@article {pmid41051678,
year = {2026},
author = {Kumar, A and Li, F and Li, Q},
title = {Quantifying Arbuscular Mycorrhizal Fungal Colonization via Anthocyanin Pigmentation in Medicago truncatula Roots.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2988},
number = {},
pages = {195-205},
pmid = {41051678},
issn = {1940-6029},
mesh = {*Medicago truncatula/microbiology/metabolism/genetics ; *Mycorrhizae/physiology/growth & development ; *Anthocyanins/metabolism ; *Plant Roots/microbiology/metabolism ; Symbiosis ; Pigmentation ; Plant Proteins/genetics/metabolism ; },
abstract = {Plant responses to environmental stimuli are often shaped by a history of previous interactions, forming the foundation for stress memory and adaptive plasticity. Arbuscular mycorrhizal (AM) fungi establish a mutualistic relationship with most land plants, enhancing nutrient uptake and stress resilience, and are increasingly recognized as biological agents contributing to plant stress memory. However, quantifying AM colonization, especially in large-scale or time-course experiments investigating priming or memory effects, remains a technical bottleneck. Conventional staining methods are time-consuming, destructive, and incompatible with live imaging. This chapter presents a robust, nondestructive, and quantitative protocol to assess AM colonization in Medicago truncatula roots using a visible anthocyanin pigmentation marker. The method employs a synthetic construct expressing the R2R3 MYB transcription factor MtLAP1, driven by the AM-inducible Kunitz Protease Inhibitor 106 (KPI106) promoter, enabling visualization of arbuscule-containing root cells through purple/red pigmentation. The protocol encompasses Agrobacterium rhizogenes-mediated hairy root transformation, standardized mycorrhization assays, and anthocyanin pigment extraction and quantification. Anthocyanin accumulation correlates strongly with conventional staining-based colonization estimates, and the system enables early detection, live imaging, and high-throughput screening of mutants with altered AM phenotypes. This method offers a powerful tool for dissecting the functional role of mycorrhizal symbiosis in plant stress memory and is especially suited for forward genetic screens, stress priming experiments, and live-tracking of root-fungus interactions over time.},
}

*Medicago truncatula/microbiology/metabolism/genetics
*Mycorrhizae/physiology/growth & development
*Anthocyanins/metabolism
*Plant Roots/microbiology/metabolism
Symbiosis
Pigmentation
Plant Proteins/genetics/metabolism

@article {pmid41051369,
year = {2025},
author = {Zhou, C and Xing, S and Ma, J and Sui, M},
title = {Synergistic Piezoelectric-Nanoscale Zero-Valent Iron Catalyst for Peroxyacetic Acid Activation: A Self-Driven Advanced Oxidation Process.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08828},
pmid = {41051369},
issn = {1520-5851},
abstract = {Conventional advanced oxidation processes (AOPs) that utilize iron-based catalysts encounter several limitations, including rapid deactivation and low electron transfer efficiency. Although piezoelectric materials have shown potential for mechanochemical energy conversion, their practical application is often hindered by the need for substantial external energy inputs. This requirement results in considerable energy consumption and waste. Herein, we innovatively designed a symbiotic self-driven nZVI@BTO catalyst through dual incorporation of nZVI within the barium titanate (BTO) lattice and its surface, achieving breakthrough synergy between piezoelectric activation and peracetic acid (PAA)-mediated oxidation. The nZVI@BTO/PAA system completely degraded sulfamethoxazole (SMX) within 10 min, exhibiting 12-fold enhancement in kobs compared to the nZVI/PAA system. The hydraulic vortex-induced piezoelectric polarization of nZVI@BTO generated a surface-enhanced built-in electric field (BIEF), creating a localized reducing microenvironment. This enhanced charge carrier separation and promoted the efficient regeneration of Fe[2+], ensuring a sustained abundance of active Fe[2+] sites on the catalyst surface. Surface Fe[2+] sites enabled rapid PAA activation, generating hydroxyl radical ([•]OH), singlet oxygen ([1]O2), and acetylperoxy radical (CH3C(O)OO[•]). Our findings demonstrated the efficiency, stability (maintaining >80% SMX removal after 5 cycles), and practicality of the nZVI@BTO/PAA system for real-world applications. The nZVI@BTO/PAA system represented a sustainable strategy for AOPs, advancing the development of environmentally resilient water treatment technologies.},
}

@article {pmid41050163,
year = {2025},
author = {Ando, M and Kito, I and Rachi, T and Matsuda, T and Oshima, K},
title = {Formation of the intestinal microbiota during mouse weaning promotes maturation of the IgA repertoire after growth.},
journal = {Bioscience of microbiota, food and health},
volume = {44},
number = {4},
pages = {261-271},
pmid = {41050163},
issn = {2186-6953},
abstract = {Secretory IgA (sIgA) is a class of antibodies that plays a pivotal role in mucosal immunity. The sIgA secreted into the intestinal tract acts to prevent luminal pathogens and food antigens from penetrating across the intestinal epithelial barrier, thereby contributing to the suppression of infections and food allergies. Furthermore, it binds extensively to symbiotic bacteria, exerting a significant impact on the gut microbiota. The antigen recognition specificity of antibodies is determined by the amino acid sequence of the variable region. Therefore, the type of IgA repertoire influences the formation and maintenance of the gut microbiota and susceptibility to infection and food allergy. The initial repertoire of IgA is induced by the extensive colonization of intestinal bacteria during the weaning period and is maintained for an extended period. However, the relationship between the initial gut microbiota and IgA repertoire development has yet to be fully analyzed. In the present study, the weaning gut microbiota was disrupted with antibiotics, and the IgA repertoire was subsequently analyzed in young adulthood. The administration of antibiotics during the weaning period resulted in the suppression of somatic hypermutation in the variable regions of IgA expressed in the small intestine, as well as an impact on multivalent reactivity in IgA during early childhood. Additionally, disturbances in the weaning gut microbiota led to alterations in the microbiota structure of adolescent mice. These findings suggest that the weaning gut microbiota plays a role in promoting the maturation of IgA function.},
}

@article {pmid41049555,
year = {2025},
author = {Lee, MH and Morris, RA and Phillips, R and Rio, RVM},
title = {mir-31 mediated control of bacteriome size in tsetse flies.},
journal = {Current research in insect science},
volume = {8},
number = {},
pages = {100117},
pmid = {41049555},
issn = {2666-5158},
abstract = {Tsetse flies are the primary vectors of African trypanosomes, which are transmitted through blood feeding. To supplement this nutritionally limited diet, tsetse evolved an obligate mutualism with the bacterium Wigglesworthia glossinidia, housed within a specialized organ called the bacteriome. While the functional contributions of this symbiosis towards tsetse fitness have been studied, host morphological changes that accommodate this relationship remain less understood. In pregnant flies, variable expression of microRNAs (miRNAs) regulates protein expression, but the specific impacts are unknown. During pregnancy, high expression of fatty acyl-CoA reductase (far) within the bacteriome is indirectly correlated with miR-31 abundance and coincides with bacteriome size increase. We explored the roles of far and miR-31 towards this morphological change. Although RNAi effectively reduced far expression, bacteriome size still increased, suggesting its expansion is independent of far. In contrast, disrupting miR-31 activity resulted in significantly enlarged bacteriomes in virgin flies, resembling those of mated females. These results suggest that gene(s) other than far are regulated by miR-31 and may contribute to bacteriome remodeling during pregnancy, potentially to meet increased symbiosis demands. Ultimately, disrupting this obligate mutualism may present a promising target for future vector control strategies.},
}

@article {pmid41049204,
year = {2025},
author = {Wang, L and Du, X and Liu, J and Zhang, J and Lv, S},
title = {Effects of grazing on plant functional groups across spatial scales in Stipa breviflora desert steppe.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1643655},
pmid = {41049204},
issn = {1664-462X},
abstract = {This study investigated the Stipa breviflora desert steppe through multi-scale (50m×50m, 25m×25m, 2.5m×2.5m) and grazing intensity (no grazing vs. heavy grazing) comparative analyses, revealing the response mechanisms of plant functional group diversity, interspecific associations, and stability. Key findings include: (1) Heavy grazing significantly reduced functional group diversity and evenness, while the Margalef richness index increased at the 25m×25m scale due to patchy invasion of grazing-tolerant species. (2) Interspecific associations exhibited scale-dependent patterns: Large-scale (50m×50m) associations were driven by environmental heterogeneity (e.g., resource competition and complementarity), whereas small-scale (2.5m×2.5m) interactions were dominated by direct species interactions (mutualism or exclusion). (3) Grazing-induced structural simplification through "environmental filtering", heavy grazing reduced functional group quantity, forming simplified symbiotic networks (PC≥0.6) between perennial grasses and annual/biennial plants, while significantly suppressing woody plants and forbs (Perennial forbs, Shrubs and semi-shrubs). (4) Stability analysis demonstrated higher stability of perennial grasses and forbs in ungrazed areas, though the overall system remained unstable. Annual/biennial plants and shrubs/semi-shrubs generally exhibited low disturbance resistance. The study proposes a multi-scale grassland restoration strategy: optimizing resource allocation at large scales while enhancing key species interactions at small scales. These findings provide theoretical foundations for the ecological restoration of degraded desert steppes and adaptive grazing regimes. Future research should integrate climate change and socioeconomic factors to develop more resilient grassland ecosystem management frameworks.},
}

@article {pmid41047046,
year = {2025},
author = {Cho, M and Choi, E and Lee, SJ and Choi, S and Kim, I and Shin, D and Kim, W and Hur, JS and Kim, JH and Rhee, JS and Park, H},
title = {Whole-genome sequence of the lichen-forming fungus Cetrariella delisei reveals an expanded repertoire of biosynthetic gene clusters.},
journal = {Genomics},
volume = {},
number = {},
pages = {111131},
doi = {10.1016/j.ygeno.2025.111131},
pmid = {41047046},
issn = {1089-8646},
abstract = {Lichens represent a distinctive symbiotic relationship between fungi and photosynthetic algae, allowing them to persist in harsh and extreme habitats. While known for their adaptability, the genomic features of lichen-forming fungi remain relatively understudied. In this study, the genome of the lichen-forming fungus Cetrariella delisei was assembled into 40 contigs, spanning 45.8 Mbp, with a BUSCO completeness of 96.7 %. Repetitive sequences comprised 18.14 % of the genome. A total of 11,716 genes were annotated, including 401 putative carbohydrate-active enzymes (CAZymes), though polysaccharide lyases were absent. Comparative analysis with five additional Parmeliaceae species showed that C. delisei contains a markedly higher number of auxiliary activity genes. Notably, C. delisei harbors 79 biosynthetic gene clusters (BGCs), exceeding the 50 to 65 clusters typically observed in related species, reflecting an expanded biosynthetic repertoire potentially underlying enhanced natural product diversity. These results improve our understanding of lichen symbiosis and provide a valuable genomic resource for future research.},
}

@article {pmid41046273,
year = {2025},
author = {Ding, Q and Tian, XY and Wu, WS and Yu, FJ and Shao, ZQ and Zeng, Z},
title = {The metabolic landscape of tomato roots during arbuscular mycorrhizal symbiosis reveals lipid-related metabolic rewiring.},
journal = {Plant cell reports},
volume = {44},
number = {10},
pages = {230},
pmid = {41046273},
issn = {1432-203X},
support = {32400186//National Natural Science Foundation of China/ ; 32270241//National Natural Science Foundation of China/ ; GZB20230303//Postdoctoral Fellowship Program of CPSF/ ; 2023ZB796//Jiangsu Excellent Postdoctoral Funding/ ; },
mesh = {*Mycorrhizae/physiology ; *Symbiosis/physiology ; *Solanum lycopersicum/metabolism/microbiology/genetics ; *Plant Roots/metabolism/microbiology ; *Lipid Metabolism ; Gene Expression Regulation, Plant ; },
abstract = {This study reveals lipid-related metabolic rewiring in tomato roots during arbuscular mycorrhizal symbiosis, identifying potential candidate lipids for fungal carbon transfer and signaling. Arbuscular mycorrhizal (AM) symbiosis induces substantial metabolic rearrangement in host plants to facilitate nutrient exchange and symbiotic efficiency. While previous metabolomic studies have characterized metabolite shifts in AM symbiosis, the lipid-related metabolic rewiring underlying nutrient exchange in host plant roots remains poorly resolved. Here, we investigated the metabolic response in tomato roots colonized by AM fungi. A total of 219 differentially accumulated metabolites (DAMs) were identified by the ultra-high-performance liquid chromatography-tandem mass spectrometry analysis, with lipids and lipid-like molecules representing the predominant classes. The most significantly upregulated metabolite was 2-(14,15-epoxyeicosatrienoyl) glycerol, a 2-monoacylglycerols (2-MAGs) mapped to arachidonic acid metabolism. This compound represents a C20-based epoxy fatty acid-derived 2-MAG, distinct from the C16:0 2-MAG induced by AM symbiosis in legumes, thereby implying the possibility of transferring diverse lipid substrates from different host plants to AM fungi. Concurrently, enhanced accumulation of dihomo-γ-linolenic acid (DGLA) and arachidonic acid (ARA) in AM fungi colonized roots underscored alterations of arachidonic acid metabolism and unsaturated fatty acid pathway. Gene set enrichment analysis based on the transcriptome data revealed significant transition of the glycerophospholipid metabolism pathway, primarily driven by multiple lysophosphatidylcholine (LPC) species that showed significant upregulation. Integrated transcriptomic and metabolomic analysis identified 31 overlapping KEGG pathways, emphasizing the importance of lipid and amino acid metabolism. In summary, our integrated analysis demonstrates that lipid-related metabolic reprogramming, represented by the induction of 2-MAGs and LPCs, is a feature of AM symbiosis that enables cross-kingdom nutrient exchange and host metabolic adaptation.},
}

*Mycorrhizae/physiology
*Symbiosis/physiology
*Solanum lycopersicum/metabolism/microbiology/genetics
*Plant Roots/metabolism/microbiology
*Lipid Metabolism
Gene Expression Regulation, Plant

@article {pmid41045972,
year = {2025},
author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X},
title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104408},
doi = {10.1016/j.ibmb.2025.104408},
pmid = {41045972},
issn = {1879-0240},
abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.},
}

@article {pmid41045963,
year = {2025},
author = {Lu, S and Miao, Y and Wang, D and Xu, D and Liu, R and Liu, X and Zhang, Y and Zhang, X and Qin, H},
title = {Engineered tumor-symbiotic bacterial membrane nanovesicles enable precise immuno-chemotherapy of colorectal cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114291},
doi = {10.1016/j.jconrel.2025.114291},
pmid = {41045963},
issn = {1873-4995},
abstract = {Gut microorganisms show promising therapeutic effects and drug delivery potential for colorectal cancer (CRC) treatment, but are limited by their insufficient targeting ability and side effects. Fusobacterium nucleatum (Fn) is a key symbiotic bacterium in CRC, which can preferentially accumulate in tumor tissues and invade tumor cells, while its tumorigenicity restricts the application in drug delivery. Herein, we engineered Fn with anchored PD-L1 antibody (αPD-L1), and then isolated the Fn membranes to construct bacterial membrane nanovesicles (ab-FMNVs) for precise delivery of chemotherapeutic drugs. The ab-FMNVs exploited Fn's inherent tumor colonization capabilities to achieve tumor-targeted delivery through the specific membrane protein FadA-mediated pathway, and modulated the PD-L1 immune checkpoint pathway for tumor immunotherapy. Simultaneously, ab-FMNVs were internalized into CT26 cells to release the chemotherapeutic agent doxorubicin, synergistically inhibiting tumor cell proliferation and metastasis. In a CRC-bearing mouse model, doxorubicin-loaded ab-FMNVs increased tumor accumulation and demonstrated superior antitumor efficacy against both primary and recurrent CRC progression without inducing any side effects. This innovative approach holds promise for precision cancer therapies by harnessing the symbiotic relationship between bacteria and CRC.},
}

@article {pmid41045882,
year = {2025},
author = {Hao, J and Shah, NS and Zhou, B},
title = {S[2]CAC: Semi-supervised coronary artery calcium segmentation via scoring-driven consistency and negative sample boosting.},
journal = {Medical image analysis},
volume = {107},
number = {Pt A},
pages = {103823},
doi = {10.1016/j.media.2025.103823},
pmid = {41045882},
issn = {1361-8423},
abstract = {Coronary artery calcium (CAC) scoring plays a pivotal role in assessing the risk for cardiovascular disease events to guide the intensity of cardiovascular disease preventive efforts. Accurate CAC scoring from gated cardiac Computed Tomography (CT) relies on precise segmentation of calcification. However, the small size, irregular shape, and sparse distribution of calcification in 3D volumes present significant challenges for automated CAC assessment. Training reliable automatic segmentation models typically requires large-scale annotated datasets, yet the annotation process is resource-intensive, requiring highly trained specialists. To address this limitation, we propose S[2]CAC, a semi-supervised learning framework for CAC segmentation that achieves robust performance with minimal labeled data. First, we design a dual-path hybrid transformer architecture that jointly optimizes pixel-level segmentation and volume-level scoring through feature symbiosis, minimizing the information loss caused by down-sampling operations and enhancing the model's ability to preserve fine-grained calcification details. Second, we introduce a scoring-driven consistency mechanism that aligns pixel-level segmentation with volume-level CAC scores through differentiable score estimation, effectively leveraging unlabeled data. Third, we address the challenge of incorporating negative samples (cases without CAC) into training. Directly using these samples risks model collapse, as the sparse nature of CAC regions may lead the model to predict all-zero maps. To mitigate this, we design a dynamic weighted loss function that integrates negative samples into the training process while preserving the model's sensitivity to calcification. This approach effectively reduces over-segmentation and enhances overall model performance. We validate our framework on two public non-contrast gated CT datasets, achieving state-of-the-art performance over previous baseline methods. Additionally, the Agatston scores derived from our segmentation maps demonstrate strong concordance with manual annotations. These results highlight the potential of our approach to reduce dependence on annotated data while maintaining high accuracy in CAC scoring. Code and trained model weights are available at: https://github.com/JinkuiH/S2CAC.},
}

@article {pmid41045547,
year = {2025},
author = {Yang, X and Li, Y and Wang, T and Li, Z and Zhuang, Q and Liang, C and Wang, X and Tian, J},
title = {GmSPX5 regulates arbuscular mycorrhizal colonization and phosphate acquisition through modifying transcription profile and microbiome in soybean.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70511},
doi = {10.1111/tpj.70511},
pmid = {41045547},
issn = {1365-313X},
support = {2021YFF1000500//National Key Research and Development Program of China/ ; 2024A1515013054//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZD04072//STI 2030-Major Project/ ; 2022B0202060005//Key Areas Research and Development Programs of Guangdong Province/ ; 2022SDZG07//the Open Competition Program of Ten Major Directions of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province/ ; 32172658//National Natural Science Foundation of China/ ; 32172659//National Natural Science Foundation of China/ ; 32302662//National Natural Science Foundation of China/ ; },
mesh = {*Glycine max/microbiology/genetics/metabolism ; *Mycorrhizae/physiology ; *Phosphates/metabolism ; Symbiosis ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Plant Roots/microbiology/metabolism ; *Microbiota/genetics ; },
abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi is a crucial strategy for plant adaptation to low phosphorus (P) stress. However, the mechanisms underlying how phosphate (Pi) signaling regulators participate in AM colonization remain largely unknown in soybean (Glycine max). In this study, the expression of GmSPX5, one member of the SPX (SYG1/Pho81/XPR1) family, was induced by AM fungal inoculation in soybean roots. Furthermore, the expression of GmSPX5 seems to overlap with AM infection structures through analyzing GUS activity of transgenic soybean plants harboring ProGmSPX5:GUS. Four transgenic lines with GmSPX5 overexpression (OX8 and OX12) and suppression (Ri9 and Ri11) were subsequently used to examine the functions of GmSPX5 on AM symbiosis and Pi acquisition. Despite no difference between Ri and wild-type (WT), the overexpression of GmSPX5 significantly increased AM colonization as reflected by 8.4% in OX8 and 8.7% in OX12, respectively. Consistently, the dry weight and total P content of OX8 and OX12 were higher than WT. Furthermore, a total of 3483 genes were found to exhibit differential expression patterns in roots between OX12 and WT, including genes related to linolenic acid metabolism and flavonoid metabolism. Meanwhile, the composition of the bacterial community in the roots of OX12 was distinct from that in WT through β-diversity analysis. Particularly, an ASV19 (Sphingomonadales) was enriched in OX12 roots, which was positively related to total P content and AM fungi colonization. Taken together, these results highlight that GmSPX5 can regulate AM symbiosis, as well as Pi acquisition in soybean. Our findings advance the understanding of SPX functions in plant-microbe interaction.},
}

*Glycine max/microbiology/genetics/metabolism
*Mycorrhizae/physiology
*Phosphates/metabolism
Symbiosis
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified
Gene Expression Regulation, Plant
Plant Roots/microbiology/metabolism
*Microbiota/genetics

@article {pmid41044905,
year = {2025},
author = {Zhang, W and Cheng, H and Yan, X and Suo, B and Wen, S and Liu, W and Wei, G and Chen, J},
title = {H2S-Mediated GH3.1 Persulfidation Regulates IAA Homeostasis to Enhance Nodulation Formation and Nitrogen Fixation in Robinia pseudoacacia.},
journal = {Molecular plant pathology},
volume = {26},
number = {10},
pages = {e70145},
doi = {10.1111/mpp.70145},
pmid = {41044905},
issn = {1364-3703},
support = {42477370//National Natural Science Foundation of China (NSFC)/ ; 2023yfd1900502//National Key Research and Development Program of China/ ; },
mesh = {*Nitrogen Fixation/drug effects/physiology ; *Indoleacetic Acids/metabolism ; Homeostasis/drug effects ; *Robinia/metabolism/drug effects/microbiology/genetics ; *Hydrogen Sulfide/pharmacology/metabolism ; *Plant Proteins/metabolism/genetics ; *Plant Root Nodulation/drug effects/physiology ; Gene Expression Regulation, Plant/drug effects ; },
abstract = {Hydrogen sulphide (H2S), a gaseous signalling molecule, plays a multifaceted role in plant physiology by enhancing adaptability to environmental stresses. However, the regulatory mechanism of symbiotic nitrogen (N) fixation by H2S in indeterminate nodules of woody legumes remains unclear. In this study, we investigated the mechanism by which H2S promotes nodulation and N fixation in the woody legume Robinia pseudoacacia. Exogenous H2S significantly enhanced rhizobium infection, nodule formation and nitrogenase activity, demonstrating its positive role in the symbiotic process. Transcriptomic analysis of roots and nodules revealed that H2S signalling modulates auxin metabolism, particularly through the regulation of indole-3-acetic acid (IAA) homeostasis. H2S was found to promote free IAA accumulation and reduce IAA conjugation (IAA-Asp and IAA-Glu). Further investigation revealed that H2S directly targets GH3.1, a key IAA-amido synthetase responsible for IAA conjugation. Specifically, H2S mediated persulfidation at Cys304 of GH3.1, inhibiting its enzymatic activity and preventing IAA inactivation. This modification was confirmed by LC-MS/MS, UPLC-ESI-MS/MS and site-directed mutagenesis. This post-translational modification maintained active IAA levels, facilitating early nodule development. These findings highlight the active role of H2S in regulating IAA homeostasis, thereby enhancing indeterminate nodule formation and N fixation through persulfidation of the Cys304 residue of GH3.1 in R. pseudoacacia.},
}

*Nitrogen Fixation/drug effects/physiology
*Indoleacetic Acids/metabolism
Homeostasis/drug effects
*Robinia/metabolism/drug effects/microbiology/genetics
*Hydrogen Sulfide/pharmacology/metabolism
*Plant Proteins/metabolism/genetics
*Plant Root Nodulation/drug effects/physiology
Gene Expression Regulation, Plant/drug effects

@article {pmid41044678,
year = {2025},
author = {Ren, C and Meng, Y and Liu, Y and Wang, Y and Wang, H and Liu, Y and Liu, C and Fan, X and Zhang, S},
title = {Probiotic Bacillus subtilis enhances silkworm (Bombyx mori) growth performance and silk production via modulating gut microbiota and amino acid metabolism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {103},
pmid = {41044678},
issn = {2524-4671},
support = {No. SDAIT-18//Modern Agricultural Technology System of Shandong Province/ ; No. CARS-18//China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Artificial diet-reared silkworms (Bombyx mori) exhibit reduced gut microbial diversity and impaired growth performance compared to mulberry-fed counterparts. While Bacillus subtilis is widely used as a probiotic in livestock and aquaculture, its impact on silkworms remains unexplored. This study investigates whether dietary supplementation with B. subtilis enhances larval development and elucidates the underlying mechanisms involving gut microbiota and metabolic pathways.

RESULTS: Supplementing artificial diets with B. subtilis (6 × 10[5] CFU/g) significantly increased larval body weight by 9.1-22.1% during instar stages and improved feed utilization efficiency (FUE) by 4.09%-6.80% compared to controls. Cocoon quality metrics, including cocoon shell weight (+ 9.77% in females) and cocoon shell ratio (+ 6.56%), also improved. Mechanistically, B. subtilis did not colonize the midgut but transiently modulated gut physiology: it elevated midgut fluid pH and enhanced α-amylase, trypsin, and lipase activities. 16 S rRNA sequencing revealed reduced gut microbial diversity (Shannon index, P < 0.01) and shifts in community structure, with decreased abundances of potential pathogens (e.g., Pseudomonas) and commensals (e.g., Lactobacillus). Targeted metabolomics identified a 3.1-fold increase in phenylalanine levels in hemolymph, linked to upregulated aromatic amino acid metabolism pathways (KEGG). Dietary phenylalanine supplementation (0.4%) replicated B. subtilis-induced growth promotion, confirming its pivotal role in host-microbe interactions.

CONCLUSIONS: B. subtilis enhances silkworm growth and silk production through multi-faceted mechanisms: reshaping gut microbiota composition, improving digestive enzyme activity, and elevating phenylalanine biosynthesis. These findings establish B. subtilis as a promising probiotic for optimizing artificial diet systems in Lepidoptera and highlight the central role of amino acid metabolism in insect-microbiome symbiosis.},
}

@article {pmid41042365,
year = {2025},
author = {Bernal-Castro, C and Camargo-Herrera, Á and Gutiérrez-Cortés, C and Díaz-Moreno, C},
title = {Probiotic and Technological Potential of Native Lactic Acid Bacteria Strains from High Andean Forest Bee Bread: In Vitro Study.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {80},
number = {4},
pages = {163},
pmid = {41042365},
issn = {1573-9104},
mesh = {*Probiotics ; *Bread/microbiology ; Animals ; Bees ; *Lactobacillales/isolation & purification/genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Pollen ; *Pediococcus pentosaceus/isolation & purification/growth & development/genetics ; *Pediococcus/isolation & purification/genetics/growth & development ; Functional Food ; Hydrogen-Ion Concentration ; Bile Acids and Salts ; },
abstract = {Bioprospecting of lactic acid bacteria with probiotic potential from apicultural products is an important key for the research in functional foods. The in vitro evaluation of the probiotic and technological potential of commercial HOWARU strains and native strains isolated from bee bread was conducted in this study. The strains were molecularly identified (16S rRNA sequencing), revealing differences between molecular characterization and the microorganisms described in the technical datasheet. Most native strains belong to the genus Pediococcus. The ability to resist simulated gastrointestinal conditions (acidic pH and bile salts), as well as tolerance to extreme conditions (high temperature and osmotic pressure), was determined. VEGE 092 culture showed survival levels above 80%, and Pediococcus pentosaceus exceeded 95%. Finally, growth on alternative substrates (by-product of supercritical fluid extraction of bee pollen, car-rot waste flour, and turmeric flour) was evaluate by the quantitative prebiotic index. This study demonstrated that the best symbiotic combination was VEGE 092 and turmeric (prebiotic index = 0.96), and P. pentosaceus with the pollen extraction by-product, demonstrating a strain-substrate relationship. This study highlights the potential use of these strains in functional food applications, emphasizing their resilience and ability to thrive in various substrates.},
}

*Probiotics
*Bread/microbiology
Animals
Bees
*Lactobacillales/isolation & purification/genetics/physiology
RNA, Ribosomal, 16S/genetics
Pollen
*Pediococcus pentosaceus/isolation & purification/growth & development/genetics
*Pediococcus/isolation & purification/genetics/growth & development
Functional Food
Hydrogen-Ion Concentration
Bile Acids and Salts

@article {pmid41042234,
year = {2025},
author = {Sathe, S and Becks, L},
title = {Reciprocal effects of programmed cell death on fitness in unicellular endosymbiotic Chlorella and its ciliate host.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf119},
pmid = {41042234},
issn = {1420-9101},
abstract = {Programmed cell death (PCD), the genetically controlled active cellular suicide mechanism in multicellular organisms, also exists in unicellular organisms. However, explaining the evolution of PCD by natural selection in these organisms remains a challenge. PCD likely emerged during early endosymbiotic events as an initial antagonistic adaptation, enabling unicellular parasitic proto-endosymbionts to exploit their hosts, for example, by triggering host death in response to nutrient depletion or releasing offspring. Over time, during endosymbiont domestication and, as proposed, through horizontal gene transfer from endosymbionts to the host, PCD evolved in the host, providing benefits to both the host and the endosymbionts. However, the underlying assumption of this hypothesis, that PCD benefits and non-PCD (necrosis) harms the endosymbionts and/or the host, remains untested. Here, we investigated the fitness consequences of heat-shock-induced PCD in the endosymbiotic chlorophyte Chlorella variabilis and its facultative symbiotic ciliate host Paramecium bursaria, the non-symbiotic C. sorokiniana, and the predatory host P. duboscqui. Heat-shock triggered PCD in C. variabilis and the two ciliate species, causing significant fitness consequences. The supernatant from C. variabilis PCD enhanced the growth of its own clones and endosymbiotic host while inhibiting the growth of the predatory host. The supernatants from necrotic C. variabilis reduced growth of both Chlorella and Paramecium. Similarly, PCD in the symbiotic Paramecium host benefited Chlorella, whereas PCD and necrosis in the predatory Paramecium host were detrimental. These results expand the understanding of unicellular PCD, highlighting its dual role in benefiting clonal populations and their specific endosymbiotic partners, thereby affecting endosymbiosis evolution.},
}

@article {pmid41041976,
year = {2025},
author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA},
title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/mec.70126},
pmid = {41041976},
issn = {1365-294X},
support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; },
abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.},
}

@article {pmid41040871,
year = {2025},
author = {Zeng, L and Qian, Y and Cui, X and Zhao, J and Ning, Z and Cha, J and Wang, K and Ge, C and Jia, J and Dou, T and Chen, H and Liu, L and Bao, Z and Jian, Z},
title = {Immunomodulatory role of gut microbial metabolites: mechanistic insights and therapeutic frontiers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675065},
pmid = {41040871},
issn = {1664-302X},
abstract = {The gut microbiota modulates host immunity through a wide array of metabolic products that function as signaling molecules, thereby linking microbial activity with both mucosal and systemic immune responses. Notably, short-chain fatty acids, secondary bile acids, tryptophan-derived indoles, polyamines, and lipid derivatives play pivotal roles in regulating innate and adaptive immune functions via G protein-coupled receptors, nuclear receptors, and epigenetic pathways. These metabolites modulate immune cell differentiation, epithelial barrier integrity, and the resolution of inflammation in a dose- and site-specific manner. Recent advancements in spatial metabolomics, synthetic biology, and nanomedicine have facilitated the spatiotemporal delivery of these immunomodulatory compounds, revealing novel therapeutic avenues for the treatment of inflammatory and autoimmune disorders. This review summarizes the biosynthesis and immunoregulatory functions of key microbial metabolites, highlights the compartmentalized and systemic mechanisms of action, and discusses emerging therapeutic approaches, including postbiotics, engineered probiotics, and receptor-targeting drugs. We also explore the challenges in achieving personalized microbiome-immune modulation and propose future directions integrating multiomics and AI-driven predictive modeling. Understanding the metabolite-immune axis paves the way for novel interventions targeting host-microbe symbiosis.},
}

@article {pmid41040407,
year = {2025},
author = {Tan, CH and Schwartz, HT and Rodak, NY and Sternberg, PW},
title = {Evolution of parasitism-related traits in nematodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.26.678730},
pmid = {41040407},
issn = {2692-8205},
abstract = {UNLABELLED: The abundant resources provided by the host provide an evolutionary rationale for parasitism and drive the metabolic and developmental divergence of parasitic and free-living animals. Two evolutionally distant nematode genera, Steinernema and Heterorhabditis , independently evolved an entomopathogenic lifestyle, in which they invade insects and kill them with the assistance of specifically associated symbiotic pathogenic bacteria. It had been generally assumed that the worm, being a bacterivore, feeds on its symbiotic bacteria, which rapidly reproduce while consuming the insect host. The evolutionary adaptations of entomopathogenic nematodes to a parasitic lifestyle developmentally, and the symbiotic relationships of entomopathogenicity, remain largely unknown. We developed an axenic culture medium that allows for robust and sustained growth of Steinernema hermaphroditum , allowing finite control of nutrients available to the nematodes. We found that, uniquely among nematodes tested, the hatchlings of S. hermaphroditum cannot endure in a nutrient-poor environment; this ability is impaired but still present in Heterorhabditis bacteriophora . Similarly, the ability to forage for food is completely lost in H. bacteriophora hatchlings and severely compromised in S. hermaphroditum . We reasoned that these traits were lost because they are unnecessary to obligate parasites that always hatch in a resource-rich host. We further found that Steinernema and, to a limited extent, Heterorhabditis nematodes can successfully invade, develop, and reproduce inside a living insect host independent of their symbiotic bacteria, apparently feeding on the hemolymph, and emerge carrying bacteria found within, explaining the evolutionary origins of entomopathogenic nematodes.

HIGHLIGHTS: A simple but robust axenic culturing method for the emerging model nematode Steinernema hermaphroditum and other invertebrate parasitic nematodes. Convergent evolution led to the loss of hatchling survival traits in entomopathogenic nematodes.Nematode adaptation to parasitism is associated with changes in modes of feeding.Entomopathogenic nematodes evolved from parasitoid ancestors.},
}

@article {pmid41040397,
year = {2025},
author = {Sankari, S and Arnold, MF and Babu, VMP and Deutsch, M and Walker, GC},
title = {Exploiting Peptide Chirality and Transport to Dissect the Complex Mechanism of Action of Host Peptides on Bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.24.678446},
pmid = {41040397},
issn = {2692-8205},
abstract = {UNLABELLED: Elucidation of the complex mechanisms of action of antimicrobial peptides (AMPs) is critical for improving their efficacy. A major challenge in AMP research is distinguishing AMP effects resulting from various protein interactions from those caused by membrane disruption. Moreover, since AMPs often act in multiple cellular compartments, it is challenging to pinpoint where their distinct activities occur. Nodule-specific cysteine-rich (NCR) peptides secreted by legumes, including NCR247, have evolved from AMPs to regulate differentiation of their nitrogen-fixing bacterial partner during symbiosis as well as to exert antimicrobial actions. At sub-lethal concentrations, NCR247 exhibits strikingly pleiotropic effects on Sinorhizobium meliloti . We used the L- and D-enantiomeric forms of NCR247 to distinguish between phenotypes resulting from stereospecific, protein-targeted interactions and those caused by achiral interactions such as membrane disruption. In addition, we utilized an S. meliloti strain lacking BacA, the transporter that imports NCR peptides into the cytoplasm. BacA plays critical symbiotic roles by reducing periplasmic peptide accumulation and fine-tuning symbiotic signaling. Use of the BacA-deficient strain made it possible to distinguish between phenotypes resulting from peptide interactions in the periplasm and those occurring in the cytoplasm. At high concentrations, both L- and D-NCR247 permeabilize bacterial membranes, consistent with nonspecific cationic AMP activity. In the cytoplasm, both NCR247 enantiomers sequester heme and trigger iron starvation in an achiral but BacA-dependent manner. However, only L-NCR247 activates bacterial two-component systems via stereospecific periplasmic interactions. By combining stereochemistry and genetics, this work disentangles the spatial and molecular complexity of NCR247 action. This approach provides critical mechanistic insights into how host peptides with pleiotropic functions modulate bacterial physiology.

AUTHOR SUMMARY: Many organisms produce antimicrobial peptides (AMPs) to fight infections, but legumes have uniquely co-opted these molecules to control their symbiotic partners. During symbiosis between Medicago truncatula and Sinorhizobium meliloti , the plant secreted Nodule-specific Cysteine-Rich (NCR) peptides, transforms free-living bacteria into differentiated bacteroids that fix nitrogen but cannot reproduce outside the host. One such peptide, NCR247, exerts pleiotropic effects on the bacteria, acting on different subcellular locations, including membrane, heme, and proteins. Using a mirror-image (D-form) peptide, we disentangled peptide effects arising from generic physiochemical interactions versus stereospecific binding. The inner membrane protein BacA is known to play a protective role by importing NCR peptides into the cytoplasm. Using a bacterium lacking BacA, we were able to distinguish the effects of the peptide within and outside the cytoplasm. It was thought that BacA safeguards symbiotic bacteria by internalizing NCR peptides, thereby limiting their toxic membrane lytic effects, yet this has not been demonstrated. We show that BacA prevents lethal overstimulation of signaling pathways in the periplasm by internalizing the peptides. Our methods provide a framework for testing mechanism of action of new peptide-based antibiotics to combat multidrug-resistant bacteria.},
}

@article {pmid41040118,
year = {2025},
author = {Bonnette, H and Savitt, LR},
title = {Optimizing Colorectal Surgery Outcomes: The Role of the Advanced Practice Provider (APP) in Developing a Center for Pelvic Floor Disorders and Maximizing Scope of Practice for APPs.},
journal = {Clinics in colon and rectal surgery},
volume = {38},
number = {6},
pages = {411-416},
pmid = {41040118},
issn = {1531-0043},
abstract = {Many patients with pelvic floor disorders who are referred to colorectal surgery do not actually need surgery. The Massachusetts General Hospital (MGH) Center for Pelvic Floor Disorders (PFDC) was established in 2008 out of a recognition of the need for a specialized comprehensive treatment for patients living with a pelvic floor disorder. To describe the model that we have created utilizing advanced practice providers (APPs) within the PFDC at the MGH as an example of a model of care for patients who historically may have been managed by colorectal surgeons. The utilization of APPs in surgery has increased, which in turn has had positive effects on patient care and can help reduce the demands put on surgeons to see patients who ultimately do not end up having surgery. There is also a potential for both direct and indirect revenue production through the utilization of APPs at the top of their scope of practice as well as increased access to care for these patients. Training APPs to work at the top of their scope within a surgical practice increases patient's access to care, allows surgeons to focus on those who ultimately require surgery, and can lead to better patient outcomes at a reduced healthcare cost. In order for this symbiotic relationship between APPs and surgeons to be successful, it is essential that there is mutual collaboration and trust between providers. It requires commitment from surgeons to appropriately train their APPs.},
}

@article {pmid41039684,
year = {2025},
author = {Xu, N and Yang, X and Li, C and Zhang, C and Guo, M},
title = {Identification and functional characterization of chemoreceptors for phenolic acids in Agrobacterium tumefaciens.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128348},
doi = {10.1016/j.micres.2025.128348},
pmid = {41039684},
issn = {1618-0623},
abstract = {Phenolic acids influence host-pathogen interactions and function as key signals in Agrobacterium-mediated transformation or plant-microbe symbiosis. Agrobacterium tumefaciens uses chemotaxis to detect plant-secreted phenolic compounds and migrates to infection sites, though the chemotactic mechanism remains unclear. In this study, starting with structurally simple phenolic acids, the chemotactic response of A. tumefaciens C58 was investigated. The chemotaxis of A. tumefaciens toward 4-hydroxybenzoate and protocatechuate is not impacted by the methyl-accepting chemotaxis proteins (MCPs) Atu0387 and Atu0738, which share a four-helix bundle domain with previously discovered phenolic-sensing MCPs. To identify chemoreceptors for phenolic acids, a heterologous expression and functional screening system was constructed in Escherichia coli. Among the 13 MCPs, Atu0872 could respond to both 4-hydroxybenzoate and protocatechuate. Furthermore, atu0872 deletion weakened chemotaxis toward vanillin, acetosyringone, guaiacol, caffeic, vanillic, salicylic, gallic, p-coumaric, syringic, and sinapinic acids. Although the ligand-binding domain of Atu0872 was predicted to be a nitrate- and nitrite-sensing domain, the A. tumefaciens deletion mutant Δatu0872 did not affect chemotaxis toward nitrate and nitrite. In addition to chemotaxis, atu0872 deletion decreased the tumor weight on Daucus carota roots, Kalanchoe daigremontiana leaves, and the number of bacterial colonies per 0.1 g of tumor, implying that atu0872 affects bacterial colonization on the host by regulating chemotactic behavior. To our knowledge, this is for the first study identifying Atu0872 as a core chemoreceptor in A. tumefaciens for phenolic compounds, providing a theoretical foundation for elucidating the chemotaxis-pathogenicity relationship in A. tumefaciens and optimizing its use in genetic transformations.},
}

@article {pmid41039422,
year = {2025},
author = {Wong, ELY and Calchera, A and Otte, J and Schmitt, I},
title = {Temperature variability and other climatic attributes linked to genomic features in the lichen-forming fungal genus Umbilicaria.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {293},
pmid = {41039422},
issn = {1741-7007},
support = {LOEWE/1/10/519/03/03.001(0014)/52//Hessisches Ministerium für Wissenschaft und Kunst/ ; },
mesh = {*Genome, Fungal ; *Temperature ; *Lichens/genetics ; *Climate ; *Ascomycota/genetics ; },
abstract = {BACKGROUND: Many species of lichen-forming fungi exhibit large geographical ranges and broad thermal niches, making them excellent models for investigating the genomics of climate adaptation. In this study, we examined the impacts of climatic variables on genomic features in 11 Umbilicaria species. We compared PacBio genomes of individuals from the same species collected in different climate zones: alpine, cold temperate, or Mediterranean.

RESULTS: Our findings revealed several links between climatic and genomic features: (1) Selection pressure: in each climate zone, specific genes are under strong selection. (2) Genomic feature correlations: certain temperature variables (BIO2: mean diurnal range, BIO4: seasonality, BIO6: minimum in coldest month, BIO7: annual range) are correlated with GC content and the usage of the amino acids arginine and valine, suggesting these variables may drive convergent evolution of these genomic features. (3) Temperature variability: bioclimatic variables representing temperature variability, e.g. BIO2,4,7 are more influential in shaping genomic features than temperature means or extrema, with BIO6 also playing a significant role. (4) Epigenetic modifications: the rate of 5-methylcytosine (5mc) methylation within species is generally higher in samples from the colder habitat, suggesting that epigenetic modifications may contribute to climate adaptation.

CONCLUSIONS: Overall, our study shows that genome evolution is partially shaped by climate and, particularly, temperature variability. This aligns with numerous ecological and climate modelling studies, which show that climate variability has a stronger impact on species behaviour and evolution than climate means and extrema. Further genomics studies are required to provide additional evidence on this topic.},
}

*Genome, Fungal
*Temperature
*Lichens/genetics
*Climate
*Ascomycota/genetics

@article {pmid41038270,
year = {2025},
author = {Liu, T and Lin, H and Tian, Z},
title = {Genetic innovations underlying the evolution of root nodule symbiosis in Leguminosae.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2025.09.008},
pmid = {41038270},
issn = {1673-8527},
abstract = {Root nodule symbiosis (RNS) is a mutualistic association formed between nitrogen-fixing rhizobia or Frankia and host plants limited to four orders within Rosid I-Fabales, Fagales, Cucurbitales and Rosales-which comprise the so-called 'Nitrogen Fixing Nodulation Clade' (NFNC). The majority of nodulation studies have focused on Leguminosae, given their agricultural and environmental importance, as well as the widespread occurrence of nodulation among members of this family. Endowing cereal crops with nitrogen fixation, like Leguminosae, presents a strategy to reduce the detrimental effects of synthetic fertilizer overuse. Different hypotheses on the origin of RNS have been proposed, however key genetic innovations underlying the evolution of RNS, even in Leguminsoae, have been rarely reported. In this review, we begin by examining current knowledge of genetic innovations-including gene gain, gene loss, and the acquisition or loss of conserved noncoding sequences (CNS) in preexisting genes. We explore the available evidence supporting these genetic innovations underlying the evolution of RNS in Leguminosae and offer the phylogenomics approach that could be applied to uncover these genetic innovations. Finally, we conclude by proposing a model of genetic innovations underlying the evolution of RNS in Leguminsoae and consider the potential implications for the development of nitrogen-fixing crops.},
}

@article {pmid41038028,
year = {2025},
author = {Almeida, AC and Reid, M and Lillicrap, A},
title = {Specific toxicity of octinoxate and octocrylene on Symbiodinium sp., a symbiotic microalga with corals.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119151},
doi = {10.1016/j.ecoenv.2025.119151},
pmid = {41038028},
issn = {1090-2414},
abstract = {The widespread use of UV filters in sunscreens and personal care products has raised concerns about their detrimental effects to the aquatic environment. This study examined the specific toxicity of two UV filters, octinoxate and octocrylene to Symbiodinium sp., a photosynthetic dinoflagellate essential for coral symbiosis, nutrient acquisition, and reef structure. The study employed a comprehensive set of sub-lethal endpoints analyzed through flow cytometry, including cell viability, pigment fluorescence, cell size, complexity, metabolic activity, production of reactive oxygen species and membrane potential. The exposure of exponentially proliferating Symbiodinium sp. to octinoxate and octocrylene demonstrated pronounced toxicity, with octinoxate exhibiting toxicity levels significantly greater than those of octocrylene. This disparity underscores the different ecological impacts of these UV filters. Even at lower concentrations, octinoxate significantly influenced cellular parameters, including cell size, complexity, viability, and metabolic activity, as evidenced by increased lipid peroxidation (LPO) and neutral lipid accumulation, alongside a reduction in cellulose levels, suggesting potential structural alterations in cellular components. In contrast, octocrylene's sub-lethal effects are manifested as enhanced cell complexity and LPO, with elevated neutral lipids and cellulose levels. However, at elevated concentrations, octocrylene adversely affected cell viability and metabolic activity, indicative of severe membrane depolarization. These findings highlight the importance of an early warning system to protect Symbiodinium sp. and consequently corals. Flow cytometry proved to be a valuable diagnostic tool for detecting sub-lethal effects, providing insights into Symbiodinium sp. health status and, consequently, the resiliency of coral reef ecosystems.},
}

@article {pmid41037855,
year = {2025},
author = {Reynoso, MA},
title = {Update on translational control modes in plant cell signaling.},
journal = {Current opinion in plant biology},
volume = {88},
number = {},
pages = {102799},
doi = {10.1016/j.pbi.2025.102799},
pmid = {41037855},
issn = {1879-0356},
abstract = {Protein synthesis can contribute to plant cell signaling at multiple regulatory levels. Recent studies have expanded the conditions that are directly impacted by translational regulation. This control can balance responses to developmental, environmental, and diverse stress stimuli. Processes with evidence of translational regulation include: immunity to bacterial pathogens, symbiotic interactions, abiotic responses, hormonal perception, light-dependent metabolism, and developmental programs for lateral root initiation, root hair growth, and sepal initiation. Translational control modes rely on the sequence and secondary structure of mRNAs due to the presence of upstream open reading frames (uORFs) and/or internal ribosome entry sites (IRES), protein-binding regions or structures, and the decoding of the epitranscriptomic mRNA modifications such as N[6]-methyladenosine, N[4]-acetylcytidine or pseudouridine. In addition, the post-translational modification of ribosomal proteins and eukaryotic initiation factors such as eIF4G, eIFiso4G, eIF2, as well as changes in ribosome protein composition contribute to translational control. These factors, mRNAs, regulatory proteins and other RNAs can be confined by the formation of biomolecular condensates such as stress granules, processing bodies and others, resulting in paths that modulate translation both globally and specifically. The covered topics place translation as a hub for cell responses during development and within the environmental context. Current understanding of translation has allowed the development of applications in crops, reinforcing the relevance of the study of translational control in plants.},
}

@article {pmid41037509,
year = {2025},
author = {Pardo-De la Hoz, CJ and Haughland, DL and Thauvette, D and Toni, S and Goyette, S and White, W and Medeiros, ID and Cornet, L and Dvořák, P and Garfias-Gallegos, D and Miadlikowska, J and Magain, N and Lutzoni, F},
title = {Rapid radiations outweigh reticulations during the evolution of a 750-million-year-old lineage of cyanobacteria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf244},
pmid = {41037509},
issn = {1537-1719},
abstract = {Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g., cycads and bryophytes) and fungi (e.g., cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e., when closely related clades of Nostoc cooccur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria.},
}

@article {pmid41036755,
year = {2025},
author = {Rahman, A and Borah, P and Hussain, S and Sen, A and Bharalee, R and Chabukdhara, M and Upadhyaya, H and Verma, AK},
title = {Chemical Diversity of Carotenoids Derived from Aquatic Animals and their Therapeutic, Biomedical, and Natural Colorant Applications.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073377688250903053348},
pmid = {41036755},
issn = {1875-5402},
abstract = {Carotenoids, prevalent in a diverse range of aquatic animals, perform critical and multifaceted roles essential for marine and freshwater ecosystems. This review examines the distribution, biological functions, and potential biomedical applications of carotenoids sourced from various aquatic animals. Carotenoids are acquired through food consumption or metabolic pathways, playing vital roles such as photoprotection, antioxidant defense, and nutritional enhancement, particularly provitamin A. Marine sponges and cnidarians display a diverse spectrum of carotenoids, crucial for symbiosis and photoprotection. Molluscs and crustaceans exhibit varied carotenoid profiles corresponding to their trophic strategies, whereas fish and echinoderms utilize carotenoids in reproductive and developmental processes. In biomedical contexts, carotenoids act as potential anti-cancer agents and antioxidants. Lycopene, β-carotene, and astaxanthin demonstrate anti-proliferative and antioxidant effects, pivotal in cancer prevention and therapeutic interventions. Their applications extend to biomedical technologies like Raman spectroscopy and drug delivery systems, underscoring their diagnostic and therapeutic potential. Carotenoids, as powerful antioxidants, neutralize free radicals and diminish oxidative stress, which is linked to chronic diseases like cardiovascular diseases, neurodegenerative disorders, and cancer. Some carotenoids, such as beta-carotene, are precursors to vitamin A, vital for vision, immune response, and cell communication. Furthermore, carotenoids have anti-inflammatory properties that modulate inflammatory pathways and provide therapeutic potential in diseases like inflammatory bowel disease and arthritis, which are marked by chronic inflammation. Furthermore, carotenoids provide photoprotection, safeguarding the skin and other tissues from damage caused by ultraviolet radiation. This paper highlights the integral role of carotenoids in biomedical advancements, emphasizing their significance in human health research.},
}

@article {pmid41035639,
year = {2025},
author = {Li, Y and Wang, S and Yao, D and Zhang, K and Yin, Y and Kong, X and Li, J and Zeng, L and Zhang, R and Zhang, Z},
title = {A taste of one's own medicine: Bacillus velezensis isolated from adult housefly intestines demonstrates effective fly control.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575292},
pmid = {41035639},
issn = {1664-3224},
mesh = {Animals ; *Bacillus/physiology/isolation & purification/immunology ; *Gastrointestinal Microbiome ; *Houseflies/microbiology/immunology ; Larva/microbiology/immunology ; *Intestines/microbiology/immunology ; Transcriptome ; *Pest Control, Biological/methods ; Symbiosis ; Immunity, Humoral ; },
abstract = {INTRODUCTION: Bacillus spp. are widely used as biological agents for managing diseases in crops, livestock, poultry, and aquatic animals. Bacillus velezensis, a novel species within the Bacillus genus, is extensively used in the biological control of animal and plant diseases. However, the association between B. velezensis and insect hosts remains a complex and poorly understood process.

METHODS: In this study, we utilized a housefly larvae model to investigate the relationship between B. velezensis and houseflies by examining the changes in intestinal microbiota, transcriptomics, and humoral immunity following symbiotic B. velezensis treatment.

RESULTS: The results revealed striking dynamic changes in the bacterial community composition of larvae in the treatment group at the genus level. Notably, Providencia and Morganella content increased, while Enterobacter content decreased, leading to inhibited larval growth. Moreover, the bacterial association with the larva significantly impacted the larval transcriptome, modulating the expression of genes involved in various biological pathways, including host growth and development, macronutrient metabolism, and energy production, which are essential for insect development and survival. Oral feeding of B. velezensis also caused significant morphological changes in the larval gut, resulting in notable larval mortality, cell degeneration, shrinkage, and the formation of various vacuoles. Additionally, we observed a significant decrease in immune response in housefly larvae, with a reduction in phenoloxidase activity and melanization ability in treated larvae compared to controls.

DISCUSSION: Therefore, B. velezensis can damage the vital functions of housefly larvae and may be utilized as a microecological regulator for the green prevention and control of housefly populations.},
}

Animals
*Bacillus/physiology/isolation & purification/immunology
*Gastrointestinal Microbiome
*Houseflies/microbiology/immunology
Larva/microbiology/immunology
*Intestines/microbiology/immunology
Transcriptome
*Pest Control, Biological/methods
Symbiosis
Immunity, Humoral

@article {pmid41035504,
year = {2025},
author = {Olaguez-Gonzalez, JM and Chairez, I and Breton-Deval, L and Alfaro-Ponce, M},
title = {In-silico assessment of dynamic symbiotic microbial interactions in a reduced microbiota related to the autism spectrum disorder symptoms.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {4078-4088},
pmid = {41035504},
issn = {2001-0370},
abstract = {The gut microbiota plays a crucial role in human health, with growing evidence linking its composition to the development of Autism Spectrum Disorder. However, inconsistencies in previous studies have hindered the identification of a definitive microbial signature associated with Autism Spectrum Disorder. Machine learning models have emerged as powerful tools for analyzing microbiome data, yet their interpretability remains limited. In this study, we integrate in silico simulations with machine learning predictions to explore microbial interactions under different dietary conditions and provide biological context to features of the intestinal microbiota that are linked to Autism Spectrum Disorder. This study employs constraint-based modeling to simulate metabolic exchanges among key bacterial taxa in order to assess their ecological relationships. Findings reveal that high-fiber diets foster mutualistic and balanced interactions, whereas Western-style diets promote competitive and parasitic dynamics, potentially contributing to gut dysbiosis in Autism Spectrum Disorder. In addition, the presence of oxygen (a factor associated with colonocyte permeability, a pathological condition of the colon) significantly alters microbial interactions, influencing metabolic dependencies and the overall structure of the community. This integrative approach enhances the interpretability of machine learning-based Autism Spectrum Disorder classifiers, bridging computational predictions with mechanistic insights. By identifying diet-dependent microbial interactions, our study highlights potential dietary interventions to modulate the composition of the gut microbiota in Autism Spectrum Disorder. These findings underscore the value of combining in silico modeling and machine learning for unraveling complex microbiome-host relationships and improving Autism Spectrum Disorder biomarker identification.},
}

@article {pmid41034188,
year = {2025},
author = {Li, S and Wang, Y and Zhang, Z and Xu, H and Wu, S and Jin, H and Han, X and Liu, Y and Wen, X and Wu, Y and Zhang, Z and Hu, L and Hu, L and Zhang, C and Wang, J and Yan, R and Chen, M and Xiao, G and Sun, G and Zhang, D and Wang, S},
title = {Sodium nitrate protects against metabolic syndrome by sialin-mediated macrophage rebalance.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {323},
pmid = {41034188},
issn = {2059-3635},
support = {82201054//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030031, L2224038//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; *Metabolic Syndrome/drug therapy/genetics/pathology/metabolism ; *Macrophages/drug effects/metabolism/pathology ; Humans ; *Nitrates/pharmacology/administration & dosage ; *Diabetes Mellitus, Type 2/drug therapy/genetics/pathology/metabolism ; Male ; Disease Models, Animal ; },
abstract = {Metabolic syndrome, characterized by metabolic dysfunction-associated steatotic liver disease (MASLD) and type 2 diabetes mellitus (T2DM), poses a significant threat to patients' health worldwide; however, efficient treatment is currently unavailable. Here, we show that oral administration of sodium nitrate (NaNO3) greatly attenuates the development and advancement of MASLD-like and T2DM-like phenotypes in mice induced by choline-deficient high-fat, western, or methionine/choline-deficient diet. NaNO3 attenuates metabolic turbulence by rebalancing CD206[+]/CD11C[+] polarization (anti-inflammatory/pro-inflammatory) and the function of bone marrow-derived macrophages (MoMFs). Using metabolic disorder animal models and bone marrow-reconstituted mice with mutated gene function in Slc17a5, which encodes sialin, we demonstrate that NaNO3 protects against metabolic disorders through the actions of sialin in MoMFs. NaNO3 can directly regulate MoMFs polarization and function in vitro and in mice, in which nitric oxide production from oral and enteral symbiotic bacteria is essentially abolished. At the molecular level, sialin, via the inhibition of the key transcription factor Rel, inhibits cathepsin L (CtsL) expression and thereby activates the Nrf2 pathway to modulate macrophage homeostasis and ameliorate metabolic abnormalities. Interestingly, the sialin-CtsL-Nrf2 pathway is downregulated in human macrophages from metabolic dysfunction-associated steatohepatitis (MASH) patients. Overall, we demonstrate the prophylactic and therapeutic effects of NaNO3 on metabolic syndrome and reveal a new macrophage rebalancing strategy involving NaNO3 through a novel sialin pathway. Our research indicates that NaNO3 may be a pharmaceutical agent for managing and alleviating metabolic turbulence in humans.},
}

Animals
Mice
*Metabolic Syndrome/drug therapy/genetics/pathology/metabolism
*Macrophages/drug effects/metabolism/pathology
Humans
*Nitrates/pharmacology/administration & dosage
*Diabetes Mellitus, Type 2/drug therapy/genetics/pathology/metabolism
Male
Disease Models, Animal

@article {pmid41033381,
year = {2025},
author = {Avgousti, K and Dushku, E and Spyropoulou, A and Kotzamanidis, C and Staikou, A and Yiangou, M},
title = {Revealing probiotic properties of Lactiplantibacillus plantarum and Enterococcus faecalis in Cornu aspersum animal model.},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105481},
doi = {10.1016/j.dci.2025.105481},
pmid = {41033381},
issn = {1879-0089},
abstract = {This study explores the probiotic potential, immunomodulatory capacity, and safety of Lactiplantibacillus plantarum and Enterococcus faecalis strains isolated from the intestinal tract of the edible terrestrial snail Cornu aspersum maxima. Although host-microbe interactions are well studied in vertebrates, such research remains limited in invertebrates, particularly snails. To address this gap, 12 lactic acid bacteria strains were isolated and screened for tolerance to the defense mechanisms of snails and probiotic-associated traits, followed by machine learning (ML) predictions of immunomodulatory potential. According to results, 10 strains exhibited high tolerance to the external and internal defense mechanisms of snails (pedal and gastric mucus, gastric juices, low gut pH) in association with increased autoaggregation and hydrophobicity values and were predicted to have 100% probability of eliciting immunomodulatory activity in vivo. Five strains, the L. plantarum Spp1 and Spp11 and E. faecalis Spp3, Spp8, Spp19, were selected for in vivo evaluation. Strain-specific immune responses were observed, with some strains mainly induced cellular immune responses, such as chemotaxis and phagocytic activity of hemocytes, while others also induced humoral responses. However, safety evaluations revealed that certain E. faecalis strains exhibited antimicrobial resistance or induced inflammatory reactions. Only two strains, the L. plantarum Spp11 and E. faecalis Spp19, were validated as safe and effective immunomodulatory probiotics in vivo. Overall, this study provides a comprehensive comparative analysis of the functionality of probiotic Lactiplantibacillus and Enterococcus strains in snails. These findings advance our understanding of snail-microbe symbiosis, particularly in the context of host-probiotic interactions, and support the use of C. aspersum as a valuable invertebrate model for probiotic research.},
}

@article {pmid41032286,
year = {2025},
author = {Krall, E and Benza, K and Kannenberg, R and Medina-Jimenez, K and Mukhia, S and Vanyo, V and Bravo, A},
title = {Conservation of Genes Required for Arbuscular Mycorrhizal Symbiosis.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-05-25-0065-CR},
pmid = {41032286},
issn = {0894-0282},
abstract = {Arbuscular mycorrhizal (AM) symbiosis is an ancient association that played a key role in the adaptation of plants to terrestrial environments. Originating over 400 million years ago at the dawn of land plants, this interaction depends on a core set of conserved genes that enable hosts to establish and maintain symbiotic relationships with AM fungi. The AM symbiotic program includes distinct genetic components for each stage of development, from signal perception to nutrient exchange. While AM-host plants have retained key genes dedicated to symbiosis, non-host lineages have independently lost these genes multiple times over evolutionary history. Recent studies in the liverwort Marchantia paleacea demonstrate that core mechanisms underlying AM symbiosis are conserved from bryophytes to angiosperms. Comparative genomic studies continue to uncover how symbiosis-specific genes are integrated with broadly conserved cellular machinery to sustain this interaction. Understanding these deeply conserved genetic modules is essential for uncovering the evolutionary foundations of plant-microbe associations and for harnessing their potential in sustainable agriculture.},
}

@article {pmid41031293,
year = {2025},
author = {Rui, J and Long, X and Wang, X and Xiong, X and Zhu, J},
title = {Soil microclimate and vegetation dynamics shape elevational and seasonal variations of diazotrophic communities in alpine grasslands.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1587343},
pmid = {41031293},
issn = {1664-462X},
abstract = {INTRODUCTION: Diazotrophs play critical roles in maintaining ecosystem nitrogen (N) cycling in alpine grasslands. However, the elevational and seasonal variations of diazotrophic communities in these ecosystems remain poorly understood. This gap in knowledge limits our ability to predict how N fixation will respond to environmental change. Here, we investigated the seasonal dynamics of soil diazotrophic communities across a 3200-4000 m elevational gradient in Qinghai-Tibetan alpine grasslands during the growing season.

METHODS: Soil samples were collected across an elevational gradient (3200-4000 m) throughout the growing season. The diazotrophic community composition was assessed by sequencing the nifH gene, which was also quantified using quantitative PCR. Soil nitrogenase activity was measured to assess N fixation potential. Key environmental variables, such as soil temperature, moisture, and plant biomass (particularly legume biomass), were monitored.

RESULTS AND DISCUSSION: Our results revealed that diazotrophic alpha-diversity followed an inverted V-shaped pattern along the elevational gradient, primarily driven by soil temperature and moisture. Beta-diversity analyses demonstrated that diazotrophic communities generally exhibited similar elevational distribution patterns throughout the growing season, also primarily influenced by temperature and moisture. Seasonal variations in diazotrophic communities were more pronounced at lower elevations, primarily associated with plant biomass dynamics, including delayed legume emergence at 3200 m in June and their subsequent biomass accumulation after July. In contrast, soil microclimate (particularly temperature) dominated community shifts at higher elevations. Notably, nifH gene abundance and soil nitrogenase activity were higher in the early growing season, suggesting free-living diazotrophs may play a crucial role in N fixation. Abundant species were key contributors to diazotrophic beta-diversity. Symbiotic Mesorhizobium was more abundant at low elevations, while free-living Geobacter at high elevations. Conversely, associative diazotrophs peaked later in the growing season, in contrast to Geobacter. Rare species played a key role in shaping alpha diversity, particularly at mid-elevations, where soil moisture was the highest. Our study underscores the complex interactions between soil microclimate change and plant dynamics in regulating diazotrophic communities. Furthermore, it highlights the essential roles of both abundant and rare species in sustaining ecosystem functions in alpine grasslands. These findings provide new insights into the biogeochemical processes supporting N cycling in alpine grasslands and highlight the potential impacts of vegetation and climate change on these fragile ecosystems.},
}

@article {pmid41030555,
year = {2025},
author = {Worku, AT and Sciarretta, A and Guarnieri, A and Falcone, M and Brancazio, N and Minwuyelet, A and Cutuli, MA and Atenafu, G and Nicolosi, D and Colacci, M and Yewhalaw, D and Di Marco, R and Petronio Petronio, G},
title = {Microbial gatekeepers: midgut bacteria in Aedes mosquitoes as modulators of arboviral transmission and targets for sustainable vector control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656709},
pmid = {41030555},
issn = {1664-302X},
abstract = {Arboviral diseases such as Dengue virus, Zika virus, Chikungunya virus, and West Nile virus pose significant global public health and economic challenges, particularly in tropical and subtropical regions. The absence of effective vaccines and sustainable vector control strategies continues to drive high morbidity and mortality rates. Symbiotic bacteria residing in the mosquito midgut can produce antimicrobial compound, stimulate the host immune response, disrupt nutrient pathways critical for pathogen development, and interfere with the pathogen's lifecycle and dissemination. Additionally, these microbes may reduce vector reproduction and shorten the lifespan of both immature and adult stages. Genetically modified symbiotic bacteria can release effector molecules that target pathogens without harming mosquitoes. Advances in genomic and metagenomic tools have deepened our understanding of the mosquito gut microbiome. This review highlights current knowledge of gut bacteria and arbovirus interactions and explores strategies to reduce arboviral transmission. Comprehensive literature searches were conducted using global databases, including PubMed, Web of Science, and Scopus, with a focus on English-language publications.},
}

@article {pmid41030195,
year = {2025},
author = {Vancaester, E and Oldrieve, GR and Reid, A and Koutsovoulos, G and Laetsch, DR and Makepeace, BL and Tanya, V and Poppert, S and Krücken, J and Wolstenholme, A and Blaxter, M},
title = {Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf226},
pmid = {41030195},
issn = {2160-1836},
abstract = {Many, but not all, parasitic filarial nematodes (Onchocercidae) carry intracellular, maternally-transmitted, alphaproteobacterial Wolbachia symbionts. The association between filarial nematodes and Wolbachia is often portrayed as mutualist, where the nematode is reliant on Wolbachia for an essential but unknown service. Wolbachia are targets for anti-filarial chemotherapeutic interventions for human disease. Wolbachia of Onchocercidae derive from four of the major supergroups (C, D, F and J) defined within the genus. We explored the evolutionary history of the filarial nematode-Wolbachia symbiosis in twenty-two nematode species, sixteen of which have current Wolbachia infections, by screening the nematode nuclear genome sequences for nuclear Wolbachia transfers, fragments of the Wolbachia genome that have been inserted into the nuclear genome. We identified Wolbachia insertions in five of the six species that have no current Wolbachia infection, showing they have previously had and have now lost Wolbachia infections. In currently-infected species we found a diversity of origins of the insertions, including many cases where they derived from a different supergroup to the current live infection. Mapping the origins of the insertions onto the filarial nematode phylogeny we derive a complex model of evolution of Wolbachia symbiosis. The history of association between Wolbachia and onchocercid nematodes includes not only cospeciation, as would be expected from a mutualist symbiosis, but also loss (in the five Wolbachia-free species), frequent symbiont replacement, and dual infection. This dynamic pattern is challenging to models that assume host-symbiont mutualism.},
}

@article {pmid41029997,
year = {2025},
author = {Ferreras-Garrucho, G and Chancellor, T and Paszkowski, U},
title = {Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf404},
pmid = {41029997},
issn = {1460-2431},
abstract = {Arbuscular mycorrhizal symbiosis (AMS) is a ubiquitous and ancient interaction between plant root systems and fungi of the Glomeromycotina subphylum. The resulting relationship is mutually beneficial and deeply intimate where the fungus intracellularly colonises root cortex cells to receive organic carbon and deliver minerals and water to the plant. Fungal colonisation of plant roots and cells is extremely dynamic and asynchronous across the root system. Symbiosis development must therefore result from spatio-temporally fine-tuned molecular control mechanisms of plant and fungus. Although the plant genetic program underpinning AMS has been extensively studied, little is known about its dynamic regulation across root cell layers and developmental stages of the association. Thus, many questions remain outstanding: how do different cell-types transcriptionally respond to AMS, how are distinct cell-type specific regulatory states coordinated, and what are the transcriptional activities in the fungus associated with discrete stages of root colonisation? The advent of single cell-based techniques now enables the high-resolution analysis to address these questions. In this review, we recapitulate the current knowledge on the spatio-temporal control of AMS, we evaluate the relevance of existing spatial datasets to AMS research and provide new perspectives for future study.},
}

@article {pmid41029519,
year = {2025},
author = {Modara, B and Rahimi, MM and Abdipour, M and Hosseinifarahi, M},
title = {Physiological and antioxidant responses of marjoram (Origanum Majorana L.) under drought stress mediated by Salicylic acid and mycorrhizal symbiosis.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1248},
pmid = {41029519},
issn = {1471-2229},
mesh = {*Mycorrhizae/physiology ; *Salicylic Acid/metabolism/pharmacology ; *Droughts ; *Antioxidants/metabolism ; *Symbiosis ; Stress, Physiological ; },
abstract = {Drought stress, exacerbated by climate change, is a major limiting factor for herbs cultivation. This study aimed to evaluate the combined effects of salicylic acid (SA) and mycorrhizal fungi (MF) on marjoram under drought stress conditions. The experiment was conducted over two years (2022-2023) using a split factorial design within a randomized complete block with three replications. The study's primary factor was drought stress at three levels: 90% (D0), 70% (D1), and 35% (D2) of field capacity (FC). The secondary factor included two sub-factors: SA concentrations (0, 100, and 300 mg L[-1]) and MF inoculation (non-inoculated (M0) and inoculated with Glomus hoi (M1)). Results demonstrated that drought stress decreased relative water content (RWC) (46.8%), chlorophyll content (35%), carotenoids (25.7%), and dry weight (49.3%), while increasing proline (38.6%), soluble sugars (29.4%), electrolyte leakage (44.8%), superoxide dismutase (35.2%), peroxidase (43.1%), and catalase activities (29.3%). Additionally, the combined treatment of SA and MF enhanced water status by 44%, proline content by 12%, and soluble sugar content by 6% under severe drought conditions. Antioxidant enzyme activities (Catalase) were also significantly increased by up to 91% with the combined treatments, supporting the hypothesis that the synergy of SA and MF can effectively mitigate the adverse effects of drought stress on marjoram. Overall, this study demonstrated that the combined application of SA and MF could be a promising strategy for enhancing drought tolerance in marjoram, especially in drought-prone areas. TRIAL REGISTRATION: This study does not involve clinical trials or human participants and, as such, does not require clinical trial registration.},
}

*Mycorrhizae/physiology
*Salicylic Acid/metabolism/pharmacology
*Droughts
*Antioxidants/metabolism
*Symbiosis
Stress, Physiological

@article {pmid41028587,
year = {2026},
author = {Anandakumar, S and Senthamilselvi, D and Kalaiselvi, T},
title = {Estimation of Foliar Volatiles Emitted by Mycorrhizal Colonized Blackgram (Vigna mungo L) Infested with Spodoptera litura.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2966},
number = {},
pages = {233-243},
pmid = {41028587},
issn = {1940-6029},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Animals ; *Spodoptera/physiology ; Gas Chromatography-Mass Spectrometry/methods ; *Mycorrhizae/physiology ; *Plant Leaves/metabolism/chemistry/parasitology ; *Vigna/metabolism/parasitology/microbiology/chemistry ; Symbiosis ; },
abstract = {Plant-emitted volatile organic compounds (VOCs) play a significant role in signaling and tolerance to biotic stressors, including insect pest infestation. Mycorrhizae, a symbiotic fungus, improves the tolerance of blackgram plants to Spodoptera litura by altering the profiling of foliage VOCs. Recently, gas chromatography-mass spectrometry (GC-MS) coupled with headspace (HS) trapping of VOCs is the most frequently used analytical technique to understand the metabolic process and responses of plants to biotic stresses. This method performs four steps such as (i) trapping of HS-VOCs, (ii) concentration and enrichment of VOCs, (iii) transfer of VOCs from air sample to analytical device, and (iv) detection and identification of compounds. HS volatiles is trapped using fiber polymers like Tenax TA and desorbed thermally in GC-MS with TD autosampler and thermal desorption (TD). The identification of VOCs compounds is performed by searching mass spectral peaks against NIST mass spectral library. This chapter provides the detailed procedure for the estimation of plant-produced VOCs using HS sapling coupled with gas chromatography-mass spectrometry (TD-GC/MS) with TD autosampler and thermal desorption method.},
}

*Volatile Organic Compounds/analysis/metabolism
Animals
*Spodoptera/physiology
Gas Chromatography-Mass Spectrometry/methods
*Mycorrhizae/physiology
*Plant Leaves/metabolism/chemistry/parasitology
*Vigna/metabolism/parasitology/microbiology/chemistry
Symbiosis

@article {pmid41027965,
year = {2025},
author = {Cao, J and Wang, J and Yang, Q and Guo, B and Colombi, T and Valverde-Barrantes, OJ and Ding, J and Zhang, Y and Wu, H and Feng, Z and Yang, X and Kong, D},
title = {Root anatomy governs bi-directional resource transfer in mycorrhizal symbiosis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8731},
pmid = {41027965},
issn = {2041-1723},
support = {32471824, 32171746, 31870522, and 31670550//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Mycorrhizae/physiology/metabolism ; *Symbiosis/physiology ; *Plant Roots/anatomy & histology/microbiology/metabolism ; Carbon/metabolism ; Models, Biological ; },
abstract = {Plants form mycorrhizal symbioses to enhance nutrient acquisition, yet the biophysical principles governing carbon and nutrient exchange remain unclear. Here, we develop a theory of bi-directional carbon-nutrient transfer that integrates root anatomy, energetic costs, and mycorrhizal positioning. We show that nutrient uptake per unit carbon or energy investment declines with increasing root diameter due to higher carbon demands across thicker cortical tissues. Mycorrhizal fungi mitigate this constraint by enabling more carbon-efficient nutrient uptake, particularly when arbuscules are positioned in inner cortical layers. This spatial optimization minimizes the carbon cost of transporting nutrients to the stele. Our framework reconciles anatomical variation, symbiotic structure, and functional efficiency across root types and mycorrhizal strategies and offers a new lens for understanding the coevolution between roots and mycorrhizal fungi.},
}

*Mycorrhizae/physiology/metabolism
*Symbiosis/physiology
*Plant Roots/anatomy & histology/microbiology/metabolism
Carbon/metabolism
Models, Biological

@article {pmid41027223,
year = {2025},
author = {Jing, X and Zhang, X and Wang, X and Chen, H and Xing, S and Jin, Z and Yang, D and Li, J and Wu, S and Hao, Z and Song, F and Chen, B},
title = {Bidirectional interference between nanoplastics and arsenic in arbuscular mycorrhizal symbiosis: Reciprocal modulation of uptake, transformation and translocation.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139983},
doi = {10.1016/j.jhazmat.2025.139983},
pmid = {41027223},
issn = {1873-3336},
abstract = {Nanoplastics, which persist in the environment with high specific surface areas, interact with the well-documented pollutant arsenic, thereby exacerbating its phytotoxicity. Arbuscular mycorrhizal fungi, forming symbiotic relationships with most plants and enhancing their arsenic tolerance, possess hyphae capable of capturing nanoplastics. However, no studies have investigated either how arbuscular mycorrhizal fungi absorb and transfer arsenic during nanoplastics co-exposure, or whether nanoplastics are internalized by arbuscular mycorrhizal fungi hyphae and translocated to mycorrhizal tissues under arsenic stress. In this study, a two-compartment in vitro monoxenic cultivation system was used to investigate the synergistic translocation and transformation of arsenic-nanoplastic co-contaminants at the plant-microbe interface. The results indicated that nanoplastics hindered the arsenic absorption by arbuscular mycorrhizal fungi hyphae and promoted the transformation of inorganic arsenic to organic arsenic via upregulating the relative expression of the RiMT-11 gene in the hyphae. Scanning electron microscopy and confocal laser scanning microscopy imaging confirmed nanoplastics internalization by hyphae and subsequent translocation to mycorrhizae under arsenic exposure. This study deciphers nanoplastic-arsenic-arbuscular mycorrhizal fungi interaction mechanisms and validates arbuscular mycorrhizal fungi's potential role in the bioremediation of arsenic-nanoplastic co-contaminated soils.},
}

@article {pmid41026427,
year = {2025},
author = {Kumar, SC and Kumar, M and Singh, R and Saxena, AK},
title = {Selection of competitive and effective rhizobial strain for enhanced chickpea production under Indo-Gangetic plains of India.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {41026427},
issn = {1678-4405},
support = {Application of Microorganisms in Agriculture and Allied Sectors (AMAAS).//Application of Microorganisms in Agriculture and Allied Sectors (AMAAS)./ ; },
abstract = {Chickpea (Cicer arietinum L.) is a vital legume crop, but its productivity is often limited by poor soil fertility. This study aimed to assess the nodulation efficacy and plant growth-enhancing activities of six Mesorhizobium spp. strains in the chickpea cultivar Pusa 362 through the Leonard jar experiment and field trial. The strains, including two strains from ICRISAT (reference strains), were tested for solubilization of phosphate, potassium, and zinc, and production of Indole-3-Acetic Acid (IAA). Strain C5 excelled in phosphate solubilization (61.40 µg/ml), while C7 was superior in potassium (26.10 µg/ml) and zinc phosphate (69.15 µg/ml) solubilization; C17 showed the highest IAA production (25.75 µg/ml). In the Leonard jar experiment, inoculation of strains M. ciceri C5 and M. helmanticense C17 exhibited the highest nodule number and root dry weight, while treatments with M. ciceri C5 and M. helmanticense C7 inoculation recorded the maximum nodule dry weight and shoot dry weight. Field trials indicated significant improvements in nodulation, biomass, and nitrogen content in chickpeas inoculated with these strains. Treatment with strain C7 led to the highest increase in nodule number and root dry weight over the control, while strain C5 inoculation recorded maximum grain yield. Correlation analysis showed positive relationships between yield and several growth parameters. Nodule occupancy tests revealed that strain C7 had the highest occupancy (32.98%), followed by C5 (31.92%), indicating superior nodulation competitiveness under field conditions. These results suggest that inoculation with specific Mesorhizobium strains can significantly enhance chickpea productivity through improved nodulation and nitrogen fixation.},
}

@article {pmid41026187,
year = {2025},
author = {Cheng, P and Liu, F and Li, L and Wu, S and Xiao, W and Zong, Q and Liu, T and Peng, Y},
title = {Impact of Tebuconazole On the Development and Symbiotic Microbial Communities of Pardosa Pseudoannulata.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {97},
pmid = {41026187},
issn = {1432-184X},
mesh = {*Triazoles/toxicity ; *Symbiosis/drug effects ; Animals ; *Microbiota/drug effects ; Bacteria/drug effects/classification/genetics/isolation & purification ; *Fungi/drug effects/classification/genetics ; *Fungicides, Industrial/toxicity ; *Spiders/microbiology/drug effects/growth & development/physiology ; RNA, Ribosomal, 16S/genetics ; Animals, Poisonous ; },
abstract = {Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.},
}

*Triazoles/toxicity
*Symbiosis/drug effects
Animals
*Microbiota/drug effects
Bacteria/drug effects/classification/genetics/isolation & purification
*Fungi/drug effects/classification/genetics
*Fungicides, Industrial/toxicity
*Spiders/microbiology/drug effects/growth & development/physiology
RNA, Ribosomal, 16S/genetics
Animals, Poisonous

@article {pmid41025674,
year = {2025},
author = {Ste-Croix, DT and Gagnon, AÈ and Mimee, B},
title = {The genome and stage-specific transcriptomes of the carrot weevil, Listronotus oregonensis, reveal adaptive mechanisms for host specialisation and symbiotic interactions.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70012},
pmid = {41025674},
issn = {1365-2583},
support = {J-002846//Alternative Pest Management Solutions initiative/ ; //Agriculture and Agri-Food Canada/ ; },
abstract = {Throughout their evolution, insects have become specialised to occupy diverse ecological niches. The carrot weevil, Listronotus oregonensis, is an important agricultural pest that exhibits a very specific host range. In this study, we characterised the genome and transcriptomes of each developmental stage of L. oregonensis and its Wolbachia endosymbiont to gain deeper knowledge of the genetic determinants controlling its biology. We annotated 14,637 genes and showed expression profiles across the developmental stages. We also compared orthologous genes between L. oregonensis and nine other species, with particular focus on chemoreceptors and detoxification genes. We identified 24 distinct odorant-binding protein genes and 41 genes for receptors involved in stimulus perception, relatively low numbers compared with other species, which would be consistent with a narrow host range. In contrast, we found a high number of detoxification genes, with significant expansion of certain gene families. Among the annotated genes, 46 were putatively acquired through horizontal gene transfer, with 17 showing strong evidence for this, including several cell-wall degrading enzymes. The phylogeny of a cytolethal distending toxin gene also suggests an initial transfer from a prokaryotic source and vertical dissemination in members of Curculionidae through recent evolution. The presence of the endosymbiotic bacterium Wolbachia (supergroup A) was confirmed in all tested L. oregonensis individuals from several regions in northeastern North America and showed very little diversity. This study enhances our understanding of the genomic, functional, and evolutionary aspects of a significant agricultural pest and makes important and useful databases available to the scientific community.},
}

@article {pmid41025407,
year = {2025},
author = {Esquinas-Ariza, RM and Villar, I and Minguillón, S and Zamarreño, Á and Pérez-Rontomé, C and Reeder, BJ and Sandal, N and Yan, D and García-Mina, JM and Duanmu, D and Martínez-Júlvez, M and Becana, M},
title = {Structural and functional comparison of hemoglobin Glb2-1 of Lotus japonicus with Glb1-1 and leghemoglobins.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf434},
pmid = {41025407},
issn = {1460-2431},
abstract = {The legume Lotus japonicus expresses nine hemoglobins, including leghemoglobins (Lbs), class 1 phytoglobin (Glb1-1), and an unusual phytoglobin (Glb2-1). Quantitative PCR, proteomics, and plant mutant analyses indicate that Glb2-1 is mainly present in nodules without replacing Lb function, but is also in roots and photosynthetic tissues. Comparison of hormonal profiles of the knock-out mutants glb1-1, glb2-1, and glb1-1/2-1 reveals that Glb1-1 and Glb2-1 have distinct functions. The increase of salicylic acid in the leaves of glb1-1 reveals a role of Glb1-1 in the defense response, which was corroborated by accumulation of pipecolic acid, a metabolite involved in plant immunity. In contrast, the decrease of bioactive jasmonoyl-isoleucine in glb2-1 is consistent with a role of Glb2-1 in the plant's reproductive stage. The mutants also showed changes in cytokinins, gibberellins, and polyamines, but without clear distinctive patterns. The crystal structure of Glb2-1 was determined to 1.6 Å resolution and compared with those of soybean Lba and Arabidopsis Glb1. In combination with mutant versions of Glb2-1, residues Tyr31, His64, and Cys65 were identified as critical for O2-binding stability. Spectral changes in heme coordination when Tyr31 is substituted for Phe highlights the importance of the residue at the B10 position for Lb and Glb function.},
}

@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation & purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}

Animals
*Microbiota/genetics
*DNA, Bacterial/isolation & purification/genetics
*Aquatic Organisms/microbiology
*Bacteria/genetics/isolation & purification/classification
*Porifera/microbiology
Symbiosis
Republic of Korea
*Invertebrates/microbiology
Anthozoa/microbiology
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
Polymerase Chain Reaction

@article {pmid41024490,
year = {2025},
author = {Speijer, D},
title = {Eukaryogenesis From FECA to LECA: Radical Steps Along the Way.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70063},
doi = {10.1002/bies.70063},
pmid = {41024490},
issn = {1521-1878},
abstract = {The characteristics of the last eukaryotic common ancestor (LECA) population and the root of the eukaryotic tree have been coming into focus lately. However, the trajectory taking the host, related to present-day Asgard archaea and the endosymbiont, related to present-day alphaproteobacteria, toward such fully integrated and complex organisms is still unclear. Here I marshal recent evidence supporting the early arrival of the "mitochondrion-to-be", setting up the evolutionary dynamic for a series of mutual adaptations leading to eukaryotes. Upon critical analysis of some presuppositions in phylogenomic reconstructions of eukaryogenesis, I again propose that pre-symbiosis, efficient ATP generation, internal reactive oxygen species (ROS) formation and enhanced retention of genes supplied by horizontal gene transfer (HGT) interdependently allowed this unique transformation to occur.},
}

@article {pmid41024329,
year = {2025},
author = {Manjili, MH},
title = {The Invisible Lens: Why Theoretical Models Are Essential for Interpreting Immune Phenomena.},
journal = {Scandinavian journal of immunology},
volume = {102},
number = {4},
pages = {e70057},
pmid = {41024329},
issn = {1365-3083},
support = {W81XWH2210793//U.S. Department of Defense/ ; P30 CA 016059/NH/NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Models, Theoretical ; *Models, Immunological ; *Immune System/immunology ; *Allergy and Immunology ; },
abstract = {Immunology progresses not merely by accumulating data but by evolving the conceptual lenses through which those data are interpreted; yet for six decades the self-non-self/infectious-non-self (SNS/INS) paradigm-casting allogeneity as activating signal and 'self' as intrinsically tolerogenic-has dominated research design, peer review and curriculum. This, in turn, systematically amplifies concordant findings while attenuating evidence for tissue integrity, metabolic, symbiotic and network-centric cues. This conceptual monoculture appears as a hidden dogma that impedes breakthroughs in our understanding of the immune system and the development of curative therapies. By institutionalising theoretical immunology as a formal discipline and treating models as explicit, testable tools rather than hidden assumptions, immunologists can sharpen hypothesis generation and achieve a better understanding of existing data. This essay provides an overview of empirically grounded theoretical models to counter monoculture, clarify how frames shape interpretation, and expand the field's conceptual toolkit.},
}

Humans
Animals
*Models, Theoretical
*Models, Immunological
*Immune System/immunology
*Allergy and Immunology

@article {pmid41024212,
year = {2025},
author = {Wang, Y and Gong, L and Dong, D and Li, X},
title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {122},
pmid = {41024212},
issn = {2524-6372},
support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.

RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.

CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.},
}

@article {pmid41023112,
year = {2025},
author = {Chakraborty, S and Sharma, R and Bhat, A and Curtin, SJ and Wen, J and Mysore, KS and Paape, T},
title = {Partners in root nodule symbiosis respond uniquely to heavy metal stresses in a host genotype-dependent manner.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33518},
pmid = {41023112},
issn = {2045-2322},
support = {3093-53000-001-000D & 5062-21000-035-000D//Agricultural Research Service/ ; },
mesh = {*Symbiosis/drug effects/genetics ; *Medicago truncatula/genetics/microbiology/drug effects ; *Root Nodules, Plant/microbiology/genetics/drug effects/metabolism ; *Metals, Heavy/toxicity ; Gene Expression Regulation, Plant/drug effects ; Genotype ; Cadmium/toxicity ; *Sinorhizobium meliloti/physiology/drug effects ; *Stress, Physiological/drug effects ; Zinc/toxicity ; Mutation ; Gene Expression Profiling ; Transcriptome ; },
abstract = {The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using the Medicago truncatula-Sinorhizobium meliloti symbiotic system. Phenotypes were measured in the wild-type Medicago truncatula and a mutant in an ABC transporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies.},
}

*Symbiosis/drug effects/genetics
*Medicago truncatula/genetics/microbiology/drug effects
*Root Nodules, Plant/microbiology/genetics/drug effects/metabolism
*Metals, Heavy/toxicity
Gene Expression Regulation, Plant/drug effects
Genotype
Cadmium/toxicity
*Sinorhizobium meliloti/physiology/drug effects
*Stress, Physiological/drug effects
Zinc/toxicity
Mutation
Gene Expression Profiling
Transcriptome

@article {pmid41022930,
year = {2025},
author = {Charaabi, K and Hamdene, H and Djobbi, W and Fadhel, S and Tanfouri, N and Saidi, M and Guerfali, MM},
title = {Assessing gut microbiota diversity and functional potential in resistant and susceptible strains of the mediterranean fruit fly.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33456},
pmid = {41022930},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ceratitis capitata/microbiology/drug effects ; *Insecticide Resistance/genetics ; Insecticides/pharmacology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Malathion/pharmacology ; Macrolides/pharmacology ; Dimethoate/pharmacology ; Drug Combinations ; },
abstract = {The Mediterranean fruit fly (Ceratitis capitata) is a destructive polyphagous pest that affects many agricultural crops. While insecticides are commonly used to control its populations, the widespread and excessive use of these chemicals has led to increased resistance globally. Gut microbiota may influence insect behavior and physiology, potentially contributing to this resistance. In this study, high throughput 16S rRNA sequencing was performed to characterize the gut microbiota of both insecticide-susceptible and insecticide-resistant strains of C. capitata, aiming to investigate the potential role of symbiotic bacteria in the medfly resistance development in. Three resistant strains were selected under laboratory conditions by exposing the adult-rearing diet to increasing concentrations of malathion, dimethoate, and spinosad over successive generations. Principal coordinate analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS) analyses revealed significant differences in gut microbiota structure between resistant and susceptible strains (p < 0.001). Insecticide-resistant strains showed a microbiota composition shift upon insecticide exposure. Notably, Serratia spp. and Buttiauxella spp. exhibited a sharp decline in resistant strains, while Enterococcus spp. and Klebsiella spp. showed a significant increase (p < 0.001). Resistant strains showed lower bacterial richness and diversity, suggesting an enrichment of bacteria that have a competitive advantage under insecticide selection pressure. Functional predictions indicated distinct metabolic differences, with resistant strains displaying enhanced activities related to xenobiotic biodegradation and metabolism. This suggests a potential association between these bacteria and insecticide resistance; however, further studies are necessary to determinate whether these bacteria directly contribute to the degradation or detoxification of insecticides.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
*Ceratitis capitata/microbiology/drug effects
*Insecticide Resistance/genetics
Insecticides/pharmacology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Biodiversity
Malathion/pharmacology
Macrolides/pharmacology
Dimethoate/pharmacology
Drug Combinations

@article {pmid41021533,
year = {2025},
author = {Matsui, H and Hata, Y},
title = {Group-level matching behavior in phototaxis of acoel flatworm Praesagittifera naikaiensis.},
journal = {Journal of comparative psychology (Washington, D.C. : 1983)},
volume = {},
number = {},
pages = {},
doi = {10.1037/com0000430},
pmid = {41021533},
issn = {1939-2087},
abstract = {The matching law, which posits that animals allocate their responses in proportion to the rate of reinforcement, has been supported across diverse animal taxa. Although originally formulated in the context of operant choice, matching also applies to time allocation in foraging and to Pavlovian responses, indicating its generality across behavioral domains. However, empirical evidence has thus far been largely limited to vertebrates and arthropods. Addressing the broader applicability of this principle requires extending investigations beyond these taxonomic groups, across a wider phylogenetic spectrum. Here, we examined phototactic behavior in the acoel flatworm Praesagittifera naikaiensis, a species that acquires nutrients through photosynthesis by symbiotic algae and exhibits positive phototaxis. Using a custom-built T-maze in which the number of illuminated LEDs varied across arms, we found that the animals distributed themselves in proportion to relative brightness, consistent with matching behavior. Moreover, prior exposure to light for 24 hr attenuated this pattern. This manipulation was intended to induce a state of nutritional sufficiency, and the resulting decline in phototactic responses suggests that internal physiological states can modulate even seemingly reflexive locomotor behaviors. (PsycInfo Database Record (c) 2025 APA, all rights reserved).},
}

@article {pmid41021075,
year = {2025},
author = {Leng, C and Yang, G and Hou, M and Huang, X and Xing, Y and Yang, B and Chen, J},
title = {Fungi of the family Psathyrellaceae are symbiotic partners of the mycoheterotrophic orchid Danxiaorchis yangii.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {56},
pmid = {41021075},
issn = {1432-1890},
support = {No. tsqn202211233//Special Fund for Taishan Scholar Project/ ; 2021-I2M-1-032//the CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {*Orchidaceae/microbiology ; *Symbiosis ; Phylogeny ; China ; Endophytes/physiology/isolation & purification/genetics ; *Mycorrhizae/physiology/genetics ; DNA, Ribosomal Spacer/genetics ; *Basidiomycota/physiology/genetics/classification/isolation & purification ; Rhizome/microbiology ; DNA, Fungal/genetics ; },
abstract = {Fully mycoheterotrophic orchids rely entirely on fungal symbionts for carbon acquisition and are often highly specialized in their fungal associations. Danxiaorchis yangii is a fully mycoheterotrophic orchid species with an extremely limited population in its endemic region of southeastern China. Its fungal symbionts remain poorly understood. In this study, we investigated the fungal associations of D. yangii using both the isolation of culturable fungal endophytes and high-throughput sequencing of the ribosomal internal transcribed spacer-1 (ITS1) region. Six strains of Psathyrellaceae were isolated from rhizomes (underground stems) of D. yangii and phylogenetic analysis revealed that they belong to two main taxa. High-throughput sequencing further confirmed that the fungal community within the rhizomes was dominated by Psathyrellaceae. Moreover, an in vitro symbiotic seed germination assay demonstrated that one of the isolated strains could promote the growth of germinating seeds to the protocorm stage. These findings are significant for advancing our understanding of the mycoheterotrophic symbiosis in D. yangii.},
}

*Orchidaceae/microbiology
*Symbiosis
Phylogeny
China
Endophytes/physiology/isolation & purification/genetics
*Mycorrhizae/physiology/genetics
DNA, Ribosomal Spacer/genetics
*Basidiomycota/physiology/genetics/classification/isolation & purification
Rhizome/microbiology
DNA, Fungal/genetics

@article {pmid41019754,
year = {2025},
author = {Foster, LR and Yang, J and Riethoven, JM and Mukhtar, H and Schachtman, DP},
title = {Inoculation frequency and maize genotype influence plant growth-promoting effects of soil bacteria under low nitrogen conditions.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1637156},
pmid = {41019754},
issn = {1664-462X},
abstract = {Global agriculture relies heavily on the use of synthetic nitrogen fertilizer to meet the current global food demand. Unfortunately, the average nitrogen-use efficiency (NUE) of maize (Zea mays ssp. mays) is as low as 50%. Improving the NUE of maize is essential for feeding the ever-increasing world population while also decreasing the negative environmental impacts of nitrogen fertilizer due to runoff and volatilization. Harnessing the symbiotic relationship between plants and soil microorganisms may be one method for increasing the NUE in crops such as maize. In the present study, a set of potentially beneficial bacterial species chosen based on genetic information from the host was investigated for their ability to improve NUE-related traits in maize grown under nitrogen-deficient conditions. This was carried out through non-repeated and repeated bacterial inoculations using different maize genotypes. We identified several growth-promoting bacterial isolates and observed a significant interaction between the bacterial isolates and the maize genotype, suggesting a strong interaction between the host genetics and the effects of bacterial isolates. In addition, our results showed a significant growth response to repeated inoculations with a beneficial bacterial isolate. In summary, when evaluating the plant-growth-promoting effects of a bacterial species, it is essential to consider the interaction between host plant genotype and bacterial isolate. In addition, when inoculating with bacterial isolates, multiple inoculations appear to be more effective than a single inoculation after bacterial seed priming.},
}

@article {pmid41019523,
year = {2025},
author = {Eaker, AA and Rowe, SL and Friesen, ML},
title = {Antagonism within mutualism: host control of symbionts through nodule-specific antimicrobial peptides.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1622262},
pmid = {41019523},
issn = {1664-302X},
abstract = {Legumes (Fabaceae) have developed a symbiotic relationship with nitrogen-fixing bacteria called rhizobia to meet their nitrogen needs. Legumes recruit rhizobia from the soil, house them in root organs called nodules, and manipulate bacterial metabolism, providing carbon and receiving bacterially fixed nitrogen in return. One mechanism of host control is through a family of antimicrobial peptides that only appears in the inverted repeat lacking clade (IRLC) of the legumes, though the Dalbergioid clade has similar peptides. They are named nodule-specific cysteine-rich (NCR) peptides due to their exclusive expression in the nodule during symbiosis and the shared 4 or 6 cysteine residue motif. These genes and subsequent proteins vary in number, sequence, and function, but evolutionary genomics research shows that they are adapted from the plant immune system for the new function of symbiont manipulation. In this review, we present the current understanding of NCR peptide biology, expression, and function. We examine NCR genomic and biochemical features and explore their roles in shaping symbiotic outcomes. Finally, we discuss emerging applications and key open questions. Understanding host manipulation of bacterial symbionts within plant tissues provides researchers with targets for engineering more efficient nitrogen-fixing symbioses. In addition, NCR peptides show promise as therapeutic agents with the potential to control both plant and animal pathogens.},
}

@article {pmid41019521,
year = {2025},
author = {Zhou, L and Liu, L and Gao, W and Li, B and Guo, S},
title = {Symbiotic relationship between Polyporus umbellatus and Armillaria gallica shapes rhizosphere bacterial community structure and promotes fungal growth.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658060},
pmid = {41019521},
issn = {1664-302X},
abstract = {AIMS: Polyporus umbellatus sclerotium, known for its diuretic properties, relies on a symbiotic association with Armillaria for its growth and quality development. However, the impact of soil microorganisms on this symbiosis remains uncertain and warrants investigation. The primary objective of this research is to characterize the microorganisms capable of enhancing the symbiotic interaction between Armillaria gallica and Polyporus umbellatus sclerotia in the rhizosphere soil.

METHODS: Symbiotic cultivation experiments were conducted in woodland habitats with four groups: symbiotic group (Z0), control group (Z1), A. gallica-only group (Z2), and P. umbellatus-only group (Z3). Rhizosphere soil community profiling analysis was conducted using high-throughput sequencing of the bacterial 16S rRNA gene. Subsequently, bacterial strains were isolated, purified, and back-inoculated with A. gallica to assess their effects on this symbiotic relationship.

RESULTS: A total of 10,009 operational taxonomic units (OTUs) were identified, with the symbiotic group (Z0) showing higher bacterial richness and diversity (ACE, Chao1, Shannon indices) compared to Z2 and Z3. Dominant phyla such as Proteobacteria, Acidobacteriota, and Bacteroidota were notably more abundant in Z0. Notably, Rhodococcus sp. Z2-1 significantly promoted A. gallica rhizomorph growth (diameter increased by 112.2%, branches by 160.9%) and symbiosis establishment (100% contact rate in inoculated pots vs. 0-22.2% in controls).

CONCLUSION: The symbiotic relationship between P. umbellatus and A. gallica shapes rhizosphere bacterial communities, with specific bacteria like Rhodococcus sp. enhancing fungal growth and symbiotic efficiency. This study presents the potential for developing a bio-bacterial fertilizer for cultivation of medicinal material.},
}

@article {pmid41019519,
year = {2025},
author = {Ning, Y and Chen, Y and Wu, Z and Yang, T and He, X and Yue, H},
title = {Seasonal and regional structuring of rhizosphere fungal communities in Macadamia integrifolia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634222},
pmid = {41019519},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere fungal communities are pivotal to plant nutrient acquisition, stress tolerance, and ecosystem functionality. However, the diversity and ecological roles of these communities in tropical cash crops like Macadamia integrifolia (macadamia) remain understudied-particularly how they respond to seasonal, geographic, and root-type variations. This knowledge gap hinders targeted management of rhizosphere microbes for sustainable macadamia production.

METHODS: To address this, we examined the spatiotemporal structuring of rhizosphere fungal communities in M. integrifolia across four major production regions in Yunnan Province, China (Changning, Yingjiang, Lancang, Yunxian). We accounted for three key variables: season (dry season: November-April; rainy season: May-October), root type (normal roots vs. cluster roots), and geography. A total of 80 soil samples were collected (4 regions × 2 seasons × 2 root types × 5 biological replicates). High-throughput sequencing of the fungal Internal Transcribed Spacer (ITS) region was used to analyze community composition, diversity, and functional guilds; co-occurrence network analysis and PERMANOVA were also employed to interpret community dynamics.

RESULTS: Season and geographic location significantly shaped fungal community structure, while the effect of root type was context-dependent. Fungal diversity was higher in the rainy season, with Ascomycota (55-65%), Basidiomycota (20-30%), and Mortierellomycota (5-10%) as the dominant phyla. Cluster roots enriched symbiotic and beneficial taxa: Glomus and Trichoderma were 1.8- and 2.3-fold more abundant in cluster roots than in normal roots, respectively. PERMANOVA confirmed significant effects of season and region on community structure (p = 0.001). Co-occurrence networks showed seasonal shifts in core taxa: dry-season networks were dominated by Talaromyces and Penicillium (Ascomycota), while rainy-season networks featured Cladosporium (Ascomycota) and Mortierellaceae (Mortierellomycota)-with 35% of edges being negative interactions in the rainy season, indicating heightened resource competition. FUNGuild predictions revealed saprotrophic fungi were predominant (50-55%), with a 10% higher proportion in rainy-season samples than in dry-season samples.

DISCUSSION: This study clarifies the dynamic and region-specific nature of M. integrifolia rhizosphere fungal communities, highlighting how environmental factors drive their composition and function. These findings fill a critical knowledge gap and provide a foundational framework for future research on rhizosphere fungi in macadamia cultivation, supporting efforts to improve crop sustainability.},
}

@article {pmid41018663,
year = {2025},
author = {Barreto, CB and Barbalho Neto, FC and Bastos-Filho, CJA and Wu, QS and da Silva, MDC and da Silva, FSB},
title = {Does Mycorrhizal Biotechnology Modulate Lectin Accumulation in the Stem of Schinus terebinthifolia Raddi Seedlings?.},
journal = {ACS omega},
volume = {10},
number = {37},
pages = {43291-43299},
pmid = {41018663},
issn = {2470-1343},
abstract = {It is well-established that mycorrhizal symbiosis can alter lectin expression in plant roots, whereas little is known about its role in lectin accumulation in other plant organs and whether such behavior is related to the production of antioxidant secondary metabolites. This study aimed to evaluate whether the lectin accumulation profile in the stems of Schinus terebinthifolia Raddi seedlings is modulated in response to inoculation with an arbuscular mycorrhizal fungus (AMF) consortium. A greenhouse experiment was set up with two inoculation treatments: a noninoculated control and an AMF treatment (consortium of Acaulospora longula, Entrophospora etunicata, and Dentiscutata heterogama). After 191 days, stem tissues were harvested to prepare aqueous extracts. Primary and secondary metabolites were quantified spectrophotometrically, and in vitro antioxidant activity was evaluated. The hemagglutinating activity assay was performed to detect lectins, and the specific hemagglutinating activity (SHA) was determined. The AMF consortium significantly (p ≤ 0.01) enhanced the accumulation of metabolites, antioxidant activity, and SHA by over 110%, in comparison to control plants. The anabolism of carbohydrates, proteins, and phenols was highly correlated (r ≥ 0.8) with stem SHA. To our knowledge, this is the first study demonstrating the effect of mycorrhizal symbiosis on the specific hemagglutinating activity of plant extracts, revealing the presence of bioactive lectins in S. terebinthifolia stems and its relation to the production of other bioactive compounds. It suggests that AMF can quantitatively and qualitatively modulate lectin accumulation, a process closely tied to the host's anabolism.},
}

@article {pmid41017241,
year = {2025},
author = {Abd-Alla, AMM and Geiger, A and Haymer, D and Herrero, S and Jehle, JA and Khamis, F and Liedo, P and Malacrida, AR and Njiokou, F and Mastrangelo, T and Pagabeleguem, S and Ramırez-Santos, EM and Ros, VID and Segura, DF and Tsiamis, G and Weiss, BL},
title = {Improvement of colony management in insect mass-rearing for sterile insect technique applications.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70081},
pmid = {41017241},
issn = {1744-7917},
support = {D42017//International Atomic Energy Agency/ ; },
abstract = {Sterile Insect Technique (SIT) applications against major insect pests and disease vectors rely on the cost-effective production of high-quality sterile males. This largely depends on the optimal management of target pest colonies by maximizing the benefits provided by a genetically rich and pathogen-free mother colony, the presence of symbiotic microorganisms, and efficient domestication, mass-rearing, irradiation, and release processes. At the same time microbial (bacteria, fungi, microsporidia, and viruses) pathogen outbreaks should be minimized or eliminated, and the use of hazardous chemicals restricted. The optimization of the colony management strategies for different SIT target insects will ensure a standardized high-quality mass-rearing process and the cost-effective production of sterile males with enhanced field performance and male mating competitiveness. The aims of the Coordinated Research Project (CRP) were to develop best practices for insect colony management for the cost-effective production of high-quality sterile males for SIT applications against major insect pests and disease vectors through a multidisciplinary approach involving entomologists, geneticists, ecologists, microbiologists, pathologists, virologists, and mass-rearing experts.},
}

@article {pmid41017211,
year = {2025},
author = {Policelli, N and Nuñez, MA},
title = {Invasive ectomycorrhizal fungi: belowground insights from South America.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70608},
pmid = {41017211},
issn = {1469-8137},
support = {//Fundación Williams/ ; //Society for the Protection of Underground Networks SPUN/ ; },
abstract = {Ectomycorrhizal fungi (EMF) are essential for nutrient cycling and plant symbiosis, yet their invasions remain understudied, particularly in South America. Large-scale forestry introductions have spread non-native EMF across the continent. Although definitions vary, EMF are invasive when they disperse, colonize new environments, and overcome natural barriers. Invasive EMF alter soil biogeochemistry and local microbial and plant communities, sometimes preceding plant invasions. Despite their importance, invasive EMF remain poorly documented, with major knowledge gaps. Research must strengthen local networks, expand access to molecular tools, and integrate traditional knowledge. In turn, unregulated commercial inoculants pose risks, requiring policy intervention. South America offers a unique opportunity to strengthen collaboration and regional research to help elucidate and prevent future EMF invasions while guiding conservation.},
}

@article {pmid41015590,
year = {2025},
author = {Hameed, AK and Rab, SO and Ahmed, TA and Chandra, M and Mohammed, JS and S, R and Nayak, PP and Tomar, P and Hussn, A and Ali, AF},
title = {CAF-derived exosomes: orchestrators of dysregulated signaling pathways in breast cancer progression.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41015590},
issn = {1432-1912},
abstract = {Cancer-associated fibroblasts (CAFs) play a pivotal role in breast cancer (BC) progression by modulating the tumor microenvironment through exosome-mediated interactions. CAF-derived exosomes are rich in bioactive molecules such as metabolites, proteins, and non-coding RNAs that influence metabolic reprogramming in BC cells. These exosomes facilitate the transfer of metabolic enzymes and signaling molecules that enhance glycolysis, lipid metabolism, and oxidative phosphorylation, thereby supporting tumor growth, therapy resistance, and metastasis. This review highlights the molecular mechanisms underlying the role of CAF-derived exosomes in BC metabolism, with a focus on their contributions to metabolic plasticity and tumor progression. Potential therapeutic strategies targeting CAF exosome biogenesis, release, or uptake will also be discussed to shed light on innovative approaches for disrupting this metabolic symbiosis.},
}

@article {pmid41015552,
year = {2025},
author = {Traubenik, S and Reynoso, MA and Sánchez-Rodríguez, F and Yacullo, M and Christ, A and Hummel, M and Blein, T and Crespi, M and Bailey-Serres, J and Blanco, FA and Zanetti, ME},
title = {Subunit 3 of the SUPERKILLER complex mediates microRNA172-directed cleavage of Nodule Number Control 1 in Medicago truncatula.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf425},
pmid = {41015552},
issn = {1532-2548},
abstract = {Legumes and rhizobia establish a nitrogen-fixing symbiosis that involves the formation of a lateral root organ, the nodule, and the infection process that allows intracellular accommodation of rhizobia within nodule cells. This process involves substantial gene expression changes regulated at the transcriptional and post-transcriptional levels. We have previously shown that a transcript encoding subunit 3 of the SUPERKILLER Complex (SKI), which guides mRNAs to the exosome for 3´-to-5´ degradation, is required for nodule formation and bacterial persistence within the nodule, as well as the induction of early nodulation genes including early nodulin40 (MtENOD40) during the Medicago truncatula-Sinorhizobium meliloti symbiosis. Here, we reveal through transcript degradome and small RNA sequencing analysis that knockdown of MtSKI3 impairs the miR172-directed endonucleolytic cleavage of the mRNA encoding Nodule Number Control 1 (MtNNC1), an APETALA2 transcription factor that negatively modulates nodulation. Knockdown of MtNNC1 enhances nodule number, bacterial infection, and the induction of MtENOD40 upon inoculation with S. meliloti, whereas overexpression of an miR172-resistant form of MtNNC1 significantly reduces nodule formation. This work identifies miR172 cleavage of MtNNC1 and its control by MtSKI3, a component of the 3´-to-5´mRNA degradation pathway, as a regulatory hub controlling indeterminate nodulation.},
}

@article {pmid41014716,
year = {2025},
author = {Řezáč, M and Řezáčová, V and Némethová, E and Gloríková, N and Tranová, S and Heneberg, P},
title = {Tissue-resident microbiomes shape stress resilience and dispersal behavior in an agrobiont spider.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127431},
doi = {10.1016/j.jenvman.2025.127431},
pmid = {41014716},
issn = {1095-8630},
abstract = {Spiders serve as key biological control agents in agroecosystems, but they face repeated disturbances due to common agricultural practices. The wolf spider Pardosa agrestis, a dominant agrobiont species, recolonizes these disrupted habitats via dispersal strategies such as ballooning, particularly during juvenile stages. This study investigated how nutrition and insecticide exposure influence ballooning behavior and the structure-function dynamics of the spider's tissue-resident microbiome. We found that dispersal behavior in P. agrestis is structured and repeatable, driven by environmental cues such as light and wind, and further modulated by previous exposure. Although diet significantly impacted growth and development, it had a minimal influence on the dispersal strategy. The tissue-resident microbiome analysis revealed a diverse, core symbiotic community with notable responsiveness to both dietary and pesticide-induced stress. Specific tissue-resident microbial taxa shifted their predicted metabolic output under nutrient deprivation, suggesting adaptive biosynthetic activity. Importantly, distinct predicted microbial metabolic profiles were associated with spider behaviors (e.g., ballooning) and physiological traits (e.g., endurance), indicating a microbiome-mediated influence on the dispersal capacity. Moreover, tissue-resident microbial community function was correlated with host survival after insecticide exposure, implicating its role in detoxification and resistance. These findings highlight the role of the tissue-resident microbiome as a functional partner in arthropod stress resilience and dispersal behavior in agroecosystems.},
}

@article {pmid41014709,
year = {2025},
author = {Domini, M and Vahidzadeh, R and Vaccari, M and Sbaffoni, S and De Marco, E and Beltrani, T and Bertanza, G},
title = {Regional industrial symbiosis networks for waste minimisation: a case study from Italy.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127376},
doi = {10.1016/j.jenvman.2025.127376},
pmid = {41014709},
issn = {1095-8630},
abstract = {Industrial symbiosis supports a circular economy by fostering resource recovery through inter-industry synergies. Despite growing network scales, regional-level industrial symbiosis networks (ISNs) remain underexplored representing a key research problem. The objective of this study is to develop and demonstrate an innovative methodological framework to investigate the ISN in the highly industrialized province of Brescia. The methodology applies Social Network Analysis (SNA) across three scenarios: the current network (ISNP), a potential network identified through facilitation and research activities (ISNR), and a hypothetical scaled-up network (ISNF) that integrates ISNP with ISNR. By integrating SNA with material flow analyses, novel indicators were developed to evaluate ISNs' impact on regional waste management (WM) performance and the influence of contextual factors. The results reveal that, despite having 459 industrial nodes, the ISNs show low density and high centralisation, dominated by metallurgical companies. The transition to ISNF reveals two key advantages over ISNP: a quantitative increase in recovery of wastes otherwise disposed of (from 1 % to 18 %) and enhanced diversity of waste flows (from 39 to 57 European Waste Codes), aligning with an increased contribution to reducing waste transportation and disposal (from 14 % to 51 %). Barriers to scaling the ISN include limited industrial diversity, insufficient partners for waste transformation, and few WM permits, while key drivers involve internal reuse strategies and untapped company participation. In conclusion, the study provides an innovative methodology and case study for analysing ISNs at a regional scale, contributing valuable insights to inform further research and support development of industrial circularity initiatives.},
}

@article {pmid41014378,
year = {2025},
author = {Upadhyay, A and Khandelwal, V},
title = {Endophytes in Medicinal Plants: A Sustainable Solution for Coping with Environmental Stresses.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {529},
pmid = {41014378},
issn = {1432-0991},
mesh = {*Endophytes/physiology ; *Plants, Medicinal/microbiology/physiology ; *Stress, Physiological ; Humans ; COVID-19 ; Symbiosis ; SARS-CoV-2 ; },
abstract = {The increasing need for integrative and alternative medical therapies, especially in the aftermath of the COVID-19 epidemic, has emphasized the importance of medicinal plants in worldwide healthcare. These plants, which contain abundant bioactive secondary metabolites, provide a sustainable and cost-effective option for medicinal, adaptogenic, and immune-boosting purposes. Blooming medicinal plants that exist are at risk of becoming extinct because of excessive harvesting, deforestation, and wildfires. Medicinal plants have complex physiological defenses against stress, which are strengthened by their symbiotic relationship with endophytes. Endophytes are microbial colonies that live within plant tissues without causing harm and play a vital role in maintaining the health of plants by helping them to tolerate stress, promoting development, acquiring nutrients, synthesizing phytohormones, breaking down toxic substances, and improving plant resistance to environmental pressures such as high salt levels, lack of water, and exposure to heavy metals. In addition, endophytes have a role in managing biotic stress by engaging in antibiosis, synthesizing lytic enzymes, producing secondary metabolites, and regulating hormones. Their function in preserving the health and well-being of the host, ensuring proper nutrition intake, and enhancing resistance against pathogens highlights their potential as agents for biological control and biofertilization, providing a safer option compared to chemical pesticides. Endophytic inoculants have the potential to significantly transform crop yield in agriculture by reducing the impact of abiotic problems and improving soil health. This review critically evaluates causal studies and recent omics-based advances, highlighting their crucial significance for sustainable bioinoculant development and practical applications in climate-resilient agriculture.},
}

*Endophytes/physiology
*Plants, Medicinal/microbiology/physiology
*Stress, Physiological
Humans
COVID-19
Symbiosis
SARS-CoV-2

@article {pmid41013533,
year = {2025},
author = {Miao, W and Zang, H and Liu, Q and Zheng, T and Zhou, Y and Liu, C and Yang, N and Zhang, H and Zhang, Y and Zhang, Y and Li, S and Zhang, S and Zhang, H},
title = {From chaos to symbiosis: exploring adaptive co-evolution strategies for generative AI and research integrity systems.},
journal = {BMC medical ethics},
volume = {26},
number = {1},
pages = {120},
pmid = {41013533},
issn = {1472-6939},
support = {2024SK02//Project supported by the Affiliated Hospital of Xuzhou Medical University/ ; 2021G10//Project supported by the Affiliated Hospital of Xuzhou Medical University/ ; KC23118//the Soft Science Research Project of Xuzhou Policy Guidance Program/ ; },
mesh = {Humans ; *Artificial Intelligence/ethics ; Research Personnel/ethics ; *Ethics, Research ; *Biomedical Research/ethics ; },
abstract = {OBJECTIVE: The information age has transformed technologies across disciplines. Generative artificial intelligence (GenAI), as an emerging technology, has integrated into scientific research. Recent studies identify GenAI-related scientific research integrity concerns. Using Complex Adaptive Systems (CAS) theory, this research examines risk factors and preventive measures for each agent within the scientific research integrity management system during GenAI adoption, providing new perspectives for integrity management.

METHOD: This study applies CAS theory to analyze the scientific research integrity management system, identifying four core micro-level agents: researchers, research subjects, scientific research administrators, and academic publishing institutions. It examines macro-system complexity, agent adaptability, and the impact of agent interactions on the overall system. This framework enables analysis of GenAI's effects on the research integrity management system.

RESULTS: The scientific research integrity management system exhibits structural, hierarchical, and multidimensional complexities, with internal circulation of policy, funding, and information elements. In response to GenAI integration, four micro-level agents-researchers, research subjects, scientific research administrators, and academic publishing institutions-adapt their behaviors to systemic changes. Through these interactions, behavioral outcomes emerge at the macro level, driving evolution of the research integrity management system.

CONCLUSIONS: Risks of scientific misconduct permeate the entire research process and require urgent governance. This study recommends that scientific research administrators promptly define applicable boundaries for GenAI in research to guide researchers. Concurrently, they should collaborate with relevant departments to establish regulatory frameworks addressing potential GenAI-related misconduct. Academic publishing institutions must assume quality assurance responsibilities by strengthening review and disclosure protocols. Furthermore, research integrity considerations should be systematically integrated into GenAI's technological development and refinement.

HIGHLIGHTS: ● Develops an analytical framework grounded in Complex Adaptive Systems (CAS) theory to map evolving interactions among researchers, research subjects, scientific research administrators, and academic publishing institutions within GenAI-integrated research ecosystems.  ● Identifies self-reinforcing dynamics between GenAI adoption and integrity governance, wherein adaptive rule adjustments by agents reshape system-wide integrity thresholds.  ● Proposes adaptive governance mechanisms that balance innovation safeguards with integrity guardrails, emphasizing context-sensitive policy calibration over universal solutions.},
}

Humans
*Artificial Intelligence/ethics
Research Personnel/ethics
*Ethics, Research
*Biomedical Research/ethics

@article {pmid41012068,
year = {2025},
author = {Paladines-Beltrán, GM and Venegas, NA and Suárez, JC},
title = {Arbuscular Mycorrhizal Fungi Enhance Antioxidant Defense Systems in Sugarcane Under Soil Cadmium Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/plants14182916},
pmid = {41012068},
issn = {2223-7747},
abstract = {Cadmium (Cd) is a toxic metal that affects living organisms even at low concentrations, causing physiological alterations and biomass reduction in plants. Arbuscular mycorrhizal fungi (AMF) represent a biological strategy that increases tolerance to heavy metals, although their specific mechanisms in sugarcane remain poorly understood. To address this knowledge gap, an open-field experiment was conducted to evaluate the effects of AMF on Cd accumulation, oxidative stress, photosynthetic pigments, enzymatic antioxidant system, and non-enzymatic antioxidant compounds in sugarcane variety CC 01-1940, using a randomized block design. Results showed that AMF established symbiosis with plants, retaining Cd in the roots and reducing its translocation to leaves. Additionally, they decreased Cd-induced oxidative stress by reducing lipid peroxidation (MDA) and proline content. Although an initial decrease in photosynthetic capacity was observed, AMF helped maintain stable levels of photosynthetic pigments, preserving photosynthetic efficiency. They also activated antioxidant enzymes and increased antioxidant compounds such as reduced glutathione (GSH), non-protein thiols (NP-SH), ascorbic acid (AA), and phytochelatins (PC). These findings demonstrate that symbiosis with AMF protects sugarcane plants from cellular oxidative damage and reduces Cd concentrations in leaves. Therefore, the use of AMF represents an effective strategy to improve the antioxidant defense and resistance of sugarcane plants to cadmium stress.},
}

@article {pmid41012062,
year = {2025},
author = {Yin, X and Zhao, J and Pan, L and Wang, E and Chen, N and Xu, J and Jiang, X and Zhao, X and Ma, J and Li, S and Xie, H and Yang, Z and Yu, S and Chi, X},
title = {Genome-Wide Identification of Arachis hypogaea LEC1s, FUS3s, and WRIs and Co-Overexpression of AhLEC1b, AhFUS3b, AhWRI1a and AhWRI1d Increased Oil Content in Arabidopsis Seeds.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/plants14182910},
pmid = {41012062},
issn = {2223-7747},
support = {CXGC2025F19 and CXGC2025C19//The Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultur-al Sciences/ ; CARS-13//The China Agriculture Research System of MOF and MARA/ ; 2022A02008-3//The Major Scientific and Technological Project in Xinjiang/ ; NO.tstp20240523 and NO.tsqn202312292//The Taishan Scholar Project Funding/ ; ZR2023QC146 and ZR2023QC177//The Natural Science Foundation of Shandong Province/ ; KF2024007//The Open Project of Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs/ ; 2024LZGC035//Shandong Province Key Research and Development Programme Project/ ; 2024ZDJH100//The Science and Technology Development Guidance Plan of Dongying Major Science and Tech-nology Innovation Project/ ; 2022E10012//Open Project of Key Laboratory of Digital Upland Crops of Zhejiang Province/ ; },
abstract = {Peanut (Arachis hypogaea) is an important oil and economic crop widely cultivated worldwide. Increasing the oil yield is a major objective for oilseed crop improvement. Plant LEAFY COTYLEDON1s (LEC1s), FUSCA3s (FUS3s), and WRINKLED1s (WRI1s) are known master regulators of seed development and oil biosynthesis. While previous studies in peanut have primarily focused on two AhLEC1s and one AhWRI1 genes, this study identified a broader set of regulators, including two AhLEC1s, two AhFUS3s, nine AhWRI1s, two AhWRI2s, and four AhWRI3s from the variety HY917. The analyses of phylogenetic trees, gene structures, conserved domains, sequence alignment and identity, and collinearity revealed that they were highly similar to their homologs in other plants. Expression profiling demonstrated that two AhLEC1s, two AhFUS3s, and three AhWRI1s (AhWRI1a/b/c) were specifically expressed in developing seeds, suggesting critical roles in seed development, whereas AhWRI1d, AhWRI1f, and AhWRI1g showed high expression in root nodules, pointing to potential functions in symbiosis and nodulation. Furthermore, co-overexpression of AhLEC1b, AhFUS3b, AhWRI1a, and AhWRI1d in Arabidopsis significantly enhanced seed oil content and thousand-seed weight, but also led to reduced germination rate, plant height, and silique length. The findings allow for the extensive evaluation of AhLEC1s, AhFUS3s, and AhWRIs gene families, establishing a useful foundation for future research into their multiple roles in peanut development.},
}

@article {pmid41011486,
year = {2025},
author = {Vuleta, S and Leggat, WP and Ainsworth, TD},
title = {Photoendosymbiosis of the Blue Subtropical Montipora Corals of Norfolk Island, South Pacific.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092155},
pmid = {41011486},
issn = {2076-2607},
abstract = {Corals exhibit complex and diverse relationships with dinoflagellates of the family Symbiodiniaceae. Montiporid corals within Norfolk Island's shallow water lagoonal reef systems have been observed to turn a deep fluorescent blue during winter, suggesting potential environmentally driven changes to their photoendosymbiosis. Here, we investigate the photoendosymbiosis of blue Montipora sp. corals over a year-long study, demonstrating that photosynthetic yield and Symbiodiniaceae densities vary seasonally, with the lowest photosynthetic yield occurring within winter periods. We also provide the first characterisation of Symbiodiniaceae species associated with corals from Norfolk Island, identifying blue Montipora sp. as predominantly associating with Cladocopium (formerly Clade C) genotypes (C3aap, C3ig, and C3aao). Finally, we also report on the impact of recent bleaching conditions (March 2024) on blue Montipora sp. photoendosymbiosis and find the genera is susceptible to increasing sea surface temperatures. Our findings provide insight into the unique biology of subtropical corals within this remote reef and the susceptibility of corals in the region to increasing sea surface temperatures.},
}

@article {pmid41011468,
year = {2025},
author = {Wei, M and Wang, Y and Xie, F and Sun, Q and Shao, H and Cheng, X and Wang, X and Tao, X and He, X and Yong, B and Liu, D},
title = {The Ecological Trap: Biodegradable Mulch Film Residue Undermines Soil Fungal Network Stability.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092137},
pmid = {41011468},
issn = {2076-2607},
support = {grant number 31800425//Dongyan Liu/ ; },
abstract = {Biodegradable mulching films are promoted as alternatives to traditional polyethylene films, but their environmental impacts remain controversial. This study investigates how biodegradable films affect microplastic pollution of soil, fungal community structure, and ecological network stability. We conducted a maize field experiment comparing conventional polyethylene (CF, PE) and biodegradable (BF, PLA + PBAT) film residues. We used scanning electron microscopy and high-throughput sequencing of fungal ITS genes. We assessed soil properties, microplastic release, fungal communities, and network stability through co-occurrence analysis. BF degraded rapidly, releasing microplastic concentrations much higher than CF. BF increased soil carbon and nitrogen and substantially enhanced maize biomass. However, it significantly reduced soil pH and decreased key functional fungi (saprotrophs and symbionts) abundance. The fungal ecological network complexity and stability declined significantly. Correlation analysis revealed positive associations between saprotrophic and symbiotic fungi abundance and network stability. In contrast, CF reduced some nutrient levels but improved fungal network complexity and stability. This study reveals that biodegradable films create an "ecological trap." Short-term nutrient benefits mask systematic damage to soil microbial network stability. Our findings challenge the notion that "biodegradable equals environmentally friendly." Environmental assessments of agricultural materials must extend beyond degradability to include microplastic release, functional microbial responses, and ecological network stability.},
}

@article {pmid41011327,
year = {2025},
author = {D'Angelo, A and Zenoniani, A and Masci, M and Aceto, GM and Piattelli, A and Curia, MC},
title = {Exploring the Microbiome in Breast Cancer: The Role of Fusobacterium nucleatum as an Onco-Immune Modulator.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13091995},
pmid = {41011327},
issn = {2076-2607},
abstract = {The breast microbiome remains stable throughout a woman's life. The breast is not a sterile organ, and its microbiota exhibits a distinct composition compared to other body sites. The breast microbiome is a community characterized by an abundance of Proteobacteria and Firmicutes, which represent the result of host microbial adaptation to the fatty acid environment in the tissue. The breast microbiome demonstrates dynamic adaptability during lactation, responding to maternal physiological changes and infant interactions. This microbial plasticity modulates local immune responses, maintains epithelial integrity, and supports tissue homeostasis, thereby influencing both breast health and milk composition. Disruptions in this balance, the dysbiosis, are closely linked to inflammatory breast conditions such as mastitis. Risk factors for breast cancer (BC) include genetic mutations, late menopause, obesity, estrogen metabolism, and alterations in gut microbial diversity. Gut microbiota can increase estrogen bioavailability by deconjugating estrogen-glucuronide moieties. Perturbations of this set of bacterial genes and metabolites, called the estrobolome, increases circulating estrogens and the risk of BC. Fusobacterium nucleatum has recently been associated with BC. It moves from the oral cavity to other body sites hematogenously. This review deals with the characteristics of the breast microbiome, with a focus on F. nucleatum, highlighting its dual role in promoting tumor growth and modulating immune responses. F. nucleatum acts both on the Wnt/β-catenin pathway by positively regulating MYC expression and on apoptosis by inhibiting caspase 8. Furthermore, F. nucleatum binds to TIGIT and CEACAM1, inhibiting T-cell cytotoxic activity and protecting tumor cells from immune cell attack. F. nucleatum also inhibits T-cell function through the recruitment of myeloid suppressor cells (MDSCs). These cells express PD-L1, which further reduces T-cell activation. A deeper understanding of F. nucleatum biology and its interactions with host cells and co-existing symbiotic microbiota could aid in the development of personalized anticancer therapy.},
}

@article {pmid41010039,
year = {2025},
author = {Fuentes-Romero, F and López-Baena, FJ and Vinardell, JM and Acosta-Jurado, S},
title = {Updated Sequence and Annotation of the Broad Host Range Rhizobial Symbiont Sinorhizobium fredii HH103 Genome.},
journal = {Genes},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/genes16091094},
pmid = {41010039},
issn = {2073-4425},
support = {US-1250546//Universidad de Sevilla/ ; PID2022-141156OB-I00//MCIN/AEI/ 10.13039/501100011033/ ; PREDOC_01119//Junta de Andalucía/ ; },
mesh = {*Genome, Bacterial ; *Symbiosis/genetics ; *Sinorhizobium fredii/genetics ; Plasmids/genetics ; Molecular Sequence Annotation ; Host Specificity/genetics ; DNA Transposable Elements ; Glycine max/microbiology ; },
abstract = {Background: Sinorhizobium fredii HH103 is a fast-growing rhizobial strain capable of infecting a broad range of legumes, including plants forming determinate and indeterminate nodules, such as Glycine max (its natural host) and Glycyrrhiza uralensis, respectively. Previous studies reported the sequence and annotation of the genome of this strain (7.25 Mb), showing the most complex S. fredii genome sequenced to date. It comprises seven replicons: one chromosome and six plasmids. Among these plasmids, pSfHH103d, also known as the symbiotic plasmid pSymA, harbors most of the genes involved in symbiosis. Due to limitations of the sequencing technology used at the time and the presence of high number of clusters of transposable elements, this plasmid could only be partially assembled as four separated contigs. Methods: In this work, we have used a combination of PacBio and Illumina sequencing technologies to resolve these complex regions, obtaining an updated genome sequence (7.27 Mb). Results: This updated version includes an increase in size of the largest replicons (chromosome, pSfHH103d, and pSfHH103e) and a complete and closed symbiotic plasmid (pSfHH103d or pSymA). Additionally, we carried out a re-annotation of the updated genome, merging the previous annotation and the new one found in the remaining gaps. Notably, we found a high number of transposable elements in the HH103 genome, especially in three plasmids (pSfHH103b, pSfHH103c, and pSymA), a feature that is common among S. fredii strains. Conclusions: The combination of PacBio and Illumina sequencing technologies has allowed us to obtain a complete version of the HH103 pSymA. The presence of a high number of mobile elements seems to be a general characteristic among S. fredii strains, a fact that might be related to a high genome plasticity.},
}

*Genome, Bacterial
*Symbiosis/genetics
*Sinorhizobium fredii/genetics
Plasmids/genetics
Molecular Sequence Annotation
Host Specificity/genetics
DNA Transposable Elements
Glycine max/microbiology

@article {pmid41010029,
year = {2025},
author = {Gomes-Domingues, C and Marques, I and Simões Costa, MC and Caperta, AD},
title = {Halotolerant Mycorrhizal Symbiosis Enhances Tolerance in Limonium Species Under Long-Term Salinity.},
journal = {Genes},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/genes16091084},
pmid = {41010029},
issn = {2073-4425},
support = {UIDB/04129/2020; UIDB/00239/2020; LA/P/0092/2020; 2021.01107.CEECIND/CP1689/CT0001//Fundação para a Ciência e Tecnologia/ ; },
mesh = {*Plumbaginaceae/microbiology/genetics/physiology ; *Mycorrhizae/physiology ; *Symbiosis ; *Salt Tolerance/genetics ; Salinity ; Gene Expression Regulation, Plant ; *Salt-Tolerant Plants/genetics/microbiology ; Plant Proteins/genetics ; Plant Leaves/microbiology ; },
abstract = {To survive in saline environments, plants establish complex symbiotic relationships with soil microorganisms, including halotolerant arbuscular mycorrhizal fungi (AMF). The main objective of this study was to uncover how inoculation with a consortium of halotolerant AMF influences recretohalophyte Limonium species tolerance to long-term salinity, at physiological and molecular levels. In this study, the physiological performance, ultrastructure of leaf epidermal cells, and expression of seven genes involved in salinity response were studied in Limonium daveaui and Limonium algarvense plants exposed to 200 mM NaCl and inoculated with an AMF consortium, dominated by Rhizoglomus invernaius. An isohydric response was observed for both species after one year in salinity. Inoculation with AMF led to higher stomatal conductance for plants in non-saline conditions and improved photosystem II efficiency under salinity. In L. algarvense, inoculation enhanced stomata and salt gland epidermal area under tap water. While salinity significantly increased salt gland, stomata and pavement cells areas but not cell size. In L. daveaui, AMF led to an increased salt gland density as well as salt gland size under saline conditions. In both species, salinity increased the expression of Na[+]/H[+] antiporter AtSOS1, aquaporin TIP5, and salt gland development related genes LbTRY, Lb7G34824 and Lb4G22721GIS2. The expression of such genes was significantly reduced in AMF-inoculated plants under salinity. Besides, higher levels of gene expression were observed in L. algarvense than in L. daveaui. Overall, our findings highlight the protective role of halotolerant AMF and emphasize their potential as sustainable effective bio-inoculants for enhancing plant salinity tolerance.},
}

*Plumbaginaceae/microbiology/genetics/physiology
*Mycorrhizae/physiology
*Symbiosis
*Salt Tolerance/genetics
Salinity
Gene Expression Regulation, Plant
*Salt-Tolerant Plants/genetics/microbiology
Plant Proteins/genetics
Plant Leaves/microbiology

@article {pmid41008602,
year = {2025},
author = {Johnson, K and Pourkeramati, D and Korf, I and Powers, T},
title = {Metabolic Adaptations Determine the Evolutionary Trajectory of TOR Signaling in Diverse Eukaryotes.},
journal = {Biomolecules},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/biom15091295},
pmid = {41008602},
issn = {2218-273X},
mesh = {*Signal Transduction ; *Eukaryota/metabolism/genetics ; *Evolution, Molecular ; *Mechanistic Target of Rapamycin Complex 2/metabolism/genetics ; Mechanistic Target of Rapamycin Complex 1/metabolism/genetics ; *TOR Serine-Threonine Kinases/metabolism/genetics ; Phylogeny ; },
abstract = {Eukaryotes use diverse nutrient acquisition strategies, including autotrophy, heterotrophy, mixotrophy, and symbiosis, which shape the evolution of cell regulatory networks. The Target of Rapamycin (TOR) kinase is a conserved growth regulator that in most species functions within two complexes, TORC1 and TORC2. TORC1 is broadly conserved and uniquely sensitive to rapamycin, whereas the evolutionary distribution of TORC2 is less well-defined. We built a sensitive hidden Markov model (HMM)-based pipeline to survey core TORC1 and TORC2 components across more than 800 sequenced eukaryotic genomes spanning multiple major supergroups. Both complexes are present in early-branching lineages, consistent with their presence in the last eukaryotic common ancestor, followed by multiple lineage-specific losses of TORC2 and, more rarely, TORC1. A striking pattern emerges in which TORC2 is uniformly absent from photosynthetic autotrophs derived from primary endosymbiosis and frequently lost in those derived from secondary or tertiary events. In contrast, TORC2 is consistently retained in mixotrophs, which obtain carbon from both photosynthesis and environmental uptake, and in free-living obligate heterotrophs. These findings suggest that TORC2 supports heterotrophic metabolism and is often dispensable under strict autotrophy. Our results provide a framework for the evolutionary divergence of TOR signaling and highlight metabolic and ecological pressures that shape TOR complex retention across eukaryotes.},
}

*Signal Transduction
*Eukaryota/metabolism/genetics
*Evolution, Molecular
*Mechanistic Target of Rapamycin Complex 2/metabolism/genetics
Mechanistic Target of Rapamycin Complex 1/metabolism/genetics
*TOR Serine-Threonine Kinases/metabolism/genetics
Phylogeny

@article {pmid41007441,
year = {2025},
author = {Hou, Y and Bao, Y and Jia, R and Zhou, L and Song, L and Yang, B and Li, B and Zhu, J},
title = {The Stone Moroko Pseudorasbora parva Altered the Composition and Stability of Sediment Microbial Communities Within the Chinese Mitten Crab (Eriocheir sinensis) Polyculture Pond.},
journal = {Biology},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biology14091297},
pmid = {41007441},
issn = {2079-7737},
support = {CARS-45//China Agriculture Research System of MOF and MARA/ ; 2023TD64//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {Integrated aquaculture, centered around polyculture involving multiple species, is a typical practice for the sustainable development of the aquaculture industry, capable of enhancing resource utilization efficiency, environmental stability, and overall productivity through establishing symbiotic interactions among species. This study employed multi-amplicon high-throughput sequencing to assess the ecological impacts of two polyculture methods involving river crabs on sediment bacteria, fungi, and protists. One method involved polyculturing river crabs with mandarin fish, silver carp, and the stone moroko (SPC), and the other involved polyculturing river crabs with only mandarin fish and silver carp (SMC). The results showed that, compared to the SMC group, the SPC group remarkably increased the Chao1 index of bacterial communities in pond sediment and decreased the Pielou_J index of protists. The relative abundances of all fungal phyla and most dominant bacterial and protistan phyla (top 10 in relative abundance) in the SPC group were considerably different from those in the SMC group. In the co-occurrence networks of bacterial, fungal, and protistan communities, the numbers of edges and nodes were higher in the SPC group than in the SMC group, and the habitat niche breadth of bacterial community was also notably increased in the SPC group. The levels of total carbon (TC), total nitrogen (TN), and phosphates within pond sediment in the SPC group were obviously lower than those in the SMC group, and were significantly correlated with the microbial communities, with TC being identified as the primary contributor driving changes in the microbial communities. All the findings collectively demonstrate that the polyculture of river crabs with mandarin fish, silver carp, and the stone moroko enhances the stability of bacterial, fungal, and protistan communities in sediment and enhances resource utilization efficiency in aquaculture, thereby preventing the environmental risks associated with excessive nutrient accumulation in sediment. Polyculture systems integrating river crabs with mandarin fish, silver carp, and the stone moroko represent a sustainable aquaculture model with significant ecological benefits.},
}

@article {pmid41007393,
year = {2025},
author = {Oh, JH and Kim, E and Cho, M},
title = {Biofilm Formation by Rice Rhizosphere Nitrogen-Fixing Microorganisms and Its Effect on Rice Growth Promotion.},
journal = {Biology},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biology14091249},
pmid = {41007393},
issn = {2079-7737},
support = {PJ017406012025//National Institute of Agricultural Sciences Program/ ; },
abstract = {Excessive nitrogen fertilizer use contributes to environmental pollution and undermines agricultural sustainability. Enhancing symbiotic interactions between rice and nitrogen-fixing microorganisms offers a promising strategy to potentially improve nitrogen use efficiency (NUE). This study investigates the role of rice root exudates in promoting biofilm formation by nitrogen-fixing microbes to enhance nitrogen fixation. Nine nitrogen-fixing microbial strains were evaluated for biofilm formation in response to flavone and apigenin treatments, with Gluconacetobacter diazotrophicus KACC 12358 serving as the reference strain. The most responsive strain was selected, and a library of 1597 natural compounds was screened to identify those that promote biofilm formation in both the selected and reference strains. A. indigens KACC 11682 exhibited the highest biofilm-forming capacity, with apigenin treatment showing an OD595 value approximately 1.4 times higher than the DMSO control. Screening identified 68 compounds that enhanced biofilm formation by more than 500% compared to the control. Among them, eight compounds induced strong biofilm formation (O.D. > 2.0) in A. indigens. Cardamomin, a chalconoid flavonoid, emerged as one of the most effective compounds, showing a 245% increase in biofilm formation. Growth promotion assays showed that A. indigens increased rice fresh weight by approximately 128% compared to untreated controls. This study demonstrates the potential of rice root exudate-derived compounds to promote beneficial symbiosis with nitrogen-fixing microbes. These findings offer a novel approach that may contribute to enhancing rice NUE. Future research will focus on evaluating the long-term effects of these compounds and microorganisms, assessing their applicability in real agricultural settings, and conducting further validation across various rice cultivars.},
}

@article {pmid41007378,
year = {2025},
author = {da Silva, MB and Medeiros, AB and Dos Anjos, AIM and Ferreira Cavalcante, JV and Santiago, BCF and Monteiro, SS and Vital, AC and Dalmolin, RJS and Lisboa, HM and Pasquali, MAB},
title = {Changes in the Microbiota of the Scale Insect (Diaspis echinocacti, Bouché, 1833) in Opuntia stricta Cladodes: Taxonomic and Metagenomic Analysis as a Function of Infestation Levels.},
journal = {Biology},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biology14091233},
pmid = {41007378},
issn = {2079-7737},
support = {306165/2023-6//National Council for Scientific and Technological Development/ ; },
abstract = {Drought-tolerant cactus Opuntia stricta sustains livestock in Brazil's semi-arid Northeast but suffers yield losses from the armored scale insect Diaspis echinocacti. Symbiotic bacteria are thought to underpin scale fitness; however, their response to pest pressure remains unexplored. We characterized the bacterial communities of D. echinocacti collected from cladodes displaying low, intermediate, and high infestation (n = 3 replicates per level) using 16S-rRNA amplicon sequencing, processed with nf-core/ampliseq. Shannon diversity declined from low to high density, and Bray-Curtis ordination suggested compositional shifts, although group differences were not significant (Kruskal-Wallis and PERMANOVA, p > 0.05). The obligate endosymbiont "Candidatus Uzinura" dominated all samples (>85% relative abundance) irrespective of density, indicating a resilient core microbiome. PICRUSt2 predicted a contraction of metabolic breadth at higher infestations, with convergence on energy- and amino acid biosynthesis pathways. Taken together, increasing pest density was associated with modest loss of diversity and functional streamlining, rather than wholesale turnover. These baseline data can guide future work on microbiome-based strategies to complement existing scale-insect control in dryland cactus systems.},
}

@article {pmid41006547,
year = {2025},
author = {Parry, AJ and Klein, SG and Duarte, CM},
title = {Thermal extremes likely trigger metabolic imbalance in coral holobionts.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33181},
pmid = {41006547},
issn = {2045-2322},
support = {BAS/1/1071-01-01//King Abdullah University of Science and Technology/ ; BAS/1/1071-01-01//King Abdullah University of Science and Technology/ ; BAS/1/1071-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {Animals ; *Anthozoa/metabolism/physiology ; *Symbiosis/physiology ; Photosynthesis ; Temperature ; Hot Temperature ; Oxygen/metabolism ; },
abstract = {Rising ocean temperatures are constraining the availability of dissolved oxygen and simultaneously increasing the respiratory oxygen requirements of marine organisms. This is particularly relevant for tropical corals, as periods of anomalously high temperature destabilize the symbiosis between corals and Symbiodiniaceae, resulting in coral bleaching. These observations point towards a possible role of mismatched rates of photosynthetic oxygen production and consumption in contributing to the breakdown of the holobiont under heat stress. Here we use a global dataset comprising experimentally derived relationships between coral metabolic rates and temperature to investigate this hypothesis. Across all available relationships, we calculated and analysed the activation energy (E), optimum temperature (Topt) of respiration, net productivity, gross productivity and where possible, P: R ratio. Despite known variations in the thermal tolerances among corals in our database, we resolved composite thermal performance curves for scleractinian corals and provide insight into differences between tropical and temperate corals and among selected genera. We show that after the theoretical Topt is exceeded, photosynthesis declines at a faster rate than respiration. At temperatures exceeding the theoretical Topt for net productivity, this metabolic mismatch could possibly contribute to the destabilization of the coral-symbiont association. Specifically, we postulate that a lack of symbiont oxygen production and heightened holobiont respiratory demand at peak temperatures represents a burden on the oxygen budget of the holobiont.},
}

Animals
*Anthozoa/metabolism/physiology
*Symbiosis/physiology
Photosynthesis
Temperature
Hot Temperature
Oxygen/metabolism

@article {pmid41005673,
year = {2025},
author = {Zhu, X and Fang, L and Xu, F and Sun, J and Zhang, X and Cai, J},
title = {Deciphering effect of complex organics on Anammox-sulfide autotrophic denitrification coupling system for landfill leachate treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133388},
doi = {10.1016/j.biortech.2025.133388},
pmid = {41005673},
issn = {1873-2976},
abstract = {The inhibitory effects of complex organics on Anammox-sulfide autotrophic denitrification (SAD) coupled systems are not well understood in full-strength leachate conditions. This research examines the removal of carbon, nitrogen, and sulfur, alongside microbial symbiosis and metabolic alterations, within an Anammox-SAD system that processes raw landfill leachate.. The system attained a total nitrogen removal rate of 98.54 ± 0.42 %, with contributions of 89.47 % from Anammox and 10.53 % from SAD. The system attained a total nitrogen removal rate of 98.54 ± 0.42 %, with contributions of 89.47 % from Anammox and 10.53 % from SAD. GC × GC-TOFMS analysis indicated removal rates of 72.33 %, 51.05 %, and 53.81 % for small-, medium-, and large-molecular-weight organics, respectively, by the Anammox system, thereby reducing stress on SAD. Metagenomics studies revealed that low-molecular-weight organics promoted DNRA, partial denitrification, and Anammox through enhancing electron transfer and functional gene expression. The role of Anammox bacteria in carbon fixation decreased, whereas sulfur metabolism in SAD became increasingly dependent on Sulfurimonas-mediated Sox pathways, indicating metabolic adaptation in response to organic stress and competition between autotrophs and heterotrophs. This study provides novel insights into the application of Anammox-SAD coupled processes for landfill leachate treatment.},
}

@article {pmid41005092,
year = {2025},
author = {Dou, XX and Mao, BD and Li, A and Gu, JJ and Zhang, XL and Fu, CW and Zhang, XJ and Lan, BJ and Xu, JW and Zhang, BX and Zheng, HJ and Gao, F},
title = {Algal-bacterial symbiosis strengthens the treatment of high-salinity phenolic wastewater and its molecular mechanism.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139957},
doi = {10.1016/j.jhazmat.2025.139957},
pmid = {41005092},
issn = {1873-3336},
abstract = {This study developed algal-bacterial symbiotic flocs (ABSF) for high-salinity phenolic wastewater treatment, showcasing superior performance over activated sludge (AS). ABSF exhibited exceptional structural stability, producing 417.64 mg g[-1] extracellular polymeric substances (EPS) and accumulating 51.2 % lipids. It achieved complete phenol removal and significantly reduced effluent total nitrogen (9.36 vs. 23.59 mg L[-1] in AS) and COD (77.76 vs. 105.34 mg L[-1]), maintaining efficiency even at a 1-day hydraulic retention time. Metagenomic analysis revealed ABSF's diverse microbial community, enriched with functional genera (Candidatus Nitrosocosmicus, Synechocystis, Thauera) linked to nitrogen and aromatic degradation. Enhanced quorum sensing was evidenced by elevated N-acyl-homoserine lactones (C6-HSL: 38.56 ng mL[-1]) and upregulated signal transduction genes (5.4 % abundance). ABSF also showed higher expression of phenol-degrading enzymes and metabolic genes (e.g., succinate dehydrogenase: 0.19 %), accelerating the TCA cycle for efficient pollutant mineralization. Key mechanisms included EPS-mediated stress resistance, microbial synergy, and robust metabolic activity. These findings highlight ABSF as a sustainable solution for refractory industrial wastewater, combining high treatment efficiency with resource recovery potential, offering both environmental and economic benefits.},
}

@article {pmid41005089,
year = {2025},
author = {Wu, R and Wang, H and Zou, D and Zhu, M and Xia, H and Wang, Y and Zhu, Y and Huang, L and Liu, L and Du, S},
title = {Herbicide enantiomer selectivity drives soil heavy metal bioavailability: An "Investment-Return" framework in plant-soil-microbe symbiosis.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139944},
doi = {10.1016/j.jhazmat.2025.139944},
pmid = {41005089},
issn = {1873-3336},
abstract = {The co-contamination of heavy metals (HMs) and herbicides in agricultural soils presents a significant environmental challenge, with stereoisomeric herbicides' impact on HMs availability remaining poorly understood. Here, we elucidated how napropamide (NAP) stereoisomers differentially modulate soil HM availability in plant-soil-microbe symbiosis, deciphering the "black-box" mechanisms. Interestingly, diametrically contrasting effects of R- and S-NAP on soil HMs availability were observed between the isolated "soil" and the "plant-soil" system, implicating root-mediated regulation of isomer-specific activities. Specifically, S-NAP reduced the secretion of menthane monoterpenoids and benzoyl derivatives by the roots, which subsequently increasing soil dissolved organic nitrogen (DON). Additionally, there are two plant adaptive strategies: (1) a resource allocation trade-off via "Cost by plant-HMs deactivation" dimension, where reduced exudate investment by S-NAP diminished the return and activated soil HMs; (2) an ecological adaptation via "DON-plant growth" dimension driven by root exudates recruiting bacteria (such as Labilithrix), enhancing growth resilience. These findings establish a novel plant-driven "investment-return" trade-off framework for soil HMs activation. It is crucial for predicting environmental risks of chiral herbicides in co-contaminated farmlands, thereby informing targeted strategies to mitigate HM bioavailability. This study provides theoretical insight into plant adaptation mechanisms under composite pollution and offering a foundation for future safe agricultural production.},
}

@article {pmid41005008,
year = {2025},
author = {Jia, R and Xiao, CX and Zhang, YH and Hu, LY and Jun-Jun, Y and Zuo, R and Hu, YF and Xie, YH and Ma, XL and Li, Q and Hou, KJ},
title = {Microbiota in drug resistance.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {84},
number = {},
pages = {101311},
doi = {10.1016/j.drup.2025.101311},
pmid = {41005008},
issn = {1532-2084},
abstract = {Drug resistance, particularly those of anticancer drugs and antibiotics, poses a significant challenge in the treatment of diseases, severely compromising therapeutic efficacy and patient survival rates. In recent years, an increasing number of studies have highlighted the dual role of microbiota in either promoting or mitigating drug resistance. The microbiome exists in symbiosis with the host, playing a crucial role in maintaining physiological functions and regulating immune responses. However, dysbiosis within the microbial community may induce or exacerbate drug resistance. While antibiotic-mediated depletion of gut microbiota has been proposed as a strategy to combat resistance, it may paradoxically lead to increased resistance or even worsen treatment outcomes. In this review, we focus on anticancer and antimicrobial agents as representative examples to elucidate the association of microbiome and drug resistance. We provide a detailed discussion on the mechanisms by which microbial dysbiosis contributes to development of drug resistance. Additionally, we systematically summarize the latest advancements in microbiota-targeted therapeutic strategies aimed at overcoming resistance, including fecal microbiota transplantation, probiotics and prebiotics, and bacterial engineering approaches. Finally, we discuss the potential clinical applications of microbiota-modulating strategies for overcoming drug resistance and examine the current challenges and future research directions in this field.},
}

@article {pmid41004340,
year = {2025},
author = {Ali, H and Khan, F and Xuan, W and Liu, Y and Huang, Y and Whitfield, D and Pang, L and Chen, P},
title = {Neuropeptide adrenomedullin remodels stemness and macrophage dynamics in glioblastoma.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116342},
doi = {10.1016/j.celrep.2025.116342},
pmid = {41004340},
issn = {2211-1247},
abstract = {The presence of self-renewing glioblastoma (GBM) stem cells (GSCs) and infiltrating pro-tumor macrophages constitutes two key hallmarks of GBM. Here, we identified the neuropeptide adrenomedullin (ADM) as a key factor regulating GSC-macrophage symbiosis. Epidermal growth factor receptor (EGFR) overexpression upregulates ADM in GSCs to enhance their self-renewal, glycolysis, and tumor growth by activating the signal transducer and activator of transcription 3 (STAT3) pathway. GSC-secreted ADM promotes macrophage infiltration and pro-tumor reprogramming through activation of ADM receptor (ADMR), thereby engaging both STAT3 and STAT6 pathways. In GBM mouse and patient-derived xenograft (PDX) models, inhibition of the ADM-ADMR axis, STAT3, or STAT6 suppresses tumor progression, GSC self-renewal, and pro-tumor macrophage abundance, with dual inhibition of STAT3 and STAT6 leading to durable complete tumor regression in a subset of tumor-bearing mice. In human GBM tumors and plasmas, ADM correlates positively with GSC stemness, pro-tumor macrophage abundance, and poor prognosis. These findings highlight ADM-triggered GSC-macrophage symbiosis as a promising therapeutic target for GBM.},
}

@article {pmid41004244,
year = {2025},
author = {Kantnerová, V and Škaloud, P},
title = {The diverse world within: Age-dependent photobiont diversity in the lichen Protoparmeliopsis muralis.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf096},
pmid = {41004244},
issn = {1574-6941},
abstract = {Understanding the initial formation and development of lichens is crucial for elucidating the mechanisms behind the formation of complex lichen thalli and their maintenance in long-term symbioses. These symbiotic relationships provide significant ecological advantages for both partners, expanding their ecological niches and allowing them, in many cases, to overcome extreme environmental conditions. The correct development of thalli likely relies on the selection of suitable photobionts from the environment. In this study, we focused on the impact of lichen age on the overall diversity of photobiont partners and examined how mycobiont preference toward their symbionts changes at different developmental stages. Using the lichen Protoparmeliopsis muralis as a model organism, we observed a strong correlation between the diversity of photobionts and lichen age, confirmed by both molecular data and morphological observations. Our findings indicate greater photobiont diversity in older thalli, suggesting that lichens retain the majority of algae they collect throughout their lifespan, potentially as an adaptation to changing environmental conditions. Additionally, we found that some lichen samples contained only low levels of Trebouxia algae, indicating that P. muralis does not consistently rely on this typical partner and that local environmental conditions may significantly influence its symbiotic composition.},
}

@article {pmid41003701,
year = {2025},
author = {Wei, L and Peng, Y and Mao, J and Hu, Q},
title = {Adaptive Evolution in the Mammalian Gut Microbiota: Insights and Discoveries.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {525},
pmid = {41003701},
issn = {1432-0991},
support = {KJZD-K202302801//Key Scientific and Technological Research Project of Chongqing Municipal Education Commission/ ; ygzrc2024104//Scientific Research Project of Chongqing Medical and Pharmaceutical College/ ; ygzrc2024108//Scientific Research Project of Chongqing Medical and Pharmaceutical College/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Mammals/microbiology ; *Biological Evolution ; *Bacteria/genetics/classification ; Humans ; Symbiosis ; Host Microbial Interactions ; Selection, Genetic ; },
abstract = {The gut microbiota is inextricably linked to the host over a long evolutionary process, and the mammalian gut microbiota is the result of the interaction between bacterial species and the host. It plays a vital role in the digestion and absorption of the host, nutrient metabolism, and immune regulation, and the host genetics, diet, age, antibiotic use, and other factors can also cause changes in the gut microbiota. Natural selection serves to maintain a stable dynamic balance between the gut microbiota and the host over an extended period, and the symbiotic system formed by the microbiota and the host under this dynamic equilibrium can clearly indicate the transmission mode of the gut microbiota during the evolutionary process. Hence, the function, influencing factors, and recent advances in the evolution of the gut microbiota in mammals were reviewed, which provides a reference for a deeper understanding of the interaction between the gut microbiota and the host.},
}

*Gastrointestinal Microbiome
Animals
*Mammals/microbiology
*Biological Evolution
*Bacteria/genetics/classification
Humans
Symbiosis
Host Microbial Interactions
Selection, Genetic

@article {pmid41003514,
year = {2025},
author = {Davis, AB and Evans, M and McKindles, K and Lee, J},
title = {Co-Occurrence of Toxic Bloom-Forming Cyanobacteria Planktothrix, Cyanophage, and Symbiotic Bacteria in Ohio Water Treatment Waste: Implications for Harmful Algal Bloom Management.},
journal = {Toxins},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/toxins17090450},
pmid = {41003514},
issn = {2072-6651},
mesh = {Ohio ; *Bacteriophages/genetics/isolation & purification ; *Cyanobacteria/virology/genetics/growth & development ; Water Purification ; *Harmful Algal Bloom ; Symbiosis ; Lakes/microbiology ; Water Microbiology ; },
abstract = {Cyanobacterial blooms are increasingly becoming more intense and frequent, posing a public health threat globally. Drinking water treatment plants that rely on algal bloom-affected waters may create waste (water treatment residuals, WTRs) that concentrates contaminants. Source waters may contain harmful cyanobacteria, cyanophages (bacteriophages that infect cyanobacteria), and bacteria. Cyanophages are known to affect bloom formation and growth dynamics, so there is a need to understand viral-host dynamics between phage and bacteria in these ecosystems for managing cyanobacteria. This study isolated and characterized lytic cyanophages from WTRs of a HAB-affected lake in Ohio that infect toxic bloom-forming filamentous cyanobacteria Planktothrix agardhii. Phage infections in the Lake Erie cyanobacteria culture were examined visually and via microscopy and fluorometry. Whole genome sequencing and metagenomic analyses were also conducted. Observed changes in Planktothrix included sheared and shriveled filaments, reduced clumping, and buoyancy changes. Photosynthetic pigmentation was unexpectedly more apparent during phage infection. Metagenomic analyses identified nineteen phages and seven other co-existing bacterial genera. Annotated bacterial genomes contained metabolic pathways that may influence phage infection efficiency. Viral genomes were successfully tied to microbial hosts, and annotations identified important viral infection proteins. This study examines cyanobacterial-phage interactions that may have potential for bioremedial applications.},
}

Ohio
*Bacteriophages/genetics/isolation & purification
*Cyanobacteria/virology/genetics/growth & development
Water Purification
*Harmful Algal Bloom
Symbiosis
Lakes/microbiology
Water Microbiology

@article {pmid41003223,
year = {2025},
author = {Baeza-Guzmán, Y and Vásquez-Jiménez, MS and Morgado-Viveros, E and Sánchez-Landero, LA and Trejo-Aguilar, D},
title = {Ectomycorrhizal Fungi Associated with Pinus cembroides subsp. orizabensis, an Endemic Pine in the Arid Zones of the Oriental Basin, Puebla, Mexico.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090677},
pmid = {41003223},
issn = {2309-608X},
abstract = {Ectomycorrhizal fungi (EMF) associated with the roots of Pinus cembroides subsp. orizabensis, a key pinyon pine species for local forestry in the Oriental Basin, Puebla, Mexico, were identified and analyzed. The study aimed to evaluate the diversity of EMF in this endemic pine across three sampling transects (T1, T2, T3), each located in sites with different vegetation compositions and pine cover. In each site, a 100 m × 25 m transect was established, and root tips colonized by EMF were collected for morphological and molecular identification. Alpha (α) and beta (β) diversity were calculated for each transect. A total of 16 EMF morphotypes were identified, and molecular analysis confirmed four taxa: Geopora arenicola, Rhizopogon aff. subpurpurascens, Tomentella sp. 1, and Tricholoma sp. 1. The transect with the highest P. cembroides cover showed the greatest fungal richness. Beta diversity, as measured by Sørensen index partitioning, revealed a 30% species turnover between T1 and T2 and a 60% turnover between T2 and T3, suggesting distinct fungal communities. In contrast, no turnover but a nested pattern was observed between T1 and T3, indicating that the less diverse community is a subset of the richer one. These results show that EMF composition varies with pine cover and vegetation heterogeneity, highlighting the influence of disturbance on fungal diversity. This is the first report of EMF fungi associated with Pinus cembroides subsp. orizabensis, as well as the first record of G. arenicola in arid pine forests in Mexico.},
}

@article {pmid41003167,
year = {2025},
author = {Qi, J and Li, XZ and Zhang, M and Liu, Y and Wang, ZX and Tang, C and Xing, R and Vadim, K and Li, M and Li, Y},
title = {Haplotype-Phased Chromosome-Level Genome Assembly of Floccularia luteovirens Provides Insights into Its Taxonomy, Adaptive Evolution, and Biosynthetic Potential.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090621},
pmid = {41003167},
issn = {2309-608X},
support = {2021YFD1600401//National Key Research and Development Program/ ; 2024NYGG010//Key Core Technology Research and Development in Shaanxi Province Agriculture/ ; },
abstract = {Floccularia luteovirens is a valuable medicinal and edible ectomycorrhizal fungus that is endemic to alpine meadows on the Qinghai-Tibet Plateau. It is of significant ecological and pharmacological importance. To overcome the genomic limitations of previous fragmented assemblies, we present the first haplotype-phased, chromosome-scale genome of the Qinghai-derived QHU-1 strain using an integrated approach of PacBio HiFi, Hi-C, and Illumina sequencing. The high-contiguity assembly spans 13 chromosomes with 97.6% BUSCO completeness. Phylogenomic analysis of 31 basidiomycetes clarified a historical misclassification by placing F. luteovirens closest to Mycocalia denudata/Crucibulum laeve, thus confirming its distinct lineage from Armillaria spp. through low synteny and divergent gene family dynamics. Analyses of adaptive evolution revealed strong purifying selection and stable transposable elements, suggesting genomic adaptations to extreme UV/cold stress. AntiSMASH identified 15 biosynthetic gene clusters (BGCs), which encode diverse terpenoids (7), NRPS-like enzymes (4), PKSs (2), and a hybrid synthase with unique KS-AT-PT-A domains, which have the potential to generate novel metabolites. This chromosome-level resource sheds light on the genetic basis of F. luteovirens' taxonomy, alpine survival, and symbiotic functions while also unlocking its potential for bioprospecting bioactive compounds.},
}

@article {pmid41003162,
year = {2025},
author = {Zhao, S and Wang, S and Song, Y and Xie, L and Xiao, B and Guo, X},
title = {Arbuscular Mycorrhizal Fungi Promote Soil Respiration Primarily Through Mediating Microbial and Root Biomass in Rocky Desertification Habitat.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090616},
pmid = {41003162},
issn = {2309-608X},
support = {32271722//National Natural Science Foundation of China/ ; 32060281//National Natural Science Foundation of China/ ; 2023J0449//Scientific Research Foundation of Yunnan Provincial Department of Education/ ; },
abstract = {Arbuscular mycorrhizal (AM) fungi can have complicated interactions with plants and soils, which play a critical role in mediating the soil carbon cycle. However, the mechanism by which AM fungi regulate soil respiration is not well documented. This study conducted a completely randomized block-design mesocosm experiment using the inoculation of AM fungi (RI: Rhizophagus intraradices; FM: Funneliformis mosseae) with Fraxinus malacophylla to identify the pathways of AM fungi controlling soil respiration in a rocky desertification habitat. We observed that the average soil respiration rates (3.78 μmol·m[-2]·s[-1]) were significantly higher in two AM fungi inoculation treatments than in the control (2.87 μmol·m[-2]·s[-1]). Soil respiration rates were 1.59-fold higher in RI fungi inoculation and 1.05-fold higher in FM inoculation than in the control. Explanation rates of microbial biomass carbon, biomass nitrogen, and root biomass in RI (57.46-76.49%) and FM (44.81-62.62%) inoculation for soil respiration variation were higher than those in the control (24.51-34.32%). The direct positive pathway of soil respiration was mainly regulated by microbial biomass (59.5%) and root biomass (34.90%), while the indirect positive contributions of soil physicochemical properties (30.00%), colonization level (3.50%), soil microclimate (19.30%), and enzyme activity (3.38%) to respiration dynamics ranked second. Thus, we conclude that soil respiration dynamics can be mainly controlled by AM fungi-mediated changes in microbial and root biomass in rocky desertification areas.},
}

@article {pmid41003088,
year = {2025},
author = {Zhang, T and Zhao, W and Nadeem, M and Zaheer, U and Rui, Y},
title = {Iron-Integrated Nitrogen-Rich Nanocarriers Boost Symbiotic Nitrogen Fixation and Growth in Soybean (Glycine max).},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/nano15181453},
pmid = {41003088},
issn = {2079-4991},
abstract = {Global food security is challenged by population growth and the environmental toll of conventional fertilizers. Enhancing biological nitrogen fixation (BNF) in legumes like soybean (Glycine max) is a sustainable fertilization alternative. This study investigates a graphitic carbon nitride/iron oxide (Fe2O3/g-C3N4 or FC) nanocomposite as a dual-functional fertilizer to improve iron (Fe) nutrition and BNF in soybeans. A pot experiment was conducted using different FC concentrations (10, 100, and 200 mg kg[-1]), alongside controls. Results showed that the 100 mg kg[-1] FC treatment (FC2) was most effective, significantly increasing soybean biomass, nodule number, and nodule fresh weight. The FC2 treatment also enhanced photosynthetic rates and chlorophyll content (SPAD values) while reducing stomatal conductance and transpiration, indicating improved water-use efficiency. Furthermore, FC application bolstered the plant's antioxidant system by increasing the activity of superoxide dismutase (SOD) and peroxidase (POD). Elemental analysis confirmed that FC treatments significantly increased the uptake and translocation of Fe and nitrogen (N) in plant tissues. These findings demonstrate that the FC nanocomposite acts as a highly effective nanofertilizer, simultaneously addressing iron deficiency and boosting nitrogen fixation to promote soybean growth. This work highlights its potential as a sustainable solution to enhance crop productivity and nutrient use efficiency in modern agriculture.},
}

@article {pmid41000969,
year = {2025},
author = {Arnold, MFF and Sankari, S and Deutsch, M and Gruber, CC and Guerra-Garcia, FJ and Beis, K and Walker, GC},
title = {The BacA(SbmA) Importer of Symbiotically Important Legume Nodule Cysteine-Rich Peptides: Insights into Protein Architecture, Function, and Evolutionary Implications.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.17.676847},
pmid = {41000969},
issn = {2692-8205},
abstract = {UNLABELLED: Some legumes encode families of NCR (Nodule-Cysteine-Rich) peptides that cause their rhizobial partners to terminally differentiate during the development of a nitrogen-fixing symbiosis. Sinorhizobium meliloti , whose plant hosts Medicago truncatula and M. sativa express ca . 600 NCR peptides during root nodule development, possesses a symbiotically essential BacA Sm protein that imports certain NCR peptides into the cytoplasm. This import permits proteolytic degradation of the NCR peptides, thereby protecting the endocytosed bacteria from their antimicrobial peptide-like lethality, while also allowing certain NCR peptides to undergo their symbiotically critical interactions with cytoplasmic components, for example heme-sequestration in the case of NCR247. BacA's Escherichia coli ortholog SbmA Ec can restore a wildtype phenotype to a ΔbacA Sm mutant. Our study employed 54 S. meliloti bacA Sm missense mutants (35 to cysteine and 19 to glycine) that we tested for protein production, ability to establish a nitrogen-fixing symbiosis, and their susceptibility to killing by higher levels of the NCR247 and the Bac7(1-35) peptides. We also used the Single Cysteine Accessibility Method to make topological inferences. Our detailed genetic, biochemical, structural, and physiological analyses have revealed that BacA Sm and SbmA homodimers function as finely tuned import machines, whose structures can be relatively easily disrupted by single amino acid changes. Our discovery that several mutations that differentially separate nitrogen-fixation, NCR247 import, and Bac7(1-35) import map to the lining of the peptide-binding cavity in the outward-open SbmA/BacA conformation suggests a molecular explanation the other otherwise paradoxical observation that SbmA/BacAs from pathogens can fully replace BacA Sm , whereas BacAs from other rhizobia cannot.

SIGNIFICANCE STATEMENT: Sinorhizobium meliloti BacA Sm and Escherichia coli SbmA Ec are closely related proteins that function as homodimeric transporters to import peptides and other cargos through the cytoplasmic membrane into the cytoplasm. BacA is critical for S. meliloti to establish a nitrogen-fixing symbiosis with its legume hosts because of its ability to import Nodule Cysteine-Rich (NCR) nodule-specific plant peptides. This import protects the bacteria inside the nodule from the potentially lethal effects of these NCR peptides while also enabling NCRs to make their intracellular interactions that are necessary for symbiosis. Our extensive multidisciplinary studies offer new insights into function of BacA/SbmA transporters and provide a molecular explanation for why BacA/SbmA orthologs from mammalian pathogens can replace BacA Sm but those from other rhizobia cannot.},
}

@article {pmid41000239,
year = {2025},
author = {Ajrithirong, P and Krasaesin, A and Sriarj, W and Gavila, P and Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Samaranayake, L and Porntaveetus, T},
title = {The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2560591},
pmid = {41000239},
issn = {2000-2297},
abstract = {OBJECTIVE: To explore the plaque biofilm microbiome associated with severe dental fluorosis (SF), and to describe its metagenome and metabolome.

METHODS: Sixteen plaque biofilm samples were collected from eight 6- to 15-year-old Thai children with SF and eight age-matched, caries-free and controls. Biofilms were analyzed using shotgun metagenomic sequencing, followed by bioinformatics evaluation.

RESULTS: Taxonomic profiling of biofilms from SF and controls identified a total of 12 phyla and 354 species. While alpha diversity was similar between the groups, beta diversity analysis (P = 0.0010) indicated distinct microbial community structures. LEfSe highlighted key discriminatory taxa: five health-associated species (Actinomyces dentalis, Tannerella sp. HOT 286, Candidatus Nanosynbacter sp, Selenomonas noxia and Treponema sp OMZ 804) were enriched in controls, while Neisseria sicca, known for fluoride-sensitive esterase production, was significantly elevated in SF. Functionally, eight metabolic pathways were altered; three of these (phosphatidylcholine acyl editing, anhydromuropeptides recycling II, ubiquinol-7 biosynthesis), hypothesized to support N. sicca activity, were upregulated in the SF group.

CONCLUSION: SF is associated with a significant shift in the biofilm microbiota, characterized by enrichment of N. sicca and a reduction in health-associated taxa. Altered metabolic pathways supporting N. sicca provide mechanistic insights into its role as a candidate biomarker for fluorosis, warranting further investigation.},
}

@article {pmid40999549,
year = {2025},
author = {Gotze, CR and Tandon, K and Philip, GK and Dungan, AM and Maire, J and Høj, L and Blackall, LL and Oppen, MJHV},
title = {Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {94},
pmid = {40999549},
issn = {2524-4671},
support = {DP210100630//Australian Research Council/ ; },
abstract = {BACKGROUND: The bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience.

RESULTS: Using long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), the latter of which suggests involvement of Endozoicomonas in host 'sex-type' steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses.

CONCLUSIONS: This study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning.},
}

@article {pmid40998528,
year = {2025},
author = {Montero, H and Freund, M and Fukushima, K},
title = {Convergent losses of arbuscular mycorrhizal symbiosis in carnivorous plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70544},
pmid = {40998528},
issn = {1469-8137},
support = {RGY0082/2021//Human Frontier Science Program/ ; 23K20050//Japan Society for the Promotion of Science/ ; //Alexander von Humboldt-Stiftung/ ; },
abstract = {Most land plants form the ancient arbuscular mycorrhizal (AM) symbiosis, while carnivory is a younger trait that evolved in several angiosperm orders. The two biotic interactions similarly help plants acquire mineral nutrients, raising the question of whether they can coexist. However, the mycorrhizal status of carnivorous plants has long remained speculative. We surveyed the occurrence of AM-associated genes across carnivorous plant lineages, performed AM fungal inoculation assays, and microscopically evaluated the patterns of colonization. We found convergent losses of the AM trait either coincident with or predating the emergence of carnivory. Exceptionally, the carnivorous plant Roridula gorgonias retains symbiosis-related genes and forms arbuscules. The youngest carnivorous lineage, Brocchinia reducta, showed signatures of the early stages of AM trait loss. An AM-associated CHITINASE gene encodes a digestive enzyme in the carnivorous plant Cephalotus, suggesting gene co-option. We uncovered a mutually exclusive trend of AM symbiosis and carnivory, with only rare instances of coexistence. These findings illuminate the largely unexplored processes by which plant nutritional strategies evolve and supplant one another over time.},
}

@article {pmid40998411,
year = {2025},
author = {Larsson, EM and Wang, OY and Murray, RM},
title = {A DNA Part Library for Reliable Engineering of the Emerging Model Nematode Symbiotic Bacterium Xenorhabdus griffiniae HGB2511.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00414},
pmid = {40998411},
issn = {2161-5063},
abstract = {Xenorhabdus griffiniae is a bacterium that lives inside the intestine of the entomopathogenic nematode Steinernema hermaphroditum and partners with the nematode to infect and kill insect larvae in soil. The construction of gene circuits, such as reporters, in X. griffiniae would provide tools to study and better understand the symbiotic relationship it has with its host. However, because X. griffiniae is not a model organism, information about gene circuit construction in X. griffiniae is limited. We developed and characterized a DNA part library similar to the CIDAR MoClo extension library for E. coli to allow more efficient construction of genetic circuits in X. griffiniae. TurboRFP expressing strains with different constitutive Anderson promoters and different ribosome binding sites (RBS) were constructed to quantify promoter and RBS strengths in X. griffiniae. Furthermore, two fluorescent proteins sfGFP and sfYFP as well as the bioluminescent luxCDABE operon were added to the part library and successfully expressed in X. griffiniae. We then used the characterized parts of the cell to build and characterize IPTG inducible constructs.},
}

@article {pmid40997807,
year = {2025},
author = {Qian, JM and Li, K and Liu, W and Zhang, J and Wylie, A and Arnall, B and Krzmarzick, MJ and Wang, E and Oldroyd, GED and Bai, Y and Feng, F and Zhang, J},
title = {Chitooligosaccharide receptors modulate root microbiota to enhance symbiosis and growth in Medicago.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.09.045},
pmid = {40997807},
issn = {1879-0445},
}

@article {pmid40997670,
year = {2025},
author = {Cho, HS and Lee, JW and Cha, HE and Seo, J and Lim, SK},
title = {Comparative analysis of skin microbiome across 10 sites in Koreans for forensic applications: a pilot study.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {78},
number = {},
pages = {102706},
doi = {10.1016/j.legalmed.2025.102706},
pmid = {40997670},
issn = {1873-4162},
abstract = {Various microorganisms have a symbiotic relationship with human skin cells, influenced by intrinsic and extrinsic factors. The composition of the human microbiome varies based on the skin site. To investigate the microbial characteristics of different skin sites in Koreans, microbiome samples were collected from the scalp, forehead, cheek, retroauricular crease, cervical vertebrae, axilla, palm, lateral finger, femur, and plantar skin. The concentrations of human and bacterial DNA were quantified, and QIIME2 and MicrobiomeAnalyst platforms were used for microbial analysis. Forehead and cheek microbiome compositions were similar, with higher proportions of Streptococcus than that at other sites. Palm and lateral finger microbiome compositions were also similar, with higher proportions of Haemophilus than that at other sites. Lawsonella was specifically observed on the scalp, while Mycoplasma was found on cervical vertebrae. Staphylococcus, observed on all sites, was particularly predominant on axilla. The microbial composition of plantar was distinct, with no prevalent genus compared to that at other sites. Further research analyzing skin microbiomes from forensic evidence could help identify the origin of skin samples, aiding in crime scene reconstruction. Comparing our findings from Korean participants with international studies, it suggests that expanding research to include diverse populations could reveal regional and national differences in skin microbiomes, providing valuable insights for forensic science.},
}

@article {pmid40997175,
year = {2025},
author = {Panchal, A and Sen, R and Agarwal, R and Rana, A and Raychoudhury, R},
title = {Fungus-farming termites can protect their crop by confining weeds with fungistatic soil boluses.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6767},
pages = {1366-1371},
doi = {10.1126/science.adr2713},
pmid = {40997175},
issn = {1095-9203},
mesh = {Animals ; *Isoptera/microbiology/physiology ; Symbiosis ; *Plant Weeds/growth & development/microbiology ; *Crops, Agricultural/microbiology ; *Soil Microbiology ; *Weed Control/methods ; Soil ; *Ascomycota/growth & development ; },
abstract = {The symbiotic agriculture of fungus-farming termites can collapse if they fail to prevent invading weeds. Previous studies suggest a role for symbiotic fungistatic microbes in bringing about weed control. However, how termites employ these microbes to suppress fungal weeds without affecting the fungal cultivar remains unknown. We show that the fungus-farming termite Odontotermes obesus uses specific behaviors to remove, isolate, and suppress the growth of the fungal weed Pseudoxylaria, primarily by encasing it with soil boluses containing fungistatic microbes. These behaviors efficiently suppress the weed without affecting the crop. This integration of specific behaviors with termite-derived microbes appears to be the proximate mechanism of how microbes are topically used by termites to confine the weed while keeping the crop unaffected.},
}

Animals
*Isoptera/microbiology/physiology
Symbiosis
*Plant Weeds/growth & development/microbiology
*Crops, Agricultural/microbiology
*Soil Microbiology
*Weed Control/methods
Soil
*Ascomycota/growth & development

@article {pmid40994815,
year = {2025},
author = {Bock, B and Scherer, J and Parrish, F and Burnside, J and Rohrer, C and Gehring, C},
title = {A simple protocol for producing axenic seeds of Sorghum bicolor.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40994815},
issn = {2578-9430},
abstract = {Microbes within seeds can confound research on microbial colonization, symbiosis, and pathogenesis. Sterilization of both external and internal seed tissues is therefore essential in certain experiments, but the method must also preserve seed viability. Here, we present a reliable and simple protocol for sterilizing Sorghum bicolor seeds by submerging them in 95% ethanol for 2 minutes followed by 3.75% sodium hypochlorite for 20 minutes. This approach yielded a low contamination rate (2 out of 95 seeds) and a robust median germination rate (63%). Its simplicity, cost-effectiveness, and accessibility make it a practical option for experiments requiring axenic seeds.},
}

@article {pmid40994444,
year = {2025},
author = {He, H and Liu, W and Xu, Y and Fang, X and Zhang, W and Kong, Z and Wang, L},
title = {Nodule-specific AhPUGN1.1 positively regulates nodulation in peanuts.},
journal = {aBIOTECH},
volume = {6},
number = {3},
pages = {542-553},
pmid = {40994444},
issn = {2662-1738},
abstract = {UNLABELLED: Peanut (Arachis hypogaea) is a widely cultivated legume crop that can fix nitrogen by forming root nodules with compatible rhizobia. The initiation and formation of these nodules require complex molecular communication between legumes and rhizobia, involving the precise regulation of multiple legume genes. However, the mechanism underlying nodulation in peanuts remains poorly understood. In this study, we identified a gene associated with nodulation in peanuts, named Peanut unique gene for nodulation 1.1 (AhPUGN1.1). Multiple lines of evidence indicate that AhPUGN1.1 is primarily expressed in peanut nodules. Silencing or knocking out AhPUGN1.1 in peanut resulted in fewer nodules, as well as lower fresh weight and nitrogenase activity, while overexpressing AhPUGN1.1 significantly enhanced nodulation ability and nitrogenase activity. Modulating the expression of AhPUGN1.1 also influenced the expression levels of genes associated with the Nod factor signaling pathway and infection via crack entry. Comparative transcriptome analysis revealed that AhPUGN1.1 likely regulates peanut nodulation by affecting the expression of genes involved in the cytokinin and calcium signaling pathways. Our data thus show that AhPUGN1.1 acts as a crucial regulator promoting symbiotic nodulation in peanuts.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00222-7.},
}

@article {pmid40993906,
year = {2025},
author = {Wang, T and Wu, F and Liu, H and Zhang, X and Zhou, Y and Zhang, S and Yang, P},
title = {Symbiotic Nodulation Enhances Legume Tolerance to Abiotic Stresses: Mechanisms and Perspectives.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70207},
pmid = {40993906},
issn = {1365-3040},
support = {//This study was surpported by the National Natural Science Foundation of China (32430073 to Peizhi Yang, 31772660 to Peizhi Yang and 32472204 to Senlei Zhang) and the Scientific Startup Foundation for Doctors of Northwest A&F University (1090124002 to Ting Wang)./ ; },
abstract = {Abiotic stresses, such as drought, salinity, heavy metal contamination and cold, pose significant challenges to global agriculture, reducing crop productivity and threatening food security. Legume-rhizobium symbiosis not only facilitates biological nitrogen fixation but also improves plant tolerance to abiotic stresses. Nodulated leguminous plants exhibit better growth and improved productivity under abiotic stress conditions. In this review, we highlight recent advances in understanding how symbiotic nodulation mitigates abiotic stresses, focusing on physiological and biochemical responses, as well as molecular pathways. We then discuss future research directions to optimise rhizobial applications for stress-tolerant and climate-adaptive farming systems. Rhizobial inoculation is presented as a promising, sustainable and eco-friendly strategy for mitigating abiotic stresses, offering significant potential for stressed agricultural systems.},
}