@article {pmid40680682,
year = {2025},
author = {Cheng, T and Zhao, J and Zhang, T and Ba, G and Fan, Q and Sun, Y and Zhang, G and Sadiq, FA and Sang, Y and Gao, J},
title = {Synthetic microbial community mimicking kefir for investigating community dynamics and interspecies interactions.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111345},
doi = {10.1016/j.ijfoodmicro.2025.111345},
pmid = {40680682},
issn = {1879-3460},
abstract = {Kefir grains serve as natural dairy starter cultures, surviving in high-altitude environments with low temperatures and limited oxygen, while maintaining robust fermentation capabilities. In this study, we reconstructed a synthetic microbial community (SMC) within the kefir microbial ecosystem and explored the strategies that keep this SMC stable and functioning within the complex environment. We investigated the interactions among kefir species by comparing their symbiotic capabilities, milk acidification properties, and fermentation profiles during growth in both individual cultures and co-cultures across various media. Additionally, to deepen our understanding of system-level responses within the SMC, we integrated metabolomics with pure culture techniques to elucidate the mechanisms that enable coexistence among SMC members. The composition of the SMC in fermented milk was determined through co-cultivation assessments and flavor profile analysis, which identified the key members as Lactobacillus kefiranofaciens CZ22, Lactococcus lactis CZ19, and Saccharomyces cerevisiae Y8. The fermented milk produced by SMC shared identical volatile compound profiles with traditional kefir milk, including seven alcohols, seven aldehydes, six ketones, five esters, two carboxylic acids, two ethers, one acyl compound, and five miscellaneous volatile compounds. Our findings revealed that the coexistence mechanism among these three species is based on cross-feeding interactions. Lc. lactis CZ19 provides L. kefiranofaciens CZ22 with amino acids such as tyrosine, proline, and arginine, promoting its growth. Moreover, S. cerevisiae Y8 supplies primary metabolic products, including purines, pyrimidines, and nucleotides, to L. kefiranofaciens CZ22, facilitating the coexistence of all three species. During the fermentation process of the SMC, L. kefiranofaciens CZ22 maintained high abundance and accelerated acidification and enhanced flavor volatiles in milk. The SMC we constructed effectively maintained the core kefir species and fermentation performance of kefir starter cultures, simplified the complex fermentation system and laid the groundwork for the modernization and improvement of the production process. This study systematically elucidates the coexistence strategies employed by synthetic microbial systems in fermented milk production, while enhancing our understanding of microbial interactions in traditional fermented foods.},
}

@article {pmid40680599,
year = {2025},
author = {Kim, J and Khan, M},
title = {Genome assembly of Diadegma fenestrale (Hymenoptera: Ichneumonidae), and genome integration of its symbiotic virus, DfIV.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104366},
doi = {10.1016/j.ibmb.2025.104366},
pmid = {40680599},
issn = {1879-0240},
abstract = {Diadegma fenestrale is a parasitic wasp of ecological and agricultural significance, regulating pest populations. However, limited genomic resources have hindered a deeper understanding of its biology and symbiotic interactions. This study presents a chromosome-level genome assembly of D. fenestrale using Nanopore and Illumina sequencing. The assembled 221.1 Mb genome comprises 68 scaffolds, including 11 at the chromosomal level, and exhibits high completeness with a BUSCO completeness score of 99.6%. A total of 13,544 protein-coding genes were predicted, with BUSCO assessment of the gene set indicating 97.5% completeness (single-copy: 96.8%, duplicated: 0.7%), 0.7% fragmented, and 1.8% missing genes. Comparative genomic analysis with closely related hymenopteran species provides new insights into genome evolution, including gene family expansion, contraction patterns, and chromosomal rearrangements. Additionally, this study examines DfIV, a symbiotic virus associated with D. fenestrale, identifying 62 genome segments integrated into the host genome. Most segments are present in one or two copies, while four segments exhibit three copies, suggesting a dynamic interaction between the virus and the host genome that may influence gene regulation and chromosomal stability. This study provides a comprehensive genomic resource for D. fenestrale, enhancing our understanding of its genomic architecture, evolutionary dynamics, and functional adaptations. The findings contribute to broader research on parasitoid wasps, and symbiotic virus-host interactions, with implications for biological pest control and evolutionary biology.},
}

@article {pmid40679585,
year = {2025},
author = {Liu, D and Chen, J and Luo, Y and Yan, S and Nan, H and Chen, X and Lin, Z and Jiang, L and Tang, H and Ma, H and Niu, Y and Fang, J and Cao, P and Yuan, L and Ma, X and Zhou, X and Lv, F and Dai, Y and Liu, H},
title = {Clinical features and fusion gene analysis of two Torque Teno Mini virus associated acute promyelocytic leukemia cases.},
journal = {Annals of hematology},
volume = {},
number = {},
pages = {},
pmid = {40679585},
issn = {1432-0584},
support = {2023013167//Langfang Science and Technology Research and Development Program/ ; 2023013167//Langfang Science and Technology Research and Development Program/ ; },
abstract = {Torque Teno Mini Virus (TTMV), a member of the Anelloviridae family, is a commensal component of the human virome. Since the initial identification of the TTMV::RARA fusion gene as a novel driver of acute promyelocytic leukemia (APL), 15 cases have been reported in retrospective studies. With advancements in diagnostic methods and increased awareness, the number of newly diagnosed cases has risen, and the clinical and molecular characteristics of TTMV::RARA-APL are becoming clearer. We systematically identified the clinical characteristics, fusion gene analysis, and treatment protocols of two pediatric APL patients harboring the TTMV::RARA fusion on this basis. While the detection of TTMV::RARA contributes to defining pathogenic fusion gene and MRD monitoring indicators in non-PML::RARA-APL cases, the precise pathogenic mechanisms of this ubiquitous symbiotic virus warrant further investigation.},
}

@article {pmid40677241,
year = {2025},
author = {T Prates, E and Demerdash, O and Shah, M and Rush, TA and Kalluri, UC and Jacobson, DA},
title = {Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {2782-2795},
pmid = {40677241},
issn = {2001-0370},
abstract = {Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.},
}

@article {pmid40677082,
year = {2025},
author = {Yin, HK and Zhao, YH and Xie, WY and Liu, ZP and Zhou, HP and Yang, ZX},
title = {[Effects of Long-term Corn Stover Return on Fungal Communities and Enzyme Activities in Brown Soil].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {7},
pages = {4699-4709},
doi = {10.13227/j.hjkx.202406205},
pmid = {40677082},
issn = {0250-3301},
mesh = {*Zea mays/growth & development ; *Soil Microbiology ; Soil/chemistry ; *Agriculture/methods ; Nitrogen/analysis ; Phosphorus/analysis ; *Fungi/classification/enzymology/growth & development ; Plant Stems ; Carbon/analysis ; Mycorrhizae ; },
abstract = {Based on a 31-year consecutive long-term positioning trial of stover return to field， including four different corn stover return methods： stover not returned to field （CK）， stover overgrown （CM）， stover crushed and directly returned to field （SC）， and stover mulched （SM）； the soil nutrient content， extracellular enzyme activity， fungal community structure， and mycorrhizal functional activity were comprehensively analyzed using high-throughput sequencing technology， FUNGuild functional prediction， and ecological network approach. We investigated the effects of different straw return modes on the nutrient content of brown soil farmland， analyzed the characteristics of soil extracellular enzymes and functional activities of fungal communities， and provided a theoretical basis for efficiently improving the soil fertility of brown soil farmland. The results showed that： ① Long-term different straw return treatments （SM， SC， and CM） significantly increased soil fertility， maize yield， and extracellular enzyme activities， and soil organic carbon （SOC）； total nitrogen （TN）； total phosphorus （TP）； total potassium （TK）； alkaline dissolved nitrogen （AN）； effective phosphorus （AP）； quick-acting potassium （AK）； cumulative yield of maize； and the contents of soil glucosidase （β-GC）， cellobiose hydrolase （CBH）， and dehydrogenase （DHA） contents were elevated from 17.0%-42.9%， 3.0%-50.0%， 2.3%-27.9%， 4.4%-11.5%， 11.2%-71.0%， 14.1%-320.8%， 17.1%-153.6%， 6.4%-23.0%， 35.6%-190.7%， 41.9%-58.6%， and 28.8%-773.8%； among them， the CM treatment had the most significant enhancement effect. ② Long-term different straw return treatments changed the structural composition of the soil fungal community， and the relative abundance of fungi in the phylum Periphyton decreased by 29.05%-31.12%， and the phylum Stachybotrys was enhanced by 24.76%-481.10%. The soil pH was an important influencing factor affecting the composition of the fungal community. ③ The results of network analysis showed that the indicator species of different straw return treatments in the long term belonged to different modules， which were significantly correlated with soil nutrient content and enzyme activity， among which Phaeoacremonium and Conocybe enriched in the CM treatment formed specific functional microbial clusters through a strong symbiotic relationship. ④ Functional prediction based on FUNGuild found that long-term different straw return treatments both increased the relative abundance of pathogenic and saprophytic trophic fungi and decreased the relative abundance of saprophytic-symbiotic trophic fungi. Long-term straw return can improve soil fertility and extracellular enzyme activity， increase the abundance of beneficial flora， significantly change the structure and composition of fungal communities， and favor carbon and nitrogen cycling， thus promoting the formation of a suitable environment for crop and fungal growth in brown soils.},
}

*Zea mays/growth & development
*Soil Microbiology
Soil/chemistry
*Agriculture/methods
Nitrogen/analysis
Phosphorus/analysis
*Fungi/classification/enzymology/growth & development
Plant Stems
Carbon/analysis
Mycorrhizae

@article {pmid40676374,
year = {2025},
author = {Velásquez, A and Cornejo, P and Carvajal, M and D'Onofrio, C and Seeger, M and Cuneo, IF},
title = {A comprehensive review of the transcriptomic and metabolic responses of grapevines to arbuscular mycorrhizal fungi.},
journal = {Planta},
volume = {262},
number = {3},
pages = {58},
pmid = {40676374},
issn = {1432-2048},
support = {3220381//Fondecyt Postdoctorado/ ; 1200756//Fondecyt Regular/ ; 1220235//Fondecyt Regular/ ; NCN2023_054//Núcleo Milenio Información y Coordinación en Redes, ICR/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology/metabolism/genetics ; *Transcriptome ; Anthocyanins/metabolism ; Wine ; Gene Expression Regulation, Plant ; Symbiosis ; Phenols/metabolism ; },
abstract = {This review discusses the molecular modifications of grapevines by arbuscular mycorrhizal fungi, increasing anthocyanins and other phenolic molecules, potentially improving wine quality and plant stress tolerance. Grapevines are naturally associated with arbuscular mycorrhizal fungi (AMF). These fungi, as obligate symbionts, are capable of influencing molecular, biochemical, and metabolic pathways, leading to alterations in the concentrations of various molecules within the host plant. Recent studies have addressed the transcriptomic and metabolic modifications triggered by AMF in grapevines. These AMF-induced alterations are involved in cell transport, sugar metabolism, plant defense mechanisms, and increased tolerance to both biotic and abiotic stressors. Notably, the shikimate pathway exhibits heightened activity following AMF inoculation in grapevines, resulting in the accumulation of anthocyanins, flavonols, phenolic acids, and stilbenes. Phenolic compounds are the main metabolites influencing grape and wine quality attributes, such as color, flavor, and potential health benefits. This review aims to provide an updated overview of current research on the transcriptomic and metabolic aspects of AMF-grapevine interactions, focusing on their impact on plant performance and quality traits.},
}

*Mycorrhizae/physiology
*Vitis/microbiology/metabolism/genetics
*Transcriptome
Anthocyanins/metabolism
Wine
Gene Expression Regulation, Plant
Symbiosis
Phenols/metabolism

@article {pmid40675103,
year = {2025},
author = {Qiang, S and Xu, C and Yan, C and Chang, Y and Jiang, Z and Bao, J and Liu, Y},
title = {Rational manipulation of interfacial-water supply and photothermal effect in Ru-CoP/Co2P nanoneedle arrays for urea-assisted water splitting at high current densities.},
journal = {Journal of colloid and interface science},
volume = {700},
number = {Pt 2},
pages = {138435},
doi = {10.1016/j.jcis.2025.138435},
pmid = {40675103},
issn = {1095-7103},
abstract = {Tailoring the dissociative water‑hydrogen bonding network at catalyst-electrolyte interface and introducing favorable photothermal effect are pivotal for propelling diverse electrocatalytic reactions. Herein, we developed an advanced Ru-CoP/Co2P/NF nanoarray catalyst, achieving the rational modulation interfacial-water and photothermal effect. In-situ Raman and electrochemical analyses show that Ru doping modifies the electronic structure of CoP/Co2P/NF, promoting the directional evolution of interfacial-water and accelerating hydrogen evolution reaction (HER) kinetics. Moreover, Ru doping enhances the photothermal effect of CoP/Co2P/NF, which counteracts the enthalpy change of urea oxidation reaction (UOR), strengthens the adsorption of urea molecules, accelerates interfacial electron transfer and activates inert reaction sites. The symbiotic photoelectric effect diminishes UOR activation energy from 27.0 to 14.2 kJ mol[-1]. Under the synergistic promotion of these effects, the Ru-CoP/Co2P/NF requires only 1.26, 1.32, 1.36 V (for UOR) and 64, 126, 161 mV (for HER) to reach 100, 500 and 1000 mA cm[-2], respectively. Further constructed HER||UOR electrolyser can deliver 100 and 500 mA cm[-2] at only 1.32 and 1.59 V, and can operate stably at a high current density of 500 mA cm[-2] for 100 h without obvious degradation. This innovative strategy of integrating interfacial-water modulation with near-infrared light excitation provides new impetus for advanced electrocatalytic system.},
}

@article {pmid40673427,
year = {2025},
author = {Grundy, E and Udvardi, M},
title = {How plants pick their friends.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40673427},
issn = {2050-084X},
mesh = {*Symbiosis ; *Glycine max/microbiology/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; *Rhizobium/physiology ; },
abstract = {A protein called RIN4 has a central role in helping legumes such as soybean and the bacteria rhizobia to develop a mutually beneficial relationship.},
}

*Symbiosis
*Glycine max/microbiology/metabolism/genetics
*Plant Proteins/metabolism/genetics
*Rhizobium/physiology

@article {pmid40672564,
year = {2025},
author = {Xu, Y and Gao, Q and Xue, L and Zhang, J and Wang, C},
title = {Optimized nitrogen fertilizer management enhances soybean (Glycine max (L.) Merril.) yield and nitrogen use efficiency by promoting symbiotic nitrogen fixation capacity.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1604251},
pmid = {40672564},
issn = {1664-462X},
abstract = {INTRODUCTION: Although the mulched drip irrigation system combined with high nitrogen input (240∼310 kg ha[-1]) in Xinjiang, China, frequently achieves record-high soybean yields (6855 kg ha[-1]), this practice is not conducive to symbiotic nitrogen fixation and compromises agricultural sustainability.

METHODS: Under the mulched drip irrigation, this study evaluation four nitrogen application treatments (N0: 0 kg ha[-1], N120: 120 kg ha[-1], N180: 180 kg ha[-1], and N240: 240 kg ha[-1]) were evaluated over two consecutive growing seasons to investigate their effects on nodule morphological and physiological traits, stem ureide content, and the percentage of nitrogen derived from the atmosphere (%Ndfa) during the reproductive growth stage.

RESULTS: The application of 180 kg ha[-1] nitrogen significantly increased nodule number, nodule dry weight, nodule sucrose content, and nodule starch content, while improving soybean yield and nitrogen agronomic use efficiency. Conversely, the application of nitrogen exceeding 180 kg ha[-1] inhibited nitrogenase activity, suppressed leghemoglobin synthesis, disrupted the glutamine synthetase/glutamate synthase metabolic pathway, and reduced ureide translocation from nodules to stems, leading to significant accumulation of ureides in nodules. Correlation and path analyses indicated that nitrogenase activity, leghemoglobin content, urate oxidase activity, and stem ureide content were significantly positively correlated with %Ndfa, whereas nodule ureide content showed a significant negative correlation with %Ndfa. Stem ureide content exhibited a strong direct positive effect on %Ndfa (path coefficient = 0.95), confirming its validity as a robust indicator for assessing SNF capacity.

DISCUSSION: In conclusion, mulched drip irrigation, applying 180 kg ha[-1] nitrogen at the beginning pod stage (R3) effectively enhances root nodulation, promotes carbohydrate allocation to nodules, sustains symbiotic nitrogen fixation activity, and ultimately increases soybean yield and nitrogen use efficiency. Thus, under mulched drip irrigation system, applying the correct rate of nitrogen fertilizer is beneficial for enhancing soybean yield and mitigating environmental risks, which holds significant importance for promoting sustainable agricultural development.},
}

@article {pmid40672331,
year = {2025},
author = {Vander Griend, JA and Nottage, HC and Mehle, A and Mandel, MJ},
title = {RtmR is a membrane-embedded RRM-family RNA-binding protein that regulates biofilm formation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.10.664275},
pmid = {40672331},
issn = {2692-8205},
abstract = {UNLABELLED: The animal symbiont Vibrio fischeri has served as a model organism for molecular processes underlying bacterial group behaviors, including quorum sensing and biofilm development. Here, using a genetic approach to identify negative regulators of biofilm formation in V. fischeri , we identified a membrane-bound RNA-binding protein, RtmR (VF_2432), that acts as an inhibitor of the symbiosis polysaccharide (SYP) biofilm. Membrane localization of the protein seems to be required for protein stability, as truncation of the transmembrane helices led to an inability to detect the protein. The conserved RNP1 and RNP2 motifs in RtmR's cytoplasmic RNA recognition motif (RRM) domain are required for function, and we demonstrate binding to RNA substrates. Identification of RtmR RNA ligands was conducted with a CLIP-seq approach that revealed a large interactome. One transcript identified was that of the biofilm regulatory histidine kinase RscS. We found that RtmR biofilm inhibition depends on RscS activity and that RtmR negatively regulates levels of RscS. Overall, this work characterizes a novel type of bacterial RNA-binding protein.

IMPORTANCE: Bacterial RNA-binding proteins (RBPs) perform key functions to regulate stress responses and development. Bacterial RBPs including the RNA chaperones Hfq and ProQ, the global regulator CsrA, and the cold shock proteins (Csps) have been extensively studied, although additional classes of RBPs have been predicted by bioinformatic methods including those carrying an RRM domain. This work expands on recent studies of RRM domain proteins in bacteria to characterize a membrane-bound RRM protein that regulates bacterial biofilm development. Given our rapidly-expanding knowledge regarding the role for RNA-binding proteins in bacterial molecular biology, this work contributes a new class of membrane-bound regulators with homologs in human pathogens and marine symbionts.},
}

@article {pmid40672138,
year = {2025},
author = {Obase, K and Yamanaka, S and Ozaki, K},
title = {Root-associated ectomycorrhizal fungal communities in and around aggregated retention patches left in logged areas of Abies sachalinensis planted forests.},
journal = {Mycoscience},
volume = {66},
number = {1},
pages = {116-119},
pmid = {40672138},
issn = {1618-2545},
abstract = {An aggregated retention system retains several groups of trees within cutblocks to maintain public functions such as biodiversity conservation. We examined ectomycorrhizal (EcM) fungal communities associated with regenerating Abies sachalinensis seedlings and their surrounding trees at different locations; inside and at the edge of the retained patches, and in clear-cut areas 10 and 50 m from the edge. The EcM fungi on the roots were grouped into operational taxonomic units (OTU) based on the similarity of their ribosomal DNA internal transcribed spacer sequences. Higher OTU richness was found inside (63 OTUs) and at the edge of the patches (59 OTUs) compared to clear-cut areas (33 or 25 OTUs). The ordination analysis inferred that location may influence the EcM fungal communities. However, further studies with more site replications are needed to clarify the effects of the patches on shaping EcM fungal communities.},
}

@article {pmid40671349,
year = {2025},
author = {Li, H and Gong, W and Xu, L and Lv, W and Wang, Y and Liu, W and Li, B and Lu, A},
title = {Behavior of Chiral Paclobutrazol in Soils: Enantioselective Degradation, Transformation Products, and Effects on Soil Microorganisms and Their Metabolic Functions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01966},
pmid = {40671349},
issn = {1520-5851},
abstract = {Paclobutrazol, a triazole chiral plant growth regulator, has been widely applied as a racemic mixture in crop and fruit tree production. However, the enantioselective fate and effects of chiral paclobutrazol in the soil ecosystem are still unclear. In this study, systemic assessments of dissipation dynamics, transformation products (TPs) and pathways, and interactions between soil microorganisms and related metabolites are first carried out using suspect and nontarget screening, high-throughput sequencing, and soil metabolomics. The dissipation half-lives of R- and S-paclobutrazol were 30.7 and 40.7 d, and interconversion between the two enantiomers occurred in soils. Nine previously unreported TPs were identified, and one was synthesized and confirmed with an authentic standard. Aerobic degradation pathways of R- and S-enantiomers were proposed, showing enantioselective degradation. 16S rRNA and ITS sequencing results showed that both R- and S-enantiomers increased bacterial diversity but decreased fungal diversity and disrupted microbial symbiosis networks' complexity. Chiral paclobutrazol enantioselectively and significantly changed the soil metabolite spectrum. Integrated analyses revealed a strong association between microorganisms and certain metabolite expressions. These findings indicate the importance of TP analysis, provide new insights into how soil microbes and metabolite profiles are affected by paclobutrazol enantiomers, and lay the foundation for conducting all-sided impact assessments.},
}

@article {pmid40671186,
year = {2025},
author = {Dadfar, B and Alemdag, B and Kabay, G},
title = {The Alchemist, the Scientist, and the Robot: Exploring the Potential of Human-AI Symbiosis in Self-Driving Polymer Laboratories.},
journal = {Macromolecular rapid communications},
volume = {},
number = {},
pages = {e00380},
doi = {10.1002/marc.202500380},
pmid = {40671186},
issn = {1521-3927},
support = {//Carl Zeiss Stiftung/ ; },
abstract = {Polymer chemistry research has progressed through three methodological eras: the alchemist's intuitive trial-and-error, the scientist's rule-based design, and the robot's algorithm-guided automation. While approaches combining combinatorial chemistry with statistical design of experiments offer a systematic approach to polymer discovery, they struggle with complex design spaces, avoid human biases, and scale up. In response, the discipline has adopted automation and artificial intelligence (AI), culminating in self-driving laboratories (SDLs), integrating high-throughput experimentation into closed-loop, AI-assisted design-build-test-learn cycles, enabling the rapid exploration of chemical spaces. However, while SDLs address throughput and complexity challenges, they introduce new forms of the original problems: algorithmic biases replace human biases, data sparsity creates constraints on design space navigation, and black-box AI models create transparency issues, complicating interpretation. These challenges emphasize a critical point: complete algorithmic autonomy is inadequate without human involvement. Human intuition, ethical judgment, and domain expertise are crucial for establishing research objectives, identifying anomalies, and ensuring adherence to ethical constraints. This perspective supports a hybrid model grounded in symbiotic autonomy, where adaptive collaboration between humans and AI enhances trust, creativity, and reproducibility. By incorporating human reasoning into adaptive AI-assisted SDL workflows, next-generation autonomous polymer discovery will be not only faster but also wiser.},
}

@article {pmid40670389,
year = {2025},
author = {Arias, SL and van Wijngaarden, EW and Balint, D and Jones, J and Crawford, CC and Shukla, PJ and Silberstein, M and Brito, IL},
title = {Environmental factors drive bacterial degradation of gastrointestinal mucus.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {133},
pmid = {40670389},
issn = {2055-5008},
mesh = {Humans ; *Mucus/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Gastrointestinal Microbiome ; Peptide Hydrolases/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; Bacterial Proteins/metabolism ; Oxidative Stress ; Bacteroides fragilis/metabolism ; },
abstract = {The mucus layer lining the gastrointestinal tract is essential for gut health, providing a protective barrier while maintaining host-microbiome symbiosis. Its disruption is a hallmark of diseases like ulcerative colitis, yet how bacterial activity impacts mucus structure remains unclear. We developed a method to collect human-cell-derived mucus that mimics human colonic mucus and used it to investigate mucus degradation by commensal bacteria. Glycan foraging by species such as Bacteroides thetaiotaomicron and Bacteroides fragilis did not alter mucus rheology. Instead, secreted proteases were the primary drivers of degradation. Protease activity by B. fragilis and Bifidobacterium longum subsp. infantis was nutrient-dependent, while Enterococcus faecalis was further influenced by oxygen. Under oxidative stress, E. faecalis upregulated carbohydrate metabolism and virulence genes. These results reveal that bacterial mucus degradation is context-dependent and shaped by environmental factors. Our findings underscore the value of human cell-derived mucus models for understanding bacteria-mucus interactions in health and disease.},
}

Humans
*Mucus/microbiology/metabolism
*Bacteria/metabolism/genetics
*Gastrointestinal Microbiome
Peptide Hydrolases/metabolism
*Gastrointestinal Tract/microbiology/metabolism
*Intestinal Mucosa/microbiology/metabolism
Bacterial Proteins/metabolism
Oxidative Stress
Bacteroides fragilis/metabolism

@article {pmid40670201,
year = {2025},
author = {Wang, W and Wang, Y and Xie, Q and Shi, J and Sun, L and He, Z and Murray, J and Wang, E and Yu, N and Zhang, X},
title = {AP2-domain transcription factor WRI5a-regulated MtABCB1 promotes arbuscule development in mycorrhizal symbiosis.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2025.06.033},
pmid = {40670201},
issn = {2095-9281},
}

@article {pmid40669785,
year = {2025},
author = {Wang, H and Qi, W and Wang, W and Elshobary, M and Feng, P and Zhu, S and Wang, Z and Qin, L},
title = {N-modulated algal-bacterial symbiosis: Dual detoxification and bioproduction enhancement from acid-lignocellulosic pretreatment wastewater.},
journal = {Bioresource technology},
volume = {436},
number = {},
pages = {132978},
doi = {10.1016/j.biortech.2025.132978},
pmid = {40669785},
issn = {1873-2976},
abstract = {The lignocellulosic biorefining process produces acid-pretreated lignocellulosic wastewater (ALPW), which is rich in fermentable sugars but also contains inhibitory compounds (furfural/5-HMF/acetic acid). This study first systematically assessed the potential for ALPW valorization through algal-bacterial symbiosis with N-regulation. The results showed that 4 × ALPW enabled optimal algal biomass (3.95 g/L). Synchronous culture of algal-bacterial symbiosis in 2 × ALPW achieved 74.7 % sugar consumption and complete inhibitor detoxification, outperforming asynchronous culture. N-regulation with 80 mg/L NO3[-]-N + 40 mg/L NH4[+]-N maximized biomass (4.30 g/L) and carbon fixation (330.60 mg/L/d). The system converted 56.2 % carbon and 68.0 % nitrogen into biomass, with 1 ton corn stalk yielding 86.7 kg biomass (protein/carbohydrate/lipid: 36.6/27.1/16.0 kg). This research not only advances algal-bacterial wastewater treatment but also offers a practical, cost-effective pathway for lignocellulosic biorefineries to transition toward a circular economy. Future studies will prioritize pilot-scale validation of the N-modulated symbiosis for ALPW treatment and integration with biorefinery processes to improve economic viability.},
}

@article {pmid40669665,
year = {2025},
author = {Ghanawi, H and Koch, SF},
title = {The Versatile Roles of Retinal Pigment Epithelium in the Pathophysiology of Retinitis Pigmentosa.},
journal = {Progress in retinal and eye research},
volume = {},
number = {},
pages = {101390},
doi = {10.1016/j.preteyeres.2025.101390},
pmid = {40669665},
issn = {1873-1635},
abstract = {Retinitis pigmentosa (RP) is a group of hereditary retinal diseases that lead to progressive vision loss, with most disease-causing genes expressed in rod photoreceptors and a smaller fraction in retinal pigment epithelium (RPE) cells. The RPE and photoreceptor cells share a symbiotic relationship characterized by close spatial and functional interactions that play a pivotal role in vision. Although the role of RPE is fundamental to the retina, its involvement in retinal pathogenesis, and, in particular, in RP remains underappreciated. In this review, we summarize morphological alterations in the RPE resulting from pathogenic mutations specific to RPE cells, as well as those occurring secondary to photoreceptor degeneration. We provide a comprehensive summary of how mutations in RPE-specific genes play a key role in the pathophysiology of RP. Finally, we discuss the latest therapeutic approaches, including AAV-mediated gene augmentation, RPE cell transplantation, and pharmacological interventions.},
}

@article {pmid40669190,
year = {2025},
author = {Feng, X and Ren, X and Zhang, L and Yang, W},
title = {Combined regulation effects of peanut meal, superphosphate, and carbonized rice husk on green waste composting.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126525},
doi = {10.1016/j.jenvman.2025.126525},
pmid = {40669190},
issn = {1095-8630},
abstract = {The low degradation efficiency and inconsistent product quality of conventional green waste (GW) composting require technological innovation. This study aimed to optimize the use of organic and inorganic bulking agents to improve GW degradation efficiency and product quality. Compound organic and inorganic bulking agents were formulated using peanut meal (PM: 0, 10, and 20 %), superphosphate (SSP: 0, 5, and 10 %), and carbonized rice husk (CRH: 0, 2, and 4 %). Monitoring of composting parameters (temperature, organic matter degradation, humification, bacterial community) and product quality (nutrients, phytotoxicity) identified T5 (10 % PM + 5 % SSP + 4 % CRH) as the optimal compound bulking agent. Compared to the control, T5 significantly prolonged the thermophilic phase by 7 days and produced the highest-quality compost product within just 28 days. T5 extended the thermophilic phase by 7 days, increased the organic matter degradation rate by 27.6 %, reduced the NH4[+]-N/NO3[-]-N ratio by 52.0 %, and increased the HA/FA ratio by 59.4 %. Network analysis revealed that most bacteria have a positive correlation, indicating that symbiotic relationships may exist in the bacterial community. Among them, Sporosarcina is regarded as the dominant species. T5 enhanced the relative abundance of dominant species in the bacterial community, including Sporosarcina and norank_f_Bacillaceae, thus fostering a more uniform bacterial community and improving the biodegradation of GW. This study provided data for the use of PM, SSP, and CRH as organic and inorganic bulking agents, enhancing GW composting efficiency and product quality while offering a feasible solution for the sustainable utilization of agricultural by-products.},
}

@article {pmid40668851,
year = {2025},
author = {He, Y and Gao, M and Wang, L},
title = {The intelligent evaluation model of the English humanistic landscape in agricultural industrial parks by the SPEAKING model: From the perspective of fish-vegetable symbiosis in new agriculture.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325332},
pmid = {40668851},
issn = {1932-6203},
mesh = {Humans ; *Agriculture/methods ; *Symbiosis ; Animals ; *Fishes ; *Parks, Recreational ; Language ; Models, Theoretical ; Conservation of Natural Resources ; },
abstract = {To more accurately capture the expression of the English humanistic landscape in agricultural industrial parks under the emerging agricultural paradigm of fish-vegetable symbiosis, and to address the limitations of unscientific evaluation standards and inadequate adaptability in Chinese-English translation within multimodal contexts, this study proposes an intelligent translation evaluation framework based on the SPEAKING model-comprising Setting, Participants, Ends, Act Sequence, Key, Instrumentalities, Norms, and Genre. The study identifies the core elements essential for articulating the English humanistic landscape of agricultural industrial parks and conducts a comprehensive analysis from the dual perspectives of translation accuracy and adaptability. Fish-vegetable symbiosis, an ecological agricultural system integrating aquaculture and plant cultivation, emphasizes resource recycling and ecological synergy. Internationally referred to as the "aquaponics system," this model has become a pivotal direction in sustainable ecological agriculture due to its efficiency and environmental compatibility. This study investigates multimodal translation tasks across text, image, and speech data. It addresses two primary challenges: (1) the absence of robust theoretical grounding in existing translation evaluation systems, which leads to partial and insufficiently contextualized assessments in agricultural industrial park translations; and (2) difficulties in maintaining consistency and readability across multimodal translation tasks, particularly in speech and visual modalities. The proposed optimization model integrates linguistic theory with deep learning techniques, providing a detailed analysis of contextual translation elements. Comparative evaluations are conducted against five prominent translation models: Multilingual T5 (mT5), Multilingual Bidirectional and Auto-Regressive Transformers (mBART), Delta Language Model (DeltaLM), Many-to-Many Multilingual Translation Model-100 (M2M-100), and Marian Machine Translation (MarianMT). Experimental results indicate that the proposed model outperforms existing benchmarks across multiple evaluation metrics. For translation accuracy, the Setting score for text data reaches 96.72, exceeding mT5's 92.35; the Instrumentalities score for image data is 96.11, outperforming DeltaLM's 93.12; and the Ends score for speech data achieves 94.83, surpassing MarianMT's 91.67. In terms of translation adaptability, the Genre score for text data is 96.41, compared to mT5's 93.21; the Key score for image data is 92.78, slightly higher than mBART's 92.12; and the Norms score for speech data is 91.78, exceeding DeltaLM's 90.23. These findings offer both theoretical insights and practical implications for enhancing multimodal translation evaluation systems and optimizing cross-modal translation tasks. The proposed model significantly contributes to improving the accuracy and adaptability of language expression in the context of agricultural landscapes, advancing research in intelligent translation and natural language processing.},
}

Humans
*Agriculture/methods
*Symbiosis
Animals
*Fishes
*Parks, Recreational
Language
Models, Theoretical
Conservation of Natural Resources

@article {pmid40668214,
year = {2025},
author = {Li, X and Møller, SH and Park, J and Chuang, YM and Hsueh, PC and Chang, TH and Kao, KC and Gallart-Ayala, H and Wang, YH and Peng, JJ and Bevilacqua, A and Yu, YR and Li, Z and Kieffer, Y and Peigney, D and Croizer, H and Xu, Y and Zippelius, A and Lopez-Mejia, IC and Fajas, L and Mechta-Grigoriou, F and Ivanisevic, J and Xiao, Z and Ho, MC and Shen, YC and Ho, PC},
title = {Tumor-instructed glutamine synthesis in cancer-associated fibroblasts promotes pro-tumor macrophages.},
journal = {The Journal of experimental medicine},
volume = {222},
number = {9},
pages = {},
doi = {10.1084/jem.20241426},
pmid = {40668214},
issn = {1540-9538},
support = {310030_215126/SNSF_/Swiss National Science Foundation/Switzerland ; 310030L_208130/SNSF_/Swiss National Science Foundation/Switzerland ; TMCG-3_213736/SNSF_/Swiss National Science Foundation/Switzerland ; IZLCZ0_206083/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_205930/SNSF_/Swiss National Science Foundation/Switzerland ; /CRI/Cancer Research Institute/United States ; //Helmut Horten Stiftung/ ; /MRA/Melanoma Research Alliance/United States ; },
mesh = {*Glutamine/biosynthesis/metabolism ; *Cancer-Associated Fibroblasts/metabolism/pathology ; Animals ; Tumor Microenvironment/immunology ; Mice ; *Tumor-Associated Macrophages/metabolism/pathology/immunology ; Humans ; Signal Transduction ; *Macrophages/metabolism ; Cell Line, Tumor ; *Neoplasms/pathology/metabolism ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Interleukin-6/metabolism ; Toll-Like Receptor 4/metabolism ; Syk Kinase/metabolism ; },
abstract = {In the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) play a crucial role in promoting tumor progression by creating an immunosuppressive environment through cytokine secretion and antigen presentation. While previous studies have demonstrated that CAFs exhibit distinct metabolic profiles compared with normal fibroblasts, it remains unclear how these metabolic programs influence the immune landscape within tumors and which factors drive metabolic reprogramming in CAFs. Here, we found that glutamine synthesis by CAFs promotes the polarization of pro-tumorigenic tumor-associated macrophages (TAMs) and supports tumor growth by altering TAM composition, highlighting the pivotal role of CAFs in shaping the immunosuppressive TME. Mechanistically, we found that tumor-derived palmitic acid activates a signaling cascade involving TLR4, Syk, and NF-κB in fibroblasts, leading to inflammatory CAF polarization and IL-6-induced glutamine synthesis. These findings uncover a novel metabolic symbiosis whereby tumor cells manipulate TAM polarization through CAF-mediated glutamine metabolism, presenting potential therapeutic targets for cancer immunotherapy.},
}

*Glutamine/biosynthesis/metabolism
*Cancer-Associated Fibroblasts/metabolism/pathology
Animals
Tumor Microenvironment/immunology
Mice
*Tumor-Associated Macrophages/metabolism/pathology/immunology
Humans
Signal Transduction
*Macrophages/metabolism
Cell Line, Tumor
*Neoplasms/pathology/metabolism
Mice, Inbred C57BL
NF-kappa B/metabolism
Interleukin-6/metabolism
Toll-Like Receptor 4/metabolism
Syk Kinase/metabolism

@article {pmid40666801,
year = {2025},
author = {Lou, J and Xiang, Z and Zhu, X and Li, J and Jin, G and Cui, S and Huang, N and Le, X and Fan, Y and Sun, Q},
title = {Skin microbiota and diabetic foot ulcers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575081},
pmid = {40666801},
issn = {1664-302X},
abstract = {Skin microbiota is the microbial population on the skin surface, which has a symbiotic relationship with the host skin and plays an important role in maintaining skin health and regulating immune responses. In patients with diabetic foot ulcers (DFUs), the skin microbiota is unbalanced. The abundance of pathogenic bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa increases, forming biofilms, destroying the skin barrier function, aggravating infection, and leading to poor wound healing. Studies have shown that the diversity of skin microbiota is positively correlated with the severity of ulcers, and regulating its composition and function may be an important strategy to improve DFUs healing. In recent years, with the development of molecular biology technology, progress has been made in the study of skin microbiota, such as 16S rRNA gene sequencing technology to understand its composition changes and explore the interaction mechanism with the host immune system. Based on this, some new therapeutic approaches are being explored, such as the use of probiotics or antibacterial drugs to modulate the composition of the microbiota and the development of microbiota-based personalized treatment regimens. However, there are still challenges in current research. For example, the composition and function of skin microbiota are affected by many factors, and there are relatively few studies on other microorganisms such as fungi and viruses. In the future, it is necessary to further explore its diversity and the interaction mechanism with the host, and develop more effective treatment methods to improve the prognosis of patients with DFUs.},
}

@article {pmid40665866,
year = {2025},
author = {Sun, Z and Zhang, K and Peng, J and Liu, B and Kong, F and Sang, Q and Du, H},
title = {Strategies for Balancing Growth and Defence Against Biotic Stress in Legumes.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70070},
pmid = {40665866},
issn = {1365-3040},
support = {//This study was also supported by the Joint Funding Project of Guangzhou Municipal Government, Universities (Academies) and Enterprises (2023A03J0049 to F.K.), Key Projects of Joint Foundation of Guangdong Provincial (Grant No. 2022B1515120045 to F.K.), Guangdong Science and Technology Plan Project (2024B1212060003 to F.K.). This study was also funded by the National Natural Science Foundation of China Grant 32301750 to H.D. and the Major Program of Guangdong Basic and Applied Research 2019B030302006 to F.K. and B.L./ ; },
abstract = {Legumes are a rich source of protein and oil for human consumption and livestock feed, but pathogens and insect pests threaten their quality and yields. Balancing growth and defence against pests and pathogens is critical for plants to maintain high productivity. Insufficient defence responses result in severe yield losses, but excessive constitutive or inducible defence responses inhibit plant growth and development, also decreasing yields. Here, we review the complex relationship between defence responses and growth of leguminous plants, focusing on important legumes such as cultivated soybean (Glycine max) and barrel clover (Medicago truncatula). In addition, we examine the interaction between symbiotic nitrogen fixation and defences in legumes and describe current plant breeding strategies to optimise the balance between plant defence and growth. This review summarises the balance between growth and defence in leguminous plants, providing a theoretical basis for breeding strategies to develop stable varieties that balance growth and resistance to improve yield.},
}

@article {pmid40665121,
year = {2025},
author = {Balasubramaniyan, M and Veeran, Y},
title = {Unravelling Evolutionary and Ecological Insights of Foraminifera by Using Next Generation Sequencing: A Review.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40665121},
issn = {1573-4927},
abstract = {Next-generation sequencing (NGS) has transformed our understanding of foraminifera biology by revealing cryptic diversity, clarifying phylogenetic relationships, and elucidating adaptive mechanisms previously inaccessible through morphological studies alone. This review delves into the potential of NGS in uncovering the secrets of foraminifera. We examine the current state of knowledge, recent breakthroughs, and future directions in applying NGS to foraminiferal research. Specifically, this study highlights how NGS enhances our understanding of foraminiferal taxonomy, adaptation to environmental changes, and functional genomics. Additionally, this review explores the potential of NGS to elucidate the genetic basis of foraminiferal shell formation, symbiotic relationships, and their responses to environmental stressors. We also address challenges and limitations associated with foraminiferal NGS, such as genome assembly complexities, intra-species heterogeneity, and sampling biases. Overall, this review aims to promote further research and collaboration in foraminiferal genomics, ultimately enhancing knowledge of these ecologically significant organisms and their contributions to marine ecosystems and paleoenvironments.},
}

@article {pmid40664836,
year = {2025},
author = {Arun, M and Barik, D and Dara, RN and P, P and Tudu, K and Praveenkumar, S and Kanti, PK and Ayanie, AG},
title = {Integrated renewable energy supply architecture for advancing hydrogen symbiosis and eco synergistic smart grid interactions with next generation combustion technologies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25619},
pmid = {40664836},
issn = {2045-2322},
abstract = {This study introduces the Smart Grid Hybrid Electrolysis-and-Combustion System (SGHE-CS), designed to seamlessly integrate hydrogen production, storage, and utilization within smart grid operations to maximize renewable energy use and maintain grid stability. The system achieves a hydrogen production efficiency of 98.5%, indicating the effective conversion rate of electrical energy to hydrogen via PEM electrolysis. Combustion efficiency reaches 98.1%, reflecting the proportion of hydrogen energy successfully converted into usable power through advanced staged combustion. Storage and transportation efficiency is 96.3%, accounting for energy losses during hydrogen compression, storage, and delivery. Renewable integration efficiency is 97.3%, representing the system's capacity to utilize variable renewable energy inputs without curtailment. Operational versatility is 99.3%, denoting the system's ability to maintain high performance across load demands and grid conditions. Real-time monitoring and adaptive control strategies ensure reliability and resilience, positioning SGHE-CS as a promising solution for sustainable, low-carbon energy infrastructure.},
}

@article {pmid40664285,
year = {2025},
author = {Chi, Y and Ren, W and Jin, P and Shi, X and Liu, L},
title = {Robust partial nitrification and anammox under low-strength nitrogen condition by regulating organic-induced symbiosis of denitrifiers and anammox bacteria.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132975},
doi = {10.1016/j.biortech.2025.132975},
pmid = {40664285},
issn = {1873-2976},
abstract = {Low-strength nitrogen usually limits the efficiency of partial nitrification and anaerobic ammonium oxidation (anammox). To address this challenge, an organic-induced regulation strategy based on microbial interaction characteristics was proposed. Short-range addition of acetate for bio-screening is essential for achieving this regulation. After bio-screening, enhanced partial nitrification and anammox performance were achieved within 47 days. In the start-up phase, denitrifiers outcompeted nitrite oxidizing bacteria (NOB) for nitrite utilization, thereby enhancing the inhibition of NOB. The relative abundance of anammox bacteria (AnAOB) was maintained at approximately 8.6 % due to an increase in extracellular proteins, which was conducive to material exchange and symbiosis between denitrifiers and AnAOB. Transcriptomic analysis revealed that bio-screening induced mixotrophic metabolism of AnAOB, characterized by up-regulating the expression of genes involved in organic carbon and energy metabolism, thereby improving the stability of the anammox process. This study provides valuable insights for enhancing anammox performance under low-strength nitrogen conditions.},
}

@article {pmid40663266,
year = {2025},
author = {Iwamori, M and Tanaka, K},
title = {Characterization of bacterial glycolipids in Pediococcus pentosaceus for fermented soybean paste (miso) and Tetragenococcus halophilus for soy sauce, in comparison with those in Lactobacillus, Streptococcus and Staphylococcus species.},
journal = {Glycoconjugate journal},
volume = {},
number = {},
pages = {},
pmid = {40663266},
issn = {1573-4986},
abstract = {Gram-positive bacterial biomembranes are composed of phosphatidyl glycerol (PG), cardiolipin (CL), and dihexaosyl diglycerides (DH-DG) as the major lipid constituents. The carbohydrate structures of DH-DG are specific to the particular bacterial species and we previously revealed them to have immunologically active properties. To characterize the species-structure relationship of glycolipids in Gram-positive bacteria, the structures of DH-DG in Pediococcus pentosaceus (PP) for producing fermented soybean paste (miso) and Tetragenococcus halophilus (TH) for soy sauce were determined in comparison with those in Lactobacillus, Streptococcus and Staphylococcus species. They were shown to be Glcα1-2Glcα1-3'DG (kojibiosyl DG) with 18:1(oleic acid) and 18:1 as the fatty acids for PP, and that with 16:0 (palmitic acid) and 18:1 for TH, and their carbohydrate structures were identical to that in Streptococcus salivarius, a symbiotic bacterium in the human oral cavity. Additionally, both bacteria contained an acidic glycolipid, in which glycerol phosphate was attached to the 6-position of the nonreducing terminal Glc residue of DH-DG. TLC immunostaining with human sera revealed antibodies to Galα1-2Glcα1-3'DG (LacDH-DG) from Lactobacillus species and Glcβ1-6Glcβ1-3'DG (StaDH-DG) from Staphylococcus species, but not to Glcα1-2Glcα1-3'DG (StrDH-DG) from Streptococcus species, in 2 out of 20 human sera. Given that one serum sample with anti-StaDH-DG antibodies was from a patient who had suffered from food poisoning due to Staphylococcus aureus 6 months previously, the antibodies to bacterial DH-DG were thought to have arisen via bacterial infection.},
}

@article {pmid40661758,
year = {2025},
author = {Xie, Y and Song, X and Lu, Y and Hu, X and Pan, S and Xu, W and Xue, Y},
title = {Different forms of nitrogen uptake in tobacco promoted by the arbuscular mycorrhizal fungi.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1600887},
pmid = {40661758},
issn = {1664-462X},
abstract = {Persistent limitations in nitrogen (N) assimilation efficiency have emerged as a critical constraint in advancing the phytochemical quality of cultivated tobacco (Nicotiana tabacum L.). Arbuscular mycorrhizal fungi (AMF), forming obligate symbiotic associations with over 80% of terrestrial vascular plant species, significantly enhance host plant performance through improved rhizospheric nutrient mobilization. This mutualistic relationship facilitates enhanced acquisition of both macronutrients (particularly phosphorus and N) and water, thereby substantially decreasing agricultural dependence on synthetic fertilizer inputs. Building upon these premises, the present study was carried out to investigate the effects of different forms of nitrogen on the infestation rate and biomass of tobacco plants after inoculation with AMF, as well as the differences in the uptake of different forms of nitrogen by tobacco plants mediated by AMF, using the isotope [15]N labelling method. The study revealed significant variations in the uptake of various nitrogen forms by AMF. Under mixed nitrogen source conditions, (NH4)2SO4, KNO3, and glutamine (Glu) constituted 48.61%, 36.10%, and 15.29% of total nitrogen uptake, respectively. Notably, AMF exhibited a preferential uptake hierarchy for NH4 [+], demonstrating 1.35-fold and 2.94-fold higher absorption rates compared to NO3 [-] and Glu. Furthermore, [15]N isotopic tracing analysis confirmed active Glu assimilation by AMF, as evidenced by significantly elevated [15]N-Glu uptake in labeled treatments relative to non-labeled controls. These findings collectively suggest that AMF symbiosis modifies tobacco plants' nutritional preferences among distinct nitrogen forms. This study establishes a theoretical foundation for optimizing nitrogen utilization efficiency and enhancing agronomic productivity in tobacco cultivation systems.},
}

@article {pmid40660619,
year = {2025},
author = {Armstrong, R},
title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.},
journal = {Microbial biotechnology},
volume = {18},
number = {7},
pages = {e70195},
pmid = {40660619},
issn = {1751-7915},
support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; },
mesh = {Humans ; Ecosystem ; *Microbiology/education ; },
abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.},
}

Humans
Ecosystem
*Microbiology/education

@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}

@article {pmid40657914,
year = {2025},
author = {Fung, BL and Musto, EG and Mugambi, LK and Lange, ML and Tepavcevic, J and Visick, KL},
title = {A single point mutation is sufficient to drive syp-dependent biofilm formation and promote colonization by Vibrio fischeri.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0013125},
doi = {10.1128/jb.00131-25},
pmid = {40657914},
issn = {1098-5530},
abstract = {Symbiotic colonization by Vibrio fischeri relies on the syp gene cluster, which encodes proteins predicted to synthesize and export a polysaccharide, SYP, that functions in cell-cell adherence. In strain ES114, four two-component sensor kinase/phosphatases, including central regulator SypF and the nitric oxide/HnoX-controlled HahK, dictate the activities of two response regulators, SypG and SypE, which in turn control SYP production. Here, we report that a single nucleotide change (C/A) upstream of the hnoX-hahK operon caused a substantial 80-fold increase in its transcription. While a search for negative regulators yielded Zur (zinc uptake regulator), loss of Zur only modestly (approximately threefold) increased transcription. We found instead that the C/A change engendered a new transcriptional start site. Furthermore, the C/A change was sufficient to robustly promote syp-dependent biofilm formation dependent on HahK and SypG but only partially dependent on the central regulator SypF. Rather, the residual biofilm formation in the absence of SypF relied on the luminescence regulator LuxU. Consistent with its ability to produce syp-dependent biofilms, a ΔsypF mutant that carried the C/A-hahK allele outcompeted its ΔsypF parent for squid colonization. Finally, bioinformatic analyses of the hnoX promoter region in various V. fischeri isolates revealed that most contained G or C nucleotides lacking in ES114, indicating an evolutionary divergence between different isolates. Together, these findings uncover the ability of HahK to signal through both SypF and LuxU to induce syp-dependent biofilm formation and host colonization, thus advancing our understanding of the regulators that control syp-dependent biofilm formation by V. fischeri.IMPORTANCEBiofilms promote the attachment of bacteria to each other and to surfaces. For Vibrio fischeri, biofilm formation dependent on the symbiosis polysaccharide (syp) locus promotes colonization of its symbiotic host. Multiple two-component regulators, including the central sensor kinase SypF and nitric oxide/HnoX-controlled sensor kinase HahK, induce SYP production. Here, we identify a C/A change in the hnoX-hahK regulatory region that substantially increases its transcription and SYP-dependent biofilm formation. We further determined that HahK signals through both SypF and the luminescence regulator LuxU to promote biofilm formation and host colonization. Our findings thus provide insight into the regulatory crossover between two major pathways, quorum sensing-controlled luminescence and biofilm formation, in V. fischeri.},
}

@article {pmid40657902,
year = {2025},
author = {Keller-Costa, T and Madureira, S and Fernandes, AS and Kozma, L and Gonçalves, J and Barroso, C and Kusuma, AB and Egas, C and Costa, R},
title = {Genome sequence of the marine bacterium Roseobacter sp. EG26, isolated from the octocoral Eunicella gazella, suggests aptitude for a host-associated lifestyle.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0043025},
doi = {10.1128/mra.00430-25},
pmid = {40657902},
issn = {2576-098X},
abstract = {We present the genome sequence of the octocoral-associated Roseobacter sp. EG26. We highlight features related to type II, III, IV, and VI secretion systems, ankyrin-repeat proteins, and taurine degradation, suggesting a preference for a host-associated lifestyle. Strain EG26 also possesses genes for the degradation of phenolic compounds with bioremediation potential.},
}

@article {pmid40654802,
year = {2025},
author = {Heo, K and Jung, DJ and Yoo, JS and Goh, B and Kasper, DL and Oh, SF},
title = {Bacterial glycosphingolipids orchestrate colonization and immune modulation in neonatal host.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.02.651985},
pmid = {40654802},
issn = {2692-8205},
abstract = {Symbiotic microbiota has co-existed with the mammalian host over millennia, conserving a stable community structure generation after generation. During the vertical transmission, gut symbionts rapidly colonize the unoccupied host lumen, nonetheless, how symbionts adapt to the dynamic changes of host environment, and contribute to the structural and immunological maturation remains elusive. Here, we show that the early gut symbiont Bacteroides fragilis produces a species- and stage-specific sphingolipid, alpha-galactosylceramide (BfaGC), that orchestrates neonatal colonization and immune modulation. BfaGC stabilizes membrane integrity and facilitates aerobic respiration, providing a critical advantage under early-life oxygen exposure. Temporally induced in the neonatal gut, BfaGC is necessary to regulate colonic type I natural killer T (NKT) cells, highlighting metabolic adaptation of the symbiont is synchronized with the time-sensitive host development. These findings reveal a mutualistic benefit exerted by endobiotic lipid metabolites in host-microbe interactions and provide new insights into species-specific mechanisms in early microbiota establishment and host immune education.},
}

@article {pmid40654299,
year = {2025},
author = {Duval, BD and Carabotta, E and de Tomas-Marin, S and Lightfoot, DC},
title = {Coincident shifts in riparian ground-active arthropod diversity and soil nutrients under an introduced symbiotic N2-fixing tree.},
journal = {Environmental entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ee/nvaf025},
pmid = {40654299},
issn = {1938-2936},
support = {//New Mexico Game and Fish/ ; },
abstract = {Symbiotic nitrogen-fixing plants such as Russian olive can significantly impact soil chemistry and invertebrate biodiversity in riparian ecosystems. Here, the effects of Russian olive on soil chemical properties and invertebrate communities in riparian zones of the southwestern United States were investigated. Russian olive stands were compared to native cottonwood stands and restoration sites by analyzing soil nitrogen (N), phosphorus (P), and moisture levels, and arthropod diversity and abundance. Sites where Russian olive is present led to a net increase in soil nitrogen, a decrease in soil phosphorus, and greater soil moisture compared to both native cottonwood stands and restoration sites. Native cottonwood stands showed lower soil N and higher P levels, as well as higher arthropod diversity. This increased diversity could be linked to the soil's nutrient stoichiometry, as there is a negative correlation between taxonomic diversity and the soil N:P ratio. Moreover, there was a greater abundance of detritivorous arthropods in Russian olive stands compared to native vegetation. Soil nitrate (NO3-) levels showed a strong positive correlation with detritivorous arthropod abundance (r2 = 0.98), but only a moderate correlation with herbivores (r2 = 0.38), and NO3- was unrelated to predator abundance (r2 = 0.01). These results suggest that Russian olive stands can alter soil chemistry in ways that disproportionately benefit detritivores, potentially disrupting the balance of arthropod communities and reducing overall biodiversity in riparian ecosystems. The study underscores the need for careful management of invasive, symbiotic N2-fixing plant species to preserve the ecological integrity of riparian habitats.},
}

@article {pmid40654156,
year = {2025},
author = {Suetsugu, K},
title = {Isotope evidence for partial mycoheterotrophy and trophic flexibility in the arbuscular mycorrhizal green plant Gentiana zollingeri.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70071},
pmid = {40654156},
issn = {1438-8677},
support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; },
abstract = {Arbuscular mycorrhizal (AM) associations are central to terrestrial ecosystems, typically facilitating the exchange of organic carbon from plants for mineral nutrients from fungi. Full mycoheterotrophy, in which plants derive all their carbon from AM fungi, is widespread among many achlorophyllous plant taxa such as Voyria and Voyriella (Gentianaceae). However, the extent and ecological significance of partial mycoheterotrophy, where green AM plants supplement photosynthesis with fungal carbon, remain under debate. This study investigates the nutritional mode of Gentiana zollingeri, a photosynthetic Gentianaceae species, using [13]C and [15]N stable isotope analysis, focusing on the relationship between isotopic enrichment and leaf ratio (leaf biomass relative to total shoot biomass). Gentiana zollingeri exhibited significantly higher [13]C and [15]N than autotrophic reference plants, suggesting a reliance on fungal-derived carbon and nitrogen. A negative correlation between [13]C enrichment and leaf ratio indicates that the enrichment reflects fungal dependence rather than alternative physiological traits. Notably, the underground stem showed [13]C enrichment comparable to that of fully mycoheterotrophic Gentianaceae, suggesting it is primarily composed of fungal carbon. These findings support the hypothesis that G. zollingeri employs a flexible nutrition strategy, adjusting fungal dependence according to photosynthetic capacity. Although modest [13]C and [15]N enrichment alone cannot confirm partial mycoheterotrophy, integrative approaches combining stable isotope data with ecological and physiological indicators (e.g., negative correlation between [13]C enrichment and leaf ratio) strongly support fungal carbon acquisition in G. zollingeri. Similar frameworks will help to rigorously assess partial mycoheterotrophy in other Paris-type AM plants with subtle isotopic enrichment.},
}

@article {pmid40654068,
year = {2025},
author = {Gill, J and Tharp, CL and Suseela, V},
title = {Arbuscular Mycorrhizal Symbiosis Enables Efficient Phosphorus Uptake in Sorghum Accessions With Contrasting Root Traits.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15666},
pmid = {40654068},
issn = {1365-3040},
support = {//The study was supported by the USDA-NIFA award 2022-67014-37145./ ; },
abstract = {Phosphorus (P), an essential nutrient, is apparently unavailable to plants due to strong sorption in soils. Plants with shallow root systems and high surface area exhibit high P acquisition efficiency (PAE). Arbuscular mycorrhizal fungal (AMF) symbiosis can also enhance PAE. However, whether AMF symbiosis will equally benefit crop accessions with contrasting root traits is less known. We selected sorghum accessions that varied in root traits to evaluate P uptake strategies and assessed changes in root traits, acid-phosphatase activity, primary and specialised metabolome in the presence of AMF, and under limited and stratified P availability. Our results revealed that regardless of the inherent accession differences in root traits, all accessions had higher shoot P and biomass with AMF inoculation. AMF-inoculated plants had lower specific root length, higher hyphal length and acid phosphatase activity than the non-inoculated control, indicating that plants can enhance PAE with AMF, irrespective of inherent accession differences. The AMF induced similar changes in root metabolome, where AMF-inoculated plants had higher organic acids and specialised metabolites necessary for a functional symbiosis. Our results emphasise the critical role of AMF in efficient P uptake regardless of inherent root traits, which should be considered while selecting crop accessions for improved PAE.},
}

@article {pmid40653935,
year = {2025},
author = {Zheng, Z and Ke, W and Liu, C and Cai, H and Zhu, D and Liu, Q and Ji, C and Feng, L and Gu, J and Huang, J and Wan, X and Zheng, Y and Gao, C},
title = {Symbiosomal Proteomic Analysis Reveals the Implication of Endosomal Regulators and CAPs in the Formation of Peanut Nodules.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70409},
doi = {10.1111/ppl.70409},
pmid = {40653935},
issn = {1399-3054},
support = {32270291//National Natural Science Foundation of China/ ; 32470797//National Natural Science Foundation of China/ ; 32470353//National Natural Science Foundation of China/ ; },
mesh = {*Arachis/metabolism/microbiology/genetics ; *Root Nodules, Plant/metabolism/ultrastructure ; *Plant Proteins/metabolism/genetics ; Proteomics/methods ; Symbiosis/physiology ; Gene Expression Regulation, Plant ; *Endosomes/metabolism ; Nitrogen Fixation ; Proteome/metabolism ; },
abstract = {Arachis hypogaea (peanut) is an important leguminous crop that obtains nitrogen through symbiotic nitrogen fixation with rhizobia, with root nodules serving as the site of this symbiosis. Although the cytological characteristics and ultrastructure of root nodules in model leguminous plants have been well elucidated, research progress on peanut root nodules remains relatively limited. In this study, we characterized the spatiotemporal developmental pattern of peanut root nodules through microscopic imaging and ultrastructural analysis. Furthermore, we isolated symbiosome-enriched fractions from peanut nodules for proteomic analysis and identified 340 and 182 peanut proteins in a comprehensive proteome atlas of the peanut symbiosome membrane (SM) and peribacteroid space (PBS), respectively. Notably, our analysis revealed a significant enrichment of endosomal regulators in the SM and CAP family proteins (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) in the PBS. Finally, we demonstrated that AhCAP21 specifically localizes to the symbiosome, and the SM-localized AhRabA2a is essential for proper symbiosome development. Together, these findings advance our understanding of peanut nodule development and provide insights into the protein compositions and regulators in symbiosome biogenesis in peanut nodules.},
}

*Arachis/metabolism/microbiology/genetics
*Root Nodules, Plant/metabolism/ultrastructure
*Plant Proteins/metabolism/genetics
Proteomics/methods
Symbiosis/physiology
Gene Expression Regulation, Plant
*Endosomes/metabolism
Nitrogen Fixation
Proteome/metabolism

@article {pmid40653356,
year = {2025},
author = {Sarath Krishnan, MP and Goyal, B and Nampui, L and Gupta, SC},
title = {The role of microbiome in gastrointestinal cancer.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {67-98},
doi = {10.1016/bs.ircmb.2024.12.009},
pmid = {40653356},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Neoplasms/microbiology/pathology/therapy ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {The human microbiome consists of the diverse microorganisms with their equally diverse functional abilities that have evolved over millions of years with humans. This microbiome creates a mutually beneficial symbiotic relationship with their host. Through their varied functions, the human gut microbiota is crucial for preserving health and homeostasis. Any imbalance in this microbial population can lead to an array of diseased states, including cancer especially of the gastrointestinal system. The focus of this chapter is to discuss the mechanisms through which the gut microbiome creates a conducive environment for initiation and progression of cancer. In addition, the effect of microbial products such as short chain fatty acids, bile acids and Trimethylamine N-oxide on the formation of gastrointestinal cancer is also discussed. The various experimental methods and new molecular techniques that have facilitated the characterization and study of microorganisms is also discussed. The developments in microbiome research have shed light on the potential role of gut microbiota for novel biomarker discovery and therapeutic interventions in gastrointestinal cancer, like fecal microbiota transplantation. The prospects of these areas for further exploration are discussed.},
}

Humans
*Gastrointestinal Neoplasms/microbiology/pathology/therapy
*Gastrointestinal Microbiome
Animals

@article {pmid40651702,
year = {2025},
author = {Yu, PF and Wang, D and Fu, YB and Ma, XG and Zheng, H and Han, LY and Wang, A and Jiang, DL and Sun, HW and Jin, X},
title = {The recovery mechanism of granular sludge fragmentation and re-granulation caused by long-term high-concentration organic matter erosion in the SAD process: performance, sludge evolution, and metagenomic sequencing.},
journal = {Bioresource technology},
volume = {436},
number = {},
pages = {132966},
doi = {10.1016/j.biortech.2025.132966},
pmid = {40651702},
issn = {1873-2976},
abstract = {The Simultaneous Anammox and Denitrification (SAD) process effectively removes organic carbon sources, the impact of high-concentration carbon sources on the SAD process remains unclear. This study investigated the performance, sludge characteristics, microbial community correlations, and metagenomic sequencing of the SAD system under conditions of excessive organic matter exposure. The results showed that the organic matter metabolism ability of SAD granular sludge increased from 90.16 ± 1.16 % to 95.2 ± 2.3 %. The Mantel test revealed that Anaerobic Ammonium Oxidation Bacteria (AnAOB) (Candidatus_Kuenenia) were positively correlated with VSS/SS and instability coefficient, while Denitrifying Bacteria (DNB) (Truepera, Ottowia, Deniratisoma, Arenimonas) were negatively correlated with wet density, settling velocity, granule size, protein/polysaccharides (PN/PS) ratio, and the complete coefficient. Following the recovery of the SAD system, the bacterial community correlations increased, and the stability and mechanical strength of the granular sludge were enhanced. Metagenomic sequencing showed that a decrease of Quorum sensing (QS) and the increase of c-di-GMP levels led to up-regulation of exopolysaccharide and extracellular protein expression, resulting in the disintegration of SAD granular sludge. As the sludge aggregated, recombined, and re-granulated, the system up-regulated the expression of the hzs gene in AnAOB nitrogen metabolism via c-di-GMP and QS signals. It also up-regulated the expression of genes such as Dissimilatory Nitrate Reduction to Ammonium (DNRA) and potential denitrification pathways, enhancing the metabolism of AnAOB and symbiotic bacteria.},
}

@article {pmid40651449,
year = {2025},
author = {Li, X and Zhang, Y and Wang, Y and Han, Y and Yang, T and Yan, C and Li, H and Li, C and Yan, X},
title = {Spatiotemporal distribution, co-occurrence patterns, and potential effects of virulence factors in bioaerosols emitted from an Anaerobic-Anoxic-Aerobic wastewater treatment plant.},
journal = {Water research},
volume = {286},
number = {},
pages = {124188},
doi = {10.1016/j.watres.2025.124188},
pmid = {40651449},
issn = {1879-2448},
abstract = {Bacterial pathogenicity poses a significant concern for both environmental and public health. Various virulence factors (VFs) contribute to the establishment and pathogenicity of bacteria, either independently or in combination. VFs are key indicators of the invasive potential of a pathogen. Increasing evidence suggests that municipal wastewater treatment plant (MWTP) act as both sinks and sources of pathogens and VFs. This study systematically evaluated the spatiotemporal distribution, co-occurrence patterns, and potential effects of pathogenic VFs in bioaerosols within a conventional anaerobic-anoxic-aerobic (A[2]/O) MWTP through longitudinal field monitoring. The results showed that after wastewater treatment, most VFs from wastewater were transferred to the dewatered sludge containing pathogens or host bacteria. During wastewater treatment and sludge dewatering, significant quantities of pathogenic VFs were released into the air. Pathogenic VFs were most abundant and stable in bioaerosols during the spring. Fine grid (FG) and sludge dewatering room (SDR) were identified as the primary units responsible for VF dissipation and pathogen accumulation. Pathogens significantly affected VF overexpression in bioaerosols, with strong positive symbiotic networks observed during all four seasons (54.14 %, 74.26 %, 59.77 %, and 59.82 %). In addition, the pathogenic VFs emitted from MWTPs were carried by wind, affecting the surrounding air quality. This study enhances understanding of the pollution caused by pathogenic VFs in MWTPs, providing important insights for assessing their environmental risks and formulating effective control strategies. It also contributes to safeguarding aquatic ecosystems and public health.},
}

@article {pmid40650573,
year = {2025},
author = {Dunken, N and Thomsen, T and Zuccaro, A},
title = {Purine-Based Infochemicals and Immunometabolites: A Comparative Review of Emerging Signaling Pathways in Plants and Animals.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf029},
pmid = {40650573},
issn = {1574-6976},
abstract = {Purine-based metabolites serve as essential mediators of signaling, immunity, and host-microbe interactions across biological kingdoms. This review explores their extracellular and intracellular functions, focusing on well-characterized molecules as well as emerging players, and examines the conserved and divergent mechanisms underlying purine-mediated responses in plants and animals, with comparative insights into microbial strategies that influence or exploit these pathways. Key topics include the role of extracellular ATP in immune responses, the dual function of NAD+ as both a metabolic cofactor and signaling molecule, and the emerging roles of deoxynucleosides and cyclic nucleotides in stress and immunity regulation. Special emphasis is placed on TIR domain-containing proteins, which generate novel purine-derived infochemicals-bioactive signaling metabolites that regulate immune responses and cell death while modulating host-microbe interactions. By integrating insights across biological kingdoms, this review underscores the potential of purine-based signaling molecules and their natural and chemically modified functional derivatives as targets for therapeutic and agricultural innovation, bridging fundamental discoveries with practical applications. Finally, moving beyond purine-based metabolites, we offer a new perspective on immunometabolism and infochemicals as fundamental regulators of host-microbe interactions, shaping defense, modulating metabolism, facilitating symbiosis, and driving broader evolutionary dynamics.},
}

@article {pmid40649804,
year = {2025},
author = {Saleem, MA and Khan, A and Tu, J and Huang, W and Liu, Y and Feng, N and Zheng, D and Xue, Y},
title = {Salinity Stress in Rice: Multilayered Approaches for Sustainable Tolerance.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40649804},
issn = {1422-0067},
support = {2024KJ31//Guangdong Provincial Department of Agriculture and Rural Affairs/ ; },
mesh = {*Oryza/genetics/physiology ; *Salt Tolerance/genetics ; *Salt Stress ; Gene Editing ; Gene Expression Regulation, Plant ; Salinity ; Stress, Physiological ; },
abstract = {Salt accumulation in arable lands causes significant abiotic stress, resulting in a 10% loss in global arable land area and jeopardizing food production and agricultural sustainability. In order to attain high and sustainable food production, it is imperative to enhance traditional agricultural practices with modern technology to enable the restoration of arable lands afflicted by salinity. This review consolidates recent rice-specific advancements aimed at enhancing salt stress resilience through integrated strategies. We explore the functions of primary and secondary metabolic pathways, organic amendments, microbial symbiosis, and plant growth regulators in reducing the negative impacts of salt. Furthermore, we highlight the significance of emerging genetic and epigenetic technologies, including gene editing and transcriptional regulation, in developing salt-tolerant rice cultivars. Physiological studies reveal salt stress responses in rice plants, biochemical analyses identify stress-related metabolites, microbial investigations uncover beneficial plant-microbe interactions, and molecular approaches enable the identification of key genes-together providing essential insights for developing salt-tolerant rice varieties. We present a comprehensive overview of the multilayered strategies-ranging from agronomic management and physiological adaptations to molecular breeding and microbial applications-that have been developed and refined over recent decades. These approaches have significantly contributed to understanding and improving salinity tolerance mechanisms in rice. This review provides a foundational framework for future research and practical implementation in stress-resilient rice farming systems.},
}

*Oryza/genetics/physiology
*Salt Tolerance/genetics
*Salt Stress
Gene Editing
Gene Expression Regulation, Plant
Salinity
Stress, Physiological

@article {pmid40648017,
year = {2025},
author = {Sun, W and Shahrajabian, MH and Guan, L},
title = {The Biocontrol and Growth-Promoting Potential of Penicillium spp. and Trichoderma spp. in Sustainable Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40648017},
issn = {2223-7747},
support = {Grant no. 2024YFA0918200//the National Key R&D Program of China/ ; MTGF2023050//the Scientific Research Project of Kweichow Moutai Liquor Co., Ltd./ ; },
abstract = {Plant-growth-promoting fungi (PGPF) play a central role in promoting sustainable agriculture by improving plant growth and resilience. The aim of this literature review is to survey the impacts of Trichoderma spp. and Penicillium spp. on various agricultural and horticultural plants. The information provided in this manuscript was obtained from randomized control experiments, review articles, and analytical studies and observations gathered from numerous literature sources such as Scopus, Google Scholar, PubMed, and Science Direct. The keywords used were the common and Latin names of various agricultural and horticultural species, fungal endophytes, plant-growth-promoting fungi, Trichoderma, Penicillium, microbial biostimulants, and biotic and abiotic stresses. Endophytic fungi refer to fungi that live in plant tissues throughout part of or the entire life cycle by starting a mutually beneficial symbiotic relationship with its host without any negative effects. They are also capable of producing compounds and a variety of bioactive components such as terpenoids, steroids, flavonoids, alkaloids, and phenolic components. Penicillium is extensively known for its production of secondary metabolites, its impact as a bioinoculant to help with crop productivity, and its effectiveness in sustainable crop production. The plant-growth-promotion effects of Trichoderma spp. are related to better absorption of mineral nutrients, enhanced morphological growth, better reproductive potential and yield, and better induction of disease resistance. Both Penicillium spp. and Trichoderma spp. are effective, affordable, safe, and eco-friendly biocontrol agents for various plant species, and they can be considered economically important microorganisms for both agricultural and horticultural sciences. The present review article aims to present the most up-to-date results and findings regarding the practical applications of two important types of PGPF, namely Penicillium spp., and Trichoderma spp., in agricultural and horticultural species, considering the mechanisms of actions of these species of fungi.},
}

@article {pmid40647982,
year = {2025},
author = {Sheng, H and Shahzad, B and Long, F and Haider, FU and Li, X and Xian, L and Huang, C and Ma, Y and Li, H},
title = {Plant Diversity and Microbial Community Drive Ecosystem Multifunctionality in Castanopsis hystrix Plantations.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647982},
issn = {2223-7747},
support = {52478053//National Natural Science Foundation of China/ ; 52078222//National Natural Science Foundation of China/ ; },
abstract = {Monoculture plantation systems face increasing challenges in sustaining ecosystem multifunctionality (EMF) under intensive management and climate change, with long-term functional trajectories remaining poorly understood. Although biodiversity-EMF relationships are well-documented in natural forests, the drivers of multifunctionality in managed plantations, particularly age-dependent dynamics, require further investigation. This study examines how stand development influences EMF in Castanopsis hystrix L. plantations, a dominant subtropical timber species in China, by assessing six ecosystem functions (carbon stocks, wood production, nutrient cycling, decomposition, symbiosis, and water regulation) of six forest ages (6, 10, 15, 25, 30, and 34 years). The results demonstrate substantial age-dependent functional enhancement, with carbon stocks and wood production increasing by 467% and 2016% in mature stand (34 year) relative to younger stand (6 year). Nutrient cycling and water regulation showed intermediate gains (6% and 23%). Structural equation modeling identified plant diversity and microbial community composition as direct primary drivers. Tree biomass profiles emerged as the strongest biological predictors of EMF (p < 0.01), exceeding abiotic factors. These findings highlight that C. hystrix plantations can achieve high multifunctionality through stand maturation facilitated by synergistic interactions between plants and microbes. Conservation of understory vegetation and soil biodiversity represents a critical strategy for sustaining EMF, providing a science-based framework for climate-resilient plantation management in subtropical regions.},
}

@article {pmid40647912,
year = {2025},
author = {Li, L and Liu, L and Zou, G and Wang, X and Xu, L and Yang, Y and Liu, J and Liu, H and Liu, D},
title = {Composted PBST Biodegradable Mulch Film Residues Enhance Crop Development: Insights into Microbial Community Assembly, Network Interactions, and Soil Metabolism.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647912},
issn = {2223-7747},
support = {KJCX20230421//Capacity-building Projects by the Beijing Academy of Agriculture and Forestry Sciences/ ; CARS-02-23//Earmarked Fund for China Agriculture Research System/ ; 2023YFD1701901-05//National Key Research and Development Program of China/ ; 2024-zz-077//Beijing Postdoctoral Research Foundation/ ; 42407035//National Natural Science Foundation of China/ ; },
abstract = {Biodegradable mulch film (BDM) is regarded as a key solution to combat plastic mulch film pollution due to its ability to degrade completely into CO2 and H2O through environmentally friendly microorganisms. However, commercial BDM often fails to degrade fully after use, leading to the accumulation of BDM residues in soil and their transformation into microplastics (MPs) via various processes, posing a threat to the soil ecosystem. Given these discrepancies between the theoretical and practical degradation performance of BDM, there is an urgent need to understand the impacts of BDM residues on plant growth and soil health. This research conducted pot experiments spanning the entire growth cycle of Chinese cabbage to evaluate the impact of PBST-BDM raw material (R), PBST-BDM residues (M), and PBST-BDM composting product (P) on crop growth and soil quality. The findings revealed that R treatments had a slight effect on Chinese cabbage growth (e.g., a 5.80% increase in emergence rate in R 1% treatment, p < 0.05), while M treatments significantly hindered the emergence rate, plant height, leaf area, and biomass accumulation of Chinese cabbage by 30.4% (p < 0.05), 2.71 cm (p < 0.05), 39.0% (p < 0.05), and 1.86 g (p < 0.05) in the M 1% treatment compared to the control group (CK). In contrast, P treatments enhanced Chinese cabbage growth, with greater improvements at higher weight ratios, resulting in increases of 8.89% (p < 0.05), 4.96 cm (p < 0.05), 36.3% (p < 0.05), and 2.31 g (p < 0.05) in the P 1% treatment. Microbial network topology in the M 1% treatment is highly variable, with the increased proportion of positive correlations in the P 1% treatment hinting at stronger symbiotic interactions between species (p < 0.05). Analysis results of PCoA and PLS-DA showed significant differences in microbial community and soil metabolites between M 1% treatment and CK (p < 0.05). These findings suggest that, although composting post-use BDM may reduce their negative ecological effects, possibly via accelerating the early breakdown of residues, the feasibility and scalability of this approach require further validation under real-world field conditions.},
}

@article {pmid40647560,
year = {2025},
author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Piątkowska, M and Czarnowski, P and Goryca, K and Zeber-Lubecka, N and Dąbrowska, M and Kaniuga, E and Cybulska-Lubak, M and Bałabas, A and Statkiewicz, M and Rumieńczyk, I and Pyśniak, K and Mikula, M and Ostrowski, J},
title = {Comparative Analysis of Gut Microbiota Responses to New SN-38 Derivatives, Irinotecan, and FOLFOX in Mice Bearing Colorectal Cancer Patient-Derived Xenografts.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
pmid = {40647560},
issn = {2072-6694},
support = {2018/31/B/NZ7/02675//National Science Center/ ; },
abstract = {BACKGROUND: Symbiotic gut microbiota can enhance cancer therapy efficacy, while treatment-induced dysbiosis may reduce effectiveness or increase toxicity. Our preclinical study compared the anticancer effects and impact on fecal microbiota and metabolites of two water-soluble SN-38 derivatives (BN-MePPR and BN-MOA), with those observed after treatment with Irinotecan, and the FOLFOX regimen in NOD scid gamma mice bearing patient-derived colon adenocarcinoma xenografts (CRC PDX).

METHODS: Five individual experiments with Irinotecan and its derivatives and eight individual experiments with FOLFOX were conducted using eight CRC PDX models. Chemotherapeutics were administered intraperitoneally 4-5 times at 5-day intervals. Fecal samples were collected before and after treatment. Microbiota composition was analyzed by 16S rRNA gene (V3-V4 regions) sequencing. Mass spectrometry was used to quantify short-chain fatty acids (SCFAs) and amino acids (AAs).

RESULTS: All treatments significantly inhibited tumor growth versus controls. However, no significant changes were observed in gut microbiota α- and β-diversity between treated and untreated groups. Tumor progression in controls was associated with increased abundance of Marvinbryantia, Lactobacillus, Ruminococcus, and [Eubacterium] nodatum group. FOLFOX-treated mice showed increased Marvinbryantia, Bacteroides, and Candidatus Arthromitus, and decreased Akkermansia. No distinct taxa changes were found in the Irinotecan or derivative groups. SCFA levels remained unchanged across groups, while BN-MePPR, BN-MOA, and Irinotecan all increased AA concentrations.

CONCLUSIONS: Contrary to earlier toxicological data, these findings indicate a relatively limited impact of the tested chemotherapeutics on the gut microbiome and metabolome, emphasizing the importance of research method selection in preclinical studies.},
}

@article {pmid40646719,
year = {2025},
author = {Tong, X and Kobayashi, Y and Ikeda, M and Wen, H and Akimoto, S-i and Shigenobu, S},
title = {Draft genome sequences of Buchnera aphidicola from three aphid species (Hemiptera: Aphididae: Eriosomatinae) associated with gall formation on elm trees.},
journal = {Microbiology resource announcements},
volume = {14},
number = {7},
pages = {e0033625},
pmid = {40646719},
issn = {2576-098X},
support = {Special Postdoctoral Researcher Fellowship//RIKEN/ ; 22K20588//Japan Society for the Promotion of Science/ ; 24-IMS-C279//National Institute for Basic Biology/ ; },
abstract = {The Buchnera aphidicola genomes from eriosomatine gall-forming aphids Tetraneura sorini, Tetraneura akinire, and Eriosoma harunire were sequenced, with genome sizes of 533,871, 530,863, and 627,315 bp, respectively. These genomes shed light on Buchnera's role in aphid symbiosis and adaptation.},
}

@article {pmid40645173,
year = {2025},
author = {Mercader, M and Ziadi-Künzli, F and Olivieri, S and Komoto, S and Rosti, ME and Frédérich, B and Laudet, V},
title = {Integrative phenotyping reveals new insights into the anemonefish adaptive radiation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.06.041},
pmid = {40645173},
issn = {1879-0445},
abstract = {Evolutionary radiations are fundamental to the generation of biodiversity, occurring when organisms rapidly diversify to exploit various ecological niches. Symbiosis can serve as a powerful catalyst for such diversification, as illustrated by the iconic association of anemonefish and sea anemones. However, a critical gap in our understanding of adaptive radiations lies in determining how ecological opportunities drive adaptive morphological, behavioral, and physiological traits and how these traits, in turn, influence diversification. Using anemonefish (Amphiprion spp.) as a model, we investigated the phenotypic diversification accompanying their evolutionary history following symbiosis with giant sea anemones. While host specificity has traditionally been viewed as the primary driver of anemonefish adaptive radiation, we present an alternative perspective, showing that distinct ecological strategies-independent of host species-may also significantly contribute to their diversification. By examining half of the described anemonefish species, we combined field observations, swimming tunnel experiments, computational simulations, and morphological analyses to empirically reveal the presence of eco-morphotypes that exist independently of host specificity. Our findings provide novel insights into the evolutionary history and processes shaping anemonefish diversity. We show that, beyond sea anemone hosts, multiple drivers significantly contributed to their diversification. Integrative phenotyping, combining in situ and laboratory observations, reveals the forces driving adaptive radiations. It uncovers an unexpected, fine-tuned diversification in anemonefish, exemplifying how natural selection precisely shapes biodiversity during radiative bursts and highlighting the complexity of ecological interactions and evolutionary mechanisms.},
}

@article {pmid40644904,
year = {2025},
author = {Zhang, H and Xu, K and Xing, R and Wang, L and Liu, R and Wang, X and Chen, L and Li, R and Yu, Z and Cao, X and Cheng, C and Su, Q},
title = {Differential response patterns of bacterial communities in seawater and sediments to the Chaetomorpha valida bloom in sea cucumber Apostichopus japonicus aquaculture ponds.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118359},
doi = {10.1016/j.marpolbul.2025.118359},
pmid = {40644904},
issn = {1879-3363},
abstract = {The microbiota play a critical role in the health of the aquaculture pond ecosystem. Green tide have been found to affect the microbial community in the marine environments, but effects of Chaetomorpha valida bloom on the microbial composition in the aquaculture ponds related to the marine economic species have been rarely investigated. To address this shortcoming, we provided baseline information on the bacterial composition and diversity in C. valida bloom areas and non-bloom areas of Apostichopus japonicus aquaculture ponds in four seasons. High-throughput 16S rRNA sequencing revealed that C. valida bloom significantly changed the bacterial community composition in seawater and bacterial richness in sediment, but has minor effects on sediment bacterial community structure. The co-occurrence network analysis indicated that the bloom of C. valida intensified interspecific competition among sedimentary bacteria, thereby enhancing their stability. In contrast, it promoted symbiotic relationships among bacteria in seawater. Importantly, there were higher proportions of potential pathogens in seawater from C. valida bloom areas compared to non-bloom areas, suggesting a higher ecological risk associated with the C. valida blooms. This study offers novel perspectives on how bacterial communities in sediments and seawater differently respond to C. valida bloom in aquaculture systems.},
}

@article {pmid40644680,
year = {2025},
author = {McGarrigal, LD and Morse, CI and Sims, DT and Stebbings, GK},
title = {Development of Stretch-Shortening Cycle Function in Girls During Maturation and in Response to Training: A Narrative Review.},
journal = {Journal of strength and conditioning research},
volume = {},
number = {},
pages = {},
doi = {10.1519/JSC.0000000000005191},
pmid = {40644680},
issn = {1533-4287},
abstract = {McGarrigal, LD, Morse, CI, Sims, DT, and Stebbings, GK. Development of stretch-shortening cycle function in girls during maturation and in response to training: A narrative review. J Strength Cond Res 39(8): e1061-e1069, 2025-The aim of this narrative review was to examine stretch-shortening cycle (SSC) function and to explore its effects on the athletic performance in girls during maturation and in response to plyometric training (PT), where there has been limited focus to date. The SSC is an integral component of explosive actions such as sprinting and jumping. Literature shows that the SSC develops during maturation because of several morphological, neurophysiological, and structural mechanisms, and that the SSC response can be amplified by training. Research suggests that boys experience "accelerated adaptation" in slow and fast SSC function as they mature, but to date, similar studies in girls are limited and often contradictory. Plyometric training capitalizes on the ability of the SSC to generate greater force production by including an eccentric muscle action quickly followed by a concentric action. However, the number of PT studies involving youth female athletes is lacking, with only 10% of all PT studies including female subjects aged <18 years. This is surprising given that PT can enhance athletic performance and reduce the risk of noncontact anterior cruciate ligament injuries in girls. After PT, boys experience "synergistic adaptation," which is the symbiotic relationship between PT strategically programmed to coincide with the development of the SSC that is being concurrently enhanced by the processes of growth and maturation. Establishing if girls experience periods of accelerated and synergistic adaptation in slow and fast SSC function after PT would likely influence future training in this population, which has traditionally been underserved.},
}

@article {pmid40644522,
year = {2025},
author = {Fercoq, F and Cormerais, C and Remion, E and Gal, J and Plisson, J and Fall, A and Alonso, J and Lhermitte-Vallarino, N and Hübner, MP and Kohl, L and Landmann, F and Martin, C},
title = {Host environment shapes filarial parasite fitness and Wolbachia endosymbionts dynamics.},
journal = {PLoS pathogens},
volume = {21},
number = {7},
pages = {e1013301},
doi = {10.1371/journal.ppat.1013301},
pmid = {40644522},
issn = {1553-7374},
abstract = {Filarial nematodes, responsible for diseases like lymphatic filariasis and onchocerciasis, depend on symbiotic Wolbachia bacteria for reproduction and development. Using the Litomosoides sigmodontis rodent model, we investigated how host type-2 immunity influences Wolbachia dynamics and parasite development. Wild-type and type-2 immune-deficient (Il4rα[-]/[-]Il5[-]/[-]) BALB/c mice were infected with L. sigmodontis, and the distribution and abundance of Wolbachia were analyzed at different developmental stages using quantitative PCR and fluorescence in situ hybridization. Our results show that type-2 immune environments selectively reduce germline Wolbachia in female filariae from wild-type mice, a change associated with disrupted oogenesis, embryogenesis, and microfilarial production, while somatic Wolbachia remain unaffected. Antibiotic treatments achieving systemic Wolbachia clearance result in similar reproductive impairments. Notably, Wolbachia-free microfilariae are observed shortly after Wolbachia depletion, suggesting that early-stage embryogenesis can proceed temporarily before progressive germline dysfunction ensues. Wolbachia-free microfilariae develop into infective larvae in the vector, but stall beyond the L4 stage in vertebrate hosts, showing arrested growth and reproductive organ maturation defects in both male and female larvae. These findings highlight the variable dependency on Wolbachia across life stages and provide insights into host-parasite-endosymbiont interactions shaped by environmental pressures.},
}

@article {pmid40643254,
year = {2025},
author = {Tian, H and Fei, G and Guan, J and Xu, Z and Qu, J and Dai, Y and Zou, X},
title = {Ophiocordyceps zhenxingensis sp. nov. and its microbiota during sexual and asexual stages in nature.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0215924},
doi = {10.1128/spectrum.02159-24},
pmid = {40643254},
issn = {2165-0497},
abstract = {UNLABELLED: Ophiocordyceps holds significant importance in forest arthropod population regulation, biological control of agricultural pests, and the development of bioactive substances. Investigating the microbial community composition of wild Ophiocordyceps is significant for understanding its individual development process, understory cultivation, and taxonomy. In this study, a novel insect pathogenic fungus, Ophiocordyceps zhenxingensis, parasitizing Hymenoptera larvae, originating from Liaoning Province, China, was delineated based on morphology and phylogenetics. The microbial communities in the sclerotium and host surface complex of its different reproductive stages (sexual and asexual) were investigated. O. zhenxingensis was detected within the Hirsutella citriformis subclade, being closely related to Hirsutella gigantea and Ophiocordyceps elongata. It was morphologically characterized by solitary or multiple stromata, semi-submerged perithecia, and viscous basidiospores. Proteobacteria, Actinobacteriota, and Bacteroidota were the major bacterial taxa, and Basidiomycota and Ascomycota were the major fungal taxa. Tomentella, Sebacina, and Russula were abundant in the host surface complex that belongs to mycorrhizal fungi. The microbial co-occurrence network suggested that microbial relationships were predominantly positive correlations, and positive correlations were more pronounced in the asexual stage than the sexual stage. The microbial co-occurrence network of O. zhenxingensis was more complex during the asexual stage; it exhibited greater metabolic activity during the asexual stage. These results have enhanced our understanding of the composition, diversity, and functions of the endophytic microbial community of Ophiocordyceps, furnishing additional evidence for classifying its sexual and asexual stages and establishing a theoretical basis for subsequent research on its individual development.

IMPORTANCE: Ophiocordyceps exhibits two distinct life stages (asexual and sexual) in its natural environment. The symbiotic microorganisms associated with the fungus play a crucial role in its growth and development. We have identified a new species, Ophiocordyceps zhenxingensis, which belongs to the Hirsutella citriformis subclade. A large number of mycorrhizal fungi were found in the insect appendages of O. zhenxingensis, whereas the fungal community within the sclerotium was predominantly composed of Ascomycota. During the asexual stage, O. zhenxingensis exhibited greater microbial diversity and stronger positive correlations among microorganisms. Additionally, it possesses a richer array of metabolic pathways. These results have deepened our knowledge of the composition, diversity, and roles of the microbial community in Ophiocordyceps, providing further evidence for distinguishing its sexual and asexual stages and laying a theoretical foundation for future research on its developmental processes.},
}

@article {pmid40642959,
year = {2025},
author = {Wilder, SM and Herzog, C and Reeves, J and Knowles, O and Cuff, JP},
title = {Bridging digestive physiology and ecology for a more integrative understanding of invertebrate predators.},
journal = {The Journal of experimental biology},
volume = {228},
number = {14},
pages = {},
doi = {10.1242/jeb.249697},
pmid = {40642959},
issn = {1477-9145},
support = {IOS-2420366//National Science Foundation/ ; //Newcastle University/ ; },
mesh = {Animals ; *Invertebrates/physiology ; *Predatory Behavior/physiology ; *Digestive System Physiological Phenomena ; *Food Chain ; Symbiosis ; Ecology ; Animal Nutritional Physiological Phenomena ; },
abstract = {Nutritional ecology aims to explore the connections between the behaviour, physiology and ecology of organisms using nutrients as the unifying currency. Although significant progress has been made in studying the nutritional ecology of vertebrates and herbivorous invertebrates, research on predatory invertebrates has lagged, despite their importance in driving ecosystem processes and services, such as nutrient cycling and pest management. However, recent methodological and conceptual advances have provided significant opportunities to explore the interface of digestive physiology and ecology in predatory invertebrates. The goal of this Commentary is to explore evidence for interactions between the ecology and physiology of invertebrate predators, and to propose hypotheses and directions for future studies to expand our understanding in this area. Connections between invertebrate predator ecology and digestive physiology are discussed in relation to four pertinent topics that allow for integrative studies of invertebrate predators: micronutrients, foraging behaviour, microbial symbiosis and the Anthropocene. We hope that these areas of research will serve as examples of how physiology and ecology can be integrated for a more holistic understanding of the nutritional ecology of predatory invertebrates.},
}

Animals
*Invertebrates/physiology
*Predatory Behavior/physiology
*Digestive System Physiological Phenomena
*Food Chain
Symbiosis
Ecology
Animal Nutritional Physiological Phenomena

@article {pmid40642887,
year = {2025},
author = {Liu, Y and Jian, J and Xu, L and Meng, L and Yang, F and Li, S and Yan, J},
title = {Arbuscular Mycorrhizal Fungi Change the Growth and Metabolites of Perilla frutescens, with Subsequent Effects on the Development and Behavior of Spodoptera exigua.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c03530},
pmid = {40642887},
issn = {1520-5118},
abstract = {Arbuscular mycorrhizal fungi (AMF) influence plant-insect interactions, yet how they modulate volatile organic compounds (VOCs) to affect insect behavior remains unclear. This study integrates physiological assays, GC-MS volatile metabolomics, and insect bioassays to investigate how Funneliformis mosseae (Fm) and Rhizophagus intraradices (Ri) inoculation affects Perilla frutescens growth and its resistance to Spodoptera exigua. The results showed that Fm and Ri inoculation both promoted plant growth but differed in defense strategies. Ri inoculation increased the tannin content (16.98%) and polyphenol oxidase activity (40.52%), whereas Fm inoculation showed neutral effects. VOC profiling revealed that Ri inoculation upregulated leaf monoterpenes and phenylpropanoids, while Fm inoculation reduced sesquiterpenes (e.g., β-selinene). Insect bioassays showed that Ri inoculation inhibited the insect growth, whereas Fm inoculation promoted the insect growth and enhanced its feeding preference. These results revealed that AMF triggers a plant growth-defense trade-off, with sesquiterpenoid regulation critical for insect behavioral shifts. The findings provide a basis for sustainable pest management using AMF-plant symbiosis.},
}

@article {pmid40641649,
year = {2025},
author = {Yu, X and Zhu, H},
title = {Enacting partner specificity in legume-rhizobia symbioses.},
journal = {aBIOTECH},
volume = {6},
number = {2},
pages = {311-327},
pmid = {40641649},
issn = {2662-1738},
abstract = {Legumes, such as peas, beans, and alfalfa, have evolved a remarkable ability to establish root nodule symbioses with nitrogen-fixing soil bacteria to fulfill their nitrogen needs. This partnership is characterized by a high degree of specificity, occurring both within and between host and bacterial species. Consequently, nodulation capacity and nitrogen-fixing efficiency vary significantly among different plant-bacteria pairs. The genetic and molecular mechanisms regulating symbiotic specificity are diverse, involving a wide array of host and bacterial genes and signals with various modes of action. Understanding the genetic basis of symbiotic specificity could enable the development of strategies to enhance nodulation capacity and nitrogen fixation efficiency. This knowledge will also help overcome the host range barrier, which is a critical step toward extending root nodule symbiosis to non-leguminous plants. In this review, we provide an update on our current understanding of the genetics and evolution of recognition specificity in root nodule symbioses, providing more comprehensive insights into the molecular signaling in plant-bacterial interactions.},
}

@article {pmid40641645,
year = {2025},
author = {Gao, JP and Su, Y and Jiang, S and Liang, W and Lou, Z and Frugier, F and Xu, P and Murray, JD},
title = {Applying conventional and cell-type-specific CRISPR/Cas9 genome editing in legume plants.},
journal = {aBIOTECH},
volume = {6},
number = {2},
pages = {346-360},
pmid = {40641645},
issn = {2662-1738},
abstract = {The advent of genome editing technologies, particularly CRISPR/Cas9, has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis. The legume-rhizobia symbiosis is crucial for sustainable agriculture, enhancing nitrogen fixation and improving soil fertility. Numerous genes with a symbiosis-specific expression have been identified, sometimes exclusively expressed in cells forming infection threads or in nitrogen-fixing nodule cells. Typically, mutations in these genes do not affect plant growth. However, in some instances, germline homozygous mutations can be lethal or result in complex pleiotropic phenotypes that are challenging to interpret. To address this issue, a rhizobia-inducible and cell-type-specific CRISPR/Cas9 strategy was developed to knock-out genes in specific legume transgenic root tissues. In this review, we discuss recent advancements in legume genome editing, highlighting the cell-type-specific CRISPR system and its crucial applications in symbiotic nitrogen fixation and beyond.},
}

@article {pmid40641644,
year = {2025},
author = {Sun, F and Zhu, F and Ran, S and Ye, Q and Wang, T and Dong, J},
title = {Heterotrimeric G-protein subunits regulate plant architecture, pod development, seed size, and symbiotic nodulation in Medicago truncatula.},
journal = {aBIOTECH},
volume = {6},
number = {2},
pages = {141-159},
pmid = {40641644},
issn = {2662-1738},
abstract = {UNLABELLED: Heterotrimeric G proteins are crucial transducers of signaling from receptors, participating in growth and development, as well as in responses to biotic and abiotic stimuli. However, little is known about their roles in regulating various yield-related traits in legumes. In this study, we systematically analyzed the functions of two G-protein-encoding genes, MtGα1 and MtGβ1, along with Regulator of G-protein Signaling1 (MtRGS1), in Medicago truncatula. All three genes were ubiquitously expressed in roots, stems, leaves, nodules, flowers, and pods. We generated the knockout mutants Mtgα1, Mtgβ1, and Mtrgs1 using CRISPR/Cas9 and assessed their growth and development. MtGα1 knockout resulted in slightly shorter plants with smaller pods and shorter spines, but larger seeds, without affecting overall biomass or other traits. MtGβ1 knockout led to dwarfism, weak root development, a severe drop in biomass production, smaller legume pods with shorter spines, and smaller seeds. However, the Mtrgs1 mutants were largely similar to wild-type plants, with few significant defects in growth and development. We also investigated the symbiotic nodulation-related phenotypes of these mutants, discovering that Mtgβ1 mutants produce lighter nodules, whereas Mtgα1 and Mtrgs1 mutants have normal nodulation phenotypes similar to those of wild-type plants. These observations suggest that MtGβ1 positively regulates nodulation, although the detailed mechanisms by which G proteins regulate symbiotic nitrogen fixation in M. truncatula remain to be explored. This work provides potentially valuable genetic resources for further functional analysis and elucidation of the molecular mechanisms of G proteins in this model legume.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00210-x.},
}

@article {pmid40639969,
year = {2025},
author = {Shi, C and Wang, C and He, J and Zhang, M and Huang, W},
title = {Epichloë Endophytes Potentially Facilitate Host Plant Recruitment of Rhizosphere Microbiota Carrying Beneficial Traits.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70397},
doi = {10.1111/ppl.70397},
pmid = {40639969},
issn = {1399-3054},
support = {31760704//National Natural Science Foundation of China/ ; 2022D01A79//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 23XJTRZW07//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
mesh = {*Rhizosphere ; *Endophytes/physiology ; Plant Roots/microbiology ; *Epichloe/physiology ; *Microbiota/physiology ; Soil Microbiology ; Symbiosis ; },
abstract = {Plant-microbe symbiotic relationships drive ecosystem evolution. This study employed metabolomics and metagenomic technologies to investigate the effects of the aboveground-restricted endophytic fungus Epichloë guerinii in the host plant Melica transsilvanica on the rhizosphere microbial community structure and functional traits. Our results revealed that the presence of E. guerinii significantly increased the secretion of organic acids, amino acids, and sugar alcohols from the host root system. These exudates correlated strongly with abundant, plant growth-promoting rhizosphere microorganisms like Pseudomonas, Bradyrhizobium, and Nitrospira. Functional genes that were significantly enriched in the host rhizosphere microbiota were predominantly associated with biofilm formation and organic acid metabolic pathways. Co-enrichment analyses of rhizosphere soil metabolites and genes highlighted pathways such as flagellar assembly and carbon/nitrogen/sulfur metabolism. Notably, the abundance of key genes governing the flagellar motor MotA protein in the host rhizosphere, as well as those involved in the reductive tricarboxylic acid (rTCA) cycle, nitrification, and thiosulfate oxidation, were significantly elevated. This study demonstrates that E. guerinii positively regulates rhizosphere microbial community functions by reprogramming the composition of host root exudates. These findings deepen the mechanistic understanding of Epichloë-plant-rhizosphere microbe interactions.},
}

*Rhizosphere
*Endophytes/physiology
Plant Roots/microbiology
*Epichloe/physiology
*Microbiota/physiology
Soil Microbiology
Symbiosis

@article {pmid40638949,
year = {2025},
author = {Zhang, S and Yuan, C and Wang, G and Zhou, Y and Tian, M and Gao, C and Li, D and Guo, L and Wei, L and Yang, J and Liu, N and Jian, S},
title = {Arbuscular mycorrhizal fungi enhance the tolerance of Casuarina equisetifolia to drought and salt stress under coral sand matrix conditions.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118400},
doi = {10.1016/j.marpolbul.2025.118400},
pmid = {40638949},
issn = {1879-3363},
abstract = {To evaluate the effects of arbuscular mycorrhizal fungi (AMF) on the stress tolerance of Casuarina equisetifolia in coral sand matrix, we inoculated seedlings with Funneliformis mosseae and Rhizophagus intraradices and subjected them to salt stress (SS) and drought stress (DS). The results indicated that AMF colonization significantly (p < 0.05) enhanced height (42-123 %), proline and soluble sugar concentrations, and the peroxidase and superoxide dismutase activities (0.65-1.78-fold) when seedlings subjected to DS or SS. Compared to non-inoculated seedlings, genes and metabolites in AM-inoculated seedlings were significantly enriched in flavonoid, anthocyanin, and phenylpropanoid biosynthesis, and citrate cycle pathways under DS. Under SS, there was significant enrichments in pathways related to MAPK signaling, plant hormone signaling, and anthocyanin biosynthesis. This study elucidates the mechanisms by which AMF enhance C. equisetifolia tolerance in coral sand matrix at physiological, transcriptional, and metabolic levels, providing a theoretical basis for coastal vegetation restoration.},
}

@article {pmid40638905,
year = {2025},
author = {Uthra, C and Muralitharan, G and Manjula, R and Nagaraj, K},
title = {High-Sensitivity Detection of Neurodegenerative Cyanotoxins in Cycas circinalis and Symbiotic Cyanobacteria Dolichospermum circinalis Using Advanced LC-MS/MS and HR-MS With Toxicological Assessment via Artemia salina Bioassay.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {e00988},
doi = {10.1002/cbdv.202500988},
pmid = {40638905},
issn = {1612-1880},
abstract = {Human exposure to β-N-methylamino-l-alanine (BMAA) and its derivatives, aminoethyl glycine (AEG) and 2,4-diaminobutyric acid (DAB), through environmental and dietary sources has been implicated in neurodegenerative diseases, necessitating the development of sensitive detection methods. We developed and validated a high-sensitivity liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to detect BMAA and its derivatives in seeds and coralloid roots of Cycas circinalis and associated cyanobacteria (Anabaena circinalis). These neurotoxins are produced by cyanobacteria and can bioaccumulate in symbiotic plant systems such as cycads, raising concerns over potential human exposure through environmental contact or dietary consumption. In this study, we developed and validated a highly sensitive LC-MS/MS and high-resolution mass spectrometry (HR-MS) method for detecting BMAA, DAB, and AEG in C. circinalis seeds and coralloid roots, as well as associated cyanobacteria. An acid hydrolysis extraction, followed by 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) derivatization, increased detection sensitivity. The structural confirmation was performed using FT-IR and ESI-MS. Our results demonstrated significant variation in toxin concentrations, with seeds containing the highest quantities of BMAA and AEG. Compared with the aqueous extract, the methanolic extracts of A. circinalis showed severe toxicity in a brine shrimp lethality assay, resulting in 100% mortality at 100 µL.},
}

@article {pmid40637797,
year = {2025},
author = {Giani, NM and Lim, SJ and Anderson, LC and Paterson, AT and Engel, AS and Campbell, BJ},
title = {Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf074},
pmid = {40637797},
issn = {1574-6941},
abstract = {Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across eight waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of C1 metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.},
}

@article {pmid40637599,
year = {2025},
author = {Shik, JZ and Dussutour, A and De Fine Licht, HH},
title = {Harnessing Nutritional Niches to Explore Fungus-Animal Symbioses.},
journal = {Ecology letters},
volume = {28},
number = {7},
pages = {e70176},
pmid = {40637599},
issn = {1461-0248},
support = {CF20-0609//Carlsbergfondet/ ; CF22-0664//Carlsbergfondet/ ; 50281//Villum Fonden/ ; },
mesh = {*Symbiosis ; Animals ; *Fungi/physiology ; Biological Evolution ; },
abstract = {Fungus-animal symbioses have evolved countless times across the tree of life. While the stability of these mutualistic or parasitic interkingdom interactions often depends on optimised nutrient exchange, we lack a framework to explore whether animal-derived nutrients are optimal for fungal symbionts. This conceptual gap has constrained studies about the ecological success and evolutionary stability of fungus-animal symbioses. We use Nutritional Geometry (NG) to harness nutritional niche theory and identify the crucial nutritional niche dimensions of fungi that mediate symbiotic stability. We hypothesise that these fungal nutritional niche dimensions are governed by symbiotic role (mutualist vs. pathogen), degree of animal host control over nutritional competition (monoculture vs. polyculture), and breadth of host associations (specialist vs. generalist). We explore the promise of integrating NG with advanced imaging and -omics approaches to test coevolutionary hypotheses at precise microscales where fungus and animal cells trade nutrients. We conclude that niche-based theory can advance studies of coevolutionary dynamics from arms races to the emergence of economically important pathogens.},
}

*Symbiosis
Animals
*Fungi/physiology
Biological Evolution

@article {pmid40637409,
year = {2025},
author = {Imes, AM and Pavelsky, MN and Badal, K and Kamp, DL and Briseño, JL and Sakmar, T and Vogt, MA and Nyholm, SV and Heath-Heckman, EAC and Grasse, B and Septer, AN and Mandel, MJ},
title = {Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0000125},
doi = {10.1128/aem.00001-25},
pmid = {40637409},
issn = {1098-5336},
abstract = {Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. Bioluminescent Vibrio fischeri colonize the light organ of the Hawaiian bobtail squid, Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity, in vivo biofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid, Euprymna berryi, can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which the E. berryi light organ symbiosis parallels known processes in E. scolopes. However, the nature of the E. berryi light organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria from E. berryi animals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes in E. berryi and E. scolopes hatchlings. This study reveals E. berryi to be a valuable comparative model to complement studies in E. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. The Euprymna scolopes-Vibrio fischeri system has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and for in vivo biofilm formation in development and specificity of an animal's microbiome. Euprymna berryi is a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifies E. berryi as a strong symbiosis model host due to features that are conserved with those of E. scolopes, which will enable the extension of functional studies in bobtail squid symbioses.},
}

@article {pmid40637407,
year = {2025},
author = {Chin, HS and Ravi Varadharajulu, N and Teo, KC and Cheong, PCH and Tang, S-L},
title = {Key findings from 15 years of Mangrovibacter research: a generalist bacterium beyond endophytes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247924},
doi = {10.1128/aem.02479-24},
pmid = {40637407},
issn = {1098-5336},
abstract = {Since the discovery of Mangrovibacter plantisponsor in 2010, research on Mangrovibacters (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as "generalist microbes" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.},
}

@article {pmid40636972,
year = {2025},
author = {Zavorskas, J and Vlahos, P and Wagstrom, K and Srivastava, R},
title = {Dynamic Flux Balance Analysis Reveals Climate-Driven Shifts in Arctic Diatom Succession and Bloom Dynamics.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70339},
doi = {10.1111/gcb.70339},
pmid = {40636972},
issn = {1365-2486},
support = {//University of Connecticut, College of Engineering/ ; },
mesh = {*Diatoms/physiology/growth & development ; *Climate Change ; Arctic Regions ; *Phytoplankton/physiology ; *Carbon Cycle ; *Eutrophication ; },
abstract = {There is a critical need to understand the impact of climate change on marine microorganisms, especially phytoplankton, which are responsible for as much as half of atmospheric oxygen and are critical for the global carbon cycle. Climate change is causing drastic alterations in marine ecosystems, with the Arctic Ocean experiencing unprecedented environmental changes such as sea ice retreat and rising temperatures. These changes threaten to have severe consequences on the global carbon cycle, specifically on processes mediated by marine phytoplankton communities. Diatoms are one of the primary carbon-fixing phytoplankton in the Arctic Ocean and represent a critical sink within the global carbon cycle and are especially vulnerable to these changes. Spring blooms of diatoms in the Arctic account for approximately 20% of annual carbon fixation, but climate change effects will fundamentally change the environmental conditions that govern these blooms' dynamics. The succession pattern of diatom communities, from early blooming Thalassiosira to later-blooming Chaetoceros, is a critical driver of carbon sequestration, yet our understanding of how these patterns will respond to climate change remains limited. To address this knowledge gap, we developed dynamic flux balance analysis models incorporating complex empirical environmental parameters to simulate the annual life cycle of Thalassiosira and Chaetoceros. Model validation against historical data successfully recreated known diatom succession patterns, predicted post-bloom diatom biomass and nutrient concentrations independently, and recreated the known diatom succession pattern. Our models predicted that climate change will cause earlier, shorter, and more intense phytoplankton blooms, which are less effective at sequestering carbon. However, we found the succession pattern including diatom-cyanobacterial symbiosis may provide resilience because blooms including both symbiotic Chaetoceros and non-symbiotic Thalassiosira did not suffer losses in carbon sequestration.},
}

*Diatoms/physiology/growth & development
*Climate Change
Arctic Regions
*Phytoplankton/physiology
*Carbon Cycle
*Eutrophication

@article {pmid40636503,
year = {2025},
author = {Lei, W and Qin, Z and Jia, B and Lu, W and Yang, J and Gao, Q},
title = {Diversity and functional analysis of gut microbiota reveal ecological adaptations in the inquilinism of Ancistrotermes dimorphus and its host Macrotermes barneyi.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1587281},
pmid = {40636503},
issn = {1664-302X},
abstract = {Inquilinism describes an interesting interspecific interaction in termite ecosystems wherein an inquiline species inhabits the host's nest structure. In this context, gut microbiota play a crucial role in mediating the ecological relationship. The facultative inquiline Ancistrotermes dimorphus (Termitidae: Macrotermitinae) frequently inhabits nests of the host Macrotermes barneyi but can also establish independent colonies. We used 16S rRNA sequencing to compare the gut microbiota of A. dimorphus and M. barneyi in independent and inquilinism nests, assessing microbial diversity and composition. Gut microbiota diversity increased under inquilinism, with greater microbial similarity between A. dimorphus and M. barneyi in shared nests. Furthermore, inquilinism altered microbial function, increasing taxa linked to environmental adaptation while reducing those involved in energy metabolism, suggesting potential metabolic trade-offs. Beta diversity analysis indicated that inquilinism drives the gut microbiota adaptation between the host and inquiline. These findings reveal how gut microbiota mediates host-inquiline interactions, advancing our understanding of microbial adaptation in social insect symbiosis.},
}

@article {pmid40636498,
year = {2025},
author = {Wang, Y and Ren, H and Zhong, Y and Song, R and Jiang, S and Lai, M and Shen, Y and Liu, S and Shi, W and Qi, G},
title = {Microbial diversity and function in bamboo ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533061},
pmid = {40636498},
issn = {1664-302X},
abstract = {Bamboo is widely distributed or cultivated globally, offering significant economic and ecological values. Soil microorganisms are crucial for plant environmental adaptation, playing essential roles in regulating plant growth and development, nutrient absorption, and resistance to environmental stresses. In recent years, substantial progress has been made in the study of bamboo soil microorganisms. This review highlights the scientific challenges in understanding the interactions between bamboo and soil microorganisms, summarizes the research progress, and discusses future research directions. The microbial community composition and diversity in various bamboo soils have been successfully characterized, with some bamboo-associated microorganisms identified and shown to promote plant growth, demonstrating considerable application potential. It has been established that the composition of soil microorganisms in bamboo is influenced by factors such as bamboo species, spatial and temporal distribution, tissue specificity, management practices, and symbiosis with other plants. Future research will likely focus on the functional genomics of bamboo, the screening and identification of bamboo-specific soil microbial communities, the dynamic responses of these microbes to environmental changes, and the molecular mechanisms regulating bamboo growth and environmental adaptation.},
}

@article {pmid40635576,
year = {2025},
author = {Mackevicius-Dubickaja, V and Gottlieb, Y and White, JA and Doremus, MR},
title = {Wolbachia Feminises a Spider Host With Assistance From Co-Infecting Symbionts.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70149},
pmid = {40635576},
issn = {1462-2920},
support = {1953223//National Science Foundation/ ; 201697//United States-Israel Binational Science Foundation/ ; 1020740//National Institute of Food and Agriculture/ ; 7007679//National Institute of Food and Agriculture/ ; 2023-67012-39352//National Institute of Food and Agriculture/ ; 2809/23//Israel Science Foundation/ ; },
mesh = {Animals ; *Wolbachia/physiology/genetics ; *Spiders/microbiology/physiology ; *Symbiosis ; Female ; Male ; Feminization ; },
abstract = {Arthropods commonly harbour maternally-transmitted bacterial symbionts that manipulate host biology. Multiple heritable symbionts can co-infect the same individual, allowing these host-restricted bacteria to engage in cooperation or conflict, which can ultimately affect host phenotype. The spider Mermessus fradeorum is infected with up to five heritable symbionts: Rickettsiella (R), Tisiphia (T), and three strains of Wolbachia (W1-3). Quintuply infected spiders are feminised, causing genetic males to develop as phenotypic females and produce almost exclusively female offspring. By comparing feminisation across nine infection combinations, we identified a Wolbachia strain, W1, that is required for feminisation. We also observed that spiders infected with both W1 and W3 produced ~10% more females than those lacking W3. This increase in feminisation rate does not seem to be due to direct changes in W1 titre, nor does W1 titre correlate with feminisation rate. Instead, we observed subtle titre interactions among symbionts, with lower relative abundance of R and T symbionts in strongly feminised infections. This synergistic effect of co-infection on Wolbachia feminisation may promote the spread of all five symbionts in spider populations. These results confirm the first instance of Wolbachia-induced feminisation in spiders and demonstrate that co-infecting symbionts can improve the efficacy of symbiont-induced feminisation.},
}

Animals
*Wolbachia/physiology/genetics
*Spiders/microbiology/physiology
*Symbiosis
Female
Male
Feminization

@article {pmid40633698,
year = {2025},
author = {Wang, C and Ji, B and Li, A and Zhang, X and Liu, Y},
title = {Shear-driven stirring optimization modulates microbial synergy for robust structural-metabolic performance in microalgal-bacterial granular sludge systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132944},
doi = {10.1016/j.biortech.2025.132944},
pmid = {40633698},
issn = {1873-2976},
abstract = {This study systematically investigates the impact of stirring speed on the performance of microalgal-bacterial granular sludge (MBGS) ranging from 0 to 250 rpm, revealing that an optimal speed of 210 rpm induces synergistic structural-metabolic adaptations in MBGS. At this optimal stirring speed, Improvements in granule morphology and homogeneity, indicated by a decreased non-uniformity coefficient, as well as enhanced roundness and an optimal microalgae-bacteria ratio were observed, which collectively contribute to structural integrity and stable granule size. Notably, at 210 rpm, a significant increase in the abundance of Pseudomonadota including key genera such as Aquimonas, Azonexus, and Dechloromonas was detected, which resulted in an up-regulation of the abundance of key functional genes involved in contaminant metabolism (e.g., DLD, SucD, glmS, and ppa). These findings highlight the importance of stirring shear force as a strategic approach for maintaining granule size and stability in MBGS technology for real-world applications.},
}

@article {pmid40633656,
year = {2025},
author = {Chakraborty, S and Banerjee, S and Kumar, S and Ghosh, S and Mukherjee, P and Das, S and Bhattacharyya, P},
title = {Biofortified vermicompost: Exploring bacterial community dynamics and enzymatic pathways through bacteriome analysis for arsenic bioremediation in mine waste.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126795},
doi = {10.1016/j.envpol.2025.126795},
pmid = {40633656},
issn = {1873-6424},
abstract = {The extraction of mica from open-cast mines generates substantial waste, often laden with arsenic, posing severe environmental risks. Addressing this waste is essential to mitigate co-contamination. Vermitechnology offers a promising solution by converting toxic waste into nutrient-enriched, sanitized compost suitable for agriculture. This study explored bioremediation of toxic mine tailings (MT) through aerobic composting, vermicomposting and enriched vermicomposting (with Bacillus subtilis K5BGRD). Earthworm fecundity was impaired in dense MT settings but improved in MT+CD (1:1) treatments. Vermicomposting stabilized pH, enhanced nutrient mineralization and increased potassium bioavailability compared to aerobic composting. Enriched vermicompost reduced bioavailable arsenic by 58-88 % post-maturity, alongside increased microbial diversity and enzymatic activity. Earthworms bioaccumulated arsenic, contributing to a total reduction of 14.25 %. Pearson correlation and PLS-SEM analyses highlighted reduced arsenic-induced stress upon compost maturity. Metataxonomic analysis revealed microbial similarities between V1 (MT+CD [1:1]) and EV1 (MT+CD+B [1:1:1]) composts, with enrichment of stress-resistant, bioremediating and plant growth-promoting taxa. Upon crop trial it was deduced that microbe-mediated vermicomposting, particularly when combined with recommended fertilizer doses (as in T2), not only minimized arsenic accumulation in tomato plants but also significantly enhanced yield, highlighting its potential as a sustainable and effective strategy for safe crop production in contaminated soils. The study demonstrated the symbiotic relationship between earthworms and microbes in waste-treated settings, establishing a novel feedstock combination to remediate hazardous mine waste. Ultimately, this approach has the potential to replace chemical fertilizers, improve crop yields and reduce arsenic exposure - offering a cost-effective and eco-friendly solution to mining waste management.},
}

@article {pmid40633640,
year = {2025},
author = {Xie, Q and Lian, Y and Li, H and Fang, C and Wang, H and Chen, Z},
title = {Response to microplastics exposure and changes in system performance: a stark contrast between domestic sewage and landfill leachate.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122317},
doi = {10.1016/j.envres.2025.122317},
pmid = {40633640},
issn = {1096-0953},
abstract = {Explored the evolution process of representative polyethylene (PE) and polystyrene (PS) in anaerobic/aerobic biological treatment of domestic sewage and landfill leachate, and their effects on system efficiency, sludge performance, and microbial community structure. The results showed that microplastics (MPs) promoted the degradation of COD and NH3-N in domestic wastewater (approximately 99.00% and 98.16%), but this result was completely opposite to that in the leachate. The biofilm formation of MPs in leachate was relatively fast in the initial stage, with a biofilm amount (9.39) higher than that in domestic sewage (1.05), showing an "S"-shaped trend, but with large fluctuations over time. The amount of PE and PS biofilm in domestic sewage varied with different oxygen concentrations, but the amount of PS biofilm in leachate was generally higher than that in PE, and PS was more sensitive to biodegradation, while PE had stronger resistance to microbial attacks. Meanwhile, the presence of MPs significantly enhanced the synthesis of extracellular polymeric substances in the leachate (139.81 mg/g MLVSS, anaerobic condition on day 15), increased the concentration of heavy metals in the supernatant (842.91 μg/L, anaerobic condition on day 15), manifested as Mn and Zn. MPs stress led to varying degrees of changes in the structure of microbial communities, but the microbial abundance on the surfaces of PE and PS in the same reactor was similar. Ottowia, unclassifiedd_f_Rhizobiaceae, and Castellaniella were potential MPs degradation genera. The proportion of Thermomonas in the leachate system was about three times that of domestic sewage. The symbiotic mode between MPs and dominant bacteria in activated sludge confirmed the shaping of microbial community structure by MPs. This study contributes to improving the overall understanding of the environmental behavior and risks of MPs in domestic wastewater and leachate biological systems.},
}

@article {pmid40633341,
year = {2025},
author = {Liu, R and Oliphant, KD and Xia, Z and Chen, Z and Hou, R and Zhang, R and Peng, T and Hänsch, R and Wang, D and Rennenberg, H and Hu, B},
title = {Rhizobial symbiosis modulates mercury accumulation and metabolic adaptation under hydrological extremes.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139141},
doi = {10.1016/j.jhazmat.2025.139141},
pmid = {40633341},
issn = {1873-3336},
abstract = {Phytoremediation offers a sustainable strategy for mitigating mercury (Hg) contamination, yet its efficacy under variable water availability remains poorly understood. Robinia pseudoacacia, a leguminous tree with notable phytoremediation potential, was investigated under combined Hg exposure and water stress-drought (HgD) or flooding (HgF)-with or without rhizobia inoculation. In a controlled greenhouse study, HgD exposure enhanced root dry biomass, increased nodule nitrogenase activity, and promoted root Hg accumulation, indicating a detoxification mechanism via root retention. In contrast, HgF suppressed plant growth and nitrogen fixation, reduced total Hg uptake, and increased Hg translocation to shoots, suggesting redistribution to protect root function. Multi-omics analyses revealed that both HgD and HgF induced genes involved in cysteine and methionine metabolism (e.g., GSS, GCLC, ACS), enhancing thiol-mediated Hg detoxification and altering sulfur allocation. L-serine biosynthesis was consistently downregulated. Hormonal responses diverged: HgD suppressed jasmonic acid biosynthesis (downregulation of AOS, AOC) and reduced 12-OPDA levels, whereas HgF activated α-linolenic acid oxidation, elevating 12-OPDA and its derivatives (e.g., colneleic acid). Rhizobial inoculation further improved root Hg retention, upregulated antioxidant enzymes (SOD, POD), and maintained membrane integrity. Under HgD, inoculation enhanced phenylpropanoid metabolism (upregulation of PAL, CCR, CAD), promoting lignification. Under HgF, it stimulated the pentose phosphate pathway (via PFK induction), optimizing carbon flux for stress resilience. These findings demonstrate that Robinia-rhizobia symbiosis mediates distinct physiological and metabolic reprogramming under drought and flooding, enabling context-specific Hg detoxification. This highlights Robinia's potential as a robust phytoremediator in Hg-contaminated environments with fluctuating water regimes.},
}

@article {pmid40631381,
year = {2025},
author = {Huang, X and Gao, X and Fan, Y and Wang, D and Chen, X and Qi, X and Yang, Z and Wang, YE and Meng, J and Zou, G and Liu, Z and Li, X},
title = {Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.},
journal = {Virulence},
volume = {},
number = {},
pages = {2530660},
doi = {10.1080/21505594.2025.2530660},
pmid = {40631381},
issn = {2150-5608},
abstract = {The contributions and interactions of multi-kingdom microbiota (i.e. bacteriome, mycobiome, archaeaome, and phageome) with serum metabolome and host phenome in healthy individuals under moderate altitude exposure remain unclear. We applied shotgun metagenomic sequencing in faeces and targeted metabolomics technology in serum to explore how the human gut multi-kingdom microorganisms influence the serum metabolome and phenome in healthy Chinese individuals following moderate altitude exposure. The results indicated that individuals with moderate altitude exposure exhibited more substantial alterations in gut bacteriome and phageome compared to those in mycobiome and archaeaome. Both intra-kingdom and inter-kingdom correlations at baseline were denser than those following moderate altitude exposure. Bacteriophages-host interactions analysis revealed symbiosis between bacteriophages and Bacteroidetes, Proteobacteria, and short-chain fatty acids (SCFAs) producers. Furthermore, bacteriophage Shirahamavirus PTm1 (odds ratio (OR) = 3.82; 95% confidence interval (CI): 1.20-12.16), archaeon Crenarchaeota (OR = 3.70; 95% CI: 1.35-10.14) and bacterium Bacteroidetes (OR = 3.69; 95% CI: 1.34-10.15) showed a positive association with lowered fasting blood glucose (FBG) benefits, while bacteriophage Candidatus Nitrosopelagicus brevis (OR = 0.30; 95% CI: 0.10-0.89) and butyric acid (OR = 0.07; 95% CI: 0.01-0.37) exhibited a negative association with lowered FBG benefits. These findings suggest that targeting gut multi-kingdom microorganisms could serve as an alternative therapeutic approach to mitigate dysglycemia and its associated metabolic disorders.},
}

@article {pmid40631325,
year = {2025},
author = {Dregni, J and Lindsey, ARI and Ferrer-Suay, M and Celis, SL and Heimpel, GE},
title = {Wolbachia -mediated parthenogenesis induction in the aphid hyperparasitoid Alloxysta brevis (Hymenoptera: Figitidae: Charipinae).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.30.662338},
pmid = {40631325},
issn = {2692-8205},
abstract = {UNLABELLED: Thelytokous parthenogenesis (thelytoky), in which females can produce female offspring without mating, can be caused by parthenogenesis-inducing endosymbiotic bacteria in the genus Wolbachia . This interaction is well known in hymenopteran parasitoids, where unfertilized eggs typically develop as males via haplo-diploidy in the absence of parthenogenesis-inducing bacteria. We report on a case of thelytoky in Alloxysta brevis (Thomson) (Hymenoptera: Figitidae), a globally widespread aphid hyperparasitoid. A previous study had shown that sex ratios of this species collected in Minnesota (USA) were extremely female biased, and we found here that unmated females reared from field-collected hosts produced female offspring without exposure to males. This result demonstrated thelytoky, and we tested for the role of bacterial endosymbionts by comparing offspring production of unmated females fed the antibiotic rifampicin to offspring production of control females not fed antibiotics. Antibiotic-fed females produced almost exclusively male offspring, and control females produced mainly females. This result showed that antibiotic treatment facilitated male production by unmated Alloxysta brevis females, thus implicating bacterial symbiosis in the expression of thelytoky. We then used molecular analyses to determine the identity of the symbiont. These analyses identified a Wolbachia strain from supergroup B, and excluded other bacteria known to mediate parthenogenesis induction, such as Cardinium and Rickettsia . While Wolbachia had been previously detected by molecular analysis in this species, these are the first experiments demonstrating Wolbachia -mediated parthenogenesis in the figitid subfamily Charipinae.

IMPORTANCE: Parthenogenesis induction in insects can have important environmental and economic consequences. This is especially true if pests or their natural enemies are affected. The case of Alloxysta brevis is of particular interest, as this species is a hyperparasitoid of aphids, meaning that they attack and kill primary parasitoids of aphids. The populations of many species of pest aphids are controlled by primary parasitoid species, and hyperparasitoids thus have the potential to interfere with this mechanism of control. The role of hyperparasitoid parthenogenesis in the suppression of aphids by primary parasitoids remains unexplored. Thus, the results of this set of studies provides a starting point for determining whether parthenogenesis-inducing Wolbachia in hyperparasitoids should be expected to improve or hinder biological control of pest aphids by primary parasitoids. The focus on Alloxysta brevis as a model for these questions could be particularly instructive, since it is a species of worldwide distribution that is involved in numerous economically important aphid-parasitoid interactions.},
}

@article {pmid40630184,
year = {2025},
author = {Regassa, GB and Zhang, Y and Shen, Y and Zhang, L and Zhang, J and Liu, Y and Li, G and Xiao, R and Yang, Z},
title = {Effects of pathogen infection and Rhizobium inoculation on instantaneous and long-term water use efficiency of peanut with and without drought.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1612341},
pmid = {40630184},
issn = {1664-302X},
abstract = {INTRODUCTION: Water Use Efficiency (WUE) is one of the critical indicators to characterize plant adaptation to arid environments, however, the effects of pathogens infection and Rhizobium symbiosis on WUE are not considered in contexts of water stress.

METHODS: A study was conducted in a greenhouse pot to examine the effects of changed soil water conditions on instantaneous Water Use Efficiency (WUEi) and long-term Water Use Efficiency (WUEL) under inoculation Rhizobium, inoculation Fusarium sp., and co-inoculation Rhizobium and Fusarium sp.

RESULTS: The results showed that inoculation Fusarium sp. and co-inoculation Rhizobium and Fusarium sp. reduced WUEi by increasing net photosynthetic rate without drought. Inoculation Fusarium sp. and co-inoculation Rhizobium and Fusarium sp. reduced WUEi by decreasing plant height with drought. Inoculation Rhizobium and Fusarium sp. significantly reduced WUEL by lowering intercellular CO2 concentration without drought. Inoculation Rhizobium reduced WUEL by increasing root nodule number with drought. In contrast, drought had no effect on either WUEi or WUEL without inoculation.

DISCUSSION: The results suggest that Fusarium sp. infection is detrimental to instantaneous Water Use Efficiency while inoculation Rhizobium is unfavorable to long-term Water Use Efficiency, regardless of drought effects. Our findings provide a new insight for developing effective water use strategies after pathogen infection or Rhizobium symbiosis under increased precipitation scenarios.},
}

@article {pmid40630045,
year = {2025},
author = {Samanta, I and Ghosh, K and Saikia, R and Savita, and Maity, PJ and Chowdhary, G},
title = {Arbuscular mycorrhizal fungi - a natural tool to impart abiotic stress tolerance in plants.},
journal = {Plant signaling & behavior},
volume = {20},
number = {1},
pages = {2525843},
pmid = {40630045},
issn = {1559-2324},
mesh = {*Mycorrhizae/physiology ; *Stress, Physiological/physiology ; Symbiosis/physiology ; *Plants/microbiology/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are crucial components of the soil microbiomes that establish symbiotic associations with most terrestrial plants. The review summarizes the basic mechanisms behind the plant-AMF symbiosis, the genes involved in the fungal and their plant counterparts, novel biomolecules and growth regulators, leading to probable signal transduction pathways. It also focuses on the involvement of lipids and strigolactones in establishing AMF-plant symbiosis. Herein, we further emphasize the role played by these AMF in enhancing plant resistance to various abiotic stresses while giving a broad outline of current research practices and attempting to dissect the mechanism behind the AMF-mediated abiotic stress signal transduction. Discussion on the mechanisms behind this stress reduction involving AMF will be valuable for the researchers, agronomists, and environmentalists involved in sustainable agriculture. Water scarcity, salinity, heavy metals, and extreme temperatures are the primary abiotic stresses that pose serious challenges to agricultural sustainability and ecosystem functioning. Conventional responses to such pressures typically rely on genetic modifications as well as chemical treatments, which could be expensive and detrimental to the environment. However, these AM fungi act in an alternative way that is natural and cost-effective too, leading to healthy plants with resilience toward stress through symbiosis, leading to the fulfillment of the United Nations Sustainable Development Goal (UNSDG) 2 of zero hunger.},
}

*Mycorrhizae/physiology
*Stress, Physiological/physiology
Symbiosis/physiology
*Plants/microbiology/metabolism

@article {pmid40629845,
year = {2025},
author = {Monnens, M and Artois, T and Briscoe, A and Diez, YL and Fraser, KPP and Leander, BS and Littlewood, DTJ and Santos, MJ and Smeets, K and Van Steenkiste, NWL and Vanhove, MPM},
title = {Signatures of Endosymbiosis in Mitochondrial Genomes of Rhabdocoel Flatworms.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70015},
doi = {10.1111/mec.70015},
pmid = {40629845},
issn = {1365-294X},
support = {1141817N//Fonds Wetenschappelijk Onderzoek/ ; GOH3817N//Fonds Wetenschappelijk Onderzoek/ ; NSERC 2019-03986//Natural Sciences and Engineering Research Council of Canada/ ; BOF15BL09//Special Research Fund (Bijzonder Onderzoeksfonds) UHasselt/ ; BOF20TT06//Special Research Fund (Bijzonder Onderzoeksfonds) UHasselt/ ; //Vlaams Instituut voor de Zee/ ; //Hakai Institute/ ; UIDB/04423/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04423/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The transition from a free-living lifestyle to endosymbiosis represents a large evolutionary shift, impacting various aspects of any organism's biology, including its molecular-genetic groundwork. So far, it has been impossible to generalise the impact this lifestyle shift has on genomic architecture. This study explores this phenomenon using a new model system: neodalyellid flatworms (Rhabdocoela), a diverse assemblage of free-living and independently evolved endosymbiotic lineages. A uniquely comprehensive mitochondrial genomic dataset, consisting of 50 complete or partial mitogenome sequences (47 of which are new to science), is constructed, increasing the genomic resources available for rhabdocoel flatworms over tenfold. A robust phylogenomic framework is built, enabling an in-depth exploration of the molecular-genetic signatures associated with evolutionary shifts towards endosymbiosis. To understand speciation influenced by host phylogeny, first steps are taken to unravel the host-switching history of the largest endosymbiotic group of neodalyellids. We test several hypotheses regarding the potential consequences of a symbiotic lifestyle and find marginally heightened AT content, more pronounced GC skew and relaxed selection on specific protein-coding genes in endosymbionts compared to their free-living counterparts. Numerous substitutions have accumulated in certain endosymbiotic lineages; however, the correlation with lifestyle remains uncertain. A high frequency of genetic rearrangements across all studied lineages is observed. Our findings affirm the variable nature of rhabdocoel mitogenomes and, for the first time, reveal distinct signatures of an endosymbiotic lifestyle in neodalyellid flatworms. This effort lays the groundwork for future research into the evolutionary and genomic consequences of a symbiotic lifestyle in this and other animal systems.},
}

@article {pmid40629841,
year = {2025},
author = {Tian, B and Hao, M and Ma, J and Feng, W and Wang, J and Fang, A and Yang, Y and Bi, C and Yu, Y},
title = {A xylan hydrolase contributes to pathogenicity and induces resistance to pathogens in a schizotrophic fungus.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8976},
pmid = {40629841},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Xylanases are widely distributed in fungi, and are involved in the breakdown of carbohydrates and polysaccharides in plant cell walls, and activating host immune responses. However, the role of xylanase in regulating the interaction between schizotrophic fungi and both the symptomatic host plant and the endophytic host is not yet clear.

RESULTS: A secretory xylanase, SsXyl3, was identified from the schizotrophic fungus Sclerotinia sclerotiorum, which contains a glycoside hydrolase family 11 domain and a signal peptide. SsXyl3 is associated with vegetative growth and sclerotial development and influences sugar metabolism in S. sclerotiorum, as demonstrated by phenotyping SsXyl3 mutants and RNA-seq analysis. Additionally, SsXyl3 is crucial for the complete virulence of S. sclerotiorum, and is further involved in establishing the symbiotic relationship between S. sclerotiorum and wheat plants. It also regulates the induction of resistance against stripe rust and Fusarium head blight (FHB) diseases in wheat by S. sclerotiorum.

CONCLUSION: These results highlight that S. sclerotiorum induces resistance to stripe rust and FHB diseases in wheat, and shows complete virulence in symptomatic hosts through secreting SsXyl3. These findings offer valuable clues for developing innovative and eco-friendly crop disease control methods for FHB and stripe rust diseases in asymptomatic wheat and Sclerotinia diseases in symptomatic hosts. © 2025 Society of Chemical Industry.},
}

@article {pmid40629501,
year = {2025},
author = {Voinnet, O},
title = {Three decades of mobile RNA-silencing movement within plants: what have we learnt?.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf312},
pmid = {40629501},
issn = {1460-2431},
abstract = {In plant RNA-silencing, small interfering (si)RNAs and micro (mi)RNAs guide ARGONAUTE (AGO) effector proteins to silence sequence-complementary RNA/DNA. This helps regulate developmental patterning, adaptation to stress, antiviral defense or genome integrity-maintenance. Remarkably, these regulations not only occur intra-cellularly, but may also manifest in remote tissues. Here, I summarize the evidence that RNA-silencing moves from cell-to-cell and via the phloem, the long-distance extension of the symplasm-the cytosolic connection-network between cells through plasmodesmata (PDs). I then illustrate several biological functions linked to RNA-silencing movement. Besides a still largely putative role for mobile virus-derived (v)siRNAs in conferring immunity, several endogenous sRNAs act as systemic signals orchestrating organismal responses to abiotic stress or symbiosis. Other mobile sRNAs act as morphogens and generate gene expression gradients by moving from cell-to-cell. If RNA-silencing indeed moves symplasmically via PDs, then processes likely regulate its transport; discovering these processes was expected to illuminate macromolecular trafficking in general. In a final part of this perspective, I describe several forward genetic systems set in Arabidopsis to specifically tackle the above issue. Some were instrumental in revealing hitherto unknown AGO-mediated mechanisms that modulate silencing movement within silencing-incipient, traversed or recipient cells. Somewhat disappointingly, however, the systems fell short of identifying factors impacting the silencing cell-to-cell trafficking channels or their regulations. I discuss here plausible reasons for these shortcomings, what could be learnt from them, how they could be remedied, and how a better understanding of their physiological foundations might illuminate so far overlooked aspects of plant RNA- silencing movement.},
}

@article {pmid40629387,
year = {2025},
author = {Kearsley, JVS and Geddes, BA and diCenzo, GC and Zamani, M and Finan, TM},
title = {A minimized symbiotic gene set from the 1.68 Mb pSymB chromid of Sinorhizobium meliloti reveals auxiliary symbiotic loci.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {204},
pmid = {40629387},
issn = {1741-7007},
mesh = {*Sinorhizobium meliloti/genetics/physiology ; *Symbiosis/genetics ; *Nitrogen Fixation/genetics ; *Medicago sativa/microbiology/genetics ; *Genes, Bacterial ; },
abstract = {BACKGROUND: Symbiotic nitrogen-fixation between bacteria called rhizobia and leguminous plants is a critical aspect of sustainable agriculture. Complex, two-way communication governs the invasion of plant roots and the formation of nodules in which the rhizobia reduce N2 to bioavailable ammonia. Research has uncovered many of the genes required for the symbiosis; however, engineering the symbiosis to function with alternative hosts such as cereal crops necessitates the establishment of a core set of symbiotic players.

RESULTS: We examined the symbiotic relevance of the genes on the 1.68 Mb pSymB chromid of the model rhizobium Sinorhizobium meliloti. By employing a strain in which pSymB was removed, we used a gain-of-function approach to assess a select group of known symbiotic regions totalling 261 kb (15.5%) of pSymB. This gene set enabled symbiotic N2-fixation with alfalfa with a high degree of plant genotype-dependent variation in which nodules often senesced prematurely. We demonstrate that additional regions lacking canonical symbiosis genes are important for the efficient formation of symbiosis with the plant host. These regions appear to contain auxiliary symbiotic loci whose genes encode products with quasi-essential functions for the symbiosis and that are redundant in nature. We further established a 673-kb pSymB genome that engages consistently in N2-fixation with alfalfa with 45% efficiency.

CONCLUSIONS: The reduction of the pSymB genome showcases the complexity and nuance of its involvement in the N2-fixing symbiosis.},
}

*Sinorhizobium meliloti/genetics/physiology
*Symbiosis/genetics
*Nitrogen Fixation/genetics
*Medicago sativa/microbiology/genetics
*Genes, Bacterial

@article {pmid40628488,
year = {2025},
author = {Fronk, DC and Ortiz-Barbosa, GS and Macedo, F and Lee, J and Wun, K and Sachs, JL},
title = {Nitrogen fertilization nullifies host sanctions against non-fixing rhizobia and drives divestment from symbiosis in Lotus japonicus.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2050},
pages = {20251055},
doi = {10.1098/rspb.2025.1055},
pmid = {40628488},
issn = {1471-2954},
support = {//NIFA/ ; //NSF/ ; //USDA/ ; },
mesh = {*Symbiosis ; *Lotus/microbiology/physiology/metabolism ; Fertilizers/analysis ; *Nitrogen/metabolism ; Nitrogen Fixation ; *Rhizobium/physiology ; Root Nodules, Plant/microbiology ; },
abstract = {Plants and animals house microbes that provide critical nutrients, but little is known about host control over microbial cooperation when resources are also accessed from the environment. Changes in nutrient access can challenge the host's ability to detect and selectively reward beneficial partners, destabilizing symbiosis. Legumes acquire nitrogen from soil and from symbiosis with rhizobia, but it is unclear if extrinsic sources of nitrogen interfere with host control systems. We inoculated the legume Lotus japonicus with rhizobia-bearing nitrogen fixation or nitrogen metabolism knockouts, and factorially varied molecular sources of nitrogen fertilizer. Lotus hosts selectively rewarded beneficial rhizobia and sanctioned non-fixing strains when extrinsic nitrogen was unavailable. Host benefits were undiminished when inoculated with rhizobia-bearing nitrogen metabolism knockouts, suggesting redundancies in nitrogen provisioning systems. However, under nitrogen fertilization, hosts did not discriminate between fixing and non-fixing rhizobia. Fertilized hosts formed miniaturized nodules housing limited rhizobia, divesting from symbiosis. Thus, sanctioning mechanisms rely on the detection of nitrogen fixation differences among rhizobia strains and can break down in nitrogen-rich environments. Nonetheless, divestment from symbiosis offers legumes robust host control, minimizing investment into rhizobia strains, irrespective of their capacity to provide benefit, when symbiosis services are not needed.},
}

*Symbiosis
*Lotus/microbiology/physiology/metabolism
Fertilizers/analysis
*Nitrogen/metabolism
Nitrogen Fixation
*Rhizobium/physiology
Root Nodules, Plant/microbiology

@article {pmid40627970,
year = {2025},
author = {Batista, A and Helgoe, J and Rodriguez-Lanetty, M},
title = {Acute dimethyl phthalate exposure impairs tissue integrity in a model cnidarian without disrupting symbiosis.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118306},
doi = {10.1016/j.marpolbul.2025.118306},
pmid = {40627970},
issn = {1879-3363},
abstract = {In addition to heat waves and diseases that continue to decimate coral reef ecosystems, corals must increasingly contend with growing concentrations of microplastics in the oceans. Phthalates (PAE), a class of commonly used plasticizers, readily leach from plastics into marine environments and may pose threats to cnidarian health and coral symbiosis. To assess the acute effect of phthalate exposure, we investigated the impact of dimethyl phthalate (DMP) on the model cnidarian Exaiptasia diaphana. Anemones were exposed to four treatments across three weeks to the following: a control, and DMP concentrations of 2.9 mg/L, 15.3 mg/L, and 29.4 mg/L. Changes to photosynthesis, symbiont density, and visual changes to the host anemone tissue integrity were measured. DMP exposure did not significantly affect symbiont density (i.e., bleaching rate) or photosynthetic efficiency (Fv/Fm) of the algal symbionts. However, marked degradation of host tissue was observed in the chemically-treated anemones. These findings raise concerns that PAEs, if their concentrations continue to rise, could contribute to the decline of reef ecosystems by weakening host resilience, even in the absence of symbiosis breakdown.},
}

@article {pmid40627646,
year = {2025},
author = {Michel, J and Lehnert, M and Nebel, M and Quandt, D},
title = {Low and facultative mycorrhization of ferns in a low-montane tropical rainforest in Ecuador.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326712},
pmid = {40627646},
issn = {1932-6203},
mesh = {*Mycorrhizae/physiology ; *Rainforest ; Symbiosis ; Ecuador ; *Ferns/microbiology ; Tropical Climate ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are amongst the most studied obligate plant symbionts and regularly found in terrestrial plants. However, global estimates of AMF abundance amongst all land plants are difficult because i) the mycorrhizal status of many non-commercial, wild plant species is still unknown, ii) numerous plant species engage in facultative symbiosis, meaning that they can, but do not always do, associate with mycorrhiza, and iii) mycorrhizal status can vary within families, genera, and species. To gain deeper insights to the distribution of the plant-AMF symbiosis we investigated the mycorrhizal status in some of the oldest lineages of extant vascular plants, Polypodiophytina (ferns) and lycophytes, in one of the hotspots of natural plant diversification, the tropical rainforest. Providing a new data set of AMF abundance for 82 fern species representing 19 families, we hypothesized that (1) AMF would be found in 60-80% of the studied plants and (2) plant species with AMF symbionts would be more abundant than non-mycorrhizal species. Both hypotheses were rejected while the following observations were made: (1) AMF occurred in 30.5% of studied species, representing 63% of the studied fern families, (2) AMF colonisation was not correlated with species abundance, (3) a small proportion of AMF-hosting ferns was epiphytic (6%) and (4) mycorrhization was inconsistent among different populations of the same species (facultative mycorrhization). While these observations align with previous studies on ferns, they emphasise that mycorrhization is not a taxonomic trait and underscore the challenges in estimating the global abundance of AMF. In addition, the occurrence of AMF in epiphytic plants and no net benefits of AMF for plant abundance indicate that the mycorrhization observed in this study likely comprises the commensalism to parasitism range of the symbiosis spectrum.},
}

*Mycorrhizae/physiology
*Rainforest
Symbiosis
Ecuador
*Ferns/microbiology
Tropical Climate

@article {pmid40627546,
year = {2025},
author = {Delbaje, E and de Castro, PA and Pupo, MT and Rokas, A and Goldman, GH},
title = {Gliotoxin Production and Self-Defense in Filamentous Fungi.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-040324-032342},
pmid = {40627546},
issn = {1545-3251},
abstract = {Gliotoxin (GT) is a sulfur-containing secondary metabolite that belongs to a class of naturally occurring 2,5-diketopiperazines produced by fungi. Although GT production has been observed only in a few species, GT is the most studied fungal secondary metabolite, and the GT biosynthetic gene cluster (BGC) is broadly present in filamentous fungi. GT has a multitarget mechanism of action: It is fungicidal and bacteriostatic, it induces apoptosis in mammalian cells, and it modulates phagocytosis and neutrophil attraction. GT is important for Aspergillus fumigatus virulence and pathogenesis in humans and in animals and for Trichoderma spp. symbiotic and antagonistic behavior. GT is also toxic for producer and nonproducer organisms. Consequently, very sophisticated mechanisms of GT self-protection have evolved in producers; some of these protective mechanisms are also found in nonproducer organisms. This review discusses the distribution of the GT BGC among filamentous fungi and discusses GT biosynthesis, mechanisms of action and self-defense, and ecological properties.},
}

@article {pmid40627541,
year = {2025},
author = {Hisatomi, A and Yoshida, T and Hasunuma, T and Ohkuma, M and Sakamoto, M},
title = {Difficult-to-culture micro-organisms specifically isolated using the liquid-liquid co-culture method - towards the identification of bacterial species and metabolites supporting their growth.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
doi = {10.1099/mic.0.001581},
pmid = {40627541},
issn = {1465-2080},
mesh = {Coculture Techniques/methods ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation & purification/genetics/classification/metabolism/growth & development ; Animals ; Phylogeny ; DNA, Bacterial/genetics ; Culture Media/chemistry ; },
abstract = {In this study, the liquid-liquid co-culture method was applied using faecal samples and specific bacterial species as growth-supporting bacteria. We aimed to isolate new, difficult-to-culture bacterial species using metabolites produced by supportive bacteria to promote the growth of small bacteria selected using filter treatment. This study aimed to identify the supporting bacteria and their metabolites that promote the growth of these isolates. Analysis of the 16S rRNA gene sequences of the isolates obtained by co-culture revealed that they were Waltera spp., Roseburia spp. and Phascolarctobacterium faecium. Roseburia spp. and Waltera spp. were isolated from several faecal samples, suggesting that they were specifically isolated using this culture method. We focused on Waltera spp. isolated from several faecal samples with unique shapes, from long to short or thin cells. The growth of Waltera spp. was not promoted by co-culture on the agar medium, suggesting that growth was only promoted by liquid-liquid co-culture. The growth of the selected small-sized Waltera spp. was promoted by co-culture, whereas the growth of the unfiltered long-cell Waltera sp. strain was suppressed by co-culture. The selected small Waltera spp. did not grow when the supporting bacterial supernatant was added, suggesting that the supporting bacteria and Waltera spp. had a symbiotic relationship through the continuous exchange of metabolites. Co-cultured supporting bacteria (diluted faecal samples) with selected small-sized Waltera spp. were predominantly Bacteroides thetaiotaomicron and Escherichia coli, compared with monoculture diluted faecal samples. We further confirmed the growth of filtered Waltera spp. by co-culturing them with B. thetaiotaomicron and E. coli. Additionally, when B. thetaiotaomicron and E. coli were co-cultured with the selected small Waltera spp., some nutrients and metabolites were reduced. Decreased metabolites were added to the medium, and selected small-sized Waltera spp. were cultured, but Waltera spp. did not grow. Therefore, it was again strongly suggested that continuous co-culturing with the supporting bacteria was important for the growth of Waltera spp. The liquid-liquid co-culture method used in this study can be used to isolate new and unique bacterial species from any environment, not just the gut microbiome. Furthermore, this co-culture method helped identify supporting bacteria and understand metabolite variations.},
}

Coculture Techniques/methods
Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/isolation & purification/genetics/classification/metabolism/growth & development
Animals
Phylogeny
DNA, Bacterial/genetics
Culture Media/chemistry

@article {pmid40627403,
year = {2025},
author = {Xue, Y and Huang, M and Zhang, J and Navin, S and Tao, Y and Zeng, G},
title = {Sex-Specific Postmortem Microbiome Dynamics in Mice: Implications for Death Definitions.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf070},
pmid = {40627403},
issn = {1574-6968},
abstract = {Gut microbes form a complex and dynamic symbiotic relationship with their host. However, the microbial response during the early stages following host death remains largely uncharacterized. In this study, we employed a mouse model to systematically characterize the postmortem response of the intestinal microbiota, and analyzed the dynamic changes in microbial composition during the early stages after death in both male and female mice (at 0, 0.5, 2, 6, 12, and 24 hours postmortem). Our findings reveal that sex-dimorphic shifts in microbiome composition occur as early as 2 hours postmortem. Male mice exhibited increased functional redundancy and delayed community restructuring, whereas female mice displayed earlier community shifts. These sex-specific patterns were accompanied by differences in metabolic pathway activity and biomarker taxa. Notably, the observed retention of regulatory capacity by intestinal microbes after host death offers a novel perspective on the conceptualization of death itself. We propose the term "ecological death" to describe the irreversible collapse of the host-associated microbial ecosystem following death, marking a critical transition in the functional and structural integrity of the intestinal microbiota.},
}

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

@article {pmid40625873,
year = {2025},
author = {Mu, D and Zhang, M and Liang, Y and Ding, C and Chen, Q and Fan, X and Meng, X and Zhang, X and Gao, S and Zhai, D and Gao, Y and Wu, Y},
title = {Piriformospora indica enhances growth and salt tolerance in a short rotation woody crop, Paulownia elongata, under NaCl stress.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1566470},
pmid = {40625873},
issn = {1664-462X},
abstract = {Salinization is a major environmental challenge that jeopardizes productivity and resilience of plants such as the short rotation woody crops (SRWC) and bioenergy crops. Leveraging beneficial microbes will enhance plant resistance to salinity with physiological adjustments. Here we investigated the efficacy of plant growth promoting fungus (Piriformospora indica) on optimizing growth and salt tolerance of SRWCs and bioenergy tree crops, using Paulownia elongata as an example. Following culture in sterile soil, the chlamydospore of P. indica were found in paulownia plants roots. We treated both inoculated and uninoculated plants with four salt concentrations (0.00%, 0.30%,0.50%, 0.70%) by soaking them in varying concentrations of NaCl solution every 7 days. After 30 days of treatment, we investigated various physiological parameters, i.e., biomass, infection rate, growth rate, photosynthetic parameters, antioxidant enzyme activity, and soluble sugar of paulownia plants. Our two-way ANOVA demonstrated that the interaction between salinity stress and P. indica inoculation significantly enhanced plant height growth rate, leaf net photosynthetic rate, superoxide dismutase (SOD) activity, and soluble protein content in Paulownia seedlings. Inoculated plants exhibited improved salt tolerance due to the mitigating effect of symbiosis across a salinity gradient. Mortality in the P. indica-treated group was reduced by approximately 5.55%, 22.22%, and 27.77% under 0.30%, 0.50%, and 0.70% NaCl treatments. Our study is the first application of P. indica to enhance salinity tolerance in Paulownia, a short-rotation woody crop. Inoculating such endophyte significantly improves the resilience and productivity of Paulownia plantations in saline environments, for a sustainable afforestation effort.},
}

@article {pmid40625865,
year = {2025},
author = {Georgopoulos, K and Bezemer, TM and Vesterdal, L and Li, K and de Nobel, L and Gomes, SIF},
title = {Nondestructive Detection of Frankia in Alnus glutinosa With NIR Spectroscopy.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e70066},
pmid = {40625865},
issn = {2575-6265},
abstract = {Nitrogen (N) is essential for plant growth, yet excessive fertilizer use contributes to environmental degradation. Actinorhizal trees like Alnus glutinosa form symbiotic relationships with nitrogen-fixing bacteria of the genus Frankia, reducing reliance on synthetic fertilizers. However, distinguishing between soil-derived and symbiotically fixed nitrogen remains a challenge. This study investigates the potential of NIR spectroscopy as a nondestructive tool for differentiating N sources in A. glutinosa. Seedlings were grown in sterilized soil under controlled conditions with and without Frankia inoculation, and across a gradient of NH4NO3 fertilization (0-20 mM). We measured leaf chlorophyll, nitrogen content, biomass, and NIR reflectance (330-1100 nm) of the third fully expanded leaf. principal component analysis (PCA) and partial least squares (PLS) regression revealed that spectral signatures significantly differed between inoculated and uninoculated plants, particularly in the visible range around 555 nm. Despite similar leaf chlorophyll levels, Frankia-inoculated plants and those fertilized with 20 mM NH4NO3 exhibited spectral differences that could otherwise not be detected by SPAD measurements. PLS regression explained up to 54.8% of spectral variance based on nitrogen source, even in the absence of unique spectral peaks. These findings highlight the potential of NIR spectroscopy for rapid, in vivo and in vitro assessment of symbiotic N-fixation in trees, offering a novel and more precise approach than SPAD measurements.},
}

@article {pmid40625831,
year = {2025},
author = {Han, Y and Ding, PH},
title = {Advancing periodontitis microbiome research: integrating design, analysis, and technology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616250},
pmid = {40625831},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; Biofilms/growth & development ; Gingiva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.},
}

Humans
*Periodontitis/microbiology
*Microbiota
Biofilms/growth & development
Gingiva/microbiology
Bacteria/genetics/classification

@article {pmid40625334,
year = {2025},
author = {Lan, B and Malik, TG and Tsai, MT and Wu, YT and Sun, SJ},
title = {No Evidence That the Phoretic Mite Poecilochirus carabi Influences Mate Choice or Fitness in the Host Burying Beetle Nicrophorus nepalensis.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71733},
pmid = {40625334},
issn = {2045-7758},
abstract = {Mate choice is a fundamental aspect of sexual selection where the "chooser" chooses a "courter" by assessing a variety of traits that communicate potential fitness. However, the role of interspecific interactions, such as symbiosis, in shaping mate choice remains poorly understood. Here, we investigate whether phoretic mites Poecilochirus carabi, which can act as either mutualists or parasites, influence female mate choice or reproductive fitness in the burying beetle Nicrophorus nepalensis. These mites affect beetle fitness in context-dependent ways, influenced by temperature, competitor presence, and mite density-factors that could potentially impact mate selection. In an olfactory-based mate choice assay, we presented female N. nepalensis hosting a range of natural mite densities (0, 5, 10, or 20) with a choice between males carrying either 0 or 10 mites. Subsequently we allowed females to breed with their chosen male before evaluating the fitness effects of the varying male and female mite densities. We found no evidence that female N. nepalensis preferred males based on mite presence, regardless of their own mite density. Furthermore, mite density did not affect beetle fitness, as measured by brood size or average larval mass. However, mite reproductive output increased with higher total mite densities per breeding pair. Our findings suggest that, under naturally occurring conditions and in the absence of competitors, P. carabi mites do not influence female mate choice or beetle reproductive success in N. nepalensis.},
}

@article {pmid40624948,
year = {2025},
author = {Lu, R and Lanooij, J and Smakowska-Luzan, E},
title = {From Roots to Reproduction: The Multifaceted Roles of RALF and EPF Peptides in Plants.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf303},
pmid = {40624948},
issn = {1460-2431},
abstract = {In plants, peptides play an irreplaceable role as intercellular communication molecules, triggering signal transduction by activating plasma membrane-localized receptors. Of specific interest here are the cysteine-rich peptides (CRPs), which are well-characterized for their disulfide bonds that enhance structural stability and functional specificity. Although the first CRP, systemin, was identified over three decades ago, our understanding of CRPs' evolutionary trajectories, functional diversity, and underlying mechanisms remains limited. This review focuses on two main families of CRPs: the Rapid Alkalinization Factor and the Epidermal Patterning Factor (EPF)/EPF-Like peptides. We thus explore the diverse and, so far, identified signalling pathways in which the peptides play a pivotal function. We organize our tour by providing a comprehensive overview of the discovery of peptides, structural diversity, and biological functions. Particularly, emphasis is placed on their roles in plant growth, development, reproduction, defence against biotic and abiotic stresses, and plant-bacteria symbiosis.},
}

@article {pmid40624256,
year = {2025},
author = {Zhang, N and Xu, X and Liu, X and Wu, J and Tang, H},
title = {Incentive mechanism of foundation model enabled cross-silo federated learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24181},
pmid = {40624256},
issn = {2045-2322},
abstract = {The integration of foundation models (FMs) into cross-silo federated learning (FL) introduces transformative capabilities but also exacerbates strategic client behaviors, such as knowledge hoarding and free-riding, which degrade global model performance and system sustainability. Existing incentive mechanisms fail to address the knowledge hoarding and free-riding in FM-enabled FL. This paper proposes a novel incentive framework to harmonize client-server interests while suppressing adversarial behaviors. First, we propose a dynamic participant screening mechanism including pre-screening mechanism and confidence attenuation monitoring to filter low-quality updates and penalize intermittent participation. Second, we propose a cost-benefit balanced contribution metric to quantify clients' impacts by jointly evaluating accuracy gains, cost, and participation patterns. Third, we model the incentive mechanism as a two-stage Stackelberg game to establish symbiotic incentives, where the server adaptively adjust pricing strategy while clients optimize participation strategies. Simulation results demonstrate that our method can achieve up to 21.9% higher model accuracy and effectively filter malicious clients compared to existing benchmarks.},
}

@article {pmid40623763,
year = {2025},
author = {Agrawal, P and Mendhey, P and Kumar, R and Patel, S and Kaushik, PK and Dadsena, A and Kumar, S},
title = {Introduction to microbiomes in health and diseases.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {1-42},
doi = {10.1016/bs.ircmb.2024.12.010},
pmid = {40623763},
issn = {1937-6448},
mesh = {Humans ; *Microbiota ; *Health ; *Disease ; Animals ; },
abstract = {The human microbiome is a complex ecological system of commensal, symbiotic, and pathogenic microorganisms that plays a crucial role in human health and disease. The microbiome includes both the living microorganisms also called microbiota and their synthesized metabolites and structural components. It is distributed to the gastrointestinal tract, skin, respiratory system, and oral cavity, each with a distinct microbial composition. Dysbiosis, or imbalance in the microbiome is linked to numerous diseases such as eczema, gastric ulcers, cardiovascular diseases, and cancer. The axes of microbial activity and their connections to disease, including the gut-skin, gut-lung, gut-brain, and gut-kidney play a crucial role in health and disease conditions. Also, the role of the microbiome in cancer development and response to therapy is examined. This book chapter underscores the importance of maintaining a balanced microbiome for overall health and the potential for microbiome-based interventions in disease prevention and treatment.},
}

Humans
*Microbiota
*Health
*Disease
Animals

@article {pmid40622550,
year = {2025},
author = {Madhukaran, SP and Yasmin, H and Kishore, U},
title = {Innate Immune Mechanisms in Normal and Adverse Pregnancy.},
journal = {Advances in experimental medicine and biology},
volume = {1476},
number = {},
pages = {339-379},
pmid = {40622550},
issn = {0065-2598},
mesh = {Pregnancy ; Humans ; Female ; *Immunity, Innate ; Animals ; Signal Transduction/immunology ; *Receptors, Pattern Recognition/immunology ; Immune Tolerance ; *Pregnancy Complications/immunology ; Inflammation/immunology ; },
abstract = {The innate immune system's recognition of microorganisms through pattern recognition receptors (PRRs) is a fundamental aspect of host defense and microbial symbiosis. During pregnancy, this system is finely tuned to accommodate the fetal allograft while still protecting against infections. Dysregulation in the recognition and response to commensal microorganisms can lead to pathological conditions, which may have implications for both maternal and fetal health. PRRs play a critical role in maintaining a balanced immune response, which is essential during pregnancy to prevent excessive inflammation that could affect pregnancy outcomes. They are involved in the regulation of immune cell proliferation and the integrity of mucosal barriers, which are vital for the protection of the maternal-fetal interface. The signaling pathways of PRRs are also key in the initiation and modulation of inflammation in response to microbial invasion. Changes in PRR function, as observed in certain animal models, indicate that the outcome of immune responses can be significantly altered by the specific signaling pathways activated in immune cells, and by the nature of the microbial environment. This is particularly relevant in pregnancy, where an altered PRR response may influence the risk of developing inflammatory conditions that could impact gestation and labor. In light of these considerations, understanding the role of PRR signaling in pregnancy is crucial for elucidating the mechanisms of maternal immune tolerance and the maintenance of a healthy pregnancy, as well as for identifying potential therapeutic targets for pregnancy-related complications arising from immune system dysregulation.},
}

Pregnancy
Humans
Female
*Immunity, Innate
Animals
Signal Transduction/immunology
*Receptors, Pattern Recognition/immunology
Immune Tolerance
*Pregnancy Complications/immunology
Inflammation/immunology

@article {pmid40622371,
year = {2025},
author = {Binay, S and Li, HH and Tsai, S and Saco, JA and Wen, ZH and Lin, C},
title = {Effects of cryopreservation on the glycan profile of Symbiodiniaceae.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70057},
pmid = {40622371},
issn = {1529-8817},
support = {MOST 110-2313-B-291 -001 -MY3//Ministry of Science and Technology, Taiwan/ ; },
abstract = {Symbiodiniaceae are crucial dinoflagellate symbionts for corals. They are affected by climate change-induced temperature rises that lead to coral bleaching, impacting coral reefs' health. Cryopreservation offers a solution to ensuring long-term storage of this species, preserving genetic diversity and viability. However, cryoinjury's impacts on glycan, a class of biomolecules with diverse biological roles including the initiation of coral-Symbiodiniaceae symbiosis, remain unknown. Thus, we examined the glycan profile of Breviolum psygmophilum cells cultured for varied periods post-thaw. The cells were subjected to two-step freezing with 2 M methanol as the cryoprotectant, and were cryopreserved for 2 h, then thawed and cultured. Lectin Array 70 was used to analyze glycan profiles of B. psygmophilum before and after cryopreservation. The results indicated that fucose and mannose differed significantly from N-acetyllactosamine, indicating its low presence in non-cryopreserved cells. Cryopreserved B. psygmophilum showed significant changes in fucose and mannose content, and several lectins contributed to the abundance of their respective carbohydrate moieties. These carbohydrates may affect cell division, repair, and energy. Lectins Gal1, CNL, DSA, BC2LCN, GRFT, HHA, NPA, Orysata, ConA, Gal3, and ACG changed in content post-cryopreservation, which may have been to mitigate the cryopreservation-induced stress, similar to their response to other stresses, while vital biological processes were maintained. This study sheds light on Symbiodiniaceae glycan profile alterations post-cryopreservation, which could influence Symbiodiniaceae's ability to establish symbiosis with corals thus highlighting the need to optimize cryopreservation protocols to minimize glycan alterations and enhance Symbiodiniaceae preservation, ultimately supporting coral reef conservation efforts.},
}

@article {pmid40621956,
year = {2025},
author = {Huang, X and Yang, L and Zhou, S and Zhong, L and Xu, G and Bi, M and Yang, X and Su, X and Rillig, MC},
title = {Plastic Biofilms as Hotspots of Nitrogen Cycling in Estuarine Ecosystems: Comparative Ecological, Genomic, and Transcriptomic Analysis Across Substrates.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70329},
doi = {10.1111/gcb.70329},
pmid = {40621956},
issn = {1365-2486},
support = {42021005//National Natural Science Foundation of China/ ; U23A20145//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo Municipal Science and Technology Innovative Research Team/ ; ANSO-PA-2023-18//Alliance of International Science Organizations/ ; },
mesh = {*Biofilms/growth & development ; *Plastics ; *Nitrogen Cycle ; *Estuaries ; Transcriptome ; Nitrogen/metabolism ; Ecosystem ; Seawater/microbiology ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; Metagenome ; },
abstract = {Biofilms represent a ubiquitous microbial lifestyle that facilitates colonization, symbiosis, and nutrient cycling, shaping environmental chemical transformations. In the Anthropocene, the proliferation of artificial surfaces, particularly plastics, has introduced novel and artificial ecological niches for microbial colonization. However, the biogeochemical potential of biofilms on these emerging artificial substrates remains largely unknown. Here, using [15]N tracing, amplicon, metagenome, and metatranscriptomic sequencing, we explore nitrogen (N) potential biogeochemistry across artificial and natural biofilms as well as the bulk seawater. Our results reveal that plastic biofilms exhibit enhanced N transformation potential, including elevated nitrification (2~45-fold), denitrification (5~44-fold), and N2O production (3~13-fold) rates, compared to natural biofilms and ambient seawater. This functional shift corresponds to distinct microbial community structures, driven by active N-cycling taxa and metabolic pathway reconfigurations on plastic surfaces. We also observe that carbohydrate metabolism pathways, such as glycolysis and the pentose phosphate pathway, were highly expressed in plastic biofilms, with transcriptional levels of glk (encoding glucokinase) and PGK (encoding phosphoglycerate kinase) increased by 6- and 2-fold, respectively. Our findings depict the role of plastic biofilms as active participants in estuarine N cycling and underscore the broader implications of plastic pollution on ecosystem biogeochemistry.},
}

*Biofilms/growth & development
*Plastics
*Nitrogen Cycle
*Estuaries
Transcriptome
Nitrogen/metabolism
Ecosystem
Seawater/microbiology
Bacteria/metabolism/genetics
Gene Expression Profiling
Metagenome

@article {pmid40621907,
year = {2025},
author = {Liang, X and Lu, X and Wei, Y and Jiang, F and Wang, M and Wei, X},
title = {Composition and driving factors of arbuscular mycorrhizal fungal communities in the roots and rhizosphere soil of naturally regenerated Phoebe bournei seedlings in Guizhou Province, China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0021025},
doi = {10.1128/spectrum.00210-25},
pmid = {40621907},
issn = {2165-0497},
abstract = {Arbuscular mycorrhizal (AM) fungi play vital roles in promoting tree growth and maintaining biodiversity and ecosystem stability in subtropical forests. Phoebe bournei, a key species endemic to the subtropical evergreen broad-leaved forests of China, forms symbiosis associations with AM fungi. However, the composition and structure of AM fungal communities associated with naturally regenerated P. bournei remain insufficiently characterized. This study used Illumina MiSeq sequencing to investigate the AM fungal communities in the root and rhizosphere soil samples. In total, 305 operational taxonomic units (OTUs) belonging to four orders and seven families were uncovered within Glomeromycota. Seven and nine AM fungal genera were detected in root and rhizosphere soil samples, respectively, with Glomus being the most dominant genus in both root and rhizosphere soil samples. Moreover, the diversity of AM fungal communities varied across sampling locations in the rhizosphere soil and roots. The co-occurrence network structure of the AM fungal community in the rhizosphere soil was more complex and robust than that of the roots. Furthermore, soil properties, latitude, and altitude influenced the changes in AM fungal α-diversity and the relative abundance of genera in roots and rhizosphere soil to varying degrees. Overall, our findings highlight the pivotal role of soil properties over geographical variables in explaining variations in the AM fungal community structure, with soil properties-particularly total phosphorus and total nitrogen-markedly driving the AM fungal community structure in the rhizosphere soil and roots of naturally regenerated P. bournei seedlings.IMPORTANCEAlthough subtropical forest ecosystems harbor rich arbuscular mycorrhizal (AM) fungal resources, insights into their communities in the rhizosphere of Phoebe bournei remain limited. This study investigates the composition and key drivers of AM fungi communities in the rhizosphere soil and roots of naturally regenerated P. bournei seedlings in Guizhou, subtropical China. The findings deepen the understanding of the potential of AM fungi in supporting the establishment and growth of mycorrhizal plants, as well as maintaining the diversity, productivity, and stability of subtropical forest ecosystems. Moreover, this study provides valuable insights into the selection and application of AM fungi resources in mycorrhizal seedling cultivation and afforestation of P. bournei.},
}

@article {pmid40621614,
year = {2025},
author = {Reichert, J and Tepavčević, J},
title = {Growing Apart: Global Warming Severely Impacts the Symbiosis of the Hawaiian Bobtail Squid and Bioluminescent Bacteria.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70308},
doi = {10.1111/gcb.70308},
pmid = {40621614},
issn = {1365-2486},
}

@article {pmid40621421,
year = {2025},
author = {Majeed, M and Ahmed, W and Javad, S and Iahtisham-Ul-Haq, and Rashid, S and Perveen, R and Farooq, U and Abid, J and Ahmad, AMR},
title = {Optimization of microwave-assisted extraction for quercetin (prebiotic) and the effect of its symbiotic combination with Lactobacillus acidophilus (probiotic) in NAFLD induced rat model.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1596758},
pmid = {40621421},
issn = {2296-861X},
abstract = {INTRODUCTION: Changing dietary patterns, lifestyle related disorders and associated metabolic syndromes have increased the prevalence of NAFLD over the last few years. It has been observed that there is a direct association between intestinal dysbiosis and NAFLD truly depicted by interconnected complex mechanisms. Besides its antioxidant activity, quercetin serves prebiotic functions as well.

OBJECTIVE: The objective of the current research was to determine the synbiotic effect of quercetin and Lactobacillus acidophilus on non-alcoholic fatty liver disease (NAFLD) induced rat models.

METHODS: Quercetin was extracted from red onions via microwave-assisted extraction technique (MAE). Response Surface Methodology (RSM) was employed to optimize MAE parameters. 25 female albino rats were divided into 5 groups of 5 rats each; 2 control (untreated and negative control) and 3 treatment groups (G1, G2, G3). High fat diet (HFD) (40% fat) in combination with 15% sucrose water and 440 mg cholesterol/100 g feed was given to rats over a period of 6 weeks to induce NAFLD. For the efficacy trial, treatment groups received different doses of quercetin; 50 mg, 80 mg and 100 mg in G1, G2 and G3, respectively, with a dose of 10[2] CFU of Lactobacillus acidophilus/200 μL of PBS in all three groups.

RESULTS: The results revealed optimal MAE conditions for maximum amount of quercetin as 600 W microwave power, 3 min irradiation time and distilled water as a solvent. Resultantly, 86.10 mg quercetin/gram of red onion extract (32.7mgQ/g onion powder) was obtained. There was no significant difference in HDL, VLDL, triglycerides, serum AST and serum ALP levels (p-value > 0.05) between all groups. However, total cholesterol, LDL cholesterol and serum ALT significantly improved in G3 (p-value < 0.05).

CONCLUSION: The synbiotic combination is effective at lowering total cholesterol, LDL cholesterol as well as serum ALT levels at a dose of 100 mg of quercetin/kg body weight for rats.},
}

@article {pmid40620226,
year = {2025},
author = {Sangwan, S and Saxena, G and Chawla, G and Prasanna, R and Bana, RS and Choudhary, AK},
title = {Propagule-Specific Bacteriome of Funneliformis mosseae Spores and Hyphae: Integrated High-Throughput and Culture-Dependent Insights.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70076},
doi = {10.1002/jobm.70076},
pmid = {40620226},
issn = {1521-4028},
support = {//This research was supported by the Indian Potash Limited, New Delhi./ ; },
abstract = {Arbuscular mycorrhizal (AM) symbiosis is increasingly recognized as a tripartite interaction involving the fungal symbiont, the host plant, and a diverse assemblage of associated bacteria. Through this study, propagule-specific bacteriome of Funneliformis mosseae was explored, particularly its taxonomic composition and plant growth-promoting (PGP) potential. Using a polyphasic approach integrating Illumina high-throughput sequencing with culture-dependent techniques, bacterial communities associated with monosporal hyphae and spores were characterized. Sequencing analyses revealed distinct taxonomic profiles between two propagule types: spores were dominated by Pseudomonas, whereas hyphae harbored higher relative abundances of Sphingobium and Rhodococcus. Culture-dependent screening on NBRIP medium yielded 53 phosphate-solubilizing bacterial isolates-21 from spores and 32 from hyphae. While hyphae-associated propagules contained a greater number of phosphate-solubilizing isolates, those from spores exhibited significantly higher solubilization capacities, ranging from 16.87 to 273 µg mL[-1], with 47.6% exceeding 100 µg mL[-1]. In contrast, hyphae-derived isolates ranged from 35.03 to 142.20 µg mL[-1], with 28.1% surpassing the 100-µg mL[-1] threshold. Functional screening further revealed that 38% of spore and 31% of hyphae-associated isolates exhibited diverse PGP traits. The five most potent strains were identified through 16S rDNA sequencing as Pseudomonas aeruginosa, Lactiplantibacillus plantarum, Bacillus haynesii, Bacillus licheniformis, and Enterococcus innesii. This study represents the first attempt to characterize a propagule-specific core bacteriome in Funneliformis mosseae, revealing clear taxonomic and functional divergence between spore and hyphae-associated bacterial communities. These findings highlight the specialized ecological roles of distinct propagule microbiomes and offer novel avenues for targeted manipulation of AM symbiosis to enhance plant nutrient acquisition and growth.},
}