoculant for improving chickpea productivity under rainfed conditions.},
}

@article {pmid41188575,
year = {2025},
author = {Botana, MT and Lewis, RE and Quaranta, A and Salamin, O and Revol-Cavalier, J and Oakley, CA and Feussner, I and Hamberg, M and Grossman, AR and Suggett, DJ and Weis, VM and Wheelock, CE and Davy, SK},
title = {Octadecanoids as emerging lipid mediators in cnidarian-dinoflagellate symbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1519},
pmid = {41188575},
issn = {2399-3642},
support = {2022-00796//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {Oxylipin signaling has been suggested as a potential mechanism for the inter-partner recognition and homeostasis regulation of cnidarian-dinoflagellate symbiosis, which maintains the ecological viability of coral reefs. Here we assessed the effects of symbiosis and symbiont identity on a model cnidarian, the sea anemone Exaiptasia diaphana, using mass spectrometry to quantify octadecanoid oxylipins (i.e., 18-carbon-derived oxygenated fatty acids). A total of 84 octadecanoids were reported, and distinct stereospecificity was observed for the synthesis of R- and S-enantiomers for symbiont-free anemones and free-living cultured dinoflagellate symbionts, respectively. Symbiont-derived 13(S)-hydroxy-octadecatetraenoic acid (13(S)-HOTE) linked to a putative 13(S)-lipoxygenase was translocated to the host anemone with a 32-fold increase, suggesting it as a biomarker of symbiosis and as a potential agonist of host receptors that regulate inflammatory transcription. Only symbiosis with the native symbiont Breviolum minutum decreased the abundance of pro-inflammatory 9(R)-hydroxy-octadecadienoic acid (9(R)-HODE) in the host. In contrast, symbiosis with the non-native symbiont Durusdinium trenchii was marked by higher abundance of autoxidation-derived octadecanoids, corroborating previous evidence for cellular stress in this association. The putative octadecanoid signaling pathways reported here suggest foundational knowledge gaps that can support the bioengineering and selective breeding of more optimal host-symbiont pairings to enhance resilience and survival of coral reefs.},
}

@article {pmid41188239,
year = {2025},
author = {Li, Y and Nie, MM and Li, DN and Bai, S and Liu, Q and Qin, DN and Li, QR and Zhou, BW and Zhuang, KX and Wu, X and Lu, JY and Shen, RF and Chen, ZC},
title = {Maintaining sulfur supply to the symbiosome delays nodule senescence in soybean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9736},
pmid = {41188239},
issn = {2041-1723},
mesh = {*Glycine max/metabolism/microbiology/genetics/physiology ; *Sulfur/metabolism ; *Root Nodules, Plant/metabolism/microbiology ; *Symbiosis/physiology ; Nitrogen Fixation/physiology ; Plant Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; Reactive Nitrogen Species/metabolism ; Nitrogen/metabolism ; Glutathione/metabolism ; Rhizobium/metabolism ; Plant Senescence ; },
abstract = {Symbiotic nitrogen fixation (SNF) in legume-rhizobia represents a sustainable and eco-friendly alternative to chemical nitrogen fertilizers in agriculture. Identifying key factors involved in nodule senescence, is crucial for enhancing SNF by effectively extending the lifespan of nodules. Here, we reveal that sulfur (S), an essential element for SNF, plays a major regulatory role in the senescence of soybean (Glycine max) nodules. Blocking S input into the symbiosome by knocking out either S transporter genes SULTR2;1 or SULTR3;5, resulted in a significant decrease in glutathione levels. This reduction impairs the capacity for reactive nitrogen species scavenging, thereby accelerating nodule senescence. Notably, reducing reactive nitrogen species (RNS) production in rhizobia or increasing S input in soybean nodules through genetic manipulation, can effectively mitigate high nitrogen-induced nodule senescence. Our findings demonstrate that SULTR-mediated S input is a pivotal step in regulating nodule senescence, and provide insights for developing strategies to enhance SNF in legumes by delaying nodule senescence.},
}

*Glycine max/metabolism/microbiology/genetics/physiology
*Sulfur/metabolism
*Root Nodules, Plant/metabolism/microbiology
*Symbiosis/physiology
Nitrogen Fixation/physiology
Plant Proteins/metabolism/genetics
Gene Expression Regulation, Plant
Reactive Nitrogen Species/metabolism
Nitrogen/metabolism
Glutathione/metabolism
Rhizobium/metabolism
Plant Senescence

@article {pmid41187913,
year = {2025},
author = {Zhang, LJ and Hembry, DH and Hao, K and Wu, YH and Yao, G and Sun, QL and Liu, TT and Luo, SX},
title = {Network structure variation across scales offers clues to the macroevolutionary persistence of specialized mutualisms.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2058},
pages = {20250926},
doi = {10.1098/rspb.2025.0926},
pmid = {41187913},
issn = {1471-2954},
support = {//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Symbiosis ; *Biological Evolution ; *Moths/physiology ; China ; *Pollination ; Ants ; },
abstract = {Highly intimate (symbiotic) mutualisms, such as ant-myrmecophyte and brood pollination mutualisms, are characterized by reciprocally specialized and modular network architecture and constitute evolutionary paradoxes. Few examples of these mutualisms are known, fewer are species-rich, and theory suggests that they should be vulnerable to extinction. However, no studies have examined their structure at both multiple local sites and regional scales. Here, we examine these phenomena using a brood pollination mutualism between leafflower trees (Phyllanthaceae: Glochidion) and leafflower moths (Lepidoptera: Gracillariidae: Epicephala) across eight sites in tropical and subtropical China. We find that significant reciprocal specialization is conserved across local and regional scales in these networks, but we also find local-regional discrepancies in whether networks are significantly modular, resulting in adjacent local networks that differ in architecture. Interaction turnover is almost entirely due to species turnover rather than interaction rewiring among widely distributed species. Unexpectedly, we find that two regional networks are significantly nested, while none of the local networks are. Theory suggests that nestedness may confer robustness to species loss but also should not evolve in symbiotic mutualisms. The finding that some regional networks are nested in this system suggests a possible explanation for the macroevolutionary persistence of such specialized mutualisms.},
}

Animals
*Symbiosis
*Biological Evolution
*Moths/physiology
China
*Pollination
Ants

@article {pmid41187175,
year = {2025},
author = {Chiwala, B and Makasa, M and Zulu, JM},
title = {Power and interest levels in safely managed sanitation services in Zambia: A stakeholder mapping.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335130},
doi = {10.1371/journal.pone.0335130},
pmid = {41187175},
issn = {1932-6203},
mesh = {Zambia ; Humans ; *Sanitation/methods ; *Stakeholder Participation ; Qualitative Research ; Focus Groups ; },
abstract = {BACKGROUND: Access to safely managed sanitation (SMS) in sub-Saharan Africa including Zambia remains a challenge. Variations in power and interest among stakeholder significantly influence access to SMS. However, there is limited contextualization of how power and interest levels among stakeholders influenced access to SMS. The study aimed to explore and analyze how stakeholders perceived their power and interest in the context of providing SMS. The study applied the Mendelow Stakeholder Matrix to identify, characterize and analyze the actors involved in the provision of SMS in peri-urban areas in Lusaka, Zambia.

METHODS: A narrative qualitative research design was employed in this study. Ninety-four (94) respondents participated in the study - 25 key informants who were representatives from Government Institutions/Departments, Cooperating Partners, NGOs and community level stakeholders; 60 discussants who participated in focus group discussions, while nine (9) community leaders took part in transect walks conducted in the target areas of Kanyama, Chawama and George. Nvivo14 was utilized for data management and analysis.

RESULTS: The main results suggested that stakeholders displayed interrelationships that were symbiotic as they depended on each other to deliver their mandates. Stakeholders categorized into Mendelow quadrants displayed varying levels of homogeneity in power and interest. In addition, some stakeholders such as the Local Authority shifted quadrants when seen to perform dual roles for example to implement and enforce the policies aimed at improved public health.

CONCLUSION: The stakeholders' quadrant position coupled with persisted changes in their positions influenced their capacity to contribute effectively to the implementation of strategies to enhance access to SMS. This equally meant that implementers of SMS interventions have to regularly assess their engagement mechanisms to foster dialogue and coordination among stakeholders. Policy implications, especially to Government, may mean allocation of adequate resources to key players to enable them deliver on their respective mandates. Similarly, implications to practitioners might be the need to periodically review stakeholders and forge alliances coupled with conducting multi-sectoral meetings aimed to streamline their functions for the successful delivery of SMS.},
}

Zambia
Humans
*Sanitation/methods
*Stakeholder Participation
Qualitative Research
Focus Groups

@article {pmid41186346,
year = {2025},
author = {Caruso, DJ and Zaferanloo, B and Palombo, EA and Moulton, SE},
title = {Development of antibacterial hydrogel using endophytic Alternaria fungus extract isolated from Australian native plant.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb01529d},
pmid = {41186346},
issn = {2050-7518},
abstract = {To address the problems associated with pathogenic bacteria in healthcare settings, the development of novel antibacterial materials is of high priority. For such purposes, endophytic fungi - symbiotic microorganisms residing within healthy plant tissues - represent a promising yet largely unexplored source of antibacterial compounds. In this study, an antibacterial extract derived from an endophytic Alternaria fungus previously isolated from Eremophila longifolia was incorporated within gelatin methacryloyl (GelMA) to produce a novel antibacterial hydrogel. Whilst rheological and compression testing revealed the addition of the extract resulted in reduction in the crosslink density of the hydrogel, all GelMA-extract formulations produced a solid mechanical stable hydrogel. The GelMA hydrogel containing a range of extract concentrations demonstrated variable inhibition of bacterial (Staphylococcus aureus) growth, with a concentration of 10 mg mL[-1] extract demonstrating complete inhibition over 24 h, while showing no toxicity toward brine shrimp nauplii, indicating good biocompatibility. The GelMA-extract demonstrated minimal rapid release from the hydrogel, followed by a slower release at longer times. As such, the developed hydrogel composite is promising for antibacterial applications in biomedical settings, while the results also highlight the potential for utilising endophytic extracts in the development of novel antibacterial materials.},
}

@article {pmid41186231,
year = {2025},
author = {Banerjee, S and Saha, KK and Pramanik, K and Biswas, R and Parveen, M and Balachandran, S and Roubík, H and Mandal, NC},
title = {Biocontrol, plant growth-promoting, and bioremediation potential of Aeromonas veronii CMF from the gut of Chrysomya megacephala.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0162225},
doi = {10.1128/spectrum.01622-25},
pmid = {41186231},
issn = {2165-0497},
abstract = {Gut system of chitinivorous insect Chrysomya megacephala was purposefully targeted to find unexplored microbial resources based on the rationale of their usual food habits. A phytobeneficial bacterial strain Aeromonas veronii CMF was successfully isolated and characterized up to genomic approaches. The gut isolate A. veronii CMF is a non-pathogenic strain, as proven by the negative results from the hemolysis and DNase tests. Antifungal enzyme production by the CMF exhibited 22.14 ± 2.12, 16.09 ± 0.476, and 1.89 ± 0.46 U/mL chitinase, protease, and β-1,3-glucanase production, respectively. Further, in vitro and in vivo studies also elucidate the effective utilization of such gut bacterial attributes against as many as nine plant pathogenic fungi, demonstrating plant growth-promoting (PGP) and root-colonizing activities with Cicer arietinum and Oryza sativa IR36, as well as heavy metal(loid)s (HMs) resistance, removal, and bioaccumulation potential. Hence, the current study revealed the potential of the gut symbiont CMF to respond against both the biotic and abiotic stresses with PGP attributes for sustainable agriculture.IMPORTANCEGut symbiont A. veronii CMF, with integrated antifungal (chitinase, protease, and β-1,3-glucanase activity), plant growth-promoting (including plant root colonizing potential), and bioremediational attributes can be harnessed as a biotechnological tool for sustainable agriculture and human welfare by fulfilling several sustainable developmental goals. On the basis of such multidimensional gut symbiotic attributes which are validated through genomic-phenotypic observations during this study, it can be suggested that this gut symbiont can perform the host beneficial attributes in the plant rhizosphere, i.e., the "plant gut system" and consequently act as "plant gut symbionts."},
}

@article {pmid41186223,
year = {2025},
author = {Denisova, EY and Kirichek, EA and Tsyganov, VE},
title = {Genome sequence of a native nitrogen-fixing Bradyrhizobium sp. strain RCAM1614 isolated from lupine nodules.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0104825},
doi = {10.1128/mra.01048-25},
pmid = {41186223},
issn = {2576-098X},
abstract = {This report describes the genome sequence of Bradyrhizobium sp. strain RCAM1614, which was isolated from the root nodules of Lupinus angustifolius L. in the Leningrad district of Russia. The genome has a size of 9.77 Mbp and shows 96.1% completeness, which enables precise taxonomic classification.},
}

@article {pmid41185456,
year = {2025},
author = {He, L and Ge, S and Li, L and Mei, Y and Liu, R and Lin, R and Wang, L and Kang, H and Yu, J and Thomas, HR and Zhou, Y},
title = {SlWRI5a and SlHY5 co-activate SlFatM-mediated fatty acid biosynthesis during arbuscular mycorrhizal symbiosis in tomato.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70691},
pmid = {41185456},
issn = {1469-8137},
support = {2023YFD2300701//National Key Research and Development of China/ ; 32330094//National Natural Science Foundation of China/ ; U21A20233//National Natural Science Foundation of China/ ; SN-ZJU-SIAS-0011//Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study/ ; },
abstract = {Arbuscular mycorrhizal symbiosis (AMS) is a ubiquitous mutualistic interaction between many terrestrial plants and fungi, with lipids playing a pivotal role in nutrient exchange. However, few genetic regulators of AMS have been functionally validated in tomato. To investigate candidate genes, we employed CRISPR-Cas9 and VIGS to generate knockout and knockdown lines. A comprehensive suite of molecular biology techniques, including yeast-1/2-hybridization, BiFC, ChIP-qPCR, and RNA-sequencing, was used to elucidate the regulatory roles of SlWRI5a, SlHY5, and SlFatM in fatty acid (FA) biosynthesis and AMS in tomato. FA composition was analyzed using gas chromatography. In this study, we validated SlWRI5a and SlFatM as key regulators of 16-carbon FA biosynthesis during AMS in tomato and demonstrated physical interactions between SlWRI5a and SlHY5. SlHY5 expression was induced by AMS and promoted root FA biosynthesis. Finally, we demonstrated that SlWRI5a and SlHY5 can co-regulate SlFatM-mediated FA accumulation, thereby influencing AMF colonization efficiency in tomato. Our findings reveal the SlWRI5a/SlHY5-SlFatM regulatory module, offering new insights into lipid-mediated AMS in tomato. This work also highlights a novel role for HY5 during fungal symbiosis, underscoring its broader significance in plant-microbe interactions.},
}

@article {pmid41185303,
year = {2025},
author = {Pérez-Bermúdez, I and Fiallos-Maravilla, N and Opazo-Navarrete, M and Petzold, G and Orellana-Palma, P},
title = {Exploring centrifugal-percolation as an innovative external force in block freeze concentration technology applied to peppermint infusion.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117550},
doi = {10.1016/j.foodres.2025.117550},
pmid = {41185303},
issn = {1873-7145},
mesh = {*Mentha piperita/chemistry ; Centrifugation/methods ; Antioxidants/analysis ; Flavonoids/analysis ; Chromatography, High Pressure Liquid ; Polyphenols/analysis ; *Freezing ; *Food Handling/methods ; *Plant Extracts/chemistry/analysis ; },
abstract = {This study investigates the use of centrifugal-percolation block freeze concentration (CP-BFC) at three cycles to obtain concentrate fractions from peppermint (Mentha piperita L.) infusion. The process parameters, physicochemical properties, bioactive compounds (total polyphenol (TPC) and flavonoid (TFC) content, and HPLC analyses), and antioxidant capacity of the concentrated fractions were evaluated. After three CP-BFC cycles, the process parameters were close to 95 % and 66 % for efficiency of separation and solute yield, respectively. Moreover, the results demonstrate that the percolation system can be incorporated in the centrifugation step, and thus, both separation steps carry out a successful extraction of concentrate solutes (11.7 % w/w and 13.5°Brix) from the ice fraction, with TPC and TFC values of 13.21 mg gallic acid equivalents/mL and 15.93 mg catequin equivalents/mL, respectively. Vanillic acid, rutin, and kampferol presented the highest concentration among all the phenolic compounds. While, antioxidant capacity changes ranged until 47 and 206 μmol trolox equivalents/mL, for DPPH and FRAP assays, respectively. These findings (high extraction and high concentration of solutes, bioactive compounds and antioxidant capacity) highlight the potential by adding a percolation system in the centrifugation process as a novel symbiotic strategy for high-quality liquid food concentration, effectively balancing process parameters and product quality, with potential for semi-industrial scale concentration of solutes and bioactive compounds. Therefore, centrifugal-percolation is an alternative external force to couple with BFC technology due to the double separation, since the process increased and preserved bioactive compounds to produce concentrated solutions with endless possibilities for multifarious food, medical, and pharmaceutical applications.},
}

*Mentha piperita/chemistry
Centrifugation/methods
Antioxidants/analysis
Flavonoids/analysis
Chromatography, High Pressure Liquid
Polyphenols/analysis
*Freezing
*Food Handling/methods
*Plant Extracts/chemistry/analysis

@article {pmid41184748,
year = {2025},
author = {Yoshioka, Y and Kawachi, M and Kawamitsu, M and Murzabaev, A and Satoh, N and Shinzato, C and Shoguchi, E},
title = {First genome sequences of the dinoflagellate Effrenium voratum strain isolated from the coral Hydnophora exesa in temperate Japanese region.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {83},
pmid = {41184748},
issn = {2730-6844},
support = {JP23KJ2129//Japan Society for the Promotion of Science/ ; JP20H03235//Japan Society for the Promotion of Science/ ; JP23K26825//Japan Society for the Promotion of Science/ ; },
abstract = {OBJECTIVES: Dinoflagellates are important unicellular eukaryotes found in freshwater and marine ecosystems. The Family Symbiodiniaceae is well-known as symbiotic algae in various marine organisms, including many endosymbiotic species living in cnidarian cells. In contrast, the genus Effrenium is non-symbiotic, exhibiting traits such as resting cyst formation and heterotrophic feeding. Effrenium strains have been used as controls in symbiosis-related comparative studies. The only described species, E. voratum, is cosmopolitan, and draft genomes of three strains have been reported. However, genomic data from strains originating in temperate Japanese regions are lacking. A high-quality draft genome of an additional E. voratum strain will provide valuable resources for molecular biology of symbiosis and comparative genomics on local adaptation in Symbiodiniaceae.

DATA DESCRIPTION: We describe the first draft genome (version 1) of E. voratum strain NIES-2908, which was isolated from the coral Hydnophora exesa in the temperate Japanese coastal water of Goto islands, Japan. Using PacBio HiFi sequencing, the genome was assembled to a total size of 1,006 Mbp, comprising 6,051 contigs. The GC content was 50.5%, and repetitive sequences accounted for 37.9% of the genome. Gene prediction identified 54,346 protein coding genes, with 68.4% completeness based on the BUSCO alveolate dataset.},
}

@article {pmid41184724,
year = {2025},
author = {Eliassen, LK and Altin, D and Andersen, T and Riemann, L and Dunthorn, M and Titelman, J},
title = {Long Term Copepod Culture Houses a Rich Microbial Eukaryotic Community Including New and Known Symbionts.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {6},
pages = {e70053},
doi = {10.1111/jeu.70053},
pmid = {41184724},
issn = {1550-7408},
support = {315892//Norges Forskningsråd/ ; //Utdannings- og forskningsdepartementet/ ; },
mesh = {*Copepoda/microbiology/parasitology ; Animals ; *Symbiosis ; RNA, Ribosomal, 18S/genetics ; *Eukaryota/classification/genetics/isolation & purification ; Phylogeny ; Microbiota ; },
abstract = {Copepods, dominant marine zooplankton, are hosts to microbial eukaryotic symbionts, but the copepod eukaryome remains largely unexplored. We used 18S rRNA gene primers with reduced metazoan amplification to identify microbial eukaryotes in a culture of Calanus finmarchicus (Copepoda). Samples were taken from the inlet water (99.5% of reads from non-copepod sources) and the contents of the culture, which included ambient water (99.7%), bulk (many crushed copepods, 60.2%), individual copepods (1%-41%, mean = 7.4), and bulk fecal pellets (74%). The microbial eukaryotic community in the culture differed from the inlet water. The culture contained saprotrophs and bacterivores typical of eutrophic aquacultures and known parasites of copepods. Individual copepod eukaryomes varied in richness (8-33 operational taxonomic units, mean = 16.1) and revealed variation in non-copepod read yields related to specific taxa. Perkinsea, not previously reported in copepods, as well as Ascomycota and Basidiomycota (Fungi), formed the core eukaryome (found in > 90% of individuals), indicating potentially important symbiosis. The small eukaryome, relative to reported microbiomes in C. finmarchicus, suggests that ecological inferences from microbiomes, which largely address bacteria, are not readily applicable to the eukaryotic microbes. The study underpins the need for investigations of eukaryomes.},
}

*Copepoda/microbiology/parasitology
Animals
*Symbiosis
RNA, Ribosomal, 18S/genetics
*Eukaryota/classification/genetics/isolation & purification
Phylogeny
Microbiota

@article {pmid41183989,
year = {2025},
author = {Kiyota, H and Watanabe, K and Oyama, H and Tachibana, M and Shimizu, T and Watarai, M},
title = {Legionella Confer Survival Benefits to Paramecium Hosts by Inhibiting Phagocytosis.},
journal = {Microbes and environments},
volume = {40},
number = {4},
pages = {},
doi = {10.1264/jsme2.ME25022},
pmid = {41183989},
issn = {1347-4405},
mesh = {*Phagocytosis ; *Paramecium/microbiology/physiology ; *Legionella/physiology/growth & development ; Symbiosis ; Microbial Viability ; },
abstract = {Legionella survive in the natural environment by remaining within protist host cells. Many protist species, including Paramecium spp., are potential hosts for Legionella. However, the factors and mechanisms involved in the establishment of this relationship are unknown. The advantages gained by Paramecium spp. when they maintain Legionella are also unclear, and the existence of these relationships has not been confirmed. In the present study, feeding with Legionella increased the number of Paramecium cells over time. However, the growth-promoting effect of Legionella was weaker than that of Klebsiella pneumoniae, which is considered the optimal bacterial feed for Paramecium. Phagocytosis was strongly inhibited in Paramecium cells fed Legionella, indicating that this relationship prevents the uptake of harmful organisms. The inhibition of phagocytosis was also observed when Paramecium cells were treated with the Legionella culture supernatant. Despite the inhibition of phagocytosis, the presence of live Legionella within host cells allowed Paramecium spp. to survive and even increase in number, as observed earlier. This result suggests that Legionella support the survival of Paramecium hosts from a nutritional aspect. Although it is difficult to definitively state whether the relationship between Legionella and Paramecium hosts is completely mutualistic, the present results provide one rationale for defining their relationship.},
}

*Phagocytosis
*Paramecium/microbiology/physiology
*Legionella/physiology/growth & development
Symbiosis
Microbial Viability

@article {pmid41182813,
year = {2025},
author = {Caiafa, MV and Rowe, MA and Healy, R and Lemmond, B and Nouhra, E and Pfister, DH and Sandoval-Leiva, P and Furci, G and Smith, ME},
title = {Unearthing two new ectomycorrhizal Pezizales truffle species from Nothofagaceae forests in southern South America.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/00275514.2025.2562792},
pmid = {41182813},
issn = {1557-2536},
abstract = {Truffles are enclosed, hypogeous fruiting bodies that have evolved hundreds of times across different fungal groups. Truffles are particularly diverse within Pezizales, a large and diverse order of Ascomycota where truffle forms have evolved multiple times. The majority of truffle species are ectomycorrhizal symbionts of trees and rely on animals for dispersal. Because of their hypogeous nature, truffles remain understudied and many new taxa remain to be discovered. Due to their obligate symbiosis with host plants and their dependence on animal dispersal, ectomycorrhizal truffle species often show distinct host associations, are restricted to certain forest types, and have notable biogeographic distribution patterns. Here, we present morphological and phylogenetic evidence in support of two new truffle species associated with Nothofagaceae trees in southern South America, Geomorium nahuelbutense (Geomoriaceae) and Paragalactinia nothofagacearum (Pezizaceae). The closest described relatives of these species form aboveground, apothecial ascomata, suggesting that these taxa are derived from independent evolutionary events leading to the truffle morphology. Paragalactinia nothofagacearum is widespread in northern Patagonia and has been documented as an ectomycorrhizal associate of Lophozonia alpina (= Nothofagus nervosa) seedlings. In contrast, Geomorium nahuelbutense has only been found in a well-preserved coastal forest in Chile toward the northern extent of the range of Nothofagaceae in South America. This is a conservation priority area that has been heavily impacted by fires, deforestation, and other human activities. This species is known only from two modern collections from Parque Nacional Nahuelbuta and one preserved specimen collected by Roland Thaxter near Concepción, Chile, in 1906.},
}

@article {pmid41181086,
year = {2025},
author = {Hiruma, K and Sugiyama, A},
title = {Preface to the special issue "Diverse Symbiotic Relationships between Plants and Microbes in the Phyllosphere and Rhizosphere".},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {189-191},
pmid = {41181086},
issn = {1342-4580},
}

@article {pmid41181081,
year = {2025},
author = {Araragi, M and Songwattana, P and Teaumroong, N and Masuda, S and Shibata, A and Shirasu, K and Kawaharada, Y},
title = {Improved rapid and efficient hairy root transformation using Rhizobium rhizogenes in legume crops.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {279-288},
pmid = {41181081},
issn = {1342-4580},
abstract = {Hairy root transformation mediated by Rhizobium rhizogenes is a widely used tool for molecular analysis and root material for secondary metabolite production. However, this method is time-intensive, technically demanding, and exhibits low transformation efficiency. To address these limitations, we developed a rapid and efficient hairy root transformation system for legume crops, optimizing protocols with the soybean (Glycine max L. Merrill) cultivar Fukuyutaka. Sterilizing seeds with vapor of 5% sodium hypochlorite and germinating them in a double-tier container resulted in over 90% healthy, straight seedlings ideal for transformation, with 3- to 5-day-old seedlings showing the highest transformation rates. Exposing the plant shoot during co-cultivation by covering only the injection area, combined with low nitrogen levels in the hydroponic solution, significantly enhanced hairy root production, yielding up to 16 transgenic hairy roots per plant. Additionally, low nitrogen concentrations were crucial for promoting nodule formation in transgenic hairy roots. These optimized conditions were validated across 12 soybean, 1 cowpea, and 1 mungbean cultivars. The protocol's effectiveness was confirmed through the induction of symbiotic gene expression of GmEnod40a and GmErn1b using a promoter β-glucuronidase (GUS) reporter system in transgenic hairy roots. Expression of these genes was detected in both premature and mature nodules, while GmErn1b expression was also observed in epidermal cells during early nodulation. This optimized hairy root transformation protocol, requiring under 22 days from seed sterilization to transgenic root induction and 61 days to expression analysis, offers a promising approach for efficient gene function studies in legume crops.},
}

@article {pmid41181077,
year = {2025},
author = {Higashi, Y and Ambiru, H and Saito, H and Egusa, M and Miura, C and Tominaga, T and Kaminaka, H},
title = {Arbuscular mycorrhiza-induced growth promotion and disease resistance are fine-tuned by growth-defense tradeoffs in Lotus japonicus and tomato.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {289-298},
pmid = {41181077},
issn = {1342-4580},
abstract = {Arbuscular mycorrhizal fungi (AMF) are representative symbiotic partners of plants, and trade nutrients with them. This symbiotic association confers plants with the agronomically beneficial traits such as plant growth promotion and stress tolerance. Arbuscular mycorrhizae (AM) are divided into two morphotypes, the Arum-type and the Paris-type, based on fungal structures within the host plant cells. Although the phylogeny of host plants typically determines the AM morphotype, the AMF, Rhizophagus irregularis and Gigaspora margarita, can form Arum-type AM and Paris-type AM, respectively, in tomato (Solanum lycopersicum). In this study, the traits resulting from the AM symbiosis and root transcriptomes between Lotus japonicus and tomato inoculated with these two phylogenetically distal AMF were compared. In L. japonicus, Arum-type AMs formed when colonized by both AMF, as expected. Shoot growth in both plants was significantly promoted when inoculated by these AMF, although the impact of G. margarita was greater than that by R. irregularis colonization. A transcriptome analysis of both plants inoculated by the two AMF strongly suggested changes in the expression levels of genes associated with defense response. AMF inoculation induced resistance against Fusarium diseases in both plants, but the level of disease resistance in Rhizophagus-colonized plants was higher than in Gigaspora-colonized plants. Thus, the colonized AMF identity, and not the AM morphotype, determines the level of AM-induced traits, plant growth promotion and disease resistance. Negative relationships between these two traits would exist as a growth-defense tradeoff to fine-tune the balance in response to limited resources, and to optimize fitness.},
}

@article {pmid41181076,
year = {2025},
author = {Suwa, S and Ando, M and Kashiwagi, K and Kyotani, T and Hasegawa, K and Safiullah, H and Kifushi, M and Nishikawa, Y and Anai, T and Ohkama-Ohtsu, N and Takeyama, H},
title = {Single-cell Raman spectroscopic analysis of bacteroids in soybean nodules to observe the relationship between biomolecular constituents and symbiotic nitrogen fixation activity.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {335-343},
pmid = {41181076},
issn = {1342-4580},
abstract = {Nitrogen fixation in soybean occurs as a result of symbiosis between the plant and rhizobia in the nodules. This process allows both the plant and the symbiont to acquire vital nutrition. To fully understand the symbiosis, many researchers have attempted to attain a deeper interpretation of the biomolecular behavior or enhance the nitrogen fixation activity of bacteroids. However, most studies have focused on forward and reverse genetics approaches to evaluate the contribution of a particular gene/enzyme in nitrogen fixation. Few studies have observed the bacteroids' overall biomolecular behavior in the nodules. Thus, we grew soybean plants and recorded acetylene reduction assay (ARA) results at several growth stages. Simultaneously, we analyzed the biomolecular compounds in the bacteroids in the nodules at the single-cell level by Raman microspectroscopy. Random forest regression, a machine learning method, was applied to discover the biomolecular contribution to the ARA, as it predicted ARA results with high accuracy. Polyhydroxybutyrate (PHB) biopolymer significantly contributed to predicting ARA results, suggesting its potential relevance in symbiotic nitrogen fixation in soybean. Further studies related to PHB behavior will lead to a deeper understanding of symbiotic nitrogen fixation and may help achieve better control of this process to increase crop yields.},
}

@article {pmid41181073,
year = {2025},
author = {Erdenetugs, E and Harada, S and Erdenetugs, E and Sentoku, T and Arai, M and Saito, K and Kobae, Y},
title = {Various types of mycorrhizal fungi sequences detected in single intracellular vesicles.},
journal = {Plant biotechnology (Tokyo, Japan)},
volume = {42},
number = {3},
pages = {299-307},
pmid = {41181073},
issn = {1342-4580},
abstract = {A diverse range of microbes have been observed to coexist in plant roots in the field, among which arbuscular mycorrhizal fungi (AMFs) are universal and have recently been shown to be of two types: one belonging to the subphylum Glomeromycotina (G-AMF) and the other to the subphylum Mucoromycotina (M-AMF). These two types of mycorrhizal fungi are known to co-occur in roots. This is because, in addition to the morphological evidence, diverse ribosomal RNA (rRNA) gene sequences, including those of G-AMF, are detected in mycorrhizae colonized with M-AMF. However, it is difficult to physically distinguish between these AMFs, and amplification bias of G-AMF and M-AMF by PCR has hampered analysis of the detailed symbiotic behaviour of both AMFs. In this study, we isolated a single vesicle of lipid-accumulating AMF in the root and sequenced its rRNA gene by PCR using uniquely designed primers with reduced amplification bias. Notably, G-AMF and M-AMF rRNA gene sequences were detected in one vesicle. These results suggest new avenues for mycorrhizal research on the overlooked morphology of AMF vesicles and their mode of genetic co-occurrence of G-AMF and M-AMF.},
}

@article {pmid41180406,
year = {2025},
author = {Xiong, Q and Zheng, L and Zhang, Q and Li, T and Zheng, L and Song, L},
title = {Comparative genomics and evolutionary analyses of Sphaeropleales.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1534646},
pmid = {41180406},
issn = {1664-462X},
abstract = {Sphaeropleales is a diverse group with over one thousand species described, which are found in a wide range of habitats showed strong environmental adaptability. This study presented comprehensive genomic analyses of seven newly sequenced Sphaeropleales strains with BUSCO completeness exceeding 90%, alongside comparative assessments with previously sequenced genomes. The genome sizes of Sphaeropleales species ranged from 39.8 Mb to 151.9 Mb, with most having a GC content around 56%. Orthologous analysis revealed unique gene families in each strain, comprising 2 to 3.5% of all genes. Comparative functional analysis indicated that transporters, genes encoding pyrroline-5-carboxylate reductase and antioxidant enzymes played a crucial role in adaptation to environmental stressors like salinity, cold, heavy metals and varying nutrient conditions. Additionally, Sphaeropleales species were found to be B12 auxotrophy, acquiring this vitamin or its precursors through a symbiotic relationship with bacteria. Phylogenetic studies based on 18S rDNA and the low copy othologues confirmed species identification and the relationships inside core Chlorophyta and between prasinophytes. Evolutionary analyses demonstrated all the species exhibited a large count of gene family expansions and contraction, with rapidly evolving and positive selected genes identified in terrestrial Bracteacoccus species, which contributed to their adaptation to terrestrial habitat. These findings enriched the genomic data for Sphaeropleales, particularly the genus Bracteacoccus, which can help in understanding the ecological adaptations, evolutionary relationships, and biotechnological applications of this group of algae.},
}

@article {pmid41179241,
year = {2025},
author = {Sotomayor-Alge, A and Inda, LA and Ángel-Beamonte, E and Zabalgogeazcoa, Í and Catalán, P},
title = {Unveiling an asymmetric plant-fungal symbiosis: morphological, cytogenetic, and molecular characterization of a haploid Epichloë festucae strain associated with three polyploid cytotypes of the Iberian endemic grass Festuca rothmaleri.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e162692},
pmid = {41179241},
issn = {2210-6340},
abstract = {The ecological and evolutionary outcomes of plant-fungal interactions are strongly influenced by genome size and ploidy, yet the ploidy level of both partners is rarely assessed simultaneously. Epichloë symbioses with Pooideae grasses are established model systems for exploring these dynamics, but associations between polyploid hosts and haploid endophytes remain poorly documented. In this study, the association of the Iberian endemic Festuca rothmaleri-which includes tetraploid, hexaploid, and octoploid cytotypes-with Epichloë fungal endophytes is documented for the first time. An integrative, method-rich framework combining cytogenetics, morphometrics, and multilocus phylogenetics revealed a strikingly asymmetric interaction, with all cytotypes harboring a single haploid strain of Epichloë festucae. Two methodological innovations were developed: (i) an image-based tool for automated measurement of asexual structures, including the novel metric "conidial area," and (ii) a flow cytometry protocol for estimating fungal genome size. Despite morphological variability, all fungal isolates shared similar genome sizes and formed a well-supported monophyletic lineage in a coalescent species tree based on nuclear loci sequences (actG, CalM, ITS, tefA, tubB). This work provides the first comprehensive characterization of a haploid Epichloë endophyte spanning multiple naturally distributed host ploidy levels and highlights a rare but promising system for future evolutionary, physiological, and ecological studies of plant-fungal interactions.},
}

@article {pmid41178244,
year = {2025},
author = {Zhu, L and Liu, D and Wu, Y and Qi, M and Ai, Z and Sun, Y and Li, Z and Guo, D and Chen, H and Wang, W and Lin, F and Yuan, J and Ye, X and Zhang, Q and Zhang, W},
title = {Sugar Transporter GmSWEET38 Controls Nodule Development and Seed Yield in Soybean.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70269},
pmid = {41178244},
issn = {1365-3040},
support = {//This study was supported by the grants from the National Key R&D Program of China (2022YFD1201700) and the Fundamental Research Funds for the Central Universities (KJJQ2024007) to Q.Z., and the National Natural Science Foundation (32171956) to W.Z./ ; },
abstract = {The transport of sugars produced by photosynthesis between source and sink tissues controls multiple biological processes in growth and development. However, the key factors, both genetic and environmental, that influence sugar transport and crop yield are largely unknown. We identified a plasma membrane-localized sugar transporter, GmSWEET38, that facilitates the translocation of sugars to seeds and nodules in soybean (Glycine max L.). GmSWEET38 exhibited both efflux and influx activities of sucrose and fructose in Xenopus oocytes. GmSWEET38 expression was high in the vascular system of roots and nodules, and overexpression of GmSWEET38 enhanced the sugar contents of roots and seeds, consequently promoting nodule development and seed production. Loss of GmSWEET38 function exerted the opposite effects. Intriguingly, GmSWEET38 specifically transported fructose into the rhizosphere, where it is used by beneficial bacteria. By modulating sugar transport and allocation to enhance symbiotic nitrogen fixation, GmSWEET38 can be used for the breeding of high-yielding soybean cultivars.},
}

@article {pmid41178122,
year = {2025},
author = {Arumugam, B and Deotale, S and Chakravarty, I and Ninawe, Y and Dadhe, P and Deshpande, KY and Mandavgane, SA},
title = {Enzyme Treated Sapota Seed Dietary Fibre Is a Novel Prebiotic Feed Additive: In Vitro Studies.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70086},
pmid = {41178122},
issn = {1470-8744},
support = {//Department of Science and Technology, Government of India/ ; //Merino Industries Limited Hapur/ ; //SreePV Foundation/ ; },
abstract = {The valorization of agro-industrial fruit by-products presents a sustainable strategy to enhance animal nutrition while reducing environmental waste. This study investigates the physicochemical attributes, dietary fiber profile, and prebiotic potential of the enzyme treated Manilkara zapota (sapota) seed powder (eSSP) for functional use in poultry feed. The eSSP flour demonstrated high crude fiber content (23.94 ± 1.86 g/100 g), with total dietary fiber comprising 83.45% insoluble and 16.54% soluble fractions. Enzymatic hydrolysis optimized at 6 h revealed peak concentrations of fermentable oligosaccharides, including galacto-oligosaccharides (12.06 ± 0.45%), manno-oligosaccharides (8.04 ± 0.30%), fructo-oligosaccharides (9.83 ± 0.25%), and xylo-oligosaccharides (10.83 ± 0.50%). Supplementation with e6SSP resulted in a significant increase in both qualitative and quantitative volatile fatty acid (VFA) production, indicating its prebiotic potential. Notably, the high xylo-oligosaccharide (XOS) content (∼10%) contributed to elevated butyric acid levels in fermentation assays, reinforcing the stimbiotic properties of eSSP. Symbiotic assays with Lactobacillus casei confirmed the eSSP's capacity to support probiotic growth, while in vitro fermentation demonstrated enhanced production of short-chain fatty acids (SCFAs), particularly butyrate. Antioxidant profiling further validated the seed's bioactive potential, with total phenolic content of 767.65 ± 1.24 mg GAE/100 g and flavonoid content of 2223.6 ± 0.87 mg QE/100 g. These findings establish eSSP as a potent, cost-effective, and natural prebiotic candidate for improving gut health and sustainability in animal feed systems.},
}

@article {pmid41177671,
year = {2025},
author = {Botero, LM and Al-Niemi, T and McDermott, TR},
title = {Observations Concerning Rhizobium tropici Bacteroid Phosphorus Stress Response During Symbiosis With Phaseolus vulgaris.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70220},
doi = {10.1111/1758-2229.70220},
pmid = {41177671},
issn = {1758-2229},
support = {923310//Montana Agricultural Experiment Station/ ; },
mesh = {*Phaseolus/microbiology/metabolism ; *Symbiosis ; *Phosphorus/metabolism ; *Rhizobium tropici/metabolism/physiology/genetics ; Root Nodules, Plant/microbiology ; Alkaline Phosphatase/metabolism/genetics ; Stress, Physiological ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Bacteroid inorganic phosphorus (Pi) metabolism in the Rhizobium-legume symbiosis differs between indeterminate and determinate legume nodules. In contrast to alfalfa bacteroids, bean (Phaseolus vulgaris) bacteroids exhibit high levels of alkaline phosphatase (AP), the native reporter enzyme for the bacterial Pi stress response. [14]C and [32]Pi whole plant labelling techniques were used in conjunction with diagnostic mutants (lacking AP or lacking high affinity Pi transport) to assess the relative importance of the Pi stress response in Rhizobium tropici bacteroids during symbiosis. The AP- mutant was not defective for symbiosis and did not differ from wildtype bacteroids for Pi acquisition. [14]C-CO2 feeding to host plants revealed [14]C-carbon uptake and accumulation in AP- mutant bacteroids, and their nodules were increased relative to wildtype bacteroids, implying that organo-P compounds may account for meaningful levels of carbon exchange between symbionts. [32]Pi tracer experiments implied that the high affinity transporter is important to bacteroid Pi acquisition and symbiotic performance in determinate nodules, but that the symbiosome Pi concentration does not meet the capacity of the high affinity transporter. [32]P tracer work also illustrated that Pi taken up into the nodule does not remain in the nodule, but rather is redistributed to the host.},
}

*Phaseolus/microbiology/metabolism
*Symbiosis
*Phosphorus/metabolism
*Rhizobium tropici/metabolism/physiology/genetics
Root Nodules, Plant/microbiology
Alkaline Phosphatase/metabolism/genetics
Stress, Physiological
Bacterial Proteins/metabolism/genetics

@article {pmid41177652,
year = {2026},
author = {Wu, L and Huang, Z and Fan, S and Zhen, L and Lv, J},
title = {Effects and interactions of freeze-thaw leaching on cadmium forms, soil chemical properties, and microbial community structure in cadmium-contaminated soil.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {70-81},
doi = {10.1016/j.jes.2025.02.048},
pmid = {41177652},
issn = {1001-0742},
mesh = {*Cadmium/analysis/chemistry ; *Soil Pollutants/analysis/chemistry ; *Soil Microbiology ; *Soil/chemistry ; Freezing ; Microbiota ; },
abstract = {Heavy metal contamination of soil is one of the major challenges to sustainable agriculture. This contamination can be transmitted through the soil food chain and poses a serious threat to human health. In this study, we found that freeze-thaw leaching (FTL) effectively complements the low removal rate of chemical leaching, and investigated the effects of different numbers of FTL on Cd contamination, soil chemical properties and microbial communities. The results showed that repeated FTL significantly reduced (P < 0.05) the total Cd content in the top soil (19.02 %-49.35 %) and subsoil (0.41 %-21.13 %) and promoted the transformation of Cd to a more stable form, mainly through various removal mechanisms such as complexation, ion-exchange, and chemical precipitation. This finding was supported by reductions in several soil properties, including pH, available potassium (AK), and available phosphorus (AP). FTL treatment initially increased the bioavailability of Cd compared to chemical leaching, but bioavailability of Cd progressively decreased as the number of freeze-thaw cycles increased. Additionally, FTL reduced the richness and diversity of bacteria communities, destabilized ecological symbiotic networks, while increasing the richness and diversity of fungi in the soil. Various model analyses indicated that FTL treatment, available Cd, soil pH, AP and AK were the key drivers influencing the changes in microbial community structure. This study provides new insights and scientific bases for the effective management of heavy metal pollution in agricultural soils, the restoration of ecosystem health, and the improvement of soil sustainability.},
}

*Cadmium/analysis/chemistry
*Soil Pollutants/analysis/chemistry
*Soil Microbiology
*Soil/chemistry
Freezing
Microbiota

@article {pmid41177600,
year = {2026},
author = {Ponce-Hernández, A and Carranza-Álvarez, C and Castro-Longoria, E and Hernández-Martínez, R and Martínez-Soto, D},
title = {Fungus Neosartorya (Aspergillus) fischeri improves the fitness, tolerance and absorption of heavy metals in Typha latifolia.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {218-230},
doi = {10.1016/j.jes.2025.05.049},
pmid = {41177600},
issn = {1001-0742},
mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism/toxicity ; *Typhaceae/physiology/microbiology/metabolism ; *Soil Pollutants/metabolism/toxicity ; Plant Roots/microbiology ; *Aliivibrio fischeri/physiology ; },
abstract = {Heavy metal contamination is a global issue caused by anthropogenic activities leading to severe negative effects on the environment and human health. To address this problem, bioremediation strategies utilizing plants such as Typha latifolia and their symbiotic fungi have been adopted to remediate contaminated areas and mitigate the harmful effects of these pollutants. In this study, the endophytic fungus Neosartorya fischeri was isolated from the roots of T. latifolia plants growing in heavy metal-contaminated sites. N. fischeri colonized the epidermis and root cortex and showed high tolerance to toxic concentrations of silver (Ag) (1 mg/kg), copper (Cu) (60 mg/kg) and cadmium (Cd) (8 mg/kg). N. fischeri removed 8.7 % ± 0.5 % Cd from the medium, biosorbed 15.24 ± 0.2 mg/kg into its biomass, and enhanced the tolerance and bioaccumulation of Cd (184.18 ± 1.14 mg/kg) in plant roots. Moreover, N. fischeri produces siderophores, volatile compounds and solubilizes phosphates, which improve plant fitness. This was evidenced by a 28 % increase in photosynthetic pigments in T. latifolia plants colonized with N. fischeri. Additionally, N. fischeri inhibits the growth of important phytopathogens from the Fusarium genus. These findings highlight the important role of N. fischeri in enhancing the fitness and resilience of T. latifolia in hostile environments, demonstrating the potential of N. fischeri-T. latifolia association for the bioremediation of contaminated sites.},
}

Biodegradation, Environmental
*Metals, Heavy/metabolism/toxicity
*Typhaceae/physiology/microbiology/metabolism
*Soil Pollutants/metabolism/toxicity
Plant Roots/microbiology
*Aliivibrio fischeri/physiology

@article {pmid41177409,
year = {2025},
author = {Lin, S and Pan, M and Ma, Y and Chen, Z and Lyu, T and Dong, R and Ruan, R and Liu, S},
title = {Microalgae-mediated shaping of bacterial communities enhances antibiotic removal and antibiotic resistance control.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133577},
doi = {10.1016/j.biortech.2025.133577},
pmid = {41177409},
issn = {1873-2976},
abstract = {The microalgae-bacteria symbiosis sludge (MBSS) system offers a promising strategy for efficient wastewater treatment and nutrients upcycling. However, maintaining stable and effective performance facing antibiotic stress remains a significant challenge. This study explored the regulation strategy of microbial succession towards sulfadiazine (SDZ)-containing wastewater remediation while controlling antibiotic resistance genes (ARGs) spread in MBSS system. The MBSS achieved efficient SDZ removal of up to 99.8%, with an optimal microalgae-to-activated sludge inoculation ratio of 1:3. However, the highest nutrient upcycling efficiencies (33.7% for nitrogen and 98.6% for phosphorus) were observed at an inoculation ratio of 1:1. Metagenomics analysis revealed that genera Chlorella and Micractinium of Chlorophyta were strongly positively correlated with SDZ removal. Moreover, microalgae inoculation significantly modulated the microbial community structure, promoting the dominance of genera Rhodanobacter and Dokdonella in MBSS. This microbial succession could potentially facilitate bacterial co-degradation of SDZ and contribute to a substantially reduced level of ARGs (with the relative abundance of sul1 and sul2 decreasing to 22.9% post-treatment). Overall, the strategy of regulating microalgae inoculation in the MBSS significantly enhanced antibiotic removal and nutrient recovery while controlling the proliferation and spread of ARGs by directing microbial community succession.},
}

@article {pmid41175869,
year = {2025},
author = {Flori, S and Mikus, F and Flaum, E and Moog, K and Guessoum, S and Beavis, T and Zwahlen, SM and Romero-Brey, I and Oorshot, V and Olivetta, M and Steele-Ogus, M and Yeh, E and , and Dudin, O and Schwab, Y and Dey, G and Vincent, F},
title = {Diatom ultrastructural diversity across controlled and natural environments.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.024},
pmid = {41175869},
issn = {1879-0445},
abstract = {Diatoms are ubiquitous aquatic microalgae critical to our planet and were among the pioneer model organisms in cell biology because of their large and transparent cell structure. However, their robust silica cell wall, which renders diatoms impermeable to many dyes and antibodies, as well as challenging for gene editing tools, likely hindered the broader establishment of diatoms as standard model species, despite their unique cellular physiology and remarkable ecological success. Here, we demonstrate that cryo-fixation combined with ultrastructural expansion microscopy (cryo-ExM) can overcome the silica barrier across diverse diatom species spanning over 80 million years of evolutionary time. We illustrate cryo-ExM's potential to provide scalable, cost-effective volumetric imaging of diatom ultrastructure in laboratory cultures, as well as field-collected samples from the pan-European TREC expedition. We first reveal striking similarities in interphase microtubule organization across diverse diatom species by characterizing cytoskeletal arrangements throughout cell cycles and populations, uniting both pennate and centric morphologies under shared principles. We further unveil diatom photosynthetic diversity through qualitative and quantitative comparative analyses of chloroplast and pyrenoid morphologies, demonstrating that each diatom species architects unique photosynthetic machinery. Using cryo-ExM on environmental samples further exposes intricate diatom symbioses, revealing tight spatial organization of ecological interactions. This methodology makes diatoms more accessible for modern and comparative cell biology research, providing new opportunities to investigate the cellular physiology of one of Earth's most successful photosynthetic groups.},
}

@article {pmid41175755,
year = {2025},
author = {Tang, K and Cao, X and Geng, X and Huang, W and Liu, H and Yan, Z and Wu, Z and Yang, C and Tang, J and Zhou, Z},
title = {Microbiome dysbiosis and decreased survival in coral larvae exposed to environmentally relevant concentrations of nanoplastics and sulfamethoxazole.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140297},
doi = {10.1016/j.jhazmat.2025.140297},
pmid = {41175755},
issn = {1873-3336},
abstract = {Scleractinian corals are increasingly threatened by environmental contaminants such as nanoplastics (NPs) and antibiotics. The early life stages of corals are particularly vulnerable to environmental stressors, yet their impacts under environmentally relevant concentrations remain poorly understood. Here, we exposed Pocillopora damicornis larvae to NPs (100 μg/L) and sulfamethoxazole (SMX, 0.1 μg/L) for 48 h to assess their effects on larval survival, settlement, tissue structure, and bacterial symbionts. Exposure to NPs and SMX significantly reduced larval survival, caused tissue necrosis and mesenterial filament dissociation, and altered the composition of bacterial symbionts, such as a decrease in Pseudoalteromonas abundance. Compared to the single exposure group, co-exposure to NPs and SMX induced more severe tissue damage and broader functional shifts in microbial communities, including elevated methylotrophy, photoheterotrophy, photoautotrophy, and reduced anaerobic respiration. These findings suggest that coral larvae are highly sensitive to NPs and SMX, which can alter bacterial symbiont community to disturb nutrient cycling and energy metabolism, cause tissue damage, and ultimately impair larval survival, thereby threatening coral reef replenishment and recovery.},
}

@article {pmid41174857,
year = {2025},
author = {Bhardwaj, A and Gupta, M and Bhattacharjee, O and Raul, B and Ghosh, AK and Nagalla, LVS and Yadav, P and Bandyopadhyay, K and Ranjan, A and Sinharoy, S},
title = {RSD-mediated suppression of NIN and NLP2 transcription is crucial for symbiotic nitrogen fixation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70697},
pmid = {41174857},
issn = {1469-8137},
support = {AB was supported by CSIR (09/803(0141)/2017-EMR-I)//Human Resource Development Centre, Council of Scientific And Industrial Research/ ; HRD-16016/23/2025-HRD-DBT-E-21386//Biotechnology Industry Research Assistance Council/ ; SPG/2022/000171-G//Science and Engineering Research Board/ ; 37WS(0043)/2023-24/EMR-II//Council of Scientific and Industrial Research, India/ ; },
abstract = {Indeterminate nodules establish a developmental gradient along their longitudinal axis, separating cell differentiation from symbiotic nitrogen fixation (SNF). The apex contains differentiating cells, while the differentiated leghemoglobin-rich cells of the nitrogen-fixation zone shield the rhizobial nitrogenase complex from oxygen to facilitate SNF. By combining biochemical, genetic, and genomic approaches, we demonstrate the pivotal role of the Regulator of Symbiosome Differentiation (RSD), a transcriptional repressor, in the transition from symbiosome development to SNF. Interacting Protein of DMI3 (IPD3) activates RSD expression in the invasion zone (ZII) and interzone (IZ). RSD interacts with Nodule Inception (NIN), and NIN-like protein 2 (NLP2) through a novel protein-protein interaction domain. RSD determines cell fate in ZII and the IZ by suppressing several targets of NIN and NLP2, including Leghemoglobins, Nodule-specific Cysteine-Rich genes, and Symbiotic Cysteine-rich Receptor-like Kinase. Our findings underscore the critical role of RSD-mediated suppression of transcription in facilitating the transition from bacteroid differentiation to SNF.},
}

@article {pmid41174492,
year = {2025},
author = {Gao, JH and Tang, F and Wang, YW and Liu, QY and Yi, FY and Zhang, ZQ and Gao, CP},
title = {Integrated proteomic and transcriptomic analyses reveal that the Rj4-mediated immunity network restricts soybean-rhizobia symbiosis.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {981},
pmid = {41174492},
issn = {1471-2164},
}

@article {pmid41174464,
year = {2025},
author = {Lamrabet, M and Missbah El Idrissi, M},
title = {Comparative genomic analysis of native Bradyrhizobium spp. nodulating Retama dasycarpa in Moroccan semi-arid ecosystems: insights into symbiotic diversity and environmental adaptation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {984},
pmid = {41174464},
issn = {1471-2164},
mesh = {*Bradyrhizobium/genetics/classification/physiology ; *Symbiosis/genetics ; *Fabaceae/microbiology ; Phylogeny ; Morocco ; *Genomics/methods ; Nitrogen Fixation/genetics ; *Genome, Bacterial ; *Ecosystem ; *Adaptation, Physiological/genetics ; Root Nodules, Plant/microbiology ; Plant Root Nodulation/genetics ; },
abstract = {BACKGROUND: Retama dasycarpa, a drought-resistant legume endemic to Morocco's High Atlas Mountains, thrives in harsh conditions due to its association with nitrogen-fixing Bradyrhizobium strains. Despite the ecological significance of this symbiosis, the genetic diversity, symbiotic mechanisms, and stress adaptation strategies of these microsymbionts remain poorly understood. In this study we employed a comparative genomic approach to elucidate the genomic and functional traits of five strains isolated from R. dasycarpa nodules, with a focus on their symbiotic and stress-responsive gene repertoires.

RESULTS: Phylogenomic analysis revealed that four of the five strains likely represent novel Bradyrhizobium species, as indicated by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below species delineation thresholds. Genomic comparisons identified core symbiotic genes, including nod, nif, and fix genes, essential for nodulation and nitrogen fixation. Interestingly, strain RDT46 lacked canonical nod genes but retained a minimal Type III Secretion System (T3SS), suggesting alternative symbiotic pathways. Pangenome analysis of 56 Bradyrhizobium genomes highlighted an open pangenome with extensive accessory gene content, reflecting adaptive versatility. Stress adaptation genes, such as those involved in osmoprotectant synthesis, oxidative stress response, and heat shock, were conserved across the five strains, underscoring their resilience to semi-arid conditions.

CONCLUSIONS: This study uncovers previously unknown genomic diversity in R. dasycarpa-associated Bradyrhizobim spp., including evidence for non-canonical symbiosis mechanisms. The strains' genetic toolkit for stress tolerance highlights their potential as inoculants for revegetation of degraded semi-arid lands.},
}

*Bradyrhizobium/genetics/classification/physiology
*Symbiosis/genetics
*Fabaceae/microbiology
Phylogeny
Morocco
*Genomics/methods
Nitrogen Fixation/genetics
*Genome, Bacterial
*Ecosystem
*Adaptation, Physiological/genetics
Root Nodules, Plant/microbiology
Plant Root Nodulation/genetics

@article {pmid41174113,
year = {2025},
author = {Besharati-Fard, M and Moosawi-Jorf, SA and Shams-Ghahfarokhi, M and Razzaghi-Abyaneh, M},
title = {First report and diversity analysis of endophytic fungi associated with Ulva sp. from Iran.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38264},
pmid = {41174113},
issn = {2045-2322},
mesh = {Iran ; *Endophytes/genetics/classification/isolation & purification ; Phylogeny ; *Ulva/microbiology ; *Fungi/genetics/classification/isolation & purification ; Biodiversity ; },
abstract = {Endophytic fungi are diverse microorganisms that colonize plants symbiotically without causing overt infections. While numerous studies have focused on endophytes in terrestrial plants, there are no prior reports of endophytes associated with algae in Iran. Samples of Ulva sp. were collected during the fall of 2022 from the Bandar Abbas Fishery Coast, Iran, and transported to the laboratory. Following surface sterilization, the samples were cultured on potato dextrose agar (PDA) medium and incubated at 25 °C for 3 weeks. The resulting isolates were purified using the hyphal tip method. This study identified 33 fungal isolates from Ulva sp. collected at the Bandar Abbas Fishery Coast, Iran. Morphological and molecular analyses classified these isolates into 7 species across 6 genera: Alternaria, Aspergillus, Chaetomium, Cladosporium, Penicillium, and Syncephalastrum. Aspergillus was the most abundant genus (34% of isolates), while Alternaria and Syncephalastrum were the least frequent (9% each). Phylogenetic analyses of ITS, β-tubulin, GAPDH, TEF, and LSU gene sequences supported the morphological identification of the isolates. Species identified included Alternaria alternate, Aspergillus caespitosus, Aspergillus terreus, Chaetomium globosum, Cladosporium cladosporioides, Penicillium digitatum, and Syncephalastrum racemosum. All species are reported here for the first time as endophytes of Ulva sp. in Iran. Furthermore, this study represents the first documentation of endophytic fungi associated with the marine alga Ulva sp. in Iranian waters. This research enhances understanding of the ecological interactions between fungal endophytes and marine algae in Iranian ecosystems, emphasizing the diversity of symbiotic relationships in aquatic environments.},
}

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

@article {pmid41172140,
year = {2025},
author = {Xie, L and Lin, G and Ma, J and Deng, J and Yu, D and Zhou, L and Wang, QW},
title = {Canopy spectral cues affect plant growth and root-associated fungal communities of tree species with different mycorrhizal types.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpaf137},
pmid = {41172140},
issn = {1758-4469},
abstract = {Soil fungi establish symbiotic associations with plant roots, which provide nutrients in exchange for photosynthate from the host. Despite the recognized importance of fungal symbiosis, how root-associated fungal communities respond to light qualities remains unclear. In this study, we conducted on a novel spectral attenuation experiment involving seedlings of two temperate tree species, Quercus mongolica (ectomycorrhizal, ECM) and Acer mono (arbuscular mycorrhizal, AM). The experimental design incorporated five spectral treatments, including ambient full-spectrum as control and various attenuations of ultraviolet (UV) and visible light. We quantified tree growth and root traits, and profiled root-associated fungal communities through high-throughput sequencing. Results showed that tree growth and root traits varied depending on tree species and spectral treatments. Blue light significantly promoted total biomass of Q. mongolica, but reduced root exudative carbon, sugar and phenolics. In contrast, A. mono showed no spectral changes in biomass and had the lowest root exudative sugar and phenolics in control. Higher root exudative carbon and phenolics were observed in A. mono than in Q. mongolica. Root-associated fungal communities also showed distinct responses to spectral treatments and tree species. Sob's and Chao1 indices of Q. mongolica fungal communities were significantly lower than those of A. mono under UV attenuation, and alterations in community structure were more pronounced in A. mono. These changes were strongly associated with root traits, particularly exudative carbon, sugar, and total phenolics. Within fungal communities, Q. mongolica was dominated by ECM and saprotrophic fungi, and A. mono by AM and saprotrophic fungi. The relative abundance of ECM fungi in Q. mongolica and that of AM fungi in A. mono was lowest when UV-B radiation was attenuated. In total, these findings highlight the crucial role of root traits and their interaction with fungi when exploring plant adaptation to varying light environments.},
}

@article {pmid41171549,
year = {2025},
author = {Sojoudi, A and SoltaniToularoud, A and GoliKalanpa, E and Nematollahzadeh, A},
title = {Effects of Ensifer meliloti and Rhizophagus intraradices on alfalfa growth indices under cadmium sulfide nanoparticle stress.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41171549},
issn = {1614-7499},
abstract = {Cadmium sulfide nanoparticles (CdS-NPs) are increasingly applied across various industries because of their unique properties. However, their accumulation in soil ecosystems and subsequent uptake by terrestrial plants can negatively affect plant growth. Beneficial microorganisms in the rhizosphere play an important role in mitigating the toxic effects of nanoparticles, thereby supporting plant health. Nevertheless, the role of these microorganisms in alleviating CdS-NP-induced stress in alfalfa remains largely unexplored. This study investigated the effects of different CdS-NPs concentrations (0, 100, 200, and 350 mg kg[-1] soil) on alfalfa, both in the presence and absence of Ensifer meliloti (a symbiotic bacterium) and Rhizophagus intraradices (an arbuscular mycorrhizal fungus). The experimental treatments included a non-inoculated control, inoculation with E. meliloti or R. intraradices individually, and dual inoculation (R. intraradices + E. meliloti). Exposure to CdS-NPs in non-inoculated alfalfa induced significant oxidative stress, as evidenced by increased peroxidase and catalase activities, which were positively correlated with NP concentration (r > 0.90**). This stress reduced cell membrane stability, chlorophyll content and index, plant height, root length, biomass, and nodule number, with the strongest effects observed at 350 mg kg[-1] soil. In contrast, dual-inoculated plants showed improved growth, with cell membrane stability increased by 35%, chlorophyll content by 8%, chlorophyll index by 12%, nodule number by 37%, and POD and CAT activities reduced by 28% and 38%, respectively. Although no significant differences were observed between individual bacterial and fungal inoculations, bacterial inoculation was numerically more effective. These results demonstrated that microbial inoculation substantially enhanced alfalfa tolerance to CdS-NP toxicity and highlighted the need for further studies to investigate the underlying molecular and physiological mechanisms.},
}

@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41170986,
year = {2025},
author = {Mallikaarachchi, KS and Huang, JL and Madras, S and Cuellar, RA and Huang, Z and Gega, A and Rathnayaka-Mudiyanselage, IW and Nandana, V and Al-Husini, N and Saldaña-Rivera, N and Ma, LH and Ng, E and Christensen, K and Pendar, N and Li, S and Deleon, NR and Chen, JC and Schrader, JM},
title = {Sinorhizobium meliloti BR-bodies promote fitness during host colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0249025},
doi = {10.1128/mbio.02490-25},
pmid = {41170986},
issn = {2150-7511},
abstract = {Biomolecular condensates are non-membrane-bound assemblies of proteins and nucleic acids that facilitate specific cellular processes. Like eukaryotic P-bodies, the recently discovered bacterial ribonucleoprotein bodies (BR-bodies) organize the mRNA decay machinery in α-proteobacteria; however, the similarities in molecular and cellular functions across species have been poorly explored. Here, we examine the functions of BR-bodies in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, which colonizes the roots of compatible legume plants. Similar to Caulobacter crescentus, assembly of BR-bodies into visible foci in S. meliloti cells requires the C-terminal intrinsically disordered region (IDR) of RNase E in vivo and in vitro, and foci fusion is readily observed in vivo, suggesting that they are liquid-like condensates that form via mRNA sequestration. Using Rif-seq to measure mRNA lifetimes, we found a global slowdown in mRNA decay in a mutant deficient in BR-bodies, indicating that compartmentalization of the degradation machinery promotes efficient mRNA turnover across α-proteobacteria. Although BR-bodies are constitutively present during exponential growth, the abundance of BR-bodies increases upon cell stress, whereby they promote resistance to environmental stresses. Finally, we show that BR-bodies enhance competitive fitness during Medicago truncatula root colonization and appear to be required for effective symbiosis, as mutants without BR-bodies failed to promote robust plant growth on nitrogen-free medium. These results suggest that BR-bodies provide a fitness advantage for bacteria during host colonization, perhaps by enabling better resistance against the host immune response.IMPORTANCEAlthough eukaryotes often organize their biochemical pathways in membrane-bound organelles, bacteria generally lack such subcellular structures. Instead, membraneless compartments called biomolecular condensates have recently been found in bacteria to organize and enhance biochemical activities. Bacterial ribonucleoprotein bodies (BR-bodies), as one of the most characterized bacterial biomolecular condensates identified to date, assemble the mRNA decay machinery via the intrinsically disordered regions (IDRs) of proteins. However, the implications of such assemblies are unclear. Using a plant-associated symbiont, we show that the absence of BR-bodies results in slower mRNA decay, sensitivity to environmental stresses, and ineffective symbiosis, suggesting that BR-bodies play critical roles in regulating biochemical pathways and promoting fitness during host colonization.},
}

@article {pmid41170502,
year = {2025},
author = {Stepchuk, I and Pérez-Fortes, M and Ramírez, A},
title = {From Feedstock to Future Chemicals: Rethinking Carbon Sources in Industrial Propylene Clusters.},
journal = {ACS sustainable chemistry & engineering},
volume = {13},
number = {42},
pages = {17869-17880},
pmid = {41170502},
issn = {2168-0485},
abstract = {The rising pressure to defossilize the chemical industry has driven research toward producing chemicals that use alternative carbon sources (ACS). However, the challenges and impacts of replacing already implemented processes and symbiotic relationships remain largely underexplored. This paper systematically assesses the impacts of defossilizing existing processes, both individually and simultaneously, in a propylene cluster in the Port of Rotterdam, the Netherlands. Nine fossil-based processes and three ACS-based processes (i.e., CO2-based polyol, biopropylene glycol (bio-PG), and biomethyl-tert-butyl-ether (bio-MTBE)) were included in the assessment. Integrating a single ACS-based process enlarges the propylene cluster and results in an excess of upstream chemicals that are no longer required by the ACS processes. Still, relatively simple technologies can reduce total energy and water use, resulting in lower direct CO2 emissions and water consumption of the cluster. Deploying multiple processes in parallel can drive the full defossilization of the cluster, but it requires a complete overhaul. The results illustrate the extent to which combining ACS-based processes could change the layout of an existing petrochemical cluster, affecting its performance. The paper stresses the importance of assessing such deployments, considering the existing conditions in industrial clusters.},
}

@article {pmid41169718,
year = {2025},
author = {Yang, Y and Yang, Y and Deng, S and Ying, Z},
title = {Role of Azolla in sustainable agriculture and climate resilience: a comprehensive review.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1661720},
pmid = {41169718},
issn = {1664-462X},
abstract = {Agriculture faces mounting challenges from climate change, soil degradation, and unsustainable agrochemical use, highlighting the need for eco-friendly solutions. Azolla, a fast-growing aquatic fern, has emerged as a multifunctional resource for sustainable farming and climate resilience. Through its symbiosis with Anabaena azollae, it fixes atmospheric nitrogen, reducing dependence on synthetic fertilizers and improving soil health. Azolla also serves as a protein-rich feed for livestock and aquaculture, suppresses weeds and pests in rice systems, and supports water conservation. Beyond agriculture, it contributes to carbon sequestration, mitigates methane emissions, and shows promise in wastewater treatment, bioremediation, and as a feedstock for biofuels and bioplastics. However, large-scale adoption is limited by challenges such as short shelf life, ecological risks, and preservation constraints. This review synthesizes current knowledge on Azolla, emphasizing its biological and ecological functions, highlights practical applications across agriculture, livestock, aquaculture, and environmental management, and outlines key research priorities needed to overcome limitations and enable its integration into climate-smart agricultural and environmental systems.},
}

@article {pmid41168779,
year = {2025},
author = {Boss, A and Toepfer, S and Erb, M and Machado, RAR},
title = {Genetic architecture of resistance to plant secondary metabolites in Photorhabdus entomopathogenic bacteria.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {975},
pmid = {41168779},
issn = {1471-2164},
support = {GRS-079/19//Gebert Rüf Foundation/ ; 186094//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Photorhabdus/genetics/metabolism/drug effects ; Animals ; *Secondary Metabolism ; Phylogeny ; Benzoxazines/pharmacology/metabolism ; Genome, Bacterial ; *Plants/metabolism ; },
abstract = {BACKGROUND: Entomopathogenic nematodes of the genus Heterorhabditis establish a symbiotic association with Photorhabdus bacteria. Together, they colonize and rapidly kill insects, making them important biological control agents against agricultural pests. Improving their biocontrol traits by engineering resistance to plant secondary metabolites (benzoxazinoids) in Photorhabdus symbiotic bacteria through experimental evolution has been shown to increase their lethality towards benzoxazinoid-defended larvae of the western corn rootworm, a serious crop pest of maize, and it is therefore a promising approach to develop more efficient biocontrol agents to manage this pest. To enhance our understanding of the genetic bases of benzoxazinoid resistance in Photorhabdus bacteria, we conducted an experimental evolution experiment with a phylogenetically diverse collection of Photorhabdus strains from different geographic origins. We cultured 27 different strains in medium containing 6-methoxy-2-benzoxazolinone (MBOA), a highly active benzoxazinoid breakdown product, for 35 24 h-cycles to select for benzoxazinoid-resistant strains. Then, we carried out genome-wide sequence comparisons to uncover the genetic alterations associated with benzoxazinoid resistance. Lastly, we evaluated the resistance of the newly isolated resistant Photorhabdus strains to eight additional bioactive compounds, including 2-benzoxazolinone (BOA), nicotine, caffeine, 6-chloroacetyl-2-benzoxazolinone (CABOA), digitoxin, fenitrothion, ampicillin, and kanamycin.

RESULTS: We found that benzoxazinoid resistance evolves rapidly in Photorhabdus in a strain-specific manner. Across the different Photorhabdus strains, a total of nineteen nonsynonymous point mutations, two stop codon gains, and one frameshift were associated with higher benzoxazinoid resistance. The different genetic alterations were polygenic and occurred in genes coding for the EnvZ/OmpR two-component regulatory system, the different subunits of the DNA-directed RNA polymerase, and the AcrABZ-TolC multidrug efflux pump. Apart from increasing MBOA resistance, the different mutations were also associated with cross-resistance to 2-benzoxazolinone (BOA), nicotine, caffeine, and 6-chloroacetyl-2-benzoxazolinone (CABOA) and with collateral sensitivity to fenitrothion, ampicillin, and kanamycin. Targeted mutagenesis will provide a deeper mechanistic understanding, including the relative contribution of the different mutation types.

CONCLUSIONS: Our study reveals several genomic features that are associated with resistance to xenobiotics in this important group of biological control agents and enhances the availability of molecular tools to develop better biological control agents, which is essential for more sustainable and ecologically friendly agricultural practices.},
}

*Photorhabdus/genetics/metabolism/drug effects
Animals
*Secondary Metabolism
Phylogeny
Benzoxazines/pharmacology/metabolism
Genome, Bacterial
*Plants/metabolism

@article {pmid41167316,
year = {2025},
author = {Liu, X and Zhang, Q and Wang, H and Li, M and Chen, J and He, Q and Dong, X},
title = {Revealing the dynamical effects of diurnal dynamics on community assembly in the electro-enhanced algal-bacterial symbiosis system for mariculture wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123235},
doi = {10.1016/j.envres.2025.123235},
pmid = {41167316},
issn = {1096-0953},
abstract = {This study evaluated the intrinsic effect of different light-dark cycles (H1-0L:12D; H2-3.5L:8.5D; H3-8L:4D) on mariculture wastewater degradation and nitrogen removal in Electro-enhanced Algal-Bacterial Symbiosis System. While chemical oxygen demand (COD) removal remained comparable (>72.9 %), H2 achieved 82 % total nitrogen removal, outperforming H1 (67 %) and H3 (68.8 %). The different nitrogen removal performance among the three systems was primarily attributable to the significant impairment of conventional nitrification and denitrification functions in both H1 and H3. Light/dark cycles caused a shift in the complexity and community structure. Microbial community assembly shifted from deterministic (R[2]=0.356, H1) to stochastic (R[2]=0.567, H3) selection with extended illumination. Crucially, H2, a unique balancer of both strategies (R[2]=0.54), enhanced bacterial-algal synergism and denitrification performance (denitrification efficiency increased 22.16 %) through stochastic-selected communities dominated by Tropicibacter (8.7 %) and Nitrogeniibacter (12.4 %), demonstrating light-cycle-induced ecological memory effects. These findings enabled engineered photoperiod control for energy-efficient mariculture wastewater treatment.},
}

@article {pmid41166108,
year = {2025},
author = {Motnenko, A and Hawkins, JP and Ordoñez, PA and Oresnik, IJ},
title = {Sinorhizobium prairiense sp. nov., a nitrogen-fixing symbiont of Phaseolus vulgaris isolated from Canadian prairie soil.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.006947},
pmid = {41166108},
issn = {1466-5034},
mesh = {*Phaseolus/microbiology ; *Soil Microbiology ; *Phylogeny ; *Symbiosis ; *Nitrogen Fixation ; DNA, Bacterial/genetics ; *Sinorhizobium/classification/genetics/isolation & purification/physiology ; Bacterial Typing Techniques ; Plasmids/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; Manitoba ; Nucleic Acid Hybridization ; Root Nodules, Plant/microbiology ; Genome, Bacterial ; },
abstract = {Three symbiotic bacteria (K101[T], C101 and M103) were obtained from nodule-trapping experiments using Phaseolus vulgaris, which was inoculated with soil samples from three distinct field sites in Manitoba, Canada. Here, we provide a phenotypic characterization and genomic analysis of these bacteria. Based on a core phylogeny (424 core genes), digital DNA-DNA hybridization and average nucleotide alignment, these isolates group within the Sinorhizobium clade and are closely related to Sinorhizobium meliloti. Each strain contains four replicons that include a chromosome (3.5 Mb), a putative chromid (1.7 Mb) and two plasmids (plasmid A, 0.56 Mb; plasmid B, 0.77 Mb). The chromosome, chromid and plasmid B are closely related to the replicons found in S. meliloti, as shown by phylogenies constructed from the concatenation of either the parAB genes for the chromosome or the repABC genes for the chromid and plasmid B. The remaining plasmid was found to group with a plasmid from Sinorhizobium americanum. Consistent with this, the nodulation genes on this plasmid were also more similar to those in S. americanum, as seen in a phylogeny generated from the concatenation of the nodABC genes. Examination of the nodC phylogeny suggests a close association with the mediterranensis symbiovar. All three isolates were capable of symbiotic nitrogen fixation with P. vulgaris. Based on genomic and phenotypic data, we propose these isolates as a novel species within the Sinorhizobium clade, named Sinorhizobium prairiense sp. nov., for which the type strain is K101[T] (=LMG 33767[T]=DSM 118657[T]).},
}

*Phaseolus/microbiology
*Soil Microbiology
*Phylogeny
*Symbiosis
*Nitrogen Fixation
DNA, Bacterial/genetics
*Sinorhizobium/classification/genetics/isolation & purification/physiology
Bacterial Typing Techniques
Plasmids/genetics
Sequence Analysis, DNA
RNA, Ribosomal, 16S/genetics
Manitoba
Nucleic Acid Hybridization
Root Nodules, Plant/microbiology
Genome, Bacterial

@article {pmid41165958,
year = {2025},
author = {Helmich, RE and Zettler, LW and Dvorak, CJ and DiSalvo, S},
title = {Fluridone stimulates in vitro seed germination of a rare hardy terrestrial orchid (Platanthera leucophaea).},
journal = {Botanical studies},
volume = {66},
number = {1},
pages = {37},
pmid = {41165958},
issn = {1817-406X},
support = {American Orchid Society//American Orchid Society/ ; U.S. Fish and Wildlife Service//U.S. Fish and Wildlife Service/ ; },
abstract = {BACKGROUND: Seeds of temperate terrestrial (hardy) orchids are considered more difficult to germinate compared to their tropical epiphytic counterparts, presumably because they have higher levels of abscisic acid (ABA) in their seed coats which prevents seeds from germinating prematurely during winter dormancy. In nature, ABA is gradually broken down (stripped) by natural weathering, triggering germination. This process can be shortened artificially, however, by using chemical bleaching agents and cold-moist stratification with mixed results. In this study, we explored the use of fluridoneto break seed dormancy in a hardy orchid native to North America, Platanthera leucophaea (Nutt.) Lindl. This organic compound (IUPAC name: 1-methyl-3-phenyl-5-[3-(trifluoromethyl) phenyl] pyridin-4(1H)-one) is a commercial herbicide that inhibits ABA biosynthesis. We added fluridone directly to agar media prior to seed sowing in vitro. Both symbiotic and asymbiotic germination techniques were applied that involved two different agar media, with and without added fluridone. Symbiotic germination was carried out using standard oatmeal agar inoculated with a mycorrhizal fungus (Ceratobasidium), whereas asymbiotic treatments utilized P723 agar medium.

RESULTS: Seedling development within some of the replicate plates progressed to Stage 3 in all treatments, but development was marked in all asymbiotic plates containing fluridone leading to leaf elongation, 385 days after sowing.

CONCLUSIONS: As an herbicide, fluridone's use as a media additive to propagate a rare photosynthetic orchid seems counterintuitive, but its use in vitro to stimulate seedling development has the potential to benefit conservation efforts for this and possibly other hardy orchid species.},
}

@article {pmid41165784,
year = {2025},
author = {Yoda, A and Kodama, K and Shimamura, M and Kyozuka, J},
title = {Spatial Localization of Strigolactone Biosynthesis and Secretion in Marchantia paleacea.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf144},
pmid = {41165784},
issn = {1471-9053},
abstract = {Phosphorus is an essential nutrient critical for plant growth and development, yet its availability in soil is often limited. Consequently, most land plants establish symbiotic relationships with arbuscular mycorrhizal fungi (AMF) to enhance phosphate uptake. Strigolactones (SLs) function as rhizosphere signaling molecules that promote AMF symbiosis, distinct from their role as phytohormones regulating various plant functions. We previously identified an SL in Marchantia paleacea and demonstrated that the SLs primarily serve as rhizosphere signals rather than phytohormones in M. paleacea due to the absence of cognate receptors. In this study, we investigate the spatial localization of SL biosynthesis and secretion in M. paleacea. We find that SL biosynthesis genes are predominantly expressed in the basal region of the thallus compared to the distal region. Using Citrine driven by the promoter of MpaCCD8B, an SL biosynthesis gene, we show expression in smooth rhizoids and the ventral epidermis adjacent to these rhizoids, under phosphate-deficient conditions. When plants are cultured on medium, fluorescence is also detected in parenchymal cells, where AMF colonization occurs. In soil conditions, AMF colonization enhances MpaCCD8B expression in parenchymal cells, where AMF colonize. Furthermore, we assess SL secretion through germination assay of root parasitic plant seeds, revealing that exudates from the basal and midrib region exhibit the highest activity. These findings underscore that SLs are synthesized in the basal ventral tissues of M. paleacea and secreted into the rhizosphere, facilitating effective communication with AMF.},
}

@article {pmid41165610,
year = {2025},
author = {Chen, X and Xie, D and Chen, H and Jia, N and Jiang, L and Pan, Z and Wang, Y and Dai, Y and Chi, D and Yu, J},
title = {Effects of Hylurgus ligniperda (Coleoptera: Curculionidae)-microorganism symbiosis complex damage severity on physiological and defensive responses in Pinus thunbergii.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf292},
pmid = {41165610},
issn = {1938-291X},
support = {2021YFD1400300//National Key Research and Development Program of China/ ; },
abstract = {To explore the defense response of Pinus thunbergii to different damage levels of Hylurgus ligniperda, 4-yr-old P. thunbergii saplings were transplanted in pots in the field. After enclosing the base of the saplings with insect-proof nets, adult H. ligniperda were introduced for infestation. Terminal and lateral shoot growth of P. thunbergii were measured at 0, 20, 40, and 60 d post-release (dpr) of adult beetles, while samples were collected at 7, 17, 37, 57, and 67 dpr. At each sampling time point, the damage area inflicted by H. ligniperda on P. thunbergii and the pest population density were recorded. Based on the damage area, the trees were classified into five severity grades: healthy pines (no pest released), and those with damage areas of <1%, 1% to 5%, 5% to 20%, and >20%. Laboratory analyses assessed changes in defense-related indices, root vitality, and nutrient content across damage grades. Additionally, H. ligniperda adults were reared on bark from differently damaged trees to evaluate the impact of P. thunbergii defensive responses. Results revealed that H. ligniperda infestation significantly inhibited shoot growth in P. thunbergii, impairing tree development and ultimately causing death. An overall trend of initial increase followed by a decrease was observed in the tree's root vitality and defense indices with increasing damage, which ultimately failed to prevent H. ligniperda colonization. Furthermore, these defensive responses suppressed weight gain and reduced reserves of glycogen, protein, and free fatty acids in adult H. ligniperda, adversely affecting their development.},
}

@article {pmid41165394,
year = {2025},
author = {Rozo-Lopez, P and Torres, V and Torres, J and Drolet, BS and Käfer, S and Parker, BJ},
title = {Heritable viral symbionts in the family Iflaviridae are widespread among aphids.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0160625},
doi = {10.1128/aem.01606-25},
pmid = {41165394},
issn = {1098-5336},
abstract = {UNLABELLED: Heritable microbes shape host phenotypes and serve as important drivers of evolution. While interactions between insects and bacterial symbionts have been extensively studied, the prevalence and evolution of insect-viral symbioses remain poorly understood. We discovered multiple new species of iflaviruses in aphids, an important model for research on symbiosis, and found these microbes to be widespread across aphid species. We show that iflaviruses are persistently maintained in asexual host lines without apparent fitness costs while being transmitted vertically from mothers to offspring. Using field data and phylogenetic evidence, we found that aphid iflaviruses move horizontally among host species, but laboratory experiments showed that horizontal transmission does not result in persistent infections. Using quantitative PCR and immunohistochemistry, we discovered that viral infections localize in the host fat bodies and developing embryos. Surprisingly, we also found viral infections inside bacteria-housing cells called bacteriocytes, along with a positive correlation between viral and bacterial symbiont density. Together, our work suggests that iflaviruses are widespread heritable symbionts in aphids.

IMPORTANCE: In recent years, the rise of metatranscriptome sequencing has led to the rapid discovery of novel viral sequences in insects. However, few studies have carefully investigated the dynamics of insect-virus interactions to produce a general understanding of viral symbiosis. Aphids are an important model for understanding the evolution and molecular basis of symbiosis, but whether viruses are forming persistent symbiotic relationships with aphids remains unclear. Here, we show that heritable iflaviruses are a widespread but previously unrecognized part of the aphid heritable microbiome. Aphid iflaviruses are transmitted alongside bacteria from mothers to offspring, potentially via specialized bacteriocytes that house symbiotic microbes. Our findings suggest that aphids establish persistent relationships with iflaviruses and are likely coevolving with these viral symbionts.},
}

@article {pmid41164861,
year = {2025},
author = {Fowler, JC and Moutouama, J and Miller, TEX},
title = {Increasing Prevalence of Plant-Fungal Symbiosis Across Two Centuries of Environmental Change.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70577},
doi = {10.1111/gcb.70577},
pmid = {41164861},
issn = {1365-2486},
support = {//Texas Ecolab Program/ ; 1754468//Division of Environmental Biology/ ; 2208857//Division of Environmental Biology/ ; },
mesh = {*Symbiosis ; *Climate Change ; *Epichloe/physiology ; *Endophytes/physiology ; *Elymus/microbiology ; *Poaceae/microbiology ; },
abstract = {Species' distributions and abundances are shifting in response to ongoing global climate change. Mutualistic microbial symbionts can provide hosts with protection from environmental stress that may promote resilience under environmental change; however, this change may also disrupt species interactions and lead to declines in hosts and/or symbionts. Symbionts preserved within natural history specimens offer a unique opportunity to quantify changes in microbial symbiosis across broad temporal and spatial scales. We asked how the prevalence of seed-transmitted fungal symbionts of grasses (Epichloë endophytes) has changed over time in response to climate change, and how these changes vary across host species' distributions. Specifically, we examined 2346 herbarium specimens of three grass host species (Agrostis hyemalis, Agrostis perennans, Elymus virginicus) collected over the past two centuries (1824-2019) for the presence or absence of Epichloë symbiosis. Analysis of an approximate Bayesian spatially varying coefficients model revealed that endophytes increased in prevalence over the last two centuries from ca. 25% to ca. 75% prevalence, on average, across three host species. Changes in seasonal climate drivers were associated with increasing endophyte prevalence. Notably, increasing precipitation during the peak growing season for Agrostis species and decreasing precipitation for E. virginicus were associated with increasing endophyte prevalence. Changes in the variability of precipitation and temperature during off-peak seasons were also important predictors of increasing endophyte prevalence. Our model performed favorably in an out-of-sample predictive test with contemporary survey data from across 63 populations, a rare extra step in collections-based research. However, there was greater local-scale variability in endophyte prevalence in contemporary data compared to model predictions, suggesting new directions that could improve predictive accuracy. Our results provide novel evidence for a cryptic biological response to climate change that may contribute to the resilience of host-microbe symbiosis through fitness benefits to symbiotic hosts.},
}

*Symbiosis
*Climate Change
*Epichloe/physiology
*Endophytes/physiology
*Elymus/microbiology
*Poaceae/microbiology

@article {pmid41163851,
year = {2025},
author = {Rai, N and Kachore, A and Julka, JM and Panigrahi, A and Das, SP and Nan, FH},
title = {Symbiotic strategies: deciphering the role of gut microbiota in the nutrition and metabolism of fish and shellfish.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1639426},
pmid = {41163851},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Fishes/microbiology/metabolism/physiology ; *Shellfish/microbiology ; Aquaculture ; *Symbiosis ; Probiotics ; Prebiotics ; Diet ; },
abstract = {The gastrointestinal microbiota is crucial for the health and physiology of aquatic organisms, influencing their nutrition, metabolism, and immune responses. This review compares the diversity and function of gut microbial communities in finfish and shellfish, highlighting differences between freshwater and marine species as well as variations within shellfish taxa. We examine how these microbes aid in digesting complex dietary substrates, assimilating nutrients, and synthesizing essential metabolites, all of which are vital for host health. The structure of these microbial communities is shaped by a complex interplay of environmental factors, such as water temperature, salinity, and pH, and host-specific factors, including genetics and diet. A comprehensive understanding of these interactions is key to improving gut health and nutrient use in aquaculture. This review also identifies future research directions, focusing on the use of probiotics, prebiotics, and dietary interventions. These strategies, combined with multi-omics approaches, have great potential to enhance the sustainability of aquaculture by improving growth performance, feed conversion efficiency, and disease resistance in farmed aquatic species.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Fishes/microbiology/metabolism/physiology
*Shellfish/microbiology
Aquaculture
*Symbiosis
Probiotics
Prebiotics
Diet

@article {pmid41163484,
year = {2025},
author = {Yu, S and Zuo, R and Zou, F and Wang, T and Chang, M and Masabni, J and Yuan, D and Xiong, H},
title = {Ectomycorrhizal Symbiosis Enhances Mineralization of Phytate by Inducing Host-Derived Purple Acid Phosphatase Secretion in Castanea henryi.},
journal = {Physiologia plantarum},
volume = {177},
number = {6},
pages = {e70614},
doi = {10.1111/ppl.70614},
pmid = {41163484},
issn = {1399-3054},
support = {32001309//National Natural Science Foundation of China/ ; 2025JJ60143//National Natural Science Foundation of Hunan/ ; 2024RC1059//Science and Technology Innovation Program of Hunan Province/ ; },
mesh = {*Acid Phosphatase/metabolism/genetics ; *Mycorrhizae/physiology ; *Phytic Acid/metabolism ; *Symbiosis/physiology ; Phosphorus/metabolism ; *Fagaceae/microbiology/metabolism/enzymology/genetics ; Soil/chemistry ; Plant Roots/metabolism/microbiology ; Plant Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; },
abstract = {Plant symbiosis with ectomycorrhizal fungi (ECMF) promotes soil phosphorus (P) uptake, and studies have suggested that acid phosphatase (ACP) produced by ECMF promotes soil organic phosphorus (Po) mineralization and thus aids in plant P uptake. However, how the host plant plays a role, if any in this process, is not clear. We explored the response of the host plant, Castanea henryi, to phytate and its utilization mechanism after inoculation with Pisolithus orientalis LY-8. In this study, ECMF inoculation significantly enhanced plant biomass, and soil available phosphorus, labile organic phosphorus, moderately labile organic phosphorus content, and Po mineralization rate. After inoculation, the ACP activity of plant root tips was higher than the sum of the ACP secreted by uninoculated root tips and the ACP secreted by fungi. Besides, alkaline phosphatase, and root tip vigor were significantly increased after inoculation. Transcriptome sequencing and RT-qPCR revealed that the relative expression of ChACP genes, especially purple acid phosphatase (ChPAPs) and phosphorus transporter genes were significantly higher in the inoculated treatment than in the uninoculated treatment. These results indicate that ECMF can induce the expression of ChPAPs, thus affecting the secretion of ACP in the root system of C. henryi, which in turn strengthens the ability to mineralize soil Po and promotes plant growth. Our results provide new insights into the understanding of the mechanisms of the role of ECMF in plant P nutrient acquisition.},
}

*Acid Phosphatase/metabolism/genetics
*Mycorrhizae/physiology
*Phytic Acid/metabolism
*Symbiosis/physiology
Phosphorus/metabolism
*Fagaceae/microbiology/metabolism/enzymology/genetics
Soil/chemistry
Plant Roots/metabolism/microbiology
Plant Proteins/metabolism/genetics
Gene Expression Regulation, Plant

@article {pmid41163404,
year = {2025},
author = {Ricks, KD and Raglin, SS and Kent, AD},
title = {Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70684},
pmid = {41163404},
issn = {1469-8137},
support = {NREC 2021-2-360190-334//Illinois Nutrient Research and Education Council/ ; ILLU-875-637//National Institute of Food and Agriculture/ ; DE-SC0018420//Biological and Environmental Research/ ; },
abstract = {Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant-microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant-microbiome recruitment. Plant-microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host-microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.},
}

@article {pmid41163130,
year = {2025},
author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD},
title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {967},
pmid = {41163130},
issn = {1471-2164},
support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; },
abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.

RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.

CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.},
}

*Mycorrhizae/genetics/physiology
*Symbiosis/genetics
*Plant Roots/microbiology
Phylogeny
*Endophytes/genetics
*Genomics
*Metagenome
*Genome, Fungal
Glomeromycota/genetics

@article {pmid41163086,
year = {2025},
author = {Mooney, R and Corbett, E and Giammarini, E and Rodgers, K and Donet, C and Mui, E and Ansari, ATA and Ransingh, A and Vernekar, PS and Walia, HK and Sharma, J and Connolly, J and Hursthouse, A and Mukherji, S and Mukherji, S and Henriquez, FL},
title = {The Microbial Trojan Horse and Antimicrobial Resistance: Acanthamoeba as an Environmental Reservoir for Multidrug Resistant Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70193},
doi = {10.1111/1462-2920.70193},
pmid = {41163086},
issn = {1462-2920},
support = {NE/T012986/1//Natural Environment Research Council/ ; BT/IN/Indo-UK/AMR-Env/01/SM/2020-21//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Acanthamoeba/microbiology ; *Bacteria/drug effects/genetics/isolation & purification ; *Drug Resistance, Multiple, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Geologic Sediments/microbiology ; Microbial Sensitivity Tests ; },
abstract = {Antimicrobial resistance (AMR) is shaped by environmental pressures, yet the role of microbial predators such as Acanthamoeba in resistance dynamics remains poorly characterized. In this study, Acanthamoeba-associated bacterial communities (AAB) exhibited significantly higher multidrug resistance than sediment-associated bacterial communities (SAB) in a polluted estuarine system. All isolated amoebae belonged to the T4 genotype, suggesting selection for resilient host organisms. AAB displayed elevated multiple antibiotic resistance (MAR) indices and increased resistance to multiple antibiotic classes, particularly aminoglycosides, macrolides, fluoroquinolones and β-lactams. Correlation analysis revealed that resistance in AAB, but not SAB, was associated with potentially toxic elements (PTEs) known to influence phagocyte survival, including arsenic, vanadium, and calcium. These elements may select for traits that confer metal and antibiotic resistance. The findings support a model where protists act as selective environments for AMR, favoring bacteria that possess enhanced tolerance mechanisms. This work provides the first direct evidence linking PTE exposure to the intracellular resistome of Acanthamoeba-associated bacteria. It underscores the need for AMR monitoring frameworks that include protist-bacteria interactions, with implications for One Health and environmental risk assessment strategies. Moreover, this approach is scalable for application in low/middle-income countries, where AMR burden is greatest and surveillance capacity remains limited.},
}

*Acanthamoeba/microbiology
*Bacteria/drug effects/genetics/isolation & purification
*Drug Resistance, Multiple, Bacterial
*Anti-Bacterial Agents/pharmacology
Geologic Sediments/microbiology
Microbial Sensitivity Tests

@article {pmid41162683,
year = {2025},
author = {Lin, Y and He, J and Zhang, Q and Li, Y and Ke, J and Lin, C and Yao, B and Zhang, C and Tan, N},
title = {Aerococcus christensenii: an emerging pathogen associated with infections and bacteremia in pregnancy-genomic insights and pathogenicity evaluation.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {229},
pmid = {41162683},
issn = {1438-7948},
support = {868-000001033222//The Scientific Foundation for Youth Scholars of Shenzhen University/ ; 868-000001033222//The Scientific Foundation for Youth Scholars of Shenzhen University/ ; 868-000001033222//The Scientific Foundation for Youth Scholars of Shenzhen University/ ; },
mesh = {Female ; Pregnancy ; Humans ; *Bacteremia/microbiology ; Animals ; *Aerococcus/genetics/pathogenicity/drug effects/isolation & purification ; Mice ; *Genome, Bacterial ; *Gram-Positive Bacterial Infections/microbiology ; Virulence/genetics ; *Pregnancy Complications, Infectious/microbiology ; Virulence Factors/genetics ; },
abstract = {Aerococcus christensenii (A. christensenii) is a symbiotic bacterium that primarily colonizes the vagina. Infections caused by A. christensenii are rare but can also pose a significant health threat. In this study, two rare cases of A. christensenii bacteremia in pregnant women complicated with chorioamnionitis were investigated; and two strains KSW23 and KWL24, which were isolated from blood samples, were analyzed for their genomic characteristics and pathogenic potential. Whole-genome sequencing revealed that the genome sizes of KSW23 and KWL24 were approximately 1.6 Mb, and predicted multiple genes associated with pathogenicity (tuf, eno, plr/gapA, galU, galE, groEL, gndA, sugC, lplA1, mgtB, clpC, clpP, and lmb), antibiotic resistance (ermB and tet(M)), and mobile genetic elements (plasmid replicon repUS43 and transposon Tn6009). Correspondingly, these strains showed multidrug resistance to Macrolides, Lincosamides, and Tetracyclines. Pangenome analysis revealed close evolutionary relationships and significant genomic conservation between these two strains and the previously isolated strains, especially with respect to genes related to pathogenicity and antibiotic resistance. Notably, a mouse bacteremia model confirmed the pathogenicity and virulence of A. christensenii strains KSW23 and KWL24, which induced bacteremia and mortality, but not as strongly as Staphylococcus aureus (S. aureus) strain ATCC25923. Additionally, A. christensenii exhibited a robust survival ability in human blood comparable to those observed in S. aureus strain ATCC25923. To our knowledge, this study is the first genomic research on A. christensenii, and confirms the species' bloodstream invasive capacity and pathogenicity based on genomic studies and experimental validation. These findings underscore its role as a pathogen in the ascending genital tract in the obstetric population.},
}

Female
Pregnancy
Humans
*Bacteremia/microbiology
Animals
*Aerococcus/genetics/pathogenicity/drug effects/isolation & purification
Mice
*Genome, Bacterial
*Gram-Positive Bacterial Infections/microbiology
Virulence/genetics
*Pregnancy Complications, Infectious/microbiology
Virulence Factors/genetics

@article {pmid41162617,
year = {2025},
author = {Salama, SG and Marie, AH and Bedair, R},
title = {Floristic assessment and soil-vegetation dynamics in an arid zone: a case study of the old Katameya-Ain Sokhna Road, Eastern Desert, Egypt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37742},
pmid = {41162617},
issn = {2045-2322},
mesh = {Egypt ; *Soil/chemistry ; *Desert Climate ; *Ecosystem ; *Plants/classification ; Biodiversity ; Conservation of Natural Resources ; },
abstract = {In the hyper-arid deserts of Egypt, where extreme environmental conditions prevail, understanding the symbiotic relationship between the sparse vegetation cover and the underlying soil is crucial for unraveling the mechanisms of plant survival and ecosystem functioning. This study investigates vegetation composition, environmental drivers, and their interactions in an unprotected area of Egypt's northern Eastern Desert, which has recently experienced substantial anthropogenic disturbances. Primary threats to vegetation include road construction, unregulated quarrying, and overexploitation of natural resources. To represent the habitats present in the study area, 20 stands were selected. In each stand, the existing plant species were recorded, soil samples were taken from each stand, and multivariate statistics (DCA) were conducted to show the relationship between the distinctive plant indicators for each stand, as well as the most influential soil factors in each stand. Then, the state of the vegetation cover in previous years (2014) was compared with the state in the study year (2024). A total of 75 plant species were documented, with Asteraceae (15 species) and Fabaceae (6 species) representing the most diverse families. Perennials (73%), chamaephytes (44%), and Saharo-Arabian species (71%) dominated the flora. Detrended Correspondence Analysis (DCA) revealed that the studied stands were divided into four groups (A, B, C, and D). Each group was ecologically similar to the other. Each group of stands had distinctive plant indicators and the soil factors most closely associated with them. Based on the IUCN Red List, conservation status assessments were provided for each species (65 species were unevaluated, while only 11% of the total species are classified as Least Concern, with no taxa appearing in the threatened category). The presence of invasive non-native taxa, such as Beta vulgaris and Centaurea calcitrapa, which threaten native biodiversity, was noted. Analysis of the Soil Adjusted Vegetation Index (SAVI) revealed a reduction in vegetation cover between 2014 (SAVI range: -0.523911 to 0.860437) and 2024 (SAVI range: -0.574714 to 1.08698). The recorded plant species include 16 medicinal plants. Escalating habitat destruction and anthropogenic pressures underscore the urgent need for targeted conservation strategies to safeguard biodiversity in this vulnerable region.},
}

Egypt
*Soil/chemistry
*Desert Climate
*Ecosystem
*Plants/classification
Biodiversity
Conservation of Natural Resources

@article {pmid41162221,
year = {2025},
author = {Hodžić, A},
title = {The contribution of the Midichloria mitochondrii endosymbiont to Borrelia infection dynamics.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.10.003},
pmid = {41162221},
issn = {1471-5007},
abstract = {Recent studies have revealed a positive correlation between the presence of the Midichloria mitochondrii endosymbiont and Borrelia species in the tick vector, suggesting potential interactions that may influence pathogen infection and the transmission dynamics of Lyme borreliosis. This article discusses the possible mechanistic pathways underlying these interactions.},
}

@article {pmid41162177,
year = {2025},
author = {Nam, Y and Seo, G and Kim, Y and Kim, SR and Kim, JN},
title = {Comparative Analysis of Microbial Communities and Biopolymer Production in Kombucha.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508004},
doi = {10.4014/jmb.2508.08004},
pmid = {41162177},
issn = {1738-8872},
mesh = {Cellulose/biosynthesis/metabolism ; Fermentation ; Biopolymers/biosynthesis/metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; *Kombucha Tea/microbiology ; Yeasts/metabolism/classification/genetics/isolation & purification ; Ethanol/metabolism ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Acetobacteraceae/metabolism/isolation & purification ; },
abstract = {While the microbial diversity of kombucha has been previously investigated, only a limited number of studies have explicitly distinguished between the symbiotic culture of bacteria and yeast (SCOBY) and the liquid broth, and even fewer have directly associated microbial diversity with bacterial cellulose production. This study investigated the microbial communities present in commercially available kombucha products by using both culture-based and molecular analysis methods, along with metabolite profiling by chemical analyses. Culture-based methods identified key cellulose-producing strains, including Komagataeibacter intermedius, K. rhaeticus, and Novacetimonas hansenii, while next-generation sequencing revealed Komagataeibacter as the dominant bacterial genus in kombucha. Yeast communities in kombucha were predominated by Zygosaccharomyces bisporus and Z. parabailii. As fermentation progressed, all kombucha samples exhibited typical fermentation dynamics, characterized by progressive sucrose depletion and an increase in ethanol and acetate production. Given the promising industrial applications of bacterial cellulose, the biopolymer content of kombucha was evaluated. Among the kombucha samples, K2 showed the highest cellulose yield (4.50 ± 2.28 g), and N. hansenii was identified as the most efficient cellulose producer among the isolates. This integrative approach provides critical insights into the role of microbial communities in regulating kombucha fermentation. Specifically, this study delineated the core microbiota required for stable fermentation and identified strains with enhanced cellulose-producing capacity. Beyond defining the key microbial taxa associated with kombucha production, these findings underscore the industrial potential of kombucha-derived cellulose producers and present a strategy for optimizing bacterial cellulose yield in large-scale applications.},
}

Cellulose/biosynthesis/metabolism
Fermentation
Biopolymers/biosynthesis/metabolism
*Bacteria/metabolism/classification/genetics/isolation & purification
*Microbiota
*Kombucha Tea/microbiology
Yeasts/metabolism/classification/genetics/isolation & purification
Ethanol/metabolism
High-Throughput Nucleotide Sequencing
Phylogeny
Acetobacteraceae/metabolism/isolation & purification

@article {pmid41161318,
year = {2025},
author = {Balmand, S and Rivard, C and Peignier, S and Santarella-Mellwig, R and Ghanem-Debbache, M and Maire, J and Engl, T and Galvão Ferrarini, M and Dell'Aglio, E and Soriano-Saiz, B and Dalverny, C and La Padula, V and Turunen, P and Rahioui, I and Vallier, A and Vincent-Monégat, C and Vierne, B and Parisot, N and Condemine, G and Da Silva, P and Jaurand, X and Schwab, Y and Kaltenpoth, M and Heddi, A and Zaidman-Rémy, A},
title = {Bacterial tubular networks channel carbohydrates in insect endosymbiosis.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.10.001},
pmid = {41161318},
issn = {1097-4172},
abstract = {Symbiosis is widespread in nature and plays a fundamental role in organism adaptation and evolution. In nutritional endosymbiosis, host cells accommodate intracellular bacteria and act as a "metabolic factory," requiring extensive metabolic exchanges between host and endosymbiont. To investigate the mechanisms supporting these exchanges, we used the association between the bacterium Sodalis pierantonius and the insect Sitophilus spp. that thrives on an exclusive cereal diet. Volume electron microscopy uncovered that endosymbionts generate complex membranous tubular networks (tubenets) that connect bacteria and drastically increase their exchange surface with the host cytosol. In situ high spatial resolution chemical analysis indicated that tubenets are enriched in carbohydrates, which are the main substrate used by bacteria to generate nutrients for the host. Multiple membranous structures favoring nutrient absorption are described in multicellular organisms. This work demonstrates that bacteria have convergently evolved a similar "biostrategy" that enhances nutrient acquisition by increasing membrane interface.},
}

@article {pmid41160691,
year = {2025},
author = {Becker-Kerber, B and Brocks, JJ and Archilha, NL and Rodella, CB and Petkov, V and deAzevedo, ER and Pimentel, T and Garcia, R and Petts, D and Czas, J and Ardakani, OH and Chappaz, A and Albuquerque, Â and Ortega-Hernández, J and Lerosey-Aubril, R and Kipp, MA and Johnson, B and Thoury, M and Oliveira, CMA and Pimentel, HHLSM and Freitas, RO and Vicentin, FC and Borges, LGF and Almer, J and Park, JS and Polo, CC and Kerber, G and Del Mouro, L and Figueiredo, M and Prado, GMEM and Ahmed, S and Basei, MAS},
title = {The rise of lichens during the colonization of terrestrial environments.},
journal = {Science advances},
volume = {11},
number = {44},
pages = {eadw7879},
doi = {10.1126/sciadv.adw7879},
pmid = {41160691},
issn = {2375-2548},
mesh = {*Lichens/physiology ; *Fossils ; *Ecosystem ; Biological Evolution ; Brazil ; Symbiosis ; },
abstract = {The origin of terrestrial life and ecosystems fundamentally changed the biosphere. Lichens, symbiotic fungi-algae partnerships, are crucial to nutrient cycling and carbon fixation today, yet their evolutionary history during the evolution of terrestrial ecosystems remains unclear due to a scarce fossil record. We demonstrate that the enigmatic Devonian fossil Spongiophyton from Brazil captures one of the earliest and most widespread records of lichens. The presence of internal hyphae networks, algal cells, possible reproductive structures, calcium oxalate pseudomorphs, abundant nitrogenous compounds, and fossil lipid composition confirms that it was among the first widespread representatives of lichenized fungi in Earth's history. Spongiophyton abundance and wide paleogeographic distribution in Devonian successions reveal an ecologically prominent presence of lichens during the late stages of terrestrial colonization, just before the evolution of complex forest ecosystems.},
}

*Lichens/physiology
*Fossils
*Ecosystem
Biological Evolution
Brazil
Symbiosis

@article {pmid41160687,
year = {2025},
author = {Okada, K and Fujiwara, T and Hirooka, S and Kobayashi, Y and Onuma, R and Miyagishima, SY},
title = {The closed nutrient recycling system in the Paramecium-Chlorella photosymbiosis contributes to survival under oligotrophic conditions.},
journal = {Science advances},
volume = {11},
number = {44},
pages = {eadz0004},
doi = {10.1126/sciadv.adz0004},
pmid = {41160687},
issn = {2375-2548},
mesh = {*Symbiosis ; *Paramecium/physiology/metabolism ; *Chlorella/physiology/metabolism ; *Nutrients/metabolism ; Nitrogen/metabolism ; Light ; },
abstract = {Endosymbiotic relationships between a heterotrophic host and a unicellular algal endosymbiont are observed across many eukaryotic lineages. Although these relationships are prevalent in oligotrophic environments, how they function and provide an advantage under such conditions remains largely unknown. To address these issues, we examined the behavior of the ciliate Paramecium bursaria hosting Chlorella endosymbionts under nitrogen- and prey-depleted conditions. The Paramecium host survived for up to 5 weeks while maintaining the number of Chlorella endosymbionts, whereas aposymbiotic Paramecium and free-living Chlorella either died or bleached, respectively, under the same conditions. In the symbiotic state, the host continuously fed on the endosymbionts without excreting nitrogenous waste into the medium, while the remaining endosymbionts continued to proliferate using heterotrophic metabolites from the host and light energy. Thus, the cyclical farming of endosymbionts by the host maintains a high concentration of nutrients within the closed system, providing a selective advantage in oligotrophic environments.},
}

*Symbiosis
*Paramecium/physiology/metabolism
*Chlorella/physiology/metabolism
*Nutrients/metabolism
Nitrogen/metabolism
Light

@article {pmid41160089,
year = {2025},
author = {Abuzahrah, SS},
title = {The microbiome of marine sponges located on the Saudi Arabia coast of the Red sea using high-throughput 16S amplicon sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {160},
pmid = {41160089},
issn = {2191-0855},
support = {PROJECT NO.: CRP/SAU24-02//International Centre for Genetic Engineering and Biotechnology (ICGEB)/ ; },
abstract = {Marine sponges (Porifera) from the Red Sea host diverse microbial communities that are integral to sponge health, nutrient cycling, and ecological resilience. Using high-throughput 16S rRNA amplicon sequencing, we characterized the bacterial diversity and functional potential across several Red Sea sponge species. Our findings revealed that these microbiomes are dominated by Alphaproteobacteria, Gammaproteobacteria, and Roseobacteraceae, with notable contributions from bacterial taxa involved in nitrogen fixation, organic matter degradation, and antimicrobial compound production. Functional predictions indicate that these symbionts support sponge nutrition, defense, and adaptation to the extreme Red Sea environment, including high salinity and temperature. Compared to sponge microbiomes from other marine regions, the Red Sea communities display unique taxonomic compositions and enhanced metabolic and defensive capacities. This highlights the essential ecological roles and potential biotechnological applications of these symbiotic assemblages. Our study underscores the significance of exploring sponge-associated microbiomes in understudied and extreme marine ecosystems. These results provide a foundation for future bioprospecting and work on adaptive mechanisms, emphasizing the value of Red Sea sponges and their microbiota for marine biotechnology and ecosystem resilience.},
}

@article {pmid41159495,
year = {2025},
author = {Kurimoto, SI and Nishie, K and Kubota, T},
title = {Absolute Configuration of Symbiodinolactone A.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01163},
pmid = {41159495},
issn = {1520-6025},
abstract = {The absolute configurations at five stereogenic centers in symbiodinolactone A, a 12-membered macrolide isolated from the symbiotic marine dinoflagellate Symbiodinium sp. associated with an acoelomorpha Amphiscolops sp., were determined to be 7R,11R,12R,13R,14R. A combination of different techniques was applied in this regard such as Rychnovsky's method, Kishi's universal NMR databases, the modified Mosher's method, and comparison of the NMR data of the bis(S)-MTPA ester of a degradation product of symbiodinolactone A with those of synthesized reference compounds. In addition, symbiodinolactone A was found to exhibit cytotoxicity against L1210 murine leukemia cells.},
}

@article {pmid41159488,
year = {2025},
author = {Ge, X and Li, N and Zhang, J and Fan, X and Chen, L and Zhao, N and Ren, A},
title = {Epichloë endophyte-infected Achnatherum sibiricum and neighbouring non-host grasses exhibit associational resistance to soil-borne diseases.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70112},
pmid = {41159488},
issn = {1438-8677},
support = {32271586//National Natural Science Foundation of China/ ; },
abstract = {Grasses and Epichloë endophytes often form mutualistic symbiotic defence systems. Studies have shown Epichloë endophytes improve resistance of host plants to airborne diseases. However, whether endophytes affect soil-borne disease resistance of host or neighbouring non-host plants remains unclear. We used endophyte-infected (EI) and endophyte-free (EF) Achnatherum sibiricum as host grass, Leymus chinensis as non-host grass, and Rhizoctonia solani as pathogen to explore the effects of endophyte infection on disease resistance of host and neighbouring non-host grasses. To clarify the contribution of root exudates to disease resistance of the non-host grass, three different root separation methods were employed between host and non-host plants: plastic barrier (PB), nylon mesh barrier (NL, allowing root exudates to pass through), or no barrier (NB). Epichloë endophytes decreased the disease index (DI) of the host A. sibiricum and reduced pathogen abundance in both host roots and soil. The DI of L. chinensis was affected by the interaction between root separation and endophyte infection. Under NL and NB treatments, the DI of L. chinensis with an EI neighbour was significantly lower than that with an EF neighbour, indicating that endophytic fungi can alleviate disease in non-host plants by influencing root exudates. Additionally, endophytic fungi increased the content of total phenolic compounds and salicylic acid in L. chinensis through activation of host root exudates, which could be one reason for the reduced DI of L. chinensis. Upon analysing root exudate components of the host, we found 2,4-di-tert-butylphenol (DTBP) and dibutyl phthalate (DBP) were the main antifungal compounds mediated by endophyte infection. Epichloë endophytes improved soil-borne disease resistance of the host and enhanced resistance of the neighbouring non-host grass through host root exudates; overall, host and non-host plants showed "associational resistance" to soil-borne diseases. This study highlights that Epichloë endophytes could potentially serve as efficient biological control agents against R. solani-associated diseases in grassland communities.},
}

@article {pmid41158803,
year = {2025},
author = {Totleben, L and Thomas, J and Austin, D},
title = {Drug-mediated disruption of the aging gut microbiota and mucosal immune system.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1603847},
pmid = {41158803},
issn = {2673-6217},
abstract = {The human gut microbiota is comprised predominantly of bacteria, and also includes archaea, fungi, and viruses. The gastrointestinal epithelium, mucosal barrier, and mucosal immune system balance protection against infection at mucosal entry points with symbiosis and tolerance to non-harmful organisms and antigens. Aging is associated with notable changes in both gut microbiota and mucosal immunity, including reduced microbial diversity, increased proportion of pathobionts relative to commensals, immunosenescence, and chronic inflammation. These changes may disrupt gastrointestinal function and homeostasis and increase susceptibility to infection and inflammatory conditions. Multiple drug classes are also associated with disruption of the gut microbiota and mucosal immunity, including antibacterials, proton pump inhibitors (PPIs), metformin, and steroidal and non-steroidal anti-inflammatory agents. This review describes the mechanisms by which these drugs affect the gut microbiota and mucosal immunity to provide perspective of the concurrent effects of drugs and age-related changes.},
}

@article {pmid41158770,
year = {2025},
author = {Peng, Y and Huang, D and Li, J and Sun, X and Zhang, Q and Zhang, R and Yang, R and Li, B and Kong, T and Xiong, Z and Huang, Y and Chang, Z and Su, Y and Shang, Y and Ghani, MU and Wang, Y and Sun, W},
title = {Investigation of the role of sulfide oxidation in the gill-associated microbiota of freshwater mussel Limnoperna fortunei.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671425},
pmid = {41158770},
issn = {1664-302X},
abstract = {INTRODUCTION: Limnoperna fortunei is a notable invasive freshwater species, altering structure and function of natural and engineered aquatic ecosystems. The host-associated microbiomes play a critical role in the survival and thriving of L. fortunei, with the gill-associated microbiomes being particularly significant due to their involvement in filter feeding, nutrient metabolism, and symbiosis. However, research on microbiomes associated with L. fortunei remains limited, and studies specifically focusing on gill-associated microbiota are scarce, leaving a significant gap in our understanding of their ecological roles.

METHODS: In this study, gill-associated bacterial communities of the L. fortunei were compared with their surrounding water microbial populations in the largest water diversion projects (the Middle Route of the South-to-North Water Diversion Project) to elucidate their environmental adaptations and potential contribution to their hosts. Analyses included assessing bacterial diversity and composition, conducting Neutral Community Model (NCM) analysis to explore community assembly processes, constructing an environmental-microbial co-occurrence network to identify key environmental factors, and performing metagenomic analysis of gill samples to investigate functional genes.

RESULTS: Significant variations were observed in bacterial diversity and composition between gills and surrounding water. Sulfur oxidizing bacteria Pirellula, SM1A02, and Roseomonas were significantly enriched in gill-associated microbiota. Neutral community model (NCM) analysis unveiled that the assembly of gill microbial communities was primarily governed by stochastic processes, constrained by determined processes. Moreover, environmental-microbial co-occurrence network identified reduced sulfur as the key factor shaping the composition of bacterial communities. Metagenomic binning of gill samples further revealed that metagenome assembled genomes associated with Pirellula within the phylum Planctomycetota contained functional genes related to sulfide oxidation and resistant to oxidative stress.

DISCUSSION: This study provides systematic insights into the microbial community diversity, assembly patterns, and functional characteristics of L. fortunei gill-asscociated microbiota, contributing to a mechanistic understanding of their ecological roles.},
}

@article {pmid41158324,
year = {2025},
author = {Fatemi, S and Kriefall, NG and Yogi, D and Weber, D and Hynson, NA and Medeiros, MCI and Sadowski, P and Amend, AS},
title = {Microbial composition and function are nested and shaped by food web topologies.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf175},
pmid = {41158324},
issn = {2730-6151},
abstract = {Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.},
}

@article {pmid41157958,
year = {2025},
author = {Stillson, PT and Sim, SB and Corpuz, RL and Ravenscraft, A},
title = {Symbiont Gene Expression Predicts Insect Host's Response to High Temperatures.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70154},
doi = {10.1111/mec.70154},
pmid = {41157958},
issn = {1365-294X},
support = {0201-88888-002-000D//Agricultural Research Service/ ; 0201-88888-003-000D//Agricultural Research Service/ ; 2040-22430-028-000-D//Agricultural Research Service/ ; 2019-67013-29407//National Institute of Food and Agriculture/ ; 2023-67013-39897//National Institute of Food and Agriculture/ ; 2024-67012-43746//National Institute of Food and Agriculture/ ; 2146512//National Science Foundation/ ; //University of Texas at Arlington/ ; },
abstract = {Microbial symbionts play crucial roles in host nutrition, defence, and detoxification. However, host-symbiont interactions are context-dependent, and environmental stressors can disrupt these benefits. Diverse hosts, including corals, insects and leguminous plants, have been shown to suffer under thermal stress due to the negative impact of high temperatures on their symbionts. This failure is often linked to a symbiont's poor transcriptional regulation of heat shock genes, causing vulnerability at high temperatures. In the bug-Caballeronia model system, insect performance at elevated temperatures varies based on the hosted symbiont species. Here, we explore the underlying mechanisms that drive this variation using comparative metatranscriptomics and two symbionts with contrasting host outcomes at high temperatures. We evaluated both host and symbiont transcriptional responses to elevated temperature, testing the hypothesis that symbionts conferring improved host outcomes at high temperatures will have more upregulated heat shock genes under thermal stress compared to those conferring worse host outcomes. Our findings reveal that host transcription did not change with different symbionts but rather only at different temperatures. Furthermore, symbionts had distinct gene expression profiles across temperatures. At 36°C, the heat-resistant symbiont not only increased expression of heat shock genes but surprisingly upregulated flagellar genes, which are normally turned off during symbiosis. This suggests that symbiont, not host, transcription underlies host benefits at low versus high temperatures and ultimately furthers our understanding of context dependence in the outcomes of symbiotic associations.},
}

@article {pmid41157763,
year = {2025},
author = {Zhuang, H and Tang, X and Ning, Z and Zhou, C and Zhao, Q and Wang, H and Xing, Y and Zhang, A},
title = {The Impact of Reduced Nitrogen Fertilizer Application and Arbuscular mycorrhizal fungi Inoculation on Nitrogen Utilization in Intercropped Areca catechu L. and Vanilla planifolia Andrews.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/plants14203207},
pmid = {41157763},
issn = {2223-7747},
support = {322RC779//Hainan Provincial Natural Science Foundation of China/ ; CATASCXTD202510//Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center/ ; 32360796//the National Natural Science Foundation of China/ ; 1630042025014//the Central Public-interest Scientific Institution Basal Research fund/ ; ZDYF2025XDNY087//Science and Technology special fund of Hainan Province/ ; },
abstract = {Areca (Areca catechu L.) is an important economic crop in tropical regions, but excessive nitrogen application leads to low nitrogen fertilizer utilization efficiency (approximately 30%). Vanilla (Vanilla planifolia Andrews) can be intercropped with areca to enhance land use efficiency. However, the impact of combined nitrogen reduction and Arbuscular mycorrhizal fungi (AMF) inoculation on the intercropping system of areca and vanilla remains unclear. This study examined the impact of nitrogen reduction (at levels of conventional fertilization, a 30% reduction and a 60% reduction) and the inoculation of AMF on the photosynthetic characteristics, physiological metabolism, and nitrogen utilization within an areca and vanilla intercropping system, employing a two-factor experimental design. The nitrogen reduction significantly inhibited SPAD value (chlorophyll content) (decreased by 46.21%), net photosynthesis (Pn) (decreased by 71.13%), and transpiration rate (Tr) (decreased by 44.34%) of vanilla without inoculation of AMF, but had little effect on the photosynthesis of areca. Inoculation with AMF, notably Funneliformis mosseae, alleviated the adverse effects of reduced nitrogen on vanilla. The net photosynthesis and intercellular CO2 concentration (Ci) significantly increased by 76.23% and 69.48%, respectively. Additionally, the nitrogen uptake efficiency of the areca was improved, with root vitality increasing by 39.96%. Additionally, AMF enhanced the activities of acid phosphatase (ACP) (increased by 38.86% in vanilla) and nitrate reductase (NR) (increased by 53.77% in areca), promoting soil mineral nutrient activation and nitrogen metabolism. The nitrogen reduction combined with AMF inoculation can improve the nitrogen use efficiency of the areca and vanilla intercropping system, revealing its synergistic mechanism in the tropical intercropping system.},
}

@article {pmid41157245,
year = {2025},
author = {Breivik, TJ and Gjermo, P and Opstad, PK and Murison, R and von Hörsten, S and Fristad, I},
title = {Brain Structures, Circuits, and Networks Involved in Immune Regulation, Periodontal Health, and Disease.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/life15101572},
pmid = {41157245},
issn = {2075-1729},
abstract = {The interaction between microorganisms in the dental microfilm (plaque) at the gingival margin, the immune system, and the brain is vital for gingival health. The brain constantly receives information regarding microbial composition and inflammation status through afferent nerves and the bloodstream. It modulates immune responses via efferent nerves and hormonal systems to maintain homeostasis. This relationship determines whether the gingiva remains healthy or develops into gingivitis (non-destructive inflammation) or periodontitis (a destructive condition), collectively referred to as periodontal disease. Factors associated with severe periodontitis heighten the responsiveness of this homeostatic system, diminishing the adaptive immune system's defence against symbiotic microorganisms with pathogenic properties, known as pathobionts. This leads to excessive innate immune system activation, effectively preventing infection but damaging the periodontium. Consequently, investigating the microbiota-brain axis is vital for understanding its impact on periodontal health and disease. Herein, we examine recent advancements in how the defence against pathobionts is organised within the brain, and how it regulates and adapts the pro-inflammatory and anti-inflammatory immune balance, controlling microbiota composition. It also discussed how pathobionts and emotional stress can trigger neurodegenerative diseases, and how inadequate coping strategies for managing daily stress and shift work can disrupt brain circuits linked to immune regulation, weakening the adaptive immune response against pathobionts.},
}

@article {pmid41156846,
year = {2025},
author = {Liu, Y and Shang, Y and Wang, X and Li, X and Yu, Z and Zeng, Z and Chen, Z and Wang, L and Xiang, T and Huang, X},
title = {Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102387},
pmid = {41156846},
issn = {2076-2607},
support = {31872181//National Natural Science Foundation of China/ ; 2021QDL062//Research Start-up Funds from the Hangzhou Normal University/ ; 2025JCXK01//Interdisciplinary Research Project of Hangzhou Normal University/ ; },
abstract = {In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.},
}

@article {pmid41156827,
year = {2025},
author = {Yüksel, E and Lahlali, R and Barış, A and Sameeullah, M and Ulaş, F and Koca, AS and Ait Barka, E and İmren, M and Dababat, A},
title = {Entomopathogenic Nematodes and Bioactive Compounds of Their Bacterial Endosymbionts Act Synergistically in Combination with Spinosad to Kill Phthorimaea operculella (Zeller, 1873) (Lepidoptera: Gelechiidae), a Serious Threat to Food Security.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102368},
pmid = {41156827},
issn = {2076-2607},
support = {FAPD-2025-15290//Erciyes University Scientific Research Projects Coordination Unit/ ; },
abstract = {As a staple food, potato (Solanum tuberosum L.) (Solanaceae) is one of the most produced food crops to ensure food security. The potato tuber moth (PTM), Phthorimaea operculella (Zeller, 1873) (Lepidoptera: Gelechiidae), is a major pest of potato, damaging both the growing and storage processes. In recent years, green pest control strategies have been gaining importance to reduce the adverse effects of chemicals and protect the environment. Entomopathogenic nematodes (EPNs) and their bacterial endosymbionts (Xenorhabdus and Photorhabdus spp.) have been one of the top topics studied in sustainable pest control approaches. In the present study, the two most common EPN species, Steinernema feltiae and Heterorhabditis bacteriophora, and their bacterial associates, Xenorhabdus bovienii and Photorhabdus luminescens subsp. kayaii were evaluated against PTM larvae separately and in combination with spinosad. The survival rates of infective juveniles (IJs) of EPNs were over 92% after 72 h of direct exposure to spinosad. Co-application of EPNs and bioactive compounds (BACs) of endosymbiotic bacteria with spinosad induced synergistic interactions and achieved the maximum mortality (100%) in PTM larvae 48 h post-treatment. Spinosad and BAC combinations were highly efficient in controlling the PTM larvae and provided LT50 values below 23.0 h. Gas chromatography mass spectrometry (GC-MS) analysis identified 29 compounds in total, 20 of which belonged to P. luminescens subsp. kayaii. The results indicate that the integration of EPNs and BACs of endosymbiotic bacteria with spinosad presents a synergistic interaction and enhances pest control efficacy.},
}

@article {pmid41156804,
year = {2025},
author = {Yang, Q and Dong, P and Chen, M and Wang, H and Wang, L and Yuan, J and Hu, C and Liu, Z and Li, Y and Fan, Q},
title = {Soybean-Bupleurum Rotation System Can Optimize Rhizosphere Soil Microbial Community via Impacting Soil Properties and Enzyme Activities During Bupleurum Seedling Stage.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102346},
pmid = {41156804},
issn = {2076-2607},
support = {the Youth Fund of the Shanxi Provincial Basic Research Program, Grant No.202203021212442;//Mengni Chen/ ; Sub-project of the Key Science and Technology Special Program with a "Revealing the Rank and Appointing the Leader" Approach in Shanxi Province, No. 202301140601014-01A//Hui Wang/ ; Surface project funded by the Shanxi Provincial Department of Science and Technology, No. 202303021211103//Hui Wang/ ; Scientific Research and Development Fund of the Cotton Research Institute, Shanxi Agricultural University, No.SJJCX2023-03//Peng Dong/ ; },
abstract = {To avoid continuous cropping problems with Bupleurum, we screened suitable preceding crops for rotation with Bupleurum through different crop rotations. Therefore, the objective of this study was to find out the relationships between microbial community characteristics, soil properties, and enzyme activities under four different rotation patterns, including fallow-Bupleurum (CK), maize-Bupleurum (M), soybean-Bupleurum (So), and sunflower-Bupleurum (Su). Results indicated that under all four rotation patterns, So treatment significantly enhanced soil nutrients and enzyme activities compared to CK. So not only optimized the composition of soil bacterial and fungal communities but markedly enhanced microbial α diversity. Additionally, So exhibited high similarity in bacterial and fungal community composition with M, and featured complex symbiotic relationships within the soil microbial network. While no clear discrepancies were detected in the abundance of the top twenty metabolic pathways in the predictive functions of bacterial and fungal communities across four rotation patterns, the metabolic pathway function MET-SAM-PWY (methionine synthesis pathway) in bacterial communities and the metabolic pathway function VALSYN-PWY (valine synthesis pathway) in fungal communities were particularly prominent under the So rotation pattern. RDA suggested that soil properties (available phosphorus and pH) and enzyme activities (sucrase and alkaline phosphatase activities) were the driving forces for bacterial community composition, while soil properties (soil organic matter and available potassium) and enzyme activities (sucrase and catalase activities) regulated fungal community composition. Hence, the soybean-Bupleurum rotation pattern represents a cultivation practice more beneficial for the sustainable development of the bupleurum industry, which can significantly improve soil fertility and the micro-ecological environment.},
}

@article {pmid41156693,
year = {2025},
author = {Aranda-Pérez, J and Sánchez-Aguilar, MDC and Cutiño-Gobea, AM and Pérez-Montaño, F and Medina, C},
title = {Cyclic di-GMP Modulation of Quorum Sensing and Its Impact on Type VI Secretion System Function in Sinorhizobium fredii.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102232},
pmid = {41156693},
issn = {2076-2607},
support = {PID2020-118279RA-I00//Spanish Minister of Science, Innovation and Universities (MICIU)/ ; PPIT2024-31787//FEDER program/ ; },
abstract = {Effective rhizobium-legume symbiosis depends on multiple molecular signaling pathways, integrating not only classical nodulation factors and surface polysaccharides but also diverse protein secretion systems. Among them, the Type VI Secretion System (T6SS) has emerged as a key player, due to its dual roles in interbacterial competition and interactions with eukaryotic hosts, though its contribution to symbiosis remains unclear. Key regulatory messengers, including the main autoinducer of the quorum sensing (QS) systems, the N-acyl homoserine lactones (AHLs), and the second messenger cyclic di-GMP (c-di-GMP), modulate the transition between motility and biofilm formation, especially in the context of bacteria interacting with eukaryotes, including rhizobia. While c-di-GMP's impact on exopolysaccharide production in these organisms is well established, its influence on protein secretion systems, particularly in conjunction with QS, is largely unexplored. To contribute to the study of such interplay, we artificially increased intracellular c-di-GMP levels by overexpressing a heterologous diguanylate cyclase in three Sinorhizobium fredii strains of agronomic relevance. This engineering revealed strain-specific outcomes, since elevated c-di-GMP enhanced biofilm development in two strains, but reduced it in another. Furthermore, using β-galactosidase expression assays, we confirmed that both high c-di-GMP and/or AHL concentrations contribute to the transcriptional activation of T6SS. These results demonstrate a direct regulatory link between c-di-GMP, QS signals, and T6SS expression, shedding light on the multilayered control mechanisms that structure beneficial rhizobia-plant interactions.},
}

@article {pmid41156619,
year = {2025},
author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB},
title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101008},
pmid = {41156619},
issn = {2076-0817},
mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; },
abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.},
}

Animals
Kazakhstan
*Metagenomics/methods
*Ixodidae/microbiology
Male
Female
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Cattle
*Microbiota
*Metagenome
DNA, Bacterial/genetics

@article {pmid41155435,
year = {2025},
author = {Kuprin, A and Baklanova, V},
title = {The Microbiome as a Protagonist of Xylophagous Insects in Adaptation to Environmental Conditions and Climate Change.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010143},
pmid = {41155435},
issn = {1422-0067},
mesh = {Animals ; *Climate Change ; *Insecta/microbiology/physiology ; *Microbiota ; *Adaptation, Physiological ; Ecosystem ; Symbiosis ; Forests ; *Gastrointestinal Microbiome ; },
abstract = {Xylophagous insects represent a diverse group of species whose life cycles are trophically associated with wood at various stages of decomposition. In forest ecosystems, they play a pivotal role in wood degradation and biogeochemical nutrient cycling. Their remarkable adaptation to feeding on structurally complex and nutrient-poor woody substrates has been largely mediated by long-term symbiotic interactions with gut microbiota. This review synthesizes current knowledge on the molecular and ecological mechanisms underlying insect-microbiota interactions, with particular attention paid to the impact of environmental stressors-including elevated temperature, shifts in moisture regimes, and pollution-on microbial community structure and host adaptive responses. We critically evaluate the strength of evidence linking climate-driven microbiome shifts to functional consequences for the host and the ecosystem. The ecological implications of microbiota restructuring, such as impaired wood decomposition, decreased disease resistance, facilitation of xylophagous species spread, and alterations in key biotic interactions within forest biocenoses, are discussed. Particular emphasis is placed on the integration of multi-omics technologies and functional assays for a deeper, mechanistic understanding of microbiota roles. We also assess the potential and limitations of microbiome-based approaches for insect population management, with the overall goal of maintaining and enhancing the resilience of forest ecosystems under ongoing climate change.},
}

Animals
*Climate Change
*Insecta/microbiology/physiology
*Microbiota
*Adaptation, Physiological
Ecosystem
Symbiosis
Forests
*Gastrointestinal Microbiome

@article {pmid41154803,
year = {2025},
author = {Zhou, Y and Tian, T and Ji, J and Tan, L and Peng, K and Liu, Z and Zhao, W and Wang, C and Liu, F and Zhang, X},
title = {Dissecting the Functional Interplay Between Heme Oxygenase LjHO1 and Leghemoglobins in Lotus japonicus Nodules.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101401},
pmid = {41154803},
issn = {2079-7737},
support = {2308085QC75//Anhui Provincial Natural Science Foundation/ ; 2023AH052250//Major Natural Science Foundation of the Anhui Educational Committee/ ; 2022BSK023, 2022BSK030//Doctoral Startup Research Fund/ ; 2024XHX216//the industry-funded project/ ; },
abstract = {Heme metabolism is crucial for the function and longevity of legume nodules, with leghemoglobins (Lbs) serving as the primary heme sink and heme oxygenase (HO) mediating heme degradation. However, the precise functional relationship between HO and Lbs remains unclear. Here, we show that Lotus japonicus HO1 (LjHO1) is strongly induced in early-stage Lb-deficient nodules, but its expression gradually decreases during nodule development. Subcellular localization analysis revealed that LjHO1 is plastid-localized in uninfected cells of lb123 mutant nodules, consistent with its localization in wild-type nodules. Using CRISPR/Cas9, we generated a quadruple ho1lb123 mutant lacking LjHO1 and all three Lb isoforms in L. japonicus. Phenotypic analyses revealed that Lbs deficiency predominantly impairs nitrogen fixation, whereas loss of LjHO1 further reduces nodule formation. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis revealed that loss of Lbs strongly decreased heme accumulation, whereas LjHO1 deficiency slightly increased heme levels in nodules. These results demonstrate that Lbs are essential for heme accumulation and nitrogen fixation, while LjHO1 fine-tunes heme turnover, highlighting their complementary roles in maintaining nodule heme homeostasis and symbiotic efficiency.},
}

@article {pmid41154716,
year = {2025},
author = {Kumru, E and Korkmaz, AF and Ekinci, F and Aydoğan, A and Güzel, MS and Akata, I},
title = {Deep Ensemble Learning and Explainable AI for Multi-Class Classification of Earthstar Fungal Species.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101313},
pmid = {41154716},
issn = {2079-7737},
abstract = {The current study presents a multi-class, image-based classification of eight morphologically similar macroscopic Earthstar fungal species (Astraeus hygrometricus, Geastrum coronatum, G. elegans, G. fimbriatum, G. quadrifidum, G. rufescens, G. triplex, and Myriostoma coliforme) using deep learning and explainable artificial intelligence (XAI) techniques. For the first time in the literature, these species are evaluated together, providing a highly challenging dataset due to significant visual overlap. Eight different convolutional neural network (CNN) and transformer-based architectures were employed, including EfficientNetV2-M, DenseNet121, MaxViT-S, DeiT, RegNetY-8GF, MobileNetV3, EfficientNet-B3, and MnasNet. The accuracy scores of these models ranged from 86.16% to 96.23%, with EfficientNet-B3 achieving the best individual performance. To enhance interpretability, Grad-CAM and Score-CAM methods were utilised to visualise the rationale behind each classification decision. A key novelty of this study is the design of two hybrid ensemble models: EfficientNet-B3 + DeiT and DenseNet121 + MaxViT-S. These ensembles further improved classification stability, reaching 93.71% and 93.08% accuracy, respectively. Based on metric-based evaluation, the EfficientNet-B3 + DeiT model delivered the most balanced performance, with 93.83% precision, 93.72% recall, 93.73% F1-score, 99.10% specificity, a log loss of 0.2292, and an MCC of 0.9282. Moreover, this modeling approach holds potential for monitoring symbiotic fungal species in agricultural ecosystems and supporting sustainable production strategies. This research contributes to the literature by introducing a novel framework that simultaneously emphasises classification accuracy and model interpretability in fungal taxonomy. The proposed method successfully classified morphologically similar puffball species with high accuracy, while explainable AI techniques revealed biologically meaningful insights. All evaluation metrics were computed exclusively on a 10% independent test set that was entirely separate from the training and validation phases. Future work will focus on expanding the dataset with samples from diverse ecological regions and testing the method under field conditions.},
}

@article {pmid41154033,
year = {2025},
author = {Gantner, M and Piotrowska, A and Kostyra, E and Hallmann, E and Ponder, A and Sionek, B and Neffe-Skocińska, K},
title = {Influence of Herbal Additives on the Physicochemical, Microbiological, Polyphenolic, and Sensory Profile of Green Tea-Based Kombucha.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/foods14203497},
pmid = {41154033},
issn = {2304-8158},
abstract = {Kombucha is a functional beverage with growing popularity due to its health-promoting properties. This study aimed to evaluate the impact of herbal infusions on the quality of green tea-based kombucha. Four variants were prepared: a control (K1) and three experimental samples combining 70% green tea with 30% (v/v) Mentha spicata (K2), Hibiscus sabdariffa (K3), or Clitoria ternatea (K4). Fermentation lasted four days at 24 ± 1 °C. Physicochemical parameters, polyphenol profile (HPLC), microbiological safety, and sensory quality were assessed using QDA and electronic tongue analysis. K3 showed the highest polyphenol content (291 mg/L), especially catechins. K4 achieved the highest overall sensory quality due to its fruity aroma, balanced sweet-sour taste, and favorable microbiological profile. K2 had the lowest caffeine content (114 mg/L) and a distinct minty flavor. All samples were microbiologically safe. Herbal additives influenced fermentative microbiota: K3 had fewer acetic acid bacteria, while K4 had the highest lactic acid bacteria count. Electronic tongue analysis confirmed sensory panel results and revealed distinct taste profiles among the variants. Herbal infusions significantly enhance the nutritional and sensory properties of kombucha. Their use offers a promising strategy for developing functional beverages with tailored characteristics.},
}

@article {pmid41153433,
year = {2025},
author = {Lalawmpuii, K and Jacob, SS and Tolenkhomba, TC and Behera, P and Lalmuanpuia, J and Lalremsanga, HT and Lalrintluanga, K and Lalchhandama, C and Biakzuala, L and Lalrinkima, H},
title = {Mitochondrial and Nuclear DNA Analyses of Rhipicephalus microplus from Mizoram, Northeast India: Insights into Genetic Diversity and Endosymbiont.},
journal = {Genes},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/genes16101216},
pmid = {41153433},
issn = {2073-4425},
mesh = {Animals ; India ; *Rhipicephalus/genetics/microbiology/classification ; Phylogeny ; *DNA, Mitochondrial/genetics ; *Genetic Variation ; Haplotypes ; *Symbiosis/genetics ; RNA, Ribosomal, 16S/genetics ; Cell Nucleus/genetics ; },
abstract = {Background/Objectives: In this study, we conducted molecular identification of R.microplus and explored the genetic diversity of R. microplus for the first time in Mizoram, a Northeastern Hill (NEH) state of India bordering Myanmar. Methods: To assess genetic variation and evolutionary relationships, we employed phylogenetic analyses, genetic divergence metrics, and haplotype network construction based on mitochondrial (COX1 and 16S rDNA) and nuclear (ITS-2 and 18S rDNA) markers. Additionally, multivariate Principal Coordinate Analysis (PCoA) was used to visualize genetic differentiation among R. microplus populations. Results: Our analyses indicated that populations of R. microplus sensu lato from India, Bangladesh, and Pakistan form a closely related matrilineal lineage distinct from R. microplus sensu stricto, clustering within clade C of the COX1-based phylogeny. Globally, 24 COX1 haplotypes were recovered, with 1 haplotype identified in India. The Mizoram population exhibited a single 16S rDNA haplotype; however, intraspecific divergence was evident across India, with seven matrilineal haplotypes detected and nineteen globally. Further, five haplotypes were identified within R. microplus using the ITS-2 marker, while five haplotypes were observed within the Rhipicephalus genus using the 18S rDNA marker. Moreover, this study revealed the presence of Coxiella-like endosymbionts in 95% of the tick specimens analyzed. Conclusions: This study fills a critical knowledge gap by providing the first molecular documentation of tick diversity in Mizoram, a strategic region along the Indo-Myanmar border, and offers novel insights into the phylogeography and symbiotic associations of R. microplus and related tick taxa.},
}

Animals
India
*Rhipicephalus/genetics/microbiology/classification
Phylogeny
*DNA, Mitochondrial/genetics
*Genetic Variation
Haplotypes
*Symbiosis/genetics
RNA, Ribosomal, 16S/genetics
Cell Nucleus/genetics

@article {pmid41152548,
year = {2025},
author = {Guedán, ML and Smykala, M and Käfer, S and Mueller, JS and Lohmus, K and Pieck, D and Engelen, B and Gerlach, G},
title = {Seasonal and spatial dynamics of the microbiome of the polychaete Lanice conchilega in the Wadden Sea.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37731},
pmid = {41152548},
issn = {2045-2322},
mesh = {Animals ; *Polychaeta/microbiology ; *Seasons ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Ecosystem ; Germany ; Oceans and Seas ; Geologic Sediments/microbiology ; },
abstract = {Rapidly changing abiotic conditions, particularly temperature variations, pose adaptation challenges to many animal communities across the globe. Lanice conchilega, a key polychaete in the ecosystem of the German Wadden Sea, faces an increasing threat hampered by its limited mobility. The microbiome can alleviate stress, alter local environmental conditions, and provide new metabolic capabilities, contributing to host adaptation. To understand the potential roles of the microbiome of L. conchilega, we analysed a broad sample set via 16 S rRNA gene amplicon sequencing. We compared the bacterial composition of the microbiome of L. conchilega with that of the surrounding sediment, and the effect of seasonality, zonation, tidal, and diurnal cycles. Our findings reveal a set of ASVs exclusive to the microbiome of L. conchilega. Community composition was mostly shaped by seasonality, slightly influenced by zonation, day/night cycles, and tides. Notably, Endozoicomonas ASVs were found only in the L. conchilega microbiome and were particularly abundant during summer. These bacteria, known for their symbiotic relationships, broad metabolic capabilities, and linked to heat resistance in corals, are predicted to contribute unique metabolic functions in L. conchilega. This work provides novel insights into the host-microbiome relationship of L. conchilega and highlights the potential role of symbionts in the environmental adaptation of these and similar animals.},
}

Animals
*Polychaeta/microbiology
*Seasons
*Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Ecosystem
Germany
Oceans and Seas
Geologic Sediments/microbiology

@article {pmid41151998,
year = {2025},
author = {Li, D and Wu, J and Zeng, X and Xie, F and Lin, H and Chen, D and Wang, L and Li, Y},
title = {The Extracellular Loop2 domain of the rhizobia outer membrane protein MhOpa22 mediates symbiotic nodulation and nitrogen fixation.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf535},
pmid = {41151998},
issn = {1532-2548},
abstract = {The Mesorhizobium huakuii opacity protein (MhOpa22) is essential for effective nodulation and nitrogen fixation in rhizobium-legume symbiosis. Astragalus sinicus AsGLP1 interacts with MhOpa22, but the molecular mechanisms underlying the ability of MhOpa22 to mediate symbiosis remain elusive. This study demonstrated that the Loop2-3 domains of MhOpa22 interact with AsGLP1 in planta. Inoculating A. sinicus with different M. huakuii loop deletion mutants revealed that the Loop2 mutant gives rise to fewer root nodules and decreased nodule nitrogenase activity relative to inoculation with the wild-type strain. The Loop2 mutation also significantly affects ROS production and the coordinated expression of defense and symbiosis genes in host plant roots during early symbiosis. Furthermore, MhOpa22 was confirmed to be a membrane protein that exerts its function via outer membrane vesicles (OMVs). Taken together, these results provide molecular insights into the function of the outer membrane protein MhOpa22 and its critical extracellular Loop2 domain during symbiosis. MhOpa22 inhibits host defense responses through OMVs during early symbiosis and plays an essential role in rhizobial infection and nodule formation.},
}

@article {pmid41151337,
year = {2025},
author = {Yurdunkulu, A and Bulut, MA and Göçen, A},
title = {From academics to Aidemics: Unpacking the human-AI symbiosis in higher education.},
journal = {Acta psychologica},
volume = {261},
number = {},
pages = {105796},
doi = {10.1016/j.actpsy.2025.105796},
pmid = {41151337},
issn = {1873-6297},
abstract = {The integration of artificial intelligence (AI) into higher education is reshaping both academic roles and organizational practices. This transformation is not merely technical; it also introduces psychological and ethical tensions as academics negotiate new forms of work. This qualitative study advances the concept of Aidemics-academics who efficiently, ethically, and critically employ AI to enhance their professional practice-and examines how AI reconfigures intellectual tasks while challenging traditional academic identities. Drawing on semi-structured interviews with twenty academics (informed by five pilot interviews), we show that Aidemics engage in a symbiotic, human-in-the-loop relationship with AI: they exploit efficiencies for routine tasks, yet safeguard creative and critical work, actively auditing AI outputs and setting clear boundaries of use. Participants also surface structural concerns-framed as AI colonialism-about the potential of AI to entrench power asymmetries and epistemic inequities in global knowledge production. Key challenges include hallucinations, erosion of human agency, and unequal access to AI tools. We argue for policies and professional-development strategies that preserve human agency and ethical judgment while enabling responsible, explainable, and context-sensitive AI use. The findings specify the competencies of Aidemics and outline supports for balanced human-AI collaboration at individual and institutional levels.},
}

@article {pmid41150878,
year = {2025},
author = {Roces, F and Bollazzi, M},
title = {Nest Building in Leaf-Cutting Ants: Behavioral Mechanisms and Adaptive Value.},
journal = {Annual review of entomology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-ento-121423-013337},
pmid = {41150878},
issn = {1545-4487},
abstract = {Leaf-cutting ants, which comprise more than 50 species distributed from Patagonia to North America, build the largest nests among ants. Workers forage plant fragments to cultivate a symbiotic fungus inside underground chambers, which serves as the primary food source for the colony. While digging the nest, workers respond to local cues such as soil temperature, moisture, and CO2 levels, resulting in the emergence of a nest architecture that provides a proper environment for fungus growth. Leaf-cutting ants have species-specific nest architectures, which evolved from a basal design consisting of a vertical tunnel and a few interconnected chambers. Some species developed, in addition, architectural innovations aimed at the control of both hygiene and nest climate, including waste chambers, ventilatory turrets, and a nest thatch. A fine-tuned climate control is achieved by the relocation of fungus gardens within the nest following the workers' environmental preferences and by nesting plasticity.},
}