@article {pmid41795945,
year = {2026},
author = {Snyder Garneau, RE and Tegeder, M},
title = {S-Methylmethionine Phloem Loading Affects Source-Sink Physiology and Assimilate Partitioning in Nitrogen-Fixing Pea Plants, Resulting in Improved Growth and Seed Protein Yields.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag031},
pmid = {41795945},
issn = {1471-9053},
abstract = {Legumes like pea (Pisum sativum L.) fix atmospheric nitrogen (N) in a symbiosis with bacteria, thus reducing the need for N fertilizer and its negative impact on the environment and human health. In addition, their seeds are a vital source of protein for human diets and animal feed. Legume productivity depends on efficient sulfur (S) partitioning within the plant to support N fixation in nodules and seed protein synthesis. S movement from source leaves to sinks occurs in the phloem, and we tested the hypothesis that phloem loading of the organic S compound S-methylmethionine (SMM) is a key regulatory step controlling sink S supply. In pea plants relying solely on N fixation for N nutrition, expression of an SMM transporter in the leaf phloem enhanced source-to-sink movement of SMM and other S assimilates, resulting in increased nodule number, N fixation, and total plant N. These changes triggered coordinated increases in S, N, and carbon acquisition, metabolism, and partitioning, leading to greater vegetative growth, seed yield, and improved seed protein quantity and quality. Overall, this study identifies source-to-sink transport of SMM as a promising target for improving legume productivity.},
}

@article {pmid41794853,
year = {2026},
author = {Zhang, Z and Yu, L and Wu, C and Guo, J and Zhu, L and Wang, J and Zhou, C},
title = {Soil acidification dismantles a citrulline-mediated microbe-metabolite-host defense axis in watermelon, exacerbating Fusarium wilt.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00951-7},
pmid = {41794853},
issn = {2055-5008},
support = {20250586//where they are referenced/ ; 2023AH020024, gxyq2022053//Natural Science Foundation of Universities in Anhui Province/ ; XK-XJGY003//University-Level Advanced Discipline/ ; DTR2024033//Discipline (Major) Leader Development Program/ ; },
abstract = {Soil acidification disrupts the structure and function of soil microbiomes, resulting in increased vulnerability to soil-borne pathogens. While the link between soil acidification and disease susceptibility is well-established, the mechanisms underlying the suppression of plant defense remain poorly understood. In this study, we found that soil acidification perturbed the co-evolved assembly process of endophytic microbiomes in watermelon roots, leading to the collapse of a critical microbe-metabolite-host defense axis essential for resistance against Fusarium oxysporum f. sp. niveum (FON). Integrated field surveys and multi-omics analyses revealed that acidification-induced dysbiosis in the root endophytic microbiomes, characterized by the depletion of keystone Pseudomonas species (Pseudomonadaceae), strongly correlated with increased Fusarium wilt incidence. Central to this interaction was citrulline, a metabolite produced by root Pseudomonas endophytes that functioned as a symbiotic effector promoting bacterial colonization and a defense modulator inhibiting FON-induced oxidative burst. Disruption of citrulline biosynthesis abolished these protective effects, whereas exogenous citrulline application restored disease resistance. These findings underscored the role of root endophyte-derived citrulline in sustaining microbial fitness and plant defense, revealing a tripartite interaction impacted by soil acidification. Collectively, this study provides insights for developing microbiome-based strategies to enhance sustainable crop protection in degraded agroecosystems.},
}

@article {pmid41794478,
year = {2026},
author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V},
title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118597},
doi = {10.1016/j.foodres.2026.118597},
pmid = {41794478},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.},
}

*Fermentation
*Microbiota
*Kombucha Tea/microbiology/analysis/economics
Food Microbiology
Bacteria/metabolism/classification
Yeasts/metabolism
Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry

@article {pmid41793892,
year = {2026},
author = {Jin, XH and Li, Y and Li, YX and Wang, YC and He, HY and Zhang, HB},
title = {Rhizomorph endophytic bacterial community of Armillaria and growth promotion of Armillaria gallica and Gastrodia elata.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128489},
doi = {10.1016/j.micres.2026.128489},
pmid = {41793892},
issn = {1618-0623},
abstract = {Armillaria is a crucial symbiotic fungus for the late-stage growth of Gastrodia elata corms. We analyzed the bacterial community colonizing the Armillaria rhizomorph through isolation culture and high-throughput sequencing methods. We found that (1) the Armillaria rhizomorphs associated with G. elata contained diverse endophytic bacteria. The core genera included Burkholderia-Caballeronia-Paraburkholderia (10.32%), Alphaproteobacteria_unclassified (9.00%), Bradyrhizobium (7.09%), Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium (5.12%), and Yersinia (3.20%). Factors, such as Armillaria species identity and soil characteristics (pH, AP, and AK), significantly influence the community structure of endophytic bacteria. (2) A total of 49 bacterial strains were isolated from the Armillaria rhizomorph, and the five dominant genera were Pseudomonas (28.57%), Bacillus (22.45%), Viridibacillus (12.24%), Rouxiella (10.20%), and Priestia (8.16%). All the isolated bacterial strains were capable of producing IAA, three strains had potassium hydrolysis ability, and 14 strains exhibited phosphorus solubilization ability. (3) In the interaction experiment between the bacteria and Armillaria gallica YSP2_1, most bacteria inhibited the laccase production and rhizomorph branching of A. gallica, but they were able to increase the biomass of A. gallica. In the triple cocultivation experiment, two bacterial strains, 1YSL_5_Viridibacillus and 1YSL_7_Peribacillus, significantly increased the yield of G. elata tubers. This study indicated that rhizomorph endophytic bacteria could facilitate interactions between Armillaria and G. elata.},
}

@article {pmid41793588,
year = {2026},
author = {Zhou, L and Wang, P and Guo, C and Kuang, T and Chen, X and Zuo, J and Wang, J and Zhao, Z and Zhang, X},
title = {Functional traits shape gut microbial assembly beyond phylogeny in estuarine fish.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41793588},
issn = {1869-1889},
abstract = {Host-specific patterns of symbiotic microbiomes are ubiquitous in nature, yet the intricate interplay among host phylogeny, functional traits, and gut microbiota remains insufficiently explored and debated. In this study, the gut microbiota of 61 fish species inhabiting the sympatric Pearl River Estuary, China, was examined by integrating host phylogeny and functional traits to elucidate the mechanisms underlying microbiota assembly. While substantial interspecies differences in gut microbiota composition were evident, the influence of phylosymbiosis was minimal. Instead, functional traits emerged as pivotal mediators of gut microbiota differentiation, emphasizing their roles in adaptive and ecological functions, such as habitat preferences, feeding strategies, and digestive efficiencies. Clustering and machine learning analyses identified three distinct enterotypes within the fish gut microbiota strongly associated with feeding habits and migratory behaviors. Gut microbiota diverged among fishes differing in estuarine use, feeding strategies, and resilience traits. Functional profiling of the gut microbiota unveiled enterotype-specific metabolic adaptations, encompassing pathways related to nutrient utilization and stress resistance. Notably, redundancy analysis indicated that functional traits-such as eye size, oral gape shape, and gut length-played significant roles in influencing enterotype clustering. Our findings introduce the concept of "functsymbiosis", defined as the functional-trait-driven congruence between hosts and their symbiotic microbiota, indicating that host functional traits, rather than phylogenetic lineage, predominantly govern gut microbiota assembly. This study highlights the complex interactions between host traits and gut microbiota in fish, providing novel insights into the adaptive mechanisms underpinning host-microbiota dynamics and the ecological significance of gut microbiota in shaping host fitness and niche differentiation.},
}

@article {pmid41791334,
year = {2026},
author = {Zhao, J and Li, R and Yang, S and Gou, J and Chen, X},
title = {Elucidating the enzyme-driven degradation of macrolide antibiotics in a bacterial-algal symbiotic system.},
journal = {Journal of environmental management},
volume = {403},
number = {},
pages = {129163},
doi = {10.1016/j.jenvman.2026.129163},
pmid = {41791334},
issn = {1095-8630},
abstract = {With the widespread use of macrolide antibiotics, their presence in aquatic environments has emerged as a significant ecological concern. Clarithromycin (CLA), a representative macrolide antibiotic, was used to investigate the stress response and metabolic degradation dynamics within a bacterial-algal symbiotic system operated in a novel photobioreactor. Ten days before the addition of CLA, the bacterial-algal system was in the period of symbiotic acclimatization and secreted considerable EPS with polysaccharide content as high as 77.84 ± 2.05 mg/g SS, which provided a high density of adsorption sites for CLA. Up to 96.74% of CLA was degraded, 0.89% was adsorbed and 0.23% was accumulated. In this study, three degradation pathways of clarithromycin were hypothesized, with N-desmethyl-Clari, 2-Phospho-Clari and de-desotamine-Clari being the major degradation products. Expression of the specific degradation enzymes phosphotransferase and erythromycin esterase increased by 7.43-fold and 23.55-fold, respectively, compared to the control. Sphingopyxis was the dominant flora. The transcriptomics results showed that the bacterial-algal system resisted stress and degraded CLA through regulatory mechanisms that enhanced energy metabolism, substance exchange, signaling responses and attenuated competitive behavioral processes. In this study, a green and efficient CLA removal method was developed and theoretical support was provided for the treatment of CLA-containing wastewater. This study not only provides a viable and eco-friendly solution for the immediate remediation of clarithromycin-contaminated water but also offers a sustainable microbial-enhanced framework with promising potential for long-term application in the treatment of wastewater containing emerging refractory antibiotics.},
}

@article {pmid41789915,
year = {2026},
author = {Chen, S and Li, Y and Xue, J and Hao, Y and Shaalan, MGA and Ghallab, EHS and Guo, Z and Jin, S and Fang, Y and I M Khater, E and Li, S},
title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Egypt: co-circulation of multiple insect-specific viruses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0213525},
doi = {10.1128/spectrum.02135-25},
pmid = {41789915},
issn = {2165-0497},
abstract = {UNLABELLED: Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganisms. In this study, a total of 654 mosquito samples-encompassing species from the Aedes and Culex genera-were collected from Egypt and subjected to metagenomic sequencing analysis. Over 130 virus species were identified, grouped into 35 families or equivalent taxonomic ranks. Detected ISVs included Culex flavivirus (CxFV), Kustavi Toti-like virus, Hanko Toti virus 5, Culex phasma-like virus (CPLV), Culex Iflavi-like virus 1, Culex Iflavi-like virus 4, Guadeloupe Culex rhabdovirus (GCRV), and Sarawak virus, confirming concurrent ISV circulation in Egyptian mosquitoes. Phylogenetic analyses of these ISVs revealed their closest evolutionary affinities to viral genome sequences originating from the Middle East, Europe, Oceania, and Asia. Specifically, Egyptian CxFV strains exhibited a closer genetic relationship with the tropical lineage within the Latin American/Caribbean/Africa genotype. Furthermore, our study uncovered 10 putative novel viruses, which are distributed across seven viral families: Amagaviridae, Chrysoviridae, Mitoviridae, Totiviridae, Virgaviridae, Narnaviridae, and Orthomyxoviridae. Collectively, our findings emphasize the necessity for more in-depth investigations into arthropod viromes-encompassing both mosquitoes and ticks-in Egypt, as well as in neighboring African and Middle Eastern countries. Such research is critical for enhancing our understanding of viral diversity and evolutionary biology, elucidating their roles in mosquito-pathogen-host interactions, and exploring their potential as biocontrol agents against vector-borne diseases of public health importance.

IMPORTANCE: Mosquito-borne viruses are estimated to cause over 100 million human infections annually, making surveillance of these pathogens increasingly crucial amid growing international travel and trade. Egypt, situated in northeastern Africa, serves as a geopolitical and geographical hub connecting Asia, Europe, and Africa-a unique location that complicates the surveillance of mosquito-borne viruses. Arboviruses persist in nature through cyclical transmission between arthropod vectors (e.g., mosquitoes, ticks, and midges) and susceptible vertebrate hosts. Despite this, systematic investigations into mosquito viromes remain relatively scarce in Egypt. The present study aimed to explore the genetic diversity and evolutionary relationships of mosquito-associated viruses in Egypt using metaviromic sequencing. Our findings significantly expand the current knowledge of both known and previously uncharacterized mosquito-associated viruses in the region, while also providing complete genome sequences of several viruses that may infect arthropods or vertebrates, and potentially interfere with the replication of pathogenic arboviruses.},
}

@article {pmid41788917,
year = {2026},
author = {Cho, H and Glasgow, E and Mukund, V and Boyle, JA and Stinchcombe, JR},
title = {Simulated drought with Polyethylene-Glycol (PEG) decreases above-ground performance and increases nodulation in the legume Medicago lupulina.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {41788917},
issn = {2578-9430},
abstract = {We investigated drought growth responses in Medicago lupulina using PEG to simulate drought stress. We grew Medicago lupulina plants inoculated with Sinorhizobium meliloti in Magenta boxes under randomly assigned treatments: a control, PEG applied to the bottom (PEG added to the bottom-watering container), or PEG applied from the top (PEG poured over the growth media). PEG treatments significantly reduced above-ground growth but unexpectedly increased nodulation. Our results suggest that while PEG effectively simulates drought stress on above-ground growth parameters, it may not accurately simulate drought effects on rhizobial symbiosis.},
}

@article {pmid41788331,
year = {2026},
author = {Li, H and Yang, YY and Chokkakula, S and Sathishkumar, K and Alam, MM and Al-Sehemi, AG and Zhang, X and Chong, S and Jeyaraj, G},
title = {Fungi between threat and promise: global perspectives on health and innovation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743670},
pmid = {41788331},
issn = {1664-302X},
abstract = {Fungi play a dual role as indispensable ecological engineers and as major agents of disease in humans, animals, and plants. Recent estimates highlight their substantial impact, with millions of invasive infections annually and severe agricultural losses threatening food security. At the same time, fungi underpin ecosystem services such as decomposition, soil aggregation, and carbon sequestration, while also serving as prolific sources of enzymes, metabolites, and sustainable biomaterials. Advances in single-cell and spatial omics, cryo-electron microscopy, AlphaFold-based structural predictions, and machine learning applied to biosynthetic gene clusters are transforming the study of fungal pathogenicity, symbiosis, and metabolism. These approaches are shifting fungal research from descriptive biology toward predictive, translational pipelines that connect mechanistic insights to drug discovery, resistance management, and biotechnological innovation. Nevertheless, challenges remain, including antifungal resistance, climate-driven emergence of new pathogens, limited therapeutic options, and bottlenecks in scaling fungal applications for sustainability. Addressing these requires integrated One Health strategies that bridge clinical, agricultural, and environmental perspectives. By uniting structural biology, omics, genome editing, and computational tools within a global framework, fungal biology can be harnessed not only to mitigate emerging risks but also to drive innovations in medicine, agriculture, and green technologies.},
}

@article {pmid41787809,
year = {2026},
author = {Mapari, SV and Gaikwad, SB and Sutar, RR and Patil, RM and Behera, BC},
title = {From Symbiosis to Cytotoxicity: Biosynthesis, Molecular Mechanisms, and Anticancer Potential of Lichen-Derived Depsides and Depsidones.},
journal = {Chemistry & biodiversity},
volume = {23},
number = {3},
pages = {e02921},
doi = {10.1002/cbdv.202502921},
pmid = {41787809},
issn = {1612-1880},
support = {DBTHRDPMU/JRF/BET-20/I/2020/AL/112//Department of Biotechnology, Government of India, New Delhi/ ; },
mesh = {Humans ; *Lichens/chemistry/metabolism ; *Depsides/pharmacology/chemistry/metabolism ; *Lactones/chemistry/pharmacology/metabolism ; *Antineoplastic Agents/pharmacology/chemistry/metabolism ; Symbiosis ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; Animals ; Drug Screening Assays, Antitumor ; Neoplasms/drug therapy/pathology ; },
abstract = {Lichen is a unique symbiotic organism that consists of fungi and photosynthetic algae and or cyanobacteria. They are known for producing a large repository of secondary metabolites, among which depsides and depsidones gain pharmacological interest. This review meticulously examines the anticancer efficacy of lichen-derived depsides and depsidones, with a focus on their chemical composition, biosynthetic pathways, and molecular mechanisms that underpin their antitumor activities across various cancer cell lines. These compounds have shown notable bioactivities, including cytotoxicity, apoptosis, and suppression of critical oncogenic cascades such as cellular proliferation, metastasis, and angiogenesis. In some studies, they have shown their selectivity for malignant cells while having minimal cytotoxicity towards healthy cells. This review also addresses the challenges for isolation and large-scale production of these metabolites and also explores the aspect of chemical synthesis or designing of synthetic analogues to increase stability, potency, and pharmacokinetic profile. In conclusion, this review emphasizes the potential application of depsides and depsidones as natural anticancer drugs, as studies strongly recommend conducting further analysis using laboratory models.},
}

Humans
*Lichens/chemistry/metabolism
*Depsides/pharmacology/chemistry/metabolism
*Lactones/chemistry/pharmacology/metabolism
*Antineoplastic Agents/pharmacology/chemistry/metabolism
Symbiosis
Cell Proliferation/drug effects
Apoptosis/drug effects
Animals
Drug Screening Assays, Antitumor
Neoplasms/drug therapy/pathology

@article {pmid41787564,
year = {2026},
author = {Luo, F and Cai, Y and Cui, Y and He, X and Xu, J and Tang, W and Wang, X and Cai, Y and Xie, H and Chen, W and Li, W and Ding, X},
title = {Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02359-z},
pmid = {41787564},
issn = {2049-2618},
support = {CARS-01-09//the earmarked fund for the China Agriculture Research System/ ; 32260023, 31560041//National Natural Science Foundation of China/ ; 20232ACB205006//Key Project of Jiangxi Natural Science Foundation/ ; },
abstract = {BACKGROUND: Crop wild relatives and their microbiomes are essential for sustainable crop production. However, the co-evolution of wild rice species and their microbiomes remains poorly understood. Herein, we investigated microbiome assembly across 17 wild rice and one cultivated rice species under controlled conditions spanning ~15 million years of evolution.

RESULTS: Our data reveal distinct eco-evolutionary patterns for bacteria and fungi. Host divergence time was the predominant driver of root microbiota structure, outweighing polyploidy and life cycle, and exerted a stronger effect on bacteria than fungi. Bacterial community exhibited a significant phylosymbiosis with its host, but fungi did not. Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased. Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly. Potentially functional taxa, including nitrogen-fixing and methane-cycle bacteria, were differentially enriched across evolutionary time and polyploidization events. Notably, co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution. Using a synthetic community (SynCom) derived from the wild rice core microbiome and four nitrogen-fixing strains enriched in early- and medium-diverging Oryza species, we demonstrated that the SynCom strongly promoted rice growth, with the removal of key members markedly reducing its impact.

CONCLUSIONS: These results reveal co-phylogenetic patterns between Oryza and root-associated bacteria, highlighting the closer functional linkage between rice traits and bacteria than fungi, likely due to their co-evolution. Our findings provide new insights into crop-microbiome symbiosis from an eco-evolutionary perspective and underscore the importance of co-speciating microbiomes from wild relatives in supporting crop growth. Video Abstract.},
}

@article {pmid41786689,
year = {2026},
author = {Bao, X and Hou, B and Guo, Z and Song, L and Chen, H and Zheng, Q and Zhao, Y and Gao, D and Fan, C and Xiong, X and Sun, C and Zhao, J},
title = {Absolute dynamic and relative static: the relationship of glycolysis and OXPHOS in cancer development.},
journal = {Cell death discovery},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41420-026-02992-5},
pmid = {41786689},
issn = {2058-7716},
abstract = {For a significant period following the postulation of the Warburg effect, mitochondrial dysfunction and aerobic glycolysis were commonly accepted as the defining features of cancer. Currently, a deeper understanding of tumor metabolism has demonstrated that the energy phenotype of tumor cells is not solely glycolytic. Most cancer cells possess active mitochondria and still maintain the ability to undergo oxidative phosphorylation (OXPHOS) and utilize the tricarboxylic acid (TCA) cycle to support tumor growth. In this review, we examine the choice of energy supply pathways in tumor cells in both static and dynamic contexts. From a static standpoint, tumors contain cells that rely on glycolysis or OXPHOS for energy supply and demonstrate metabolic heterogeneity. Additionally, the simultaneous operation of glycolysis and OXPHOS establishes metabolic symbiosis. In contrast, cancer cells can also exhibit metabolic plasticity by dynamically shifting between glycolysis and OXPHOS to support tumor growth. This process is influenced by a variety of factors, such as the ever-changing tumor microenvironment, specific biological activities of tumor cells, and the effects of drug therapies. The relationship between glycolysis and OXPHOS suggests that in the process of cancer development, the stable state of energy metabolism is temporary, while the dynamic changes in energy metabolism are eternal, which is in line with the category of dialectical materialism and provides us with a new perspective for treating cancer.},
}

@article {pmid41785622,
year = {2026},
author = {Dörfler, P and Wolffers, M and Eggenberger, U and Kruspan, P and Kuba, M},
title = {Evaluation of alternative bed materials in fluidized bed incineration for ash recycling as supplementary cementitious material.},
journal = {Waste management (New York, N.Y.)},
volume = {215},
number = {},
pages = {115413},
doi = {10.1016/j.wasman.2026.115413},
pmid = {41785622},
issn = {1879-2456},
abstract = {This study evaluates different alternative bed materials, sourced from waste materials, to replace quartz sand in fluidized bed incineration of wood. Using alternative bed materials is not only beneficial in terms of the circular economy, but it also aims at tailoring the chemical and mineralogical composition of the resulting bed ash to enable its use as supplementary cementitious material (SCM) in sustainable cements. Seven alternative bed materials were investigated: Construction and demolition waste fine-fraction (CDW-ff), Electric arc furnace slag (EAF slag), Steel Refinement slag (SR slag), two types of used foundry sands, and Municipal solid waste incineration bottom ash. These materials are likely to present more latent hydraulic or pozzolanic properties than the commonly used quartz sand. The study focuses on (i) the physical and mechanical properties of the alternative bed materials relevant to fluidization, and (ii) their chemical and mineralogical properties relevant for upcycling as SCM. The developed testing scheme involves three stages from the laboratory to the pilot scale. First, materials were characterized using XRF, XRD, and particle analysis, followed by XRD-heating-stage, rotary kiln experiments, and cold-flow fluidization. Finally, the most promising materials (CDW-ff and EAF Slag) were tested in bench scale wood incineration reactors. The produced bed ash contains cement-reactive phases, indicating a high potential for use as SCM. This reuse option will help closing material cycles in the sense of a circular economy. These promising findings should be validated at industrial scale, through cement performance testing and critical evaluation of the composition of the resulting ash regarding heavy metal content.},
}

@article {pmid41785342,
year = {2026},
author = {Qiao, L and Sun, H and Tang, J and Hernández-Reyes, C and Lace, B and Knerr, J and Schulze, E and Lee, T and Keller, J and Libourel, C and Yao, J and Zhao, F and Ni, Y and Jia, Y and Xu, X and Yang, G and Zhang, L and Zhang, Y and Grosse, R and Tian, C and Oldroyd, GED and Delaux, PM and Ott, T and Liang, P},
title = {Nanodomain-localized formin gates symbiotic microbial entry in legume and solanaceous plants.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6789},
pages = {1036-1045},
doi = {10.1126/science.adx8542},
pmid = {41785342},
issn = {1095-9203},
mesh = {*Symbiosis ; *Medicago truncatula/microbiology/genetics/physiology ; *Root Nodules, Plant/microbiology ; *Mycorrhizae/physiology/genetics ; Nitrogen Fixation ; *Solanum lycopersicum/microbiology/genetics ; *Plant Proteins/genetics/metabolism/chemistry ; Plant Root Nodulation/genetics ; Actins/metabolism ; *Microfilament Proteins/metabolism/genetics/chemistry ; },
abstract = {Colonization of plant roots by symbionts requires substantial morphodynamic reorganization. Examples are actin-scaffolded microcompartments called infection pockets formed during root nodule symbiosis (RNS) by legumes. We demonstrate that the actin-binding formin SYFO2 is indispensable for rhizobial infection in Medicago truncatula, where it drives actin polymerization in phase-separated and symbiosis-specific nanodomains. SYFO2 also regulates symbiotically active arbuscules formed during mycorrhizal symbiosis in plants outside the nodulating clade, indicating that it was additionally recruited to promote rhizobial infections in legumes. As part of our aim to enable nitrogen fixation in nonlegumes, we activated endogenous SYFO2 by stably introducing the RNS master regulator NODULE INCEPTION (NIN) into the natural nonhost tomato. This demonstrates the possibility of recruiting arbuscular mycorrhizae-related genes into an engineered nodulation-specific pathway.},
}

*Symbiosis
*Medicago truncatula/microbiology/genetics/physiology
*Root Nodules, Plant/microbiology
*Mycorrhizae/physiology/genetics
Nitrogen Fixation
*Solanum lycopersicum/microbiology/genetics
*Plant Proteins/genetics/metabolism/chemistry
Plant Root Nodulation/genetics
Actins/metabolism
*Microfilament Proteins/metabolism/genetics/chemistry

@article {pmid41784839,
year = {2026},
author = {Dymo, AM and Kozyulina, PY and Dolgikh, AV and Kantsurova, ES and Danko, KV and Pavlova, OA and Leonova, TS and Bovin, AD and Smirnova, NV and Kulesh, PA and Frolov, AA and Dolgikh, EA},
title = {Rhizobial Nod factors modulate reactive oxygen species, jasmonates, and pattern-recognizing receptors to suppress immune response.},
journal = {Plant molecular biology},
volume = {116},
number = {2},
pages = {},
pmid = {41784839},
issn = {1573-5028},
support = {RSF 24-16-00180//Russian Science Foundation/ ; },
mesh = {*Reactive Oxygen Species/metabolism ; *Cyclopentanes/metabolism ; *Receptors, Pattern Recognition/metabolism/genetics ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; *Oxylipins/metabolism ; Symbiosis ; *Plant Immunity ; *Rhizobium/physiology ; *Pisum sativum/microbiology/immunology/genetics/metabolism ; Plant Roots/microbiology/metabolism/immunology ; },
abstract = {Fine-tuning of the immune response plays a key role in legume-rhizobial symbiosis. Rhizobial Nod factors can suppress the defense responses during symbiosis, but the possible mechanisms of such regulation remain poorly understood. Here, we observe that Nod factors effectively suppress the expression of genes encoding defense markers (WRKYs, PRs, PALs), the reactive oxygen species (ROS) formation, and reduce the content of pattern recognition receptor (PRR) LYK9 induced by treatment with deacetylated chitooligosaccharide CO8-DA in pea roots. Since PRR LYK9 may recognize both chitin/COs and peptidoglycan, it likely plays an important role in the activation of defense responses during rhizobial inoculation. To identify potential regulators through which Nod factors suppress the immune response in plants during symbiosis with rhizobia, proteome and transcriptome analyses were performed. This allowed identifying several potential candidates activated by Nod factors, such as superoxide dismutase and catalase enzymes, which prevent excessive ROS accumulation and the development of oxidative stress. We also found ubiquitin ligases and ubiquitin-conjugating enzymes that may target PRRs activated in response to rhizobial inoculation. LYK9 degradation via ubiquitinylation was shown to prevent a hypersensitive response in plants. Nod factors activate enzymes involved in jasmonic acid biosynthesis, which in turn activates the transcription factor ABR1, suppressing the abscisic acid-induced responses and decreasing the immune response. Finally, we showed that LysM-receptor-like kinases PsLYK11/MtLYK11, probable homologs of Arabidopsis AtLYK3 in pea and Medicago, are involved in regulation of the immune response.},
}

*Reactive Oxygen Species/metabolism
*Cyclopentanes/metabolism
*Receptors, Pattern Recognition/metabolism/genetics
Gene Expression Regulation, Plant
Plant Proteins/metabolism/genetics
*Oxylipins/metabolism
Symbiosis
*Plant Immunity
*Rhizobium/physiology
*Pisum sativum/microbiology/immunology/genetics/metabolism
Plant Roots/microbiology/metabolism/immunology

@article {pmid41781251,
year = {2026},
author = {Hasegawa, R and Poulin, R},
title = {Colorful parasites: an overlooked frontier in animal coloration research.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.01.004},
pmid = {41781251},
issn = {1471-5007},
abstract = {The diverse coloration of animals has fascinated researchers over the past centuries. A growing body of evidence has documented the many functions of animal coloration, ranging from mate attraction to predator avoidance. Yet, the adaptive functions of parasite coloration have been largely neglected in this context, despite the fact that many parasites across diverse taxonomic groups exhibit colorful body patterns. In this opinion article, we discuss the potential adaptive functions of color in parasites. We first summarize some potential functions of parasite coloration based on an intensive review of the existing literature. We then propose several possible ecological, evolutionary, and biogeographical hypotheses regarding patterns in parasite coloration and outline future directions for this intriguing study frontier.},
}

@article {pmid41780388,
year = {2026},
author = {Guérineau, M and Mayer, J and Pedehour, P and Poinet, L},
title = {Exploring social acceptability of energy sufficiency policies.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129104},
doi = {10.1016/j.jenvman.2026.129104},
pmid = {41780388},
issn = {1095-8630},
abstract = {Energy sufficiency is increasingly recognized as a crucial component in achieving carbon neutrality and reducing human pressure on natural ecosystems. France has incorporated sufficiency as a key pillar of its energy transition, aiming for a 50% reduction in final energy consumption by 2050. While there is growing interest in sufficiency policies, it remains unclear whether there is social acceptance of the proposed measures. This paper employs an exploratory study and Q-method analysis to investigate the acceptability of sufficiency policies. Three distinct sufficiency strategies are identified: monitored sufficiency, symbiotic sufficiency and governed sufficiency. Our study shows that, while sufficiency measures are conceived as overarching policy tools, their acceptance by populations is far from guaranteed. We demonstrate that the level of acceptability is dependent on a number of individual parameters, including the level of maturity with regard to sufficiency practices, or personal values. Moreover, while policies based on governed sufficiency are more widely accepted, radical measures associated with symbiotic sufficiency appear to face greater resistance. These results offer valuable insights for policymakers seeking to balance political ambition with public acceptance in sufficiency strategies, suggesting that these should be adapted to local contexts and individual capacities.},
}

@article {pmid41780383,
year = {2026},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhancing methane production in anaerobic digestion of food waste by Fe-MOF and Fe-MOF-derived carbon composites: Insights into properties, multi-omics analyses, and mechanisms.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129181},
doi = {10.1016/j.jenvman.2026.129181},
pmid = {41780383},
issn = {1095-8630},
abstract = {In this work, Fe-MOF and Fe-MOF-derived carbon composites (Fe-MDCs) derived at 300, 500, and 700 °C were first applied in anaerobic digestion to achieve efficient renewable energy production from food waste. The enhancement mechanism of methane yield was further explored using metagenomic and metaproteomic analysis. The results showed that compared with the control group, methane yield was enhanced by 9.66%-13.99%, 16.21%-23.56%, and 7.99%-19.84% in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups, respectively. Among them, Fe-MDC-500 possessed superior electronic conductivity and a higher specific surface area, which was beneficial for improving methane production by facilitating interspecies electron transfer and providing abundant surface sites for microbial attachment. Metagenomic analysis demonstrated that the functional microorganisms, key genes related to methane metabolism, and the activity of corresponding coenzymes were increased in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups. The poor syntrophic interaction resulted in the lowest methane yield under Fe-MOF-300 addition. Metaproteomic analysis indicated that the expressions of proteins related to quorum sensing system, transcription, and translation were also up-regulated, indicating that Fe-MDC-500 potentially promoted microbial communication among methanogenic and symbiotic microorganisms, ultimately boosting the metabolic activity of anaerobic digestion system. Meanwhile, the expressions of vital proteins involved in enzyme synthesis and catalytic bioconversion, including RNA polymerase, Ribosome, and Aminoacyl-tRNA biosynthesis, were significantly upregulated. This research clarified the mechanism of exogenous materials enhanced methane production by elucidating the key metabolic pathways and functional genes, which provided valuable insights for optimizing energy recovery system.},
}

@article {pmid41779834,
year = {2026},
author = {Li, M and Li, Y and Mao, SH and Zhang, Z and Chen, C and Nie, X and Liu, X and Wang, H and Liu, X and Zhang, W and Lin, Q and Zhuang, GC and Sun, J},
title = {Intricate chemosymbiosis in a widespread shallow-water thyasirid clam.},
journal = {Science advances},
volume = {12},
number = {10},
pages = {eadw8163},
pmid = {41779834},
issn = {2375-2548},
mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology/physiology/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism ; Ecosystem ; Gills/microbiology ; },
abstract = {Chemosynthetic symbioses between animals and bacteria are common in marine ecosystems, but the symbioses in shallow-water thyasirid clams inhabiting suboxic sediments remain understudied despite their widespread occurrence. Here, we report that the shallow-water thyasirid clam Thyasira tokunagai, dominant in Yellow Sea sediments, harbors sulfur-oxidizing Sedimenticola symbionts in pouch-like structures on the gill; the symbionts exhibit highly consistent genomic content and functionality across the region. Two phylotypes of symbionts are present, differing by a single base in the 16S rRNA gene while sharing key functional genes with minimal differences. Spatial metabarcoding analyses of gills showed that individuals also vary in the level of spatial heterogeneity concerning the two phylotypes. These symbionts exhibit active Calvin cycle gene expressions and close-knit host-symbiont metabolic integration. Furthermore, we estimated the capacity of dissolved inorganic carbon assimilation in the live holobiont by radiocarbon tracing (29.3 ± 8.7 nmol C·clam[-1]·day[-1]). Our findings provide the basis for understanding chemosymbiosis in thyasirid clams, highlight the potential of T. tokunagai as a model for studying symbiosis, and underscore the ecological significance of shallow-water chemosymbioses overall.},
}

Animals
*Symbiosis
*Bivalvia/microbiology/physiology/genetics
RNA, Ribosomal, 16S/genetics
Phylogeny
*Bacteria/genetics/classification/metabolism
Ecosystem
Gills/microbiology

@article {pmid41779084,
year = {2026},
author = {Mallmann, GC and Tomazelli, D and Camargo, LS and da Cruz, SP and de Oliveira Filho, LCI and Sousa, JP and Klauberg-Filho, O},
title = {Risk assessment of fungicides on symbiotic phase of arbuscular mycorrhizal fungi.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {4},
pages = {},
pmid = {41779084},
issn = {1573-3017},
abstract = {UNLABELLED: The widespread use of plant protection products (PPPs) may lead to soil contamination, potentially compromising the symbiotic integrity of arbuscular mycorrhizal fungi (AMF) in agricultural systems. However, the effects of PPPs on AMF are underexplored due to the absence of standardized methodology for ecotoxicological assessments. The objective of this study was to introduce an in vivo method for assessing the effects of PPP pollutants on the AMF symbiotic phase and to evaluate the suitability of this method as an intermediate-tier protocol in risk assessment frameworks. Four tests were conducted using combinations of: (1) Gigaspora albida + Glycine max; (2) G. albida + Urochloa brizantha; (3) Rhizophagus clarus + G. max; (4) R. clarus + U. brizantha). All assays were performed in tropical artificial soil (TAS) under a gradient of chlorothalonil concentrations (0, 12, 18, 24, 36, 48, and 72 mg a.i. kg[-][1]). The evaluated endpoints included total root colonization, percentage of arbuscules colonization, total extraradical mycelial length (ERM), and spore number. All endpoints were sensitive to the presence of PPPs in TAS, with mycorrhizal colonization and ERM being the most sensitive, meeting the validity criteria (CV < 30%). The Inhibitory concentration (IC50) values for all endpoints were higher than the predicted environmental concentrations (PECs). Therefore, this method can be considered suitable as an intermediate-tier protocol, as it exhibits key characteristics of a standardized approach and can be applied to ecotoxicological studies involving other potentially contaminating PPPs, as well as additional classes of environmental contaminants.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10646-026-03059-y.},
}

@article {pmid41776601,
year = {2026},
author = {Hong, W and Long, S and Ashrafizadeh, M and Sethi, G and Duan, C},
title = {From symbiosis to immunity: the evolutionary revival of mitochondrial defense programs in inflammatory diseases.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-026-02736-z},
pmid = {41776601},
issn = {1478-811X},
support = {Nos. 82472182 and 82272252//National Natural Science Foundation of China/ ; CSTB2023NSCQ-MSX0192//General Project of the Chongqing Natural Science Foundation/ ; HBRC202419//Chongqing National Talent Reserve Project/ ; },
}

@article {pmid41776170,
year = {2026},
author = {Hammond, M and Chmelová, Ľ and van Geelen-Kuenzel, NA and Maurya, AK and Ferreira, ER and Puente, V and Cadena, LR and Záhonová, K and Dowle, A and Mottram, JC and Nowack, ECM and Lukeš, J and Yurchenko, V},
title = {Subcellular proteomics reveals a blueprint for endosymbiont integration in trypanosomatid Angomonas deanei.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41776170},
issn = {2041-1723},
support = {25-15298S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 221944/A/20/Z//Wellcome Trust (Wellcome)/ ; SFB1535//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Symbiosis/physiology ; *Proteomics/methods ; *Trypanosomatina/metabolism/microbiology/genetics ; *Protozoan Proteins/metabolism/genetics ; Proteome/metabolism ; Microbodies/metabolism ; Bacterial Proteins/metabolism ; },
abstract = {The acquisition of endosymbionts is a fundamental process that has driven the evolution of eukaryotes. The tree of life is filled with cases of internalised prokaryotes that have become integrated into their hosts, often forming mutually beneficial relationships. The trypanosomatid Angomonas deanei is one such case, harbouring a single β-proteobacterial endosymbiont. This symbiotic relationship is highly advanced, as evidenced by the identification of host-encoded proteins that are targeted to the bacterium and control its division. To deeper understand this integration, we performed an in-depth subcellular proteomic analysis to determine the compartmental localisation of both host and endosymbiont proteins. Our analysis resolved over 5,000 host proteins and over 400 endosymbiont proteins. We used this rich dataset to identify several novel host-encoded proteins targeted to the bacterium, and validated our predictions using genetic manipulations and microscopy. By mapping the localised enzymatic repertoire, we were able to shed light on metabolic interplay between the two organisms. We confirmed an energetic basis for the previously observed association between the host's glycosomes and its endosymbiont, and discovered an interaction between the endosymbiont and the host's acidocalcisomes. This subcellular proteomic dataset provides a comprehensive foundation for future research into the remarkable process of bacterial integration.},
}

*Symbiosis/physiology
*Proteomics/methods
*Trypanosomatina/metabolism/microbiology/genetics
*Protozoan Proteins/metabolism/genetics
Proteome/metabolism
Microbodies/metabolism
Bacterial Proteins/metabolism

@article {pmid41774389,
year = {2026},
author = {Bidvi, S and Choure, R and Padul, M and Jadhav, R and Mandavkar, S and Bhadane, A and Posam, M},
title = {A Bioinformatics Pipeline for Screening Nodule-Specific Cysteine-Rich (NCR) Like Peptides from Trigonella foenum-graecum and Medicago truncatula Genomes.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41774389},
issn = {1867-1314},
support = {IF220359//INSPIRE Fellowship , Department of Science and Technology/ ; },
}

@article {pmid41774148,
year = {2026},
author = {Paraginski, JA and Moraes, MP and Mayer, NA and Bianchi, VJ},
title = {Synergism Between Controlled-Release Fertilization and Microbial Bioinputs Modulates the Morphophysiological Quality of Prunus Rootstock Genotypes.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774148},
issn = {1432-0991},
mesh = {*Fertilizers/analysis ; Genotype ; *Prunus/genetics/microbiology/growth & development ; *Trichoderma/physiology ; *Plant Roots/microbiology/growth & development/genetics ; Bacillus amyloliquefaciens/physiology ; Soil Microbiology ; Symbiosis ; Seedlings/growth & development/microbiology/genetics ; Rhizosphere ; Microbial Consortia ; },
abstract = {The production of high-quality Prunus seedling rootstocks in soilless systems requires optimizing the interaction between genetics, nutrient availability, and rhizosphere microbiology. This study evaluated the morphophysiological response of four peach rootstock genotypes ('Capdeboscq', "Okinawa Roxo", "NR0060408", and "NR0160305") to inoculation with Trichoderma asperellum and a microbial consortium (Bacillus amyloliquefaciens + Trichoderma harzianum), under contrasting doses of controlled-release fertilizer (0 and 4 g dm[- 3] of CRF). Longitudinal analysis (0-120 days) demonstrated that nutrient availability is the primary limiting factor; microbial bioinputs did not compensate for the absence of fertilization due to the metabolic cost of symbiosis. However, under nutrient sufficiency (4 g dm[- 3]), strong synergism was observed. The new selections ("NR0060408" and "NR0160305") exhibited high phenotypic plasticity, maximizing the conversion of biostimulation into shoot biomass and outperforming the "Okinawa Roxo" genotype, which displayed a conservative growth strategy. The Bacillus-Trichoderma consortium was superior to single inoculation in responsive genotypes, potentiating seedling leaf area and height. Furthermore, inoculation promoted the "stay-green" effect, maintaining chlorophyll index stability until the end of the cycle. It is concluded that the use of bioinputs, especially in a consortium, acts as a metabolic catalyst in responsive genotypes, but their efficacy depends on adequate basal nutritional management.},
}

*Fertilizers/analysis
Genotype
*Prunus/genetics/microbiology/growth & development
*Trichoderma/physiology
*Plant Roots/microbiology/growth & development/genetics
Bacillus amyloliquefaciens/physiology
Soil Microbiology
Symbiosis
Seedlings/growth & development/microbiology/genetics
Rhizosphere
Microbial Consortia

@article {pmid41773902,
year = {2026},
author = {Vidal, VM and Montes-Cobos, E and Canto, FB and Bozza, MT},
title = {The different meanings of tolerating the gut microbiome.},
journal = {mBio},
volume = {},
number = {},
pages = {e0173624},
doi = {10.1128/mbio.01736-24},
pmid = {41773902},
issn = {2150-7511},
abstract = {Multicellular life arose in a world dominated by microorganisms, a reality that has imposed a constant and pervasive selective pressure on all subsequent complex organisms. The immune system has been historically defined by its role in pathogen clearance through resistance mechanisms. However, a complementary and equally critical strategy is to enable the peaceful and inevitable coexistence with microorganisms, allowing each host species to shelter a unique associated microbiome. The term tolerance holds multiple meanings in immunology, yet all underlie a balanced and cooperative host-microorganism relationship. Each represents a different aspect of how the immune system limits tissue damage while maintaining functionality in the presence of microbial or inflammatory stimuli. Using the intestinal mucosa as a paradigm, we explore how epithelial barrier integrity, toxin neutralization, tissue repair, and stress response underpin disease tolerance; how microbial exposure calibrates innate immunity via epigenetic and metabolic reprogramming (LPS tolerance); and how the gut microenvironment fosters the generation of tolerogenic antigen-presenting cells and microbe-specific regulatory T cells to enforce immunological tolerance. We further explore how the microbiota itself is a potent inducer of these tolerogenic pathways and highlight IL-10 as a major hub, connecting different tolerogenic circuits. Finally, we examine the hygiene hypothesis, arguing that lifestyle changes during the Anthropocene disrupt these finely tuned tolerance mechanisms, thereby contributing to the rising incidence of immune-mediated diseases. We posit that these tolerance programs are fundamental prerequisites for engendering host-microbiota symbiosis, a relationship forged over millennia of co-evolution and endangered in the contemporary world.},
}

@article {pmid41773510,
year = {2026},
author = {Chakrabarti, D and Paul, A and Molla, F and Bhattacharyya, S and Das, S and Chakraborty, S and Ghosh, D and Biswas, A and Kundu, A and Sinharoy, S and DasGupta, M},
title = {Conserved hinge regions in SYMRK enable release of Malectin-like Domain for symbiont passage during rhizobia-legume symbiosis.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koag053},
pmid = {41773510},
issn = {1532-298X},
abstract = {Symbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in the Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to constitute a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2 enabling cleavage of SYMRK ectodomain for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring ectodomain cleavage. Substitution of either Proline restricted cortical progression of symbionts forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that conservation of distinct Prolines in hinge-regions of SYMRK orthologues in legumes generates a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.},
}

@article {pmid41772922,
year = {2026},
author = {López-Román, MI and De la Rosa, L and Castaño-Herrero, C and Marcos-Prado, MT and Ramírez-Parra, E},
title = {Influence of genetic diversity, drought stress and rhizobial symbiosis on the nutritional quality of common vetch (Vicia sativa L.) grain.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70410},
pmid = {41772922},
issn = {1097-0010},
support = {//This work was supported by grants PDI2021-122138OR-I00, from the Spanish Ministerio de Ciencia e Innovacion (MCIN/AEI/10.13039/501100011033 /FEDER; UE); and by the "Severo Ochoa Program for Centres of Excellence in R&D" (Agencia Estatal de Investigación of Spain, grant CEX-2020-000999-S to the CBGP). CCH is supported by PRE2022-104860 funded by MCIN/AEI. CSIC partially supports open-access publication fees./ ; PDI2021-122138OR-I00//Spanish Ministerio de Ciencia e Innovacion/ ; CEX-2020-000999-S//Agencia Estatal de Investigación of Spain/ ; PRE2022-104860//MCIN/AEI/ ; },
abstract = {BACKGROUND: Legumes are the primary source of plant protein in both human and livestock diets and, therefore, play an essential role in nutrition. Common vetch (Vicia sativa L.) is a grain legume widely used in animal feed. Its nutritional properties, particularly its high protein content, make it an adequate component to enrich feedstuffs. Common vetch, like other legumes, is essential in sustainable agriculture systems in mitigating soil degradation and reducing the need for chemical fertilizers, due to its ability to fix atmospheric nitrogen, but it is increasingly being affected by drought - one of the main environmental factors that reduces its production. The genetic diversity among different varieties and environmental conditions may significantly impact the productivity and nutritional composition of legume grains.

RESULTS: In this study, we explore the effect of intra-species genetic diversity on protein levels, carbohydrates, minerals and the composition of specific nutrients, antioxidants and antinutritional factors. We have also analyzed the impact of drought stress and rhizobial symbiosis on the nutritional quality of vetch grain. Our results indicate that there are specific alterations in the selective enrichment or depletion of certain nutrients and ANFs among the diverse V. sativa accessions that have been analyzed but, interestingly, there are also differences in grain composition under different treatments, such as water deprivation, or in plants that have established rhizobial symbiosis.

CONCLUSION: Our findings suggest that the combined effect of genotype and environment, such as drought or symbiosis, plays an important role in the nutritional composition of the grain legume V. sativa. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid41772829,
year = {2026},
author = {Silva, LMD and Souza, DJ},
title = {Aspergillus conicus Endophyte Improves the Development of Eucalyptus camaldulensis Seedlings In Vitro.},
journal = {Journal of basic microbiology},
volume = {66},
number = {3},
pages = {e70156},
pmid = {41772829},
issn = {1521-4028},
support = {Project 420109/2021-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {*Eucalyptus/microbiology/growth & development ; *Seedlings/microbiology/growth & development ; *Endophytes/physiology/genetics/isolation & purification ; *Aspergillus/physiology/genetics/isolation & purification/classification ; Symbiosis ; Plant Roots/microbiology/growth & development ; Plant Leaves/microbiology/growth & development ; Brazil ; Seeds/microbiology/growth & development ; Indoleacetic Acids/metabolism ; Germination ; Biomass ; },
abstract = {Fungi of the genus Aspergillus promote plant growth and resistance, enhance nutrient uptake, protect plants against pathogens, and increase tolerance to environmental stress. We examined the symbiosis between Aspergillus conicus and seedlings of Eucalyptus camaldulensis, a forest species widely grown in Brazil for its valuable wood and resilience. The fungus was identified as an endophyte of E. camaldulensis seeds grown in Murashige and Skoog basal medium. We observed that inoculated seedlings developed faster than those without the fungus. In xerophilic medium, A. conicus produced abundant spores. Analysis of the internal transcribed spacer region grouped the isolate with other A. conicus species. Seedlings grown on Murashige and Skoog medium with fungal fragments showed significant shoot growth, more leaves, and greater biomass than uninoculated seedlings. Seeds immersed in A. conicus filtrate for 24 h showed less contamination by other fungi and a higher germination rate than those in the control group. Indole acetic acid production was below the detection limit. The fungus was endophytic, extensively colonizing the roots and present in the stems and leaves of inoculated plants. We investigated the implications of this fungal association with E. camaldulensis seedlings and highlighted its potential benefits for plant growth and development.},
}

*Eucalyptus/microbiology/growth & development
*Seedlings/microbiology/growth & development
*Endophytes/physiology/genetics/isolation & purification
*Aspergillus/physiology/genetics/isolation & purification/classification
Symbiosis
Plant Roots/microbiology/growth & development
Plant Leaves/microbiology/growth & development
Brazil
Seeds/microbiology/growth & development
Indoleacetic Acids/metabolism
Germination
Biomass

@article {pmid41772232,
year = {2026},
author = {Tinoco, AI and Henderson, CF and Meier, EK and Swinhoe, N and Cleves, PA},
title = {Efficient genome editing using CRISPR-Cas9 in reef-building corals.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {41772232},
issn = {1750-2799},
support = {2128073//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; },
abstract = {Coral reefs are one of the most biodiverse and productive ecosystems on Earth. However, corals are currently under threat from increasing ocean temperatures driven by climate change. Despite the known importance of these fragile ecosystems, our understanding of the molecular mechanisms driving ecologically important traits has been constrained by a lack of genetic tools for functional characterization. To address this limitation, we have developed straightforward and efficient methods to genetically modify corals and study gene function throughout various life history stages using CRISPR-Cas9-based mutagenesis. In this protocol, we first describe how to spawn and collect gametes from the coral Acropora millepora during seasonal spawning events. Next, we describe a method for microinjection of one-cell coral zygotes with CRISPR-Cas9 reagents. We include considerations about effective single-guide RNA design, methods for identifying successfully injected animals, strategies for rearing mutant larvae and juveniles, and methods for the detection and quantification of genomic modifications. This protocol is currently the only way to perform gene editing in corals and takes ~2-4 weeks to complete and has been successfully applied to study genes controlling heat tolerance in coral larvae and skeleton formation in coral juveniles. These technical advances set the foundation for a new field using reverse genetics to study ecologically important traits in corals, such as the establishment of symbiosis and its breakdown upon heat stress.},
}

@article {pmid41769719,
year = {2026},
author = {Czerwinski, J and Engelmann, D and Mayer, A and Lutz, T and Rubino, L},
title = {Nanoparticle Emissions of Internal Combustion Engines: From Retrospective to Outlook.},
journal = {Chimia},
volume = {80},
number = {1-2},
pages = {29-35},
doi = {10.2533/chimia.2026.29},
pmid = {41769719},
issn = {0009-4293},
mesh = {*Nanoparticles/analysis ; Humans ; *Vehicle Emissions/analysis ; *Air Pollutants/analysis ; Aerosols ; },
abstract = {Nanoparticles (NP) in the sub-micrometer measuring range are invisible. NPs from combustion processes, consisting of carbon, metal and ash nuclei and organic substances, enter the human organism through the olfactory nerves and lungs, where they can have various effects (toxic, carcinogenic, mutagenic), some of which are long-lasting (chronic). These invisible nanoparticles were identified in the second half of the last century. Since then, a great deal of research has been carried out in various fields, and nanofiltration has demonstrated and realised ways of efficiently removing nanoparticles. The greatest progress has been made in the aftertreatment of exhaust gases from combustion engines. Nevertheless, further efforts are needed here, as in other areas such as indoor and outdoor air pollution control. The authors have been involved in important stages of these developments and, in this article, they attempt to provide a brief review and a desirable outlook, along with a few examples. In summary, it can be said that all types of engines and numerous other anthropogenic sources emit harmful nanoaerosols. During the pandemic, it was proven that nanofiltration used for exhaust gas aftertreatment in engines effectively eliminates bio-nanoaerosols, i.e. viruses and larger pathogens such as bacteria, fungi, allergens and others. We are all constantly surrounded and permeated by nanoaerosols and must live in symbiosis with them. It is therefore advisable for society to gain a better understanding of this issue, take it seriously and be even more concerned about the quality of the air surrounding the general population.},
}

*Nanoparticles/analysis
Humans
*Vehicle Emissions/analysis
*Air Pollutants/analysis
Aerosols

@article {pmid41769655,
year = {2026},
author = {Ray, S and Shankaran, P},
title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1761992},
pmid = {41769655},
issn = {2296-861X},
abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.},
}

@article {pmid41769401,
year = {2026},
author = {White, E and Ruggeri, M and Weis, VM},
title = {Heterotrophy and symbiosis affect energy reserves for pedal lacerates in the sea anemone Exaiptasia diaphana.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20851},
pmid = {41769401},
issn = {2167-8359},
mesh = {Animals ; *Symbiosis/physiology ; *Sea Anemones/physiology/metabolism/growth & development ; *Heterotrophic Processes/physiology ; *Energy Metabolism/physiology ; Dinoflagellida/physiology ; },
abstract = {Nutrient exchange between corals and their dinoflagellate symbionts is the foundation of the stable symbiosis that underpins coral reef ecosystem success. The cnidarian-dinoflagellate holobiont engages in both autotrophy (photosynthates supplied by the symbiont) and heterotrophy (feeding by the host on microscopic organisms and particulate matter) to meet their nutritional demands. While considerable research has been devoted to understanding nutrient dynamics in adult corals and other symbiotic cnidarians, less is known about how the combination of heterotrophy and autotrophy influences nutrition within and across generations. We investigated the role of symbiosis and heterotrophy in the sea anemone Exaiptasia diaphana (commonly called Aiptasia), a model system for the study of coral symbiosis. We examined how different feeding regimens affected parental growth and how nutritional status of the adult influenced nutrition of asexual offspring (pedal lacerates). After one-month, heterotrophic feeding resulted in larger pedal disk sizes in aposymbiotic adults regardless of lighting. However, in symbiotic groups, a lack of heterotrophy and/or autotrophy resulted in almost no growth or a decrease in body size. This suggests that symbiosis incurs a cost on the host when it is deprived of multiple food sources, and that autotrophy needs to be paired with heterotrophy for significant growth to occur in symbiotic adults. In pedal lacerates, we found that heterotrophic feeding and symbiotic state have an interactive effect on metabolite abundance. Symbiotic lacerates with access to food and light had significantly greater carbohydrates compared to all other groups, suggesting that the symbionts require both to produce carbohydrates in high quantities. Lipid content varied by symbiotic state, with aposymbiotic lacerates having more total lipids, while symbiotic lacerates had more nutrient-rich neutral lipids, indicating that symbiosis alters the production and abundance of different lipid classes. Symbiosis and heterotrophy significantly increased total protein in lacerates. Our results show that the combination of heterotrophy and autotrophy greatly increases growth rate and the abundance of carbohydrates and protein in symbiotic cnidarians, but nutritional lipids only differ based on symbiotic state, which suggests that the symbionts greatly increase the overall metabolic pool of the holobiont. In addition, our results show that there is a cost to hosting symbionts when autotrophy and/or heterotrophy are removed. This highlights the importance of heterotrophy in the success of symbiotic cnidarians within and across generations.},
}

Animals
*Symbiosis/physiology
*Sea Anemones/physiology/metabolism/growth & development
*Heterotrophic Processes/physiology
*Energy Metabolism/physiology
Dinoflagellida/physiology

@article {pmid41768381,
year = {2025},
author = {Titus, KR and Castellon, R and Washington, C and Cooper, J and Grupstra, C and Bloomberg, J and Coy, SR and Farmer, BH and Karrick, CE and Meiling, S and Quetel, J and Rossin, AM and Veglia, A and Watkins, J and Evans, K and Apprill, A and Holstein, DM and Mydlarz, L and Brandt, M and Correa, AMS},
title = {Caribbean fish feces are an environmental hotspot of viable Symbiodiniaceae.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715855},
pmid = {41768381},
issn = {1664-302X},
abstract = {Approximately 85% of stony coral species initially acquire their nutritional symbionts (Family Symbiodiniaceae) from the environment (horizontal transmission). Recent studies have identified live Symbiodiniaceae cells in the feces of coral-eating (corallivorous) and herbivore/detritivore fish, and thus these fish could vector Symbiodiniaceae to prospective stony coral hosts. However, nearly all data on viable Symbiodiniaceae cell densities in fish feces are from Pacific reefs. This study quantifies the density and diversity of viable Symbiodiniaceae cells in the feces of six Caribbean corallivore and herbivore/detritivore fish species in the U.S. Virgin Islands, enabling comparisons of consumer-symbiont pathways between ocean basins. Caribbean fish feces contained an average of 5 million viable Symbiodiniaceae cells ml[-1], comparable to previously reported values for Pacific corallivores. However, unlike on Pacific reefs, where Symbiodiniaceae cell densities varied in feces by fish trophic group, in the Caribbean, high densities of Symbiodiniaceae cells were documented in fish feces across feeding categories. In Caribbean herbivore/detritivore feces, high Symbiodiniaceae densities likely reflect observed, yet unexpected, feeding by these fishes on corals. Contributions of sloughed diseased coral tissue to detritus on U.S. Virgin Islands reefs may have also increased the number of Symbiodiniaceae cells consumed by detritivorous fishes. Symbiodiniaceae genera Symbiodinium, Breviolum, Cladocopium, Durusdinium, and Fugacium were detected in Caribbean fish feces. These findings demonstrate that corallivore and herbivore/detritivore fish feces constitute environmental hotspots of viable Symbiodiniaceae on Caribbean reefs.},
}

@article {pmid41767969,
year = {2026},
author = {Crust, RM and Fronk, D and Macedo, F and Huynh, BL and Light, SE and Clark, NE and Sachs, JL},
title = {Growth Response of Crop Legumes to Soil Microbiota Is Linked With Soil Nutrients and Planting History.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {2},
pages = {e70130},
pmid = {41767969},
issn = {2575-6265},
abstract = {Soil microbiota provide essential services to plants, but predicting or manipulating these benefits is difficult. Here, we investigated microbial benefits to legume crops at a landscape level to uncover factors that predict those services and can be modified by growers. We sampled cultivated soils across a 1000 km transect of production farms and experiment stations with cowpea cultivation. Bioinoculant practices and crop histories were evaluated. Soils were characterized using bacterial metabarcoding and physicochemical analysis, and soil microbial extracts were created to test the capacity of the microbiota to induce root nodulation and growth effects in six legume cultivars, including cowpea, soybean, and lima bean. Resident soil microbiota enhanced cowpea growth, whereas soybean and lima bean experienced negligible benefits. Grower application of bioinoculants was associated with altered microbial communities and enhanced root nodulation but did not affect crop growth. Soil nutrient makeup was correlated with changes in the resident microbial communities and growth benefits to plants, growth effects that were eliminated in sterile soil inoculation treatments, suggesting that they are microbially mediated. Our findings that both planting practices and abiotic soil factors can indirectly affect plant performance, mediated by restructuring of the soil microbial community, suggest how soils could be inexpensively modified to enhance microbial services.},
}

@article {pmid41766944,
year = {2026},
author = {Ghomshei, M and Abbaspour, KC},
title = {Free will as structured unpredictability: toward a symbiotic human-AI relationship.},
journal = {Frontiers in artificial intelligence},
volume = {9},
number = {},
pages = {1694537},
pmid = {41766944},
issn = {2624-8212},
abstract = {Human history has been shaped by revolutions of varying pace, with artificial intelligence (AI) emerging in mere decades. This paper introduces a preliminary framework for fostering a symbiotic human-AI relationship by integrating human free will into AI systems. We conceptualize free will as 'structured unpredictability' and propose a speculative extension of Shannon's information theory to model its informational contributions. By framing free will as an informational surplus, we envision AI as a mirror and amplifier of human creativity. While theoretical, this framework lays the foundation for future empirical and computational research to preserve human autonomy and diversity in AI-driven systems.},
}

@article {pmid41766386,
year = {2026},
author = {Jenab, K and Alteio, L and Guseva, K and Gorka, S and Darcy, S and Fuchslueger, L and Canarini, A and Martin, V and Wiesenbauer, J and Spiegel, F and Imai, B and Schmidt, H and Hage-Ahmed, K and Pötsch, EM and Richter, A and Jansa, J and Kaiser, C},
title = {Arbuscular mycorrhizal fungal families and exploration-based guilds exhibit distinct responses to long-term N, P and K deficiencies and imbalances.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70969},
pmid = {41766386},
issn = {1469-8137},
support = {Consolidator Grant 819446/ERC_/European Research Council/International ; Cluster of Excellence COE7//Austrian Science Fund/ ; CZ.02.01.01/00/22_008/0004597//Czech Ministry of Education, Youth and Sports/ ; },
abstract = {Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF) and the abundance of exploration-based AMF guilds (rhizophilic, edaphophilic and ancestral) remains largely unknown. We studied a 70-yr nutrient deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty acid biomarkers, alongside soil and plant community properties. Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing up to 50% biomass reduction, particularly when N was abundant. We observed a shift from rhizophilic to ancestral guilds under P deficiency in soil, and under K deficiency in roots. Families within each guild, particularly ancestral, showed differential responses, indicating complementary nutrient specializations at the family level. Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.},
}

@article {pmid41765571,
year = {2026},
author = {Shen, W and Yan, C and Yan, H and Zhou, X and Wang, Y and Yang, X and Peng, X and Gu, S and Wang, D and Feng, K and He, Q and Wang, S and Lu, G and Deng, Y},
title = {Organic fertilization shapes diazotrophic microbiomes in legume and grass rhizospheres of the Qinghai-Tibet Plateau.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {710-718},
doi = {10.1016/j.jes.2025.07.031},
pmid = {41765571},
issn = {1001-0742},
mesh = {*Fertilizers ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Nitrogen Fixation ; Tibet ; Medicago sativa/microbiology ; *Elymus/microbiology ; Poaceae/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {Diazotrophs play a crucial role within the rhizosphere by fixing atmospheric nitrogen and promoting plant growth. However, the diversity of diazotrophic communities and the influences of human activity are largely unclear. This study investigated the composition and structure of diazotrophic communities associated with two Plateau forage plants, Medicago sativa (M. sativa) (legume) and Elymus sibiricus (E. sibiricus) (grass), in response to organic fertilizer application. The epicPCR method, which fuses nifH and 16S rRNA genes from individual cells, identified 347 diazotrophic species in the rhizospheres of these two forages, revealing a relatively limited but dominant nitrogen-fixing capacity within the whole bacterial community. Diazotrophic diversity and community structure analyses revealed significant differences between legume and grass rhizospheres (p < 0.05). Only M. sativa exhibited a significant correlation between its growth characteristics (height, fresh weight, and dry weight of plants) and diazotrophic community under natural conditions, suggesting a solid symbiotic and promoting relationship. Organic fertilizer application had differential impacts on diazotrophs. It significantly altered the diazotrophic structure in the legume rhizosphere, notably suppressing the relative abundance of Rhizobium while increasing Pantoea, with no significant effect observed on the grass rhizosphere. Therefore, organic fertilizer application disrupted the natural symbiotic relationship between diazotrophs and legume, but had little impact on the relationship between diazotrophs and grass. This study provided crucial insights into the ecological implications of organic fertilizer application and highlighted the complex influences of plant-microbe interactions in the soil ecosystem.},
}

*Fertilizers
*Rhizosphere
*Microbiota
*Soil Microbiology
Nitrogen Fixation
Tibet
Medicago sativa/microbiology
*Elymus/microbiology
Poaceae/microbiology
RNA, Ribosomal, 16S

@article {pmid41765453,
year = {2026},
author = {Arashida, H and Maita, H and Sato, S and Minamisawa, K},
title = {Genome Plasticity Depends on Positions both Inside and Outside of the Symbiosis Island of Bradyrhizobium diazoefficiens.},
journal = {Microbes and environments},
volume = {41},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME25074},
pmid = {41765453},
issn = {1347-4405},
mesh = {*Bradyrhizobium/genetics/physiology ; *Symbiosis/genetics ; *Genome, Bacterial ; *Genomic Islands ; DNA Transposable Elements ; Recombination, Genetic ; Genomic Instability ; Bacterial Proteins/genetics ; },
abstract = {Insertion sequences (ISs) are major drivers of genomic plasticity in rhizobia, frequently promoting local recombination events. To quantitatively compare the stability of genomic regions inside and outside of the symbiosis island, we engineered Bradyrhizobium diazoefficiens USDA122 mutants carrying a sacB/aadA counter-selectable cassette at four distinct loci-three on symbiosis island A (SymA) and one in the core genome. During 5 days of saprophytic growth, cassette deletion occurred at frequencies of up to 1.77×10[-3] within SymA, whereas the deletion rate in core genomic regions was markedly lower (3.29×10[-6]). Within SymA, cassettes inserted adjacent to the nif and rhc clusters, where IS copies with the same orientation were enriched, were lost more frequently than those placed in other SymA regions, indicating marked intra-island variability in genomic stability. Similar yet overall lower deletion frequencies were observed in B. diazoefficiens USDA110. These results demonstrate that SymA contains genomic loci with greater susceptibility to IS-mediated rearrangements and also that such recombination events may contribute to the diversification of Bradyrhizobium symbiosis islands. Based on our comparative IS mapping in B. japonicum and B. ottawaense, we discuss the potential for the IS-mediated deletion of genome regions harboring nod genes.},
}

*Bradyrhizobium/genetics/physiology
*Symbiosis/genetics
*Genome, Bacterial
*Genomic Islands
DNA Transposable Elements
Recombination, Genetic
Genomic Instability
Bacterial Proteins/genetics

@article {pmid41765452,
year = {2026},
author = {Konno, Y and Imamura, I and Nemoto, T and Kajiwara, M and Ohtsubo, Y and Itakura, M and Sakai, T and Mitsui, H and Minamisawa, K and Sugawara, M},
title = {Symbiosis Islands of Bradyrhizobium Determine Relationships with Host Legumes Lespedeza cuneata and Glycine max.},
journal = {Microbes and environments},
volume = {41},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME25072},
pmid = {41765452},
issn = {1347-4405},
mesh = {*Bradyrhizobium/genetics/classification/isolation & purification/physiology ; *Symbiosis ; *Glycine max/microbiology ; Phylogeny ; Root Nodules, Plant/microbiology ; RNA, Ribosomal, 16S/genetics ; Nitrogen Fixation ; *Fabaceae/microbiology ; DNA, Bacterial/genetics/chemistry ; Japan ; Sequence Analysis, DNA ; Host Specificity ; },
abstract = {Symbiotic N2-fixing bradyrhizobia nodulate various leguminous plants and possess a large symbiosis island (SI) encoding symbiotic functions in their genomes. We obtained 30 rhizobial isolates from root nodules of the tribe Desmodieae of native leguminous plants in northern Japan. Based on their 16S rRNA gene sequences, most isolates (24/30=80%) phylogenetically belonged to Bradyrhizobium. Two isolates (LCT1 and LCT2) from Lespedeza cuneata were placed phylogenetically with Bradyrhizobium diazoefficiens USDA110[T], a well-studied soybean (Glycine max [L.] Merr.) symbiont. Genomic comparisons revealed different SIs in the Met-tRNA and Val-tRNA genes on the respective genomes. In contrast, core genomic regions outside the SI regions showed strong collinearity between strains LCT2 and USDA110. Phenotypically, LCT2 formed N2-fixing root nodules on L. cuneata, an original host plant, but not on soybean, whereas USDA110 formed N2-fixing root nodules on soybean, but not on L. cuneata. Therefore, the SI variants were expected to contain the genes responsible for this host specificity. Genes relevant to the type III secretion system (T3SS) showed less homology between LCT2 and USDA110 than nod genes encoding Nod factor biosynthesis. Host plant inoculations with T3SS mutants suggested the involvement of T3SS effectors in differential host specificity. Therefore, the acquisition of distinct SI variants may confer strong host specificity through symbiotic interactions between Bradyrhizobium and host legumes. We discuss the possible pathway of symbiotic bradyrhizobial evolution and its application to the mitigation of greenhouse gas emissions.},
}

*Bradyrhizobium/genetics/classification/isolation & purification/physiology
*Symbiosis
*Glycine max/microbiology
Phylogeny
Root Nodules, Plant/microbiology
RNA, Ribosomal, 16S/genetics
Nitrogen Fixation
*Fabaceae/microbiology
DNA, Bacterial/genetics/chemistry
Japan
Sequence Analysis, DNA
Host Specificity

@article {pmid41764643,
year = {2026},
author = {Zeller, LM and Schorn, S and Nicolas-Asselineau, L and Zopfi, J and Ahmerkamp, S and Schubert, CJ and Lepori, F and Kuypers, MMM and Graf, JS and Milucka, J},
title = {Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag043},
pmid = {41764643},
issn = {1751-7370},
abstract = {Bacterial endosymbionts of the family Ca. Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of ATP, analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes Zug and Lugano (Switzerland) over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundances of ciliates with denitrifying endosymbionts in the water column suggests that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Candidatus Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lakewaters.},
}

@article {pmid41764270,
year = {2026},
author = {Yao, B and Zhu, H and He, X and Yang, W and Luo, C and Li, Y and Yang, A and Zhang, Y and Jiang, L and Li, Y and Guo, L and He, X and Du, Y and Liu, C},
title = {Cascaded regulatory network composed of small RNAs involves in the symbiosis of Panax notoginseng and fungus Acremonium sp. D212.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40644-x},
pmid = {41764270},
issn = {2045-2322},
support = {32260085, 31660501,32570377//the National Natural Science Foundation of China/ ; },
}

@article {pmid41763044,
year = {2026},
author = {Lu, B and Zhao, C and Wang, Z and Zhao, Y and Zhang, J and Yuan, X},
title = {Optimizing red-blue light ratio enhances nutrient and antibiotic removal by an algal-based symbiotic consortium in aquaculture wastewater.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129029},
doi = {10.1016/j.jenvman.2026.129029},
pmid = {41763044},
issn = {1095-8630},
abstract = {Exploring effective techniques for the removal of nutrient and antibiotic contaminants is critical to addressing aquaculture wastewater pollution. A novel approach was adopted in this study, which aimed to optimize the red-blue light ratio specifically to enhance a three-member (algae-bacteria-fungi) symbiotic consortium for efficient pollutant removal. Four systems were evaluated: Chlorella vulgaris monoculture (Strain 1), Chlorella vulgaris + S395-2 (Strain 2), Chlorella vulgaris + Clonostachys rosea (Strain 3), and Chlorella vulgaris + S395-2 + Clonostachys rosea (Strain 4). Results demonstrated that a 5:5 red-blue light ratio provided optimal growth conditions, under which Strain 4 emerged as a stable and highly efficient dominant consortium. This system achieved the highest average removal rates for conventional pollutants, with COD (78.96 ± 3.21%), TN (82.37 ± 5.31%), NH4[+]-N (63.16 ± 4.17%), and TP (84.51 ± 3.71%). Furthermore, under optimal lighting conditions at an antibiotic concentration of 0.25 mg L[-1], Strain 4 exhibited superior removal efficiency for oxytetracycline (OTC, 96.23 ± 2.01%), ciprofloxacin (CPFX, 79.62 ± 5.31%), and sulfamethoxazole (SMZ, 82.16 ± 4.76%). Density functional theory (DFT) calculations revealed that the exceptional degradation performance of OTC was attributed to its moderate amphiphilicity (ω = 1.23 eV, N = 2.79 eV), the narrowest HOMO-LUMO gap (4.28 eV), and abundant distribution of reactive sites. These findings provide valuable scientific insights into pollutant mitigation mechanisms in aquaculture environments.},
}

@article {pmid41762238,
year = {2026},
author = {Phauk, S and Sin, S and Terenius, O},
title = {Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02724-3},
pmid = {41762238},
issn = {1432-184X},
}

@article {pmid41761404,
year = {2026},
author = {Zhang, P and Huang, LT and Yu, XL and Zhang, YY and Liu, S and Jiang, L and Huang, H},
title = {Distinction in Symbiodiniaceae and Bacterial Communities and Symbiodiniaceae Lineage-Specific Transcriptome Underpinning the Superior Heat Tolerance of Intertidal Acropora Corals.},
journal = {Molecular ecology},
volume = {35},
number = {5},
pages = {e70286},
doi = {10.1111/mec.70286},
pmid = {41761404},
issn = {1365-294X},
support = {U23A2035//National Natural Science Foundation of China/ ; 2021-05//National Key Research and Development Program of China/ ; 2024A1515011041//Basic and Applied Basic Research Foundation of Guangdong Province/ ; SCSIO2023QY03//South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; 2023B1212060047//Science and Technology Planning Project of Guangdong Province/ ; },
mesh = {Animals ; *Anthozoa/microbiology/genetics/physiology ; *Transcriptome/genetics ; Symbiosis/genetics ; *Thermotolerance/genetics ; RNA, Ribosomal, 16S/genetics ; *Dinoflagellida/genetics ; Coral Reefs ; *Bacteria/genetics/classification ; Hot Temperature ; },
abstract = {Fine-scale thermal heterogeneity within intertidal and subtidal microhabitats could drive divergence in organismal heat tolerance. Reef corals from the extreme intertidal may hold optimism for the future of coral reefs and give insights into the mechanisms by which coral may persist under future conditions. Here, we compared the thermal sensitivities of intertidal and subtidal Acropora digitifera and evaluated their bleaching phenotypes, transcriptomes, host genetic differentiation and bacterial communities. Results showed that only heat-exposed subtidal corals displayed significantly reduced photochemical efficiency, symbiont densities, pigment and host protein concentrations, suggesting bleaching and host starvation. Despite being genetically similar, heat-exposed subtidal corals mounted stronger immune activation and amino acid degradation but downregulated monocarboxylate transport and calcification compared to intertidal corals. In contrast to the prevalence of Cladocopium in subtidal corals, intertidal corals were dominated by Durusdinium, whose transcriptional signature was characterised by lineage-specific and constitutively high transcript abundance of orthologs involved in stress response, metabolism, photosynthesis, cell cycle and symbiotic interactions. Furthermore, 16S rRNA sequencing demonstrated an origin-dependent bacterial composition, with Endozoicomonas being more abundant and important in co-occurrence networks of intertidal corals. Our findings suggest that distinction in Symbiodiniaceae and bacterial communities and Symbiodiniaceae lineage-specific transcriptional footprint largely underpin the exceptional thermotolerance of intertidal Acropora. Although these corals provide promising avenues for restoration, such a mechanism may bring attention to the risk of using them in selective breeding, particularly given the horizontal transmission of algal symbionts in Acropora.},
}

Animals
*Anthozoa/microbiology/genetics/physiology
*Transcriptome/genetics
Symbiosis/genetics
*Thermotolerance/genetics
RNA, Ribosomal, 16S/genetics
*Dinoflagellida/genetics
Coral Reefs
*Bacteria/genetics/classification
Hot Temperature

@article {pmid41761369,
year = {2026},
author = {Shu, Y and He, Y and Chen, T and Zhou, Y and Liu, Y and Fu, P and Xu, J},
title = {Reconstruction of coral holobionts and elucidation of the causal relationships among symbiodiniaceae, bacteria, and coral through single-cell raman spectroscopy metabolomics.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02338-4},
pmid = {41761369},
issn = {2049-2618},
support = {KYQD_ZR2017212//Research Start-Up Funds from Hainan University/ ; },
abstract = {BACKGROUND: The global decline of coral reefs underscores the urgency of understanding how corals enhance resilience in stressful environmental conditions. As metaorganisms, or holobionts, corals rely on dynamic interactions with their associated microbial communities, with bacterial restructuring proposed as a potential mechanism of holobiont adaptation. Here, we reconstructed coral symbiosis in the bleached tissues of Acropora hyacinthus by introducing beneficial bacteria and thermally domesticated Symbiodiniaceae to assess their roles in bleaching recovery. Raman spectroscopy metabolomics (RS metabolomics) enables in situ detection, providing temporal evidence of metabolic exchange within the tripartite relationship among corals, Symbiodiniaceae, and associated bacteria.

RESULTS: This study highlights the potential of acclimation-based approaches in the development of thermotolerant Symbiodiniaceae strains. Furthermore, by manipulating this bacterial community, we identified a bacterium that enhances the thermal and light tolerances of acclimated Symbiodiniaceae, offering new insights into coral reef homeostasis strategies. Our results also indicate that the introduction of beneficial bacterial strains and thermotolerant Symbiodiniaceae, including proteins, lipids, and carbohydrates, increased nutrient levels in the coral host.

CONCLUSIONS: This work introduces a microbial-assisted holobiont reconstitution framework that advances understanding of cross-kingdom metabolic integration and offers a mechanistic basis for engineering coral resilience under climate stress. The findings could provide insights into leveraging beneficial microbiota to mitigate thermal-induced coral bleaching, ultimately informing conservation strategies for marine ecosystems. Video Abstract.},
}

@article {pmid41760926,
year = {2026},
author = {Wang, Y and Moriyama, M and Koga, R and Oguchi, K and Hosokawa, T and Takai, H and Shigenobu, S and Nikoh, N and Fukatsu, T},
title = {Tryptophanase disruption promotes insect-bacterium mutualism.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {759-769},
pmid = {41760926},
issn = {2058-5276},
support = {JPMJER1902//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; JP25221107//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP17H06388//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22128001//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22128007//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Symbiosis/genetics ; Animals ; *Pantoea/genetics/physiology/enzymology ; Tryptophan/metabolism ; *Escherichia coli/genetics/enzymology/physiology ; *Tryptophanase/genetics/metabolism ; Operon ; Indoles/metabolism ; *Heteroptera/microbiology ; Mutation ; Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Animal-microorganism symbioses are omnipresent, with both partners often gaining benefits as mutualists. A single mutation in the carbon catabolite repression system in Escherichia coli enables mutualism with the stinkbug Plautia stali. Here we find that this mutation is not present in natural symbioses. Given that the carbon catabolite repression pathway affects the expression of >500 downstream genes, we investigated their role in mutualisms. We find that disruption of a single gene, tnaA, encoding tryptophanase makes E. coli mutualistic to P. stali, resulting in the accumulation of tryptophan and the reduction of toxic indole. A survey of wild populations of P. stali and other stinkbug species revealed that their typical microbial symbionts, Pantoea, consistently lack the tnaA gene. Some Pantoea species such as Pantoea ananatis retain the tnaA gene and cannot establish symbiosis with P. stali, but tnaA-disrupted P. ananatis partially restored the symbiotic capability. When a natural Pantoea mutualist of P. stali was transformed with a functional tna operon, its symbiotic capability reduced significantly. Our finding suggests that tryptophanase disruption may have facilitated the evolution of gut bacterial mutualists in insects.},
}

*Symbiosis/genetics
Animals
*Pantoea/genetics/physiology/enzymology
Tryptophan/metabolism
*Escherichia coli/genetics/enzymology/physiology
*Tryptophanase/genetics/metabolism
Operon
Indoles/metabolism
*Heteroptera/microbiology
Mutation
Escherichia coli Proteins/genetics/metabolism

@article {pmid41760915,
year = {2026},
author = {Asari, S and Kodama, Y},
title = {Mitochondrial density and cell area changes in the ciliate Paramecium bursaria under constant darkness: effects of symbiotic Chlorella variabilis and nutrient availability.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41878-5},
pmid = {41760915},
issn = {2045-2322},
support = {Grant-in-Aid for Scientific Research (B) (grant number 23H02529)//Japan Society for the Promotion of Science/ ; SDGs Research Project//Shimane University/ ; },
abstract = {Paramecium bursaria and its symbiotic association with Chlorella variabilis influence host organelles. Previous studies have reported reduced mitochondria and trichocysts in algae-bearing P. bursaria cells, suggesting that the digestion of symbiotic algae may provide nutrients for trichocyst synthesis. However, the response of host mitochondria to symbiont loss under prolonged darkness remains unclear. Here, we examined the mitochondrial dynamics and cell morphology in algae-bearing and alga-free P. bursaria under constant darkness combined with feeding or starvation. Algal reduction was quantified using differential interference contrast image intensity, and host mitochondria were visualized using MitoBright LT Green. Under dark conditions with starvation, symbiotic algae and cell area decreased markedly, whereas mitochondrial fluorescence remained largely unchanged in algae-bearing cells. Gradual loss of algae despite feeding preserved both cell area and mitochondrial density. In alga-free cells, starvation caused early mitochondrial decline, followed by partial recovery, whereas feeding supported maintenance or enhancement. These findings indicate that mitochondrial density does not increase as algae decrease; instead, nutrient availability is critical for sustaining mitochondria in prolonged darkness. Our results provide insights into organelle-level responses to symbiont loss and the mechanisms underlying endosymbiotic resilience under environmental stress, with implications for mutualistic stability in changing ecosystems.},
}

@article {pmid41760845,
year = {2026},
author = {Rípodas, C and Cretton, M and Eylenstein, A and Rivero, C and Zanetti, ME and Blanco, F},
title = {Cullin 3 substrate-adaptor protein 1 (MtCSP1) modulates nodulation through interaction with the GTPase ARFA1.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41112-2},
pmid = {41760845},
issn = {2045-2322},
support = {2020-00053//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2019/00029 and 2021-00170//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
abstract = {Legume plants have the capacity to incorporate atmospheric nitrogen by establishing an endosymbiotic interaction with soil bacteria resulting in the formation of nitrogen-fixing nodules. Bacteria are internalized through a tightly regulated process that requires membrane remodelling and vesicle trafficking, which are controlled by small GTPases. Members of the ARF family of GTPases mediate vesicle budding in a wide range of biological processes; however, the modulation of ARF members, their subcellular localization and the formation of complexes with other proteins during the root nodule symbiosis has not been fully investigated. Here, we identify a BTB/POZ protein that physically interacts with MtARFA1 in a yeast two-hybrid screening. BTB/POZ proteins are present in substrate-specific adaptors that form complexes with the Ubiquitin ligase E3 Cullin3 (CUL3), thus the interactor was designated as M. truncatula CUL3 substrate-adaptor protein 1 (MtCSP1). Physical interaction between MtARFA1 and MtCSP1 was verified in planta by co-immunopurification assays and bimolecular fluorescence complementation, revealing that the interaction takes place in vesicles of the late endosome. The MtCSP1 promoter is active in lateral roots and in the meristem of indeterminate nodules. Phenotypic analysis of transgenic roots with altered mRNA levels of MtCSP1 evidenced the requirement of this gene for the progression of rhizobial infection and nodule organogenesis. This work establishes a link between small GTPases and protein degradation by the ubiquitin system in the context of the nitrogen-fixing symbiosis.},
}

@article {pmid41760692,
year = {2026},
author = {Zhou, C and Zhong, Z and Guo, Y and Yan, Y and Wang, J and Wang, M and Li, C},
title = {Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06755-w},
pmid = {41760692},
issn = {2052-4463},
support = {42376058//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42221005 to WMX//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024YFC2816000//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Solemyidae, an ancient lineage of protobranch bivalves, are characterized by unique morphology and obligate symbiosis with sulfur-oxidizing bacteria, enabling survival in sulfide-rich sediments. However, limited genomic resources have hindered understanding of their evolutionary history, symbiotic interactions, and environmental adaptation. Here, we report a chromosome-level reference genome of Acharax haimaensis, assembled using PacBio, Illumina, and Hi-C sequencing. The 4.27 Gb genome, with a scaffold N50 of 195.52 Mb, was anchored to 22 chromosomes and achieved high completeness (98.2%) based on BUSCO. Transposable elements occupy 50.17% of the assembly, dominated by long interspersed nuclear elements (14.20%). We predicted 38,343 protein-coding genes, of which 87.25% were functionally annotated. Macrosynteny analysis revealed each chromosome comprises two to four segments of ancestral linkage groups, indicating extensive chromosomal breakage and fusion in early bivalve evolution. Phylogenetic inference suggested A. haimaensis diverged from the common ancestor of Autobranchia ~550 Mya. This first deep-sea protobranch genome provides an essential resource for exploring bivalve evolution and the genetic basis of symbiosis and adaptation to extreme environments.},
}

@article {pmid41760684,
year = {2026},
author = {Zhang, J and Tong, Q and Lin, F and An, X and Huang, H and Chen, H and Ye, J and Xu, H and Lv, X and Lv, Z and Zeng, F and Zhang, T and Wu, X and Xie, B and Ming, R and Deng, Y},
title = {Polymorphism and evolutionary origins of accessory chromosomes in the basidiomycete Tremella fuciformis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70078-y},
pmid = {41760684},
issn = {2041-1723},
support = {32472810//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Accessory chromosomes are non-essential for growth but poorly characterized in basidiomycetes, unlike in Ascomycota. Here, we report whole-genome sequencing of 16 strains of the basidiomycete Tremella fuciformis (silver ear fungus), generating 27 complete haplotypes (5 monokaryons and 11 dikaryons, each contributing two distinct haplotypes). Genome size varied by over one-third, driven by accessory chromosomes and repetitive sequences in core chromosomes (essential for basic biology). Each strain harbored 8-10 core chromosomes (polymorphic via fusion/fission) and 2-10 accessory chromosomes (total 108), whose distribution reflects phylogeny and symbiotic specificity with the ascomycete Annulohypoxylon stygium. Accessory chromosomes are small, transposon-rich, gene-poor, and exhibit higher sequence similarity but more diverse structural variations than core chromosomes, with few shared genes across phylogenetic branches. Both chromosome types show frequent copy number variation during cell type transformation. Most accessory chromosome genes lack homologs in core chromosomes or existing gene databases. Our study reveals basidiomycete accessory chromosome diversity, suggesting an origin from unexplored species pre-dating T. fuciformis speciation.},
}

@article {pmid41758921,
year = {2026},
author = {Qu, S and Zhou, G and Chen, Y},
title = {Research on the configurational paths for establishing high-level municipal industry-education consortiums in China: from the perspective of symbiosis theory.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0336145},
pmid = {41758921},
issn = {1932-6203},
mesh = {China ; *Industry ; Humans ; *Symbiosis ; *Education/organization & administration ; },
abstract = {The municipal industry-education consortium(MIEC) is a crucial component of the development of education in China, and the provincial-level administrative regions (PARs) are committed to building high-level MIECs. However, there are significant differences in the efficiency of building MIECs in different regions across China. A province is a macro-level industry-education integration ecosystem, whereas a MIEC is a micro-level ecosystem. Symbiotic units such as industrial parks, universities, and enterprises within the provincial industry-education integration ecosystem(PIEIE) cooperate and exchange resources with each other in institutional, innovative, and digital environments to achieve the symbiotic model of industry-education integration, ultimately forming high-level MIECs. Based on the theory of symbiosis and employed the fuzzy set qualitative comparative analysis (fsQCA), this study analyzed the complex causal mechanisms through which symbiotic elements of PIEIEs influenced the construction of high-level MIECs, using data from the 31 PARs in China, excluding Hong Kong, Macao and Taiwan. This paper found that the development of high-level MIECs was not determined by any single symbiotic element; instead, it resulted from the coordinated development and combined effects of three key symbiotic factors: symbiotic units, symbiotic environment, and symbiotic models. There were six configurational pathways to building high-level MIECs, grouped into three types: the "Economy-Driven" model, the "Digital-Enabled Industry-Education Integration" model, and the "Assistance-Driven" model. The findings provide a theoretical foundation and practical guidance for PARs in developing high-level MIECs.},
}

China
*Industry
Humans
*Symbiosis
*Education/organization & administration

@article {pmid41757865,
year = {2026},
author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y},
title = {Characterization of the dynamic microbiome evolution across thrips species.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70265},
pmid = {41757865},
issn = {1744-7917},
support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; },
abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.},
}

@article {pmid41756731,
year = {2026},
author = {Maxwell, MWH and Fernando, AH and Papp, A and Bell, CA},
title = {Mycorrhizal symbiosis drives tolerance to potato cyst nematodes.},
journal = {iScience},
volume = {29},
number = {3},
pages = {114923},
pmid = {41756731},
issn = {2589-0042},
abstract = {Host plant tolerance to pathogens is increasingly relevant as resistance sources and control options become scarce. Arbuscular mycorrhizal (AM) fungi are known to enhance plant stress tolerance, but it remains unclear whether they are essential for, or complement, innate tolerance. We observed that potato cultivars described as tolerant to G. pallida suffered yield loss under nematode pressure when grown in sterile soils, indicating a lack of tolerance. The introduction of Rhizophagus irregularis increased tuber biomass during nematode parasitism, with cultivars commercially labelled as tolerant exhibiting a stronger response to AM fungi. The data suggest cultivar differences in mycorrhizal responsiveness with the differential expression of a range of plant sugar transporter genes in "tolerant" cultivars inferring a role of sugar allocation in host tolerance. Overall, AM fungi are critical for conferring tolerance against G. pallida and revealing the underpinning genes may provide useful targets to explore in current commercially desirable yet intolerant cultivars.},
}

@article {pmid41756261,
year = {2026},
author = {Cai, X and Hu, X and Yan, F and Chen, D and Xiao, B and Zheng, X and Zhang, K and Zhou, J and Ma, Z and Sun, F and Peng, Y and Ma, X and Paramsothy, J and Xue, R and Liu, L},
title = {Arbuscular Mycorrhizal Fungi Orchestrate Soil Microbial Community Assembly Along a Salix cupularis Restoration Chronosequence in a Desertified Alpine Grassland.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73133},
pmid = {41756261},
issn = {2045-7758},
abstract = {Belowground microbes are emerging targets for ecosystem restoration. Understanding the assembly mechanisms of these microbial communities is critical for predicting ecosystem trajectories and optimizing restoration interventions. Arbuscular mycorrhizal fungi (AMF) are hypothesized to be key drivers of these eco-evolutionary dynamics as a crucial and unique functional group associating with approximately 80% of terrestrial plant species. However, relatively little empirical information is available on the role of AMF in the soil microbial community assembly. Here, we used Salix cupularis, a native pioneer shrub species of desertified alpine meadows, to investigate the temporal dynamics of soil rhizosphere microbial communities across a restoration chronosequence (5, 10, and 20 years), with a particular focus on the AMF community. The results showed that minimal changes occurred in bacterial community structure, whereas fungal community exhibited more pronounced shifts along the chronosequence. Bacterial community assembly was initially deterministic and then became stochastic, while fungal assembly was consistently stochastic. Shrub planting enhanced the complexity of both bacterial and fungal networks over time. Co-occurrence networks and Pearson correlation analysis revealed the "time-dependent" regulatory role of the AMF community in soil microbial assembly. AMF acted as an orchestrator in the 10th year after planting (the edge density of AMF peaking at 15.0) prior to the transition to a stable, ECM-dominated state in response to shifts in soil nutrient availability, particularly significant increases in MAOC and AP, as well as a decrease in DON. Our findings indicate that fungal communities exhibit higher sensitivity and highlight the dynamic regulatory function of AMF, especially under dual-mycorrhizal symbiosis. These results provide novel mechanistic insights into soil microbe trajectories, suggesting that targeted AMF inoculation is crucial for the early-to-mid establishment phase of restoring desertified alpine meadows.},
}

@article {pmid41754250,
year = {2026},
author = {Oliveira, EM and Besen, K and Santos, LCD and Uller, MF and Lovato, PE and Guerra, MP and Mayer, JLS},
title = {Symbiotic Germination in Cattleya purpurata: An Ultrastructural Journey from Fungal Dependence to Autotrophy.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {41754250},
issn = {2223-7747},
abstract = {Orchids depend on mycorrhizal fungi for seed germination, a critical process especially for endangered species such as Cattleya purpurata. This study elucidates the ultrastructural ontogeny of the symbiosis between C. purpurata and the fungus Tulasnella sp. We demonstrate a defined spatiotemporal colonization pattern: hyphae penetrate exclusively via suspensor cells, migrate through the basal region of the embryo, and only then colonize the apical region. Upon colonization, the fungus triggers changes in the embryonic cells, including nuclear hypertrophy and peloton formation. Ultrastructural analysis revealed a sequence of fungal degradation, from intact hyphae to senescent hyphae containing myelin-like bodies and an electron-dense cytoplasm, suggesting that programmed senescence precedes peloton digestion. This supports the novel hypothesis of active fungal participation in modulating its own digestion, challenging classical models. Simultaneously, embryonic cells exhibited rapid metabolic conversion, with the transition from proplastids to amyloplasts, and then to chloroplasts in less than 20 days, marking the onset of autotrophy. This integrated morphological study not only expands fundamental knowledge about symbiotic development in orchids but also provides an optimized protocol for producing symbiotic seedlings, offering a direct tool for the reintroduction and conservation of this species.},
}

@article {pmid41753741,
year = {2026},
author = {Arossa, S and Klein, SG and Alva Garcia, JV and Steckbauer, A and Pluma, N and Genchi, L and Laptenok, SP and Hung, SH and Salazar, OR and Aranda, M and Liberale, C and Duarte, CM},
title = {Differential Responses to Heat Stress Between Freshly Isolated and Long-Term Cultured Symbiodinium.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753741},
issn = {2076-2607},
support = {//King Abdullah University of Science and Technology and the Tarek Ahmed Juffali Research Chair on Red Sea Ecology, including the baseline research funds of CD, MA, and CL./ ; },
abstract = {Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. While laboratory culturing of symbionts has enabled controlled studies of thermal stress, prolonged culturing may lead to physiological changes that do not reflect in hospite conditions. Here, we examined the thermal stress responses of two axenic cultures of Symbiodinium A1, freshly isolated and long-term cultured (2.5 years), originally from the jellyfish Cassiopea andromeda in the Red Sea. Both cultures were exposed to a daily temperature increase of 1 °C, up to 37 °C. Freshly isolated symbionts consistently showed higher photochemical efficiency (0.515 ± 0.007) and growth rates (1.68 ± 0.60 µ day[-1]) compared to long-term cultured cells (0.401 ± 0.007; -2.25 ± 0.38 µ day[-1]), which collapsed at 37 °C. Heat stress also led to decreases in O2 and increases in pCO2 across treatments. Long-term cultured symbionts exhibited greater lipid body accumulation, suggesting a shift to anaerobic metabolism. These findings demonstrate that extended batch culturing alters symbiont physiology and stress responses, highlighting the need to consider culture history in experimental designs to avoid bias in interpreting holobiont resilience.},
}

@article {pmid41753667,
year = {2026},
author = {Li, Y and Vigil, J and Pradhan, R and Zhu, J and Libault, M},
title = {Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753667},
issn = {2076-2607},
support = {2414183//National Science Foundation (NSF)/ ; 2425989//National Science Foundation (NSF)/ ; 2022-67013-36144//USDA National Institute of Food and Agriculture (USDA-NIFA)/ ; },
abstract = {Understanding the intimate interactions between plants and their microbiota at the cellular level is essential for unlocking the full potential of plant holobionts in agricultural systems. Traditional bulk and microbial community-level sequencing approaches reveal broad community patterns but fail to resolve how distinct plant cell types interact with or regulate microbial colonization, as well as the diverse antagonistic and synergistic interactions and responses existing between various microbial populations. Recent advances in single-cell and spatial multi-omics have transformed our understanding of plant cell identities as well as gene regulatory programs and their dynamic regulation in response to environmental stresses and plant development. In this review, we highlight the single-cell discoveries that uncover the plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation, particularly in roots, nodules, and leaves. We further discuss how integrating transcriptomic, epigenomic, and spatial data can reconstruct multilayered interaction networks that connect plant cell-type-specific regulatory states with microbial spatial niches and inter-kingdom signaling (e.g., ligand-receptor and metabolite exchange), providing a foundation for developing new strategies to engineer crop-microbiome interactions to support sustainable agriculture. We conclude by outlining key methodological challenges and future research priorities that point toward building a fully integrated cellular interactome of the plant holobiont.},
}

@article {pmid41752923,
year = {2026},
author = {Gou, S and Zhao, X and Ni, Y and Shi, T and Zhao, Z and Tang, L and Li, W and Wan, Y},
title = {Revisiting the Nutritional Mode of Floccularia luteovirens: A Case for Facultative Saprobic Capacity.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
pmid = {41752923},
issn = {2075-1729},
abstract = {Floccularia luteovirens is a rare and edible fungus endemic to the Qinghai-Tibet Plateau. Traditional viewpoints have inferred it to be a mycorrhizal fungus based on its spatial association with Kobresia, yet direct morphological evidence (e.g., Hartig net) and molecular evidence is lacking. Through a systematic review of the existing literature, this study found that all current evidence supporting a mycorrhizal relationship is merely indirect inference. In contrast, experiments conducted by our research team demonstrated that this fungus colonizes well on sawdust-based substrates, which is compatible with saprobic growth capacity and does not exclude the possibility of conditional mycorrhizal symbiosis in natural environments. Based on these findings, we propose that F. luteovirens may adopt a facultative nutritional mode to adapt to the alpine environment. Genomic analysis revealed that the CAZyme repertoire of F. luteovirens (including key enzyme families such as GH6, GH7, and AA1) shows high similarity to that of the saprobic fungus Agaricus bisporus and appears to be more comprehensive than that of the ectomycorrhizal fungus Boletus edulis, based on current annotation data. This pattern suggests its potential capacity for lignocellulose degradation. The successful cultivation of its closely related species Lepista sordida on various lignocellulosic substrates further supports this functional potential. This study proposes that F. luteovirens employs a 'facultative nutrition' strategy, which presents an alternative perspective to the traditional view of obligate dependence on mycorrhizal symbiosis. These findings contribute to our understanding of fungal adaptation in alpine environments and may inform strategies for artificial domestication of this valuable species.},
}

@article {pmid41752469,
year = {2026},
author = {Lowen, E and Moulton, SE and Palombo, EA and Kwa, F and Zaferanloo, B},
title = {Harnessing Endophytic Fungi as a Sustainable Source of Novel Anticancer Agents: Opportunities, Challenges, and Future Directions.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {4},
pages = {},
pmid = {41752469},
issn = {1420-3049},
mesh = {*Endophytes/chemistry/metabolism ; Humans ; *Antineoplastic Agents/pharmacology/chemistry ; *Fungi/chemistry/metabolism ; Animals ; *Neoplasms/drug therapy ; Signal Transduction/drug effects ; Biological Products/pharmacology ; },
abstract = {Despite significant advances in oncology, current cancer therapies remain constrained by toxicity, resistance, and limited selectivity. Endophytic fungi symbiotic microorganisms inhabiting plant tissues represent a sustainable and underexplored source of structurally diverse anticancer metabolites. These include alkaloids, terpenoids, polyketides, and peptides that disrupt microtubule dynamics, interfere with DNA replication, and induce mitochondrial-mediated apoptosis. They also modulate key oncogenic signalling pathways such as nuclear factor kappa B (NF-κB), signal transducer and activator of transcription 3 (STAT3), and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt), thereby enhancing the efficacy of existing chemotherapies. Endophyte derived compounds further inhibit angiogenesis, suppress metastasis, and stimulate immune responses, offering multi-target mechanisms with reduced toxicity. This review examines strategies that enhance the discovery and yield of these bioactive metabolites, including One Strain Many Compounds (OSMAC), microbial co-culture, epigenetic activation, genome mining, and synthetic biology. A comparative assessment of endophyte-derived versus conventional anticancer agents highlights their potential for scalable, eco-sustainable production. Collectively, endophytic fungi are positioned as promising contributors to the next generation of accessible, cost-effective, and environmentally responsible anticancer therapies.},
}

*Endophytes/chemistry/metabolism
Humans
*Antineoplastic Agents/pharmacology/chemistry
*Fungi/chemistry/metabolism
Animals
*Neoplasms/drug therapy
Signal Transduction/drug effects
Biological Products/pharmacology

@article {pmid41752167,
year = {2026},
author = {Abd-Alla, MH and Hassan, EA and Khalaf, DM and Mohammed, EA and Bashandy, SR},
title = {Harnessing Silicon and Nanosilicon Formulations with Rhizobium/Bradyrhizobium for the Sustainable Enhancement of Biological Nitrogen Fixation in Legumes and Climate Change Mitigation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752167},
issn = {1422-0067},
support = {51395//This research is based on the work supported by the Science, Technology & Innovation Funding Authority of Egypt (STDF) under grant number 51395/ ; },
mesh = {*Nitrogen Fixation/drug effects ; *Silicon/chemistry/pharmacology ; *Fabaceae/microbiology/metabolism ; *Silicon Dioxide/chemistry/pharmacology ; Climate Change ; *Nanoparticles/chemistry ; Symbiosis ; *Bradyrhizobium/physiology/metabolism ; *Rhizobium/physiology/metabolism ; Rhizosphere ; Soil Microbiology ; },
abstract = {Silicon has long been recognized as a beneficial element in plant biology. Recent advances in nanosilicon technology have revealed its transformative potential in legume-rhizobia symbiosis. This review synthesizes current knowledge on how silicon and SiO2 nanoparticles (Si-NPs) influence nodulation, microbial metabolism, and soil-plant interactions. We highlight emerging evidence that Si-NPs enhance symbiotic signaling, strengthen infection pathways, and mitigate oxidative stress, thereby supporting nitrogen fixation efficiency. Beyond the rhizosphere, nanosilicon improves soil structure, microbial diversity, and plant resilience under abiotic stress, offering a multifaceted approach to sustainable agriculture. The novelty of this review lies in its integrative perspective, connecting molecular mechanisms with ecological impacts and climate-smart applications. By examining Si-NPs across three domains-soils, rhizosphere metabolites, and plants-we provide a framework for understanding their role in enhancing productivity while reducing environmental costs. Importantly, we identify critical research gaps, including the need for standardized application protocols, large-scale field validation, sustainable nanosilicon production, and robust regulatory frameworks. These insights position nanosilicon as a promising tool for advancing legume productivity, reducing reliance on synthetic fertilizers, and contributing to global food security. This review underscores silicon's potential not only as a plant nutrient but also as a strategic agent in climate-resilient agriculture.},
}

*Nitrogen Fixation/drug effects
*Silicon/chemistry/pharmacology
*Fabaceae/microbiology/metabolism
*Silicon Dioxide/chemistry/pharmacology
Climate Change
*Nanoparticles/chemistry
Symbiosis
*Bradyrhizobium/physiology/metabolism
*Rhizobium/physiology/metabolism
Rhizosphere
Soil Microbiology

@article {pmid41751747,
year = {2026},
author = {Yang, J and Huang, KW},
title = {Joint Sensing and Secure Communications in RIS-Based Symbiotic Radio Systems.},
journal = {Entropy (Basel, Switzerland)},
volume = {28},
number = {2},
pages = {},
pmid = {41751747},
issn = {1099-4300},
support = {62201206//National Natural Science Foundation of China/ ; },
abstract = {We study the problem of joint sensing and secure communications in a reconfigurable intelligent surface (RIS)-based symbiotic radio (SR) system. In the considered system, a dual-functional radar and communication base station (DFRC-BS) achieves secure communications with multiple user terminals (UTs), and at the same time, performs a target sensing task. An RIS simultaneously assists the secure communications between the DFRC-BS and the multiple UTs and conveys its own data to the UTs by modulating the radio frequency signal from the DFRC-BS. Two different SR settings are investigated, namely, parasitic SR (PSR) and commensal SR (CSR). In both the PSR and the CSR situations, the echo signal from the sensing target is interfered by the backscattered signal from the RIS. We propose two strategies for the DFRC-BS to handle with the interference from the RIS, namely, (1) directly sensing without interference cancelation, and (2) performing interference cancelation before sensing. For both the two strategies, we aim to maximize the sum secrecy rate from the DFRC-BS to the multiple UTs while ensuring satisfactory performances for the sensing and the backscatter links. A block coordinate ascend algorithm is proposed to solve the established non-convex optimization problems. Simulation results reveal that at the DFRC-BS, performing interference cancelation leads to an improved system performance. Furthermore, compared with PSR, CSR leads to a higher sum secrecy rate between the DFRC-BS and the UTs.},
}

@article {pmid41751071,
year = {2026},
author = {Quezada-Rubio, JA and Estrada-Angulo, A and Castro-Pérez, BI and Urías-Estrada, JD and Ponce-Barraza, E and Escobedo-Gallegos, LG and Mendoza-Cortez, DA and Barreras, A and Carrillo-Muro, O and Plascencia, A},
title = {Effect of Combining a Prebiotic (Autolyzed Yeast from Saccharomyces cerevisiae) and Probiotic (Bacillus subtilis) Added in a High-Energy Diet on Growth Performance, Dietary Energetics, and Carcass Traits of Fattening Hairy Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
pmid = {41751071},
issn = {2076-2615},
abstract = {Due to their specific properties, the autolyzed yeast Saccharomyces cerevisiae (SC) and bacterial Bacillus subtilis (BS) theoretically can have a synergistic effect when combined and offered in ruminant diets. Thus, the aim of this experiment was to evaluate the effect of their combination as feed additives on growth performance, dietary energy, carcass traits, and visceral organ mass in finishing lambs. For this reason, 48 Pelibuey × Katahdin lambs (98 ± 17 d age; initial weight = 20.25 ± 3.37 kg) were used in a feeding trial lasting 83 d. Lambs were blocked by weight and assigned to 24 pens. Treatment consisted in supplementing a high-energy diet with probiotic and/or prebiotic as follows: (1) finishing diet without probiotic or prebiotic supplementation (Control), (2) finishing diet supplemented with 1.5 g SC/kg diet, (3) finishing diet supplemented with 1.5 g BS/kg diet, and (4) finishing diet supplemented with 1.5 g SC plus 1.5 g BS/kg diet. There were no synergistic (interaction) effects by combining SC + BS in any of the variables evaluated. Lambs that were supplemented with BS showed a very similar response on dry matter intake (DMI, p = 0.41), average daily gain (ADG, p = 0.64), carcass traits (p ≥ 0.08), tissue composition (p ≥ 0.32), and relative visceral organ mass (g/kg EBW, p ≥ 0.15) than non-supplemented lambs. Compared to the control group, lambs that received SC alone or in combination with BS showed greater average daily gain (12.0%, p = 0.03), gain efficiency (6.1%, p = 0.04) and observed-to expected dietary energy efficiency (5.5%, p = 0.04). Supplemental SC and SC + BS increased hot carcass weight (p = 0.04) without effects on the rest of the variables evaluated including the shoulder tissue composition whole cuts, and visceral organ mass. It was concluded that SC improves growth performance and dietary energy in finishing lambs without changes in carcass traits or carcass composition. Combining SC with BS did not improve the magnitude of the response of SC supplemented alone. In this study, the inclusion of a 1.5 g/kg diet of BS during a long-term period (83 d) did not show benefits to finishing lambs.},
}

@article {pmid41750402,
year = {2026},
author = {Au, S and Cruz, WD and Lala, M and Karthikeyan, S and Venketaraman, V},
title = {The Evolution of Symbiosis in Staphylococcus epidermidis: From a Protective Mutualist to a Parasitic Pathogen.},
journal = {Biomolecules},
volume = {16},
number = {2},
pages = {},
pmid = {41750402},
issn = {2218-273X},
mesh = {*Staphylococcus epidermidis/genetics/physiology/pathogenicity/drug effects ; *Symbiosis/genetics ; Humans ; Drug Resistance, Multiple, Bacterial/genetics ; Biofilms/growth & development ; Staphylococcal Infections/microbiology ; Gene Transfer, Horizontal ; Quorum Sensing ; Anti-Bacterial Agents/pharmacology ; Evolution, Molecular ; Genomic Islands ; Bacterial Proteins/genetics ; },
abstract = {Staphylococcus epidermidis is more often known as a human skin commensal, serving as a primary protective bacterium on the skin's surface. However, more recent literature highlights the role of S. epidermidis as a nosocomial pathogen and a multidrug-resistant organism that poses a global threat. The evolution of S. epidermidis can be owed to its accumulation of resistance mechanisms, including adhesion, biofilm formation, genomic islands, phage elements, integrated plasmids, and quorum sensing. It is suspected that through gene transfer, S. epidermidis is partially responsible for the feared multidrug-resistant Staphylococcus aureus through the mecA gene and many other genomic island transfers. Overall, prolonged nosocomial exposure and misuse of antibiotics have driven dramatic genomic remodeling in S. epidermidis, characterized by many methods of genetic recombination, SCCmec and insertion sequence acquisition, and accumulation of multiple resistance genes. Our review reviews the role of S. epidermidis as both a commensal and a pathogenic bacterium, summarizes the genes responsible for its multidrug resistance, and describes methods of combatting its invasion.},
}

*Staphylococcus epidermidis/genetics/physiology/pathogenicity/drug effects
*Symbiosis/genetics
Humans
Drug Resistance, Multiple, Bacterial/genetics
Biofilms/growth & development
Staphylococcal Infections/microbiology
Gene Transfer, Horizontal
Quorum Sensing
Anti-Bacterial Agents/pharmacology
Evolution, Molecular
Genomic Islands
Bacterial Proteins/genetics

@article {pmid41749416,
year = {2026},
author = {Lu, L and Zhang, Q and Liu, J and Shi, J and Zou, X and Wang, M and Wang, S and Dai, H and Zhang, X and Jiang, Y},
title = {The LIN and LINL E3 ligases function redundantly in arbuscular mycorrhizal symbiosis and nodulation of Medicago truncatula.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71052},
pmid = {41749416},
issn = {1469-8137},
support = {2023ZD04072//Biological Breeding-National Science and Technology Major Project/ ; 2023YFF1000300//National Key Research and Development Program of China/ ; 32500211//National Natural Science Foundation of China/ ; },
abstract = {LUMPY INFECTION (LIN) is known to direct the polar growth of infection threads during nodulation in Medicago. However, the role of LIN in the arbuscular mycorrhizal (AM) symbiosis has yet to be characterized. Here, we identified a novel lin allele mutant lin-6 (FN9104) in Medicago that exhibited impaired nodulation and reduced efficiency of AM symbiosis. LIN and its four LIN-like homologs (LINL1-4) are involved in both nodulation and AM symbiosis in Medicago. RNAi knockdown assays in both lin-6/LINL1-3-RNAi hairy roots and lin-4 linl1-1 double-mutant roots demonstrated that LIN and LINL1-3 exhibit functional redundancy in the AM symbiosis. Furthermore, the U-box domain, Armadillo-like domain, and WD40 repeat domain of LIN are essential for its functions in nodulation and mycorrhizal symbiosis, and the U-box domains of LIN and LINL1 exhibit E3 ubiquitin ligase activity in vitro. Interestingly, the interactions of LIN and LINL1 with DELLAs, scaffold proteins in the common symbiosis signaling pathway (CSSP), rely on their U-box domain. Our findings revalidate that LIN is a key component of the CSSP, redundant with LINLs in AM symbiosis. The U-box-mediated DELLA interaction suggests LIN's E3 ligase activity may regulate this central signaling hub to enable intracellular accommodation in root endosymbiosis.},
}

@article {pmid41747566,
year = {2026},
author = {García-Tomsig, NI and Guedes-García, SK and Robledo, M and Jiménez-Zurdo, JI},
title = {A single small RNA shapes multiple symbiotic traits in rhizobia.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128480},
doi = {10.1016/j.micres.2026.128480},
pmid = {41747566},
issn = {1618-0623},
abstract = {Bacterial small non-coding RNAs (sRNAs) remain understudied in the ecologically crucial nitrogen (N2)-fixing root-nodule Rhizobium-legume symbiosis. The only known rhizobial RNA regulator with broad symbiotic influence is the N-responsive trans-acting sRNA NfeR1, identified in the alfalfa symbiont Sinorhizobium meliloti. To pinpoint NfeR1 function, we profiled its RNA targets using MS2 affinity purification coupled with RNA sequencing (MAPS) in N stressed bacteria, a condition that drives nodulation. NfeR1 targets distinct regions of numerous mRNAs and sRNAs via three redundant anti-Shine-Dalgarno motifs, with downregulation constituting the primary regulatory outcome observed among the subset of validated targets. Target mRNAs span pathways differentially regulated throughout symbiosis, including N metabolism, motility, osmotolerance, and cell cycle control. Notably, NfeR1 modulates cell morphology and DNA replication by pervasive regulation of cell cycle mRNAs. It also silences gdhA, suggesting repression of glutamine dehydrogenase-dependent N assimilation, thereby promoting expression of nodulation genes, which is further fine-tuned by a novel RNA feedback loop involving NfeR1 and the dual-function sRNA SmelC549. Our findings position NfeR1 as a central hub within a structurally and functionally complex RNA network that coordinates N signaling and symbiotic performance in S. meliloti.},
}

@article {pmid41746445,
year = {2026},
author = {Higazy, AE and Sindi, RA and Alharbi, HM and Alwutayd, KM and Bahgat, LB and Naiel, MAE and Abdelnour, SA},
title = {Potential symbiotic effects of Artemia franciscana extract on post-metabolic response, antioxidant defense, reproductive performance, and tissue integrity in rabbit does.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41746445},
issn = {1573-7446},
abstract = {This research was conducted to evaluate the effects of dietary supplementation with Artemia franciscana extract (AFE) on blood hematology, biochemical variables, antioxidant defense, adipokines, ovarian activity, reproductive performance, and ovarian and uterine integrities in rabbit does. A total of 120 female rabbits were fed diets fortified with 0 (AFE0), 100 (AFE1), 200 (AFE2), or 400 (AFE4) mg/kg of AFE. The HPLC analysis of AFE identified several main phenolic compounds, p-coumaric acid, caffeic acid, ferulic acid, catechol, syringic acid, gallic acid, and benzoic acid. The most prominent flavonoid identified in AFE was rutin, followed by quercetin, kaempferol, naringin, and catechin. Feeding rabbits with AFE resulted in a significant increase in red blood cell (RBC) and platelet counts (P < 0.01), while white blood cell (WBC) counts were significantly reduced (P < 0.05). Supplementation with AFE significantly enhanced circulating total protein and albumin levels and reduced the level of gamma glutamyl transferase (GGT, P < 0.01). Supplementation with 200 or 400 mg/kg AFE significantly elevated superoxide dismutase (SOD) and catalase (CAT) activities (P < 0.05), with the AFE2 group exhibiting the highest (P < 0.05) levels of total antioxidant capacity (TAC), and glutathione peroxidase (GPx). Conversely, malondialdehyde (MDA) levels declined substantially across all treated groups (P < 0.01). The serum levels of adipokines, such as leptin and adiponectin, were significantly increased in all AFE-added groups (P < 0.01). All AFE-supplemented diets resulted in significantly higher serum levels of the reproductive hormones such as progesterone (PG), luteinizing hormone (LH), and follicle-stimulating hormone (FSH), compared to the AFE0 diet (P < 0.01). Dietary AFE supplementation significantly increased the number of corpora lutea, with the highest count observed in the AFE4 group, followed by the AFE1 and AFE2 groups (P < 0.01). AFE supplementation enhanced reproductive performance throughout the second and third parities, as evidenced by increased litter sizes and weights. Histological analysis revealed that AFE maintained the structural integrity of ovarian and uterine tissues. Furthermore, AFE administration significantly downregulated the immune-expression of Caspase-3 (P < 0.01). Overall, this study demonstrates that dietary supplementation with Artemia franciscana extract (AFE) at 200 or 400 mg/kg significantly modulates metabolic responses and enhances reproductive health in female rabbits. These benefits are driven by the regulation of adipokines and reproductive hormones, improved ovarian activity, and a strengthened antioxidant defense system.},
}

@article {pmid41745266,
year = {2026},
author = {Yuan, Y and Feng, Z and Song, H and Yuan, A and Chang, L and Zou, Y and Dashdorj, M and Bian, Z},
title = {Effects of Powdered and Granular AMF on Maize Growth Under Low Fertilizer Conditions.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {41745266},
issn = {2309-608X},
support = {2024YFC3909300//National Key R&D Program/ ; 202304290000011//Key R&D Program of Shanxi Province/ ; GZSTCKP [2025]019//Science and Technology Program of Shanxi Province/ ; 202523anull050017//Anhui Provincial Science and Technology Innovation and Development Program/ ; },
abstract = {Excessive fertilizer use drives soil degradation and resource waste. This study investigates how arbuscular mycorrhizal fungi (AMF) formulations (powder vs. granular) optimize maize (Zea mays L.) yield, soil microbiome, and economic benefits under 50% and 75% fertilizer reduction. Field trials showed that the AMF powder formulation under 50% fertilizer reduction (AP50) increased maize yield by 14.67%. This increase was associated with rapid root colonization (85.3%), enhanced phosphorus availability, and the recruitment of beneficial fungi such as Mortierellomycota. Granular formulation at 75% reduction (AG75) achieved 7.18% yield gain via sustained symbiosis. Fungal communities exhibited greater sensitivity to fertilization than bacteria (Chao1, p = 0.0094), with AMF suppressing Fusarium by 42% while enriching functional taxa (Actinobacteria, Mortierellomycota). Economic analysis confirms that AP50 (30,435 CNY/ha) and AG75 (26,954 CNY/ha) yield higher net profits, where CNY denotes Chinese Yuan. Powder formulations maximize immediate benefits in medium- to low-fertility soils, whereas granules support long-term soil health in high-organic systems, providing a precision strategy for sustainable agriculture.},
}

@article {pmid41745265,
year = {2026},
author = {Huang, Y and Bi, L and Zhu, Y and Chen, L and Yao, R},
title = {Characterization of the Effector Candidate Repertoire in the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {41745265},
issn = {2309-608X},
support = {YLS-2025-ZY01004//Yuelushan Laboratory Breeding Program/ ; YLS-2025-ZY03001//Yuelushan Laboratory Breeding Program/ ; 32470340//National Natural Science Foundation of China/ ; 32270334//National Natural Science Foundation of China/ ; 32401441//National Natural Science Foundation of China/ ; 2023RC1050//Department of Science and Technology of Hunan Province/ ; 2025ZY1003//Hunan Science and Technology Innovation Plan/ ; 2024ZYC029//Central Guidance for Local Science and Technology Development Fund Project in Hunan/ ; 2025RCXM056//Key Talent Project of Gansu Province, China/ ; 25RCKA034//Science and Technology Program of Gansu Province/ ; },
abstract = {The majority of terrestrial plants can interact with arbuscular mycorrhizal fungi (AMF) to form symbiotic relationships. AMF colonization not only enhances the host plant's uptake of mineral nutrients but also improves its tolerance to biotic and abiotic stresses. In return, the host plant supplies the AMF with carbon sources essential for completing its life cycle. How AMF overcome the plant immune system to successfully establish symbiosis has remained an unresolved question. During colonization, AMF also secrete effector proteins, similar to how pathogenic fungi utilize effectors to promote virulence. In this study, we employed machine learning models such as SignalP 6.0 and EffectorP 3.0 to predict potential effectors in Rhizophagus irregularis, leading to the identification of 227 effector candidates. Using EffectorP 3.0, ApoplastP, and LOCALIZER, most R. irregularis effectors were predicted to be localized in the cytoplasm rather than the apoplast, suggesting a functional role in regulating symbiotic development. Only 26% of the predicted effectors were annotated by Pfam, indicating that the majority are proteins of unknown function. Effector proteins from 14 microbial species representing five ecological types (Ectomycorrhizae, Ericoid mycorrhizae, Endophyte, Arbuscular mycorrhizae, and Pathogen) clustered distinctly by species, highlighting the high degree of species specificity among effectors. Two R. irregularis effectors containing the RxLR motif were identified. Although these effectors localized to the cytoplasm, they did not exhibit virulence factor activity. Additionally, we characterized a functionally conserved chitin deacetylase effector, RiPDA1, which localized to the apoplastic space. The Y2H assay indicated that RiPDA1 forms homodimers. The in vitro chitin-binding assay showed that RiPDA1 has an affinity for chitin. RiPDA1 may function as a secretory polysaccharide deacetylase that facilitates symbiosis by deacetylating chitin oligomers. In summary, this study systematically identified and characterized effector proteins in R. irregularis. Similar to pathogenic fungi, AMF appear to employ cell wall-modifying enzymes to overcome plant immune defenses.},
}

@article {pmid41745230,
year = {2026},
author = {Zhang, YY and Wang, TT and Li, YZ},
title = {Environmental Drivers Override Host Phylogeny in a Locoweed-Endophyte Symbiosis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {41745230},
issn = {2309-608X},
support = {32061123004//National Natural Science Foundation of China/ ; 2022YFD1401103//National Key R & D Program of China/ ; 20220104//National Forestry and Grassland Administration/ ; CARS-34//The Earmarked Fund for CARS/ ; },
abstract = {Plant endophytes, often termed the "second genome", critically shape host adaptability. However, the complexity of their interactions, regulated by microbial traits, host species, and environment, has limited both our understanding of symbiosis and the application of beneficial endophytes. The symbiosis between locoweeds (Oxytropis and Astragalus species) and the endophyte Alternaria sect. Undifilum, which produces the neurotoxin swainsonine, serves as an ideal model for investigating these relationships. Through extensive national surveys (2021-2023) across China's major locoweed habitats, combining field sampling with cultivation, molecular, quantitative, and modeling approaches, a central question emerged: To what extent are the distribution and function of this symbiosis shaped by the contemporary environment versus host evolutionary history? The results showed that: (1) Among 32 surveyed species of Oxytropis, Astragalus, and Sphaerophysa, the endophyte Alternaria sect. Undifilum colonized 11 species. In colonized plants, endophyte loads ranged from 0.02 to 58.87 pg/ng total DNA, and swainsonine concentrations varied from 0.00003% to 1.00%. (2) Environmental factors, rather than host phylogeny, were the key driver governing the geographical distribution and expression of the symbiosis. (3) Low temperature and drought stress regulated the symbiotic relationship and chemical defense through both direct effects on the symbionts and indirect pathways involving grazing pressure. This study demonstrates that the environment is the core force dominating the geographical pattern and functional expression of the locoweed-endophyte symbiosis at ecological scales. These findings provide new perspectives for understanding the general principles of plant-endophyte symbiosis and establish a scientific foundation for predicting and utilizing endophyte resources in changing environments.},
}

@article {pmid41744672,
year = {2026},
author = {Liu, W and Li, J and Zhao, Z and Wei, J and Huang, J and Zheng, Q and Qin, Y and Ma, H and Yu, Z and Pan, Y and Zhang, Y},
title = {Comparative Analysis of Eye Traits and Visual Resolution Among Three Hatchery-Bred Giant Clams (Tridacna crocea, T. squamosa, T. maxima).},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744672},
issn = {2079-7737},
abstract = {Bivalves possess a diverse array of photoreceptive organs that are significant for their evolutionary success and systematic classification. Giant clams are the largest bivalve mollusks, with mantle tissue permanently extended in nature to maintain symbiosis with zooxanthellae and perceive environmental cues. Eyes serve as critical sensory organs for these organisms, yet the structural and functional characteristics of tridacnine eyes remain inadequately understood. This study systematically investigated the ocular traits and visual resolution of three ecologically distinct giant clam species (Tridacna crocea, T. squamosa, T. maxima) using morphometric analysis, hematoxylin-eosin (HE) staining, transmission electron microscopy (TEM), and grating stimulation assays. Significant interspecific differences were observed in eye count, diameter, and pupil-to-eye ratio (PER): T. maxima exhibited the highest mean eye count (221 ± 8), T. squamosa the largest mean eye diameter (0.490 ± 0.082 mm), and T. crocea the highest mean PER (0.363 ± 0.041). Eyes were numerically symmetric on the left and right mantles but positionally asymmetric, showing random distribution patterns along the mantle margin without fixed corresponding locations across species. All three species possessed typical pinhole eyes lacking lenses and retinas, primarily composed of filler cells, receptor cells, and sparse neurons, with symbiotic zooxanthellae distributed in the surrounding mantle tissue. Grating stimulation assays revealed resolvable stripe periods of 5.82-11.64° (T. crocea), 8.62-13.16° (T. squamosa), and 10.15-12.26° (T. maxima), confirming T. crocea as the species with the highest visual resolution. These ocular variations are inferred to reflect adaptive evolution driven by ecological niches and habitat-specific factors (water depth or light intensity), while the simplified pinhole morphology is consistent with their sedentary lifestyle and metabolic dependence on symbiotic zooxanthellae. These ocular variations provide potential morphological markers for the systematic classification of Tridacninae and offer valuable insights for researchers studying the evolutionary plasticity of bivalve visual systems.},
}

@article {pmid41744623,
year = {2026},
author = {Li, H and Liu, L and Lin, G and Zhao, F and Sun, R and He, B and Huang, Z},
title = {Comparative Analysis of Gut Microbiota in Two Cucurbit Leaf Beetles Reveals Divergent Adaptation Strategies Linked to Host Plant Range.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744623},
issn = {2079-7737},
support = {32460304//the National Natural Science Foundation of China/ ; jxsq2023201063//the Jiangxi "Double Thousand Plan"/ ; 20212ACB205006, 20252BAC200373//the Natural Science Foundation of Jiangxi Province/ ; GJJ190538//the Science and Technology Foundation of Jiangxi Provincial Department of Education/ ; },
abstract = {Insects' gut microbiota and their hosts share a mutually dependent symbiotic relationship. However, how insect dietary breadth relates to microbial diversity remains unclear. This study compared the gut bacterial communities of the polyphagous Aulacophora indica and the oligophagous Aulacophora lewisii. Using an integrated approach of cultivation, 16S rRNA high-throughput sequencing, and bioinformatic analyses, we assessed their composition, diversity, and functional potential. Using cultivation-based methods revealed that A. indica showed a greater abundance and diversity of culturable bacteria, dominated by Proteobacteria and Actinobacteria, compared to A. lewisii (Proteobacteria and Firmicutes). In contrast, high-throughput sequencing revealed the opposite pattern: A. lewisii exhibited significantly higher overall species richness and diversity. This apparent paradox highlights the methodological complementarity between cultivation and sequencing. Furthermore, the community composition differed notably at the genus level. Functional prediction via PICRUSt2 v2.2.0 indicated that core metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and energy metabolism, were more enriched in A. indica. In summary, this study reveals systematic multi-dimensional differences in the gut microbiomes of these beetles, providing a theoretical foundation and microbial resources for understanding ecological adaptation and developing targeted control strategies based on gut microbiota.},
}

@article {pmid41744620,
year = {2026},
author = {Abude, RRS and Hendrickx, ME and Salgado-Barragán, J and Grano-Maldonado, MI and García-Varela, M and Migotto, AE and de Paula, JC and Augusto, M and Moreira, DA and Parente, TE and Lôbo-Hajdu, G and Cabrini, TMB},
title = {Ecological Interactions on Sandy Beach Ecosystems: A Global Synthesis of Mole Crabs and New Insights into Emerita brasiliensis and Emerita rathbunae (Crustacea, Decapoda, Anomura, Hippidae).},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744620},
issn = {2079-7737},
support = {E-26/211.433/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; E-26/203.020/2023//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {Sandy beaches are dynamic intertidal ecosystems where ecological interactions play a critical yet often overlooked role in shaping community structure and population dynamics. This study presents a global synthesis of ecological interactions involving mole crabs of the genus Emerita (Crustacea: Decapoda: Hippidae), complemented by new field and laboratory findings. Through a literature review and targeted sampling, we documented multiple interaction types, including predation, parasitism, epibiosis, competition, and symbiosis, highlighting their ecological and potential evolutionary implications. Predation and parasitism were the most frequently reported interactions worldwide. Our new empirical observations revealed, for the first time, the association of Eucheilota (Hydrozoa) and Maritrema sp. (Digenea) with E. rathbunae, as well as annual infection patterns by Profilicollis altmani (Acanthocephala) and algal epibiosis in E. brasiliensis. These interactions influence key biological processes such as burrowing, reproduction, and survival, ultimately affecting species distribution and population structure. Overall, our findings reinforce the central role of ecological interactions in the functioning and conservation of sandy beach ecosystems, particularly under growing anthropogenic pressures.},
}

@article {pmid41744165,
year = {2026},
author = {López-Lorca, VM and López-Castillo, O and Molina-Luzón, MJ and Ferrol, N},
title = {Arbuscular Mycorrhiza Modulates Iron Distribution and Vacuolar Iron Transporter Expression in Tomato, Whereas Iron Limitation Reduces Mycorrhization.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70463},
pmid = {41744165},
issn = {1365-3040},
support = {//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {Plants have evolved highly efficient strategies to maintain iron (Fe) homeostasis. In this study, we investigate the impact of arbuscular mycorrhizal (AM) symbiosis on the Fe-deficiency response and ionomic profile of tomato plants, as well as how Fe availability affects AM symbiosis. Fe deficiency and AM colonization both reduced shoot Fe concentrations, while root Fe concentrations increased in AM plants. Notably, Fe accumulated in cortical cells colonized by arbuscules. We further show that Fe deficiency reduces expression of AM-related tomato genes (SlEXO84, SlRAM1, SlAMT2.2 and SlPT4) and of the fungal RiEF1α gene. These findings indicate that Fe availability is crucial for sustaining AM colonization and symbiotic functionality. Under Fe-limiting conditions, AM symbiosis enhances the Strategy I Fe acquisition pathway (SlFRO1, SlIRT1), an effect not observed under Fe-sufficient conditions. Four vacuolar transporter genes of the VIT/VTL family were identified in the tomato genome. Yeast complementation assays revealed that SlVIT1, SlVTL1, and SlVTL2 function as dual Fe/Mn transporters, whereas SlVIT2 appears to function as a Mn transporter. The high Fe demand of AM symbiosis is supported by the reduced expression of SlVIT1 and SlVTL1 in mycorrhizal roots. Ionomic analysis shows that AM colonization partially alleviates Fe deficiency-induced nutrient imbalances, highlighting its contribution to improved mineral homeostasis under Fe stress.},
}

@article {pmid41743129,
year = {2026},
author = {Li, Z and Liao, X and Mo, L and Liao, Q and Lin, K and Bao, X and Sun, J and Zhang, X},
title = {Composition, diversity and functional potential of bacterial community in four stony coral species from the South China Sea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759094},
pmid = {41743129},
issn = {1664-302X},
abstract = {Recent investigations of coral symbiotic microorganisms have largely centered on their ecological functions, while systematic analyses of the community composition, diversity, and functional potential of bacteria associated with different coral species remain limited. This study presents the first systematic analysis of the distinct community structures and highly conserved core functions of symbiotic bacteria in four species of stony corals Favites abdita (Fa), Favia speciosa (Fs), Montipora digitata (Md), and Porites solida (Ps) from the South China Sea by high-throughput sequencing. The results identified 23 phyla and 250 genera of bacterial taxa, revealing considerable taxonomic richness in these coral-associated bacterial communities. Significant differences (p < 0.05) in bacterial community composition were observed among four coral species. Proteobacteria was the absolutely dominant phylum in Fa, Fs, and Ps, whereas Md was dominated by the phylum Firmicutes. At the genus level, the core microbial communities of the four coral species were similar in composition but exhibited marked differences in abundance. Md showed the highest species richness and diversity, and Fs the lowest. Among them, the Fa, Fs, and Ps groups were dominated by Ruegeria, while the Md group was characterized by a high abundance of Paramaledivibacter, which was significantly more abundant than in other groups. Functional prediction indicated that the relative abundances of core functional categories, such as amino acid transport and metabolism and energy production and conversion, were highly consistent across the four coral species, reflecting functional conservation within these communities. These findings enrich the basic data on the diversity and function of Coral symbiotic microorganisms in the South China Sea, revealing the connection between coral community variability and the conservation of core functions.},
}

@article {pmid41743060,
year = {2026},
author = {Kolařík, M and Vadkertiová, R and Knížek, M and Sklenář, F and Vakula, J and Zúbrik, M and Kolář, M and Hulcr, J},
title = {The ambrosial mycobiota of Treptoplatypus oxyurus (Coleoptera, Platypodidae): a unique island of fungal diversity revealing Wilhelmdebeerea oxyuri gen. et sp. nov. (Ophiostomatales), and two new yeast species Blastobotrys sasensis sp. nov., and Sugiyamaella casensis sp. nov. (Dipodascales).},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e177075},
pmid = {41743060},
issn = {2210-6340},
abstract = {Ambrosia beetles (Coleoptera, Curculionidae) form obligate nutritional symbioses with ambrosia fungi cultivated within their galleries. Among them, the pinhole borers (Platypodinae) are predominantly tropical, with only two representatives native to Europe. One of them, the rare and understudied Treptoplatypus oxyurus, primarily colonises Abies alba. We investigated its fungal symbionts using a cultivation-dependent approach. We identified three numerically dominant associates in the prothorax containing mycangia: Candida schatavii, Magnusiomyces fungicola, and a novel member of Ophiostomatales. The latter, Wilhelmdebeerea oxyuri gen. et sp. nov., was the most abundant and exhibited both leptographium-like and hyalorhinocladiella-like morphs. Additionally, two new yeast species of low abundance and uncertain ecological roles were isolated and described: Blastobotrys sasensis sp. nov. and Sugiyamaella casensis sp. nov., both belonging to the family Trichomonascaceae (Dipodascales). Multigene and phylogenomics analyses confirmed the distinct taxonomic placement of all three new species. The ecological roles of the identified fungi and the strength of their association with T. oxyurus require confirmation through further studies at additional locations. Our findings reveal a previously undocumented fungal diversity tightly linked to a unique pinhole borer, T. oxyurus, thereby enriching our understanding of the fungi associated with conifer-colonising beetles and their ecological and biotechnological importance.},
}

@article {pmid41742901,
year = {2026},
author = {Lynch, M and Ellington, A},
title = {A symbiotic origin of the ribosome?.},
journal = {PNAS nexus},
volume = {5},
number = {2},
pages = {pgag019},
pmid = {41742901},
issn = {2752-6542},
abstract = {The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means by which the genetic code inscribed on chromosomes is converted into reliable protein sequences) remains the most enigmatic. A resolution of this problem is unlikely to be advanced by focusing on the features of the complex system found in today's species, as the reliable production of complex proteins could not possibly have been the function of the earliest ribosome. Although exact answers may be beyond reach, we propose that the protoribosome was a parasite that through mutually constrained coevolution with the host eventually led to the emergence of a molecular machine no longer reflecting its simpler beginnings. If this view is correct, then like the spliceosome and perhaps the mitochondrion in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from a largely RNA world.},
}

@article {pmid41742393,
year = {2026},
author = {Zhang, J and Wang, Z and Zhang, B and Wang, R and Yan, M and Zhang, H and Dong, C and Feng, Q and He, Z and Pan, Z and Zhang, L and Yang, W},
title = {Evolutionary history and expression analysis of the RWP-RK gene family and its potential regulatory network in root nodules.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag092},
pmid = {41742393},
issn = {1532-2548},
abstract = {The RWP-RK protein family is divided into two subfamilies: NODULE INCEPTION (NIN) -like proteins (NLPs) and RWP-RK domain proteins (RKDs), which are involved in key biological processes including nitrate response, symbiotic nitrogen fixation, and embryonic development. We investigated the evolutionary history and functional divergence of these two subfamilies in green plants through phylogenetic analysis, motif analysis, expression profiling, and regulatory network construction. Both NLPs and RKDs originated from the early green algae ancestor, with multiple duplications during the seed plant period driving their lineage-specific expansion. Conserved motifs are more abundant among NLP proteins, whereas the number of conserved motifs among RKDs is relatively smaller. Expression analysis in various samples showed that GmNLP2a/b in soybean exhibit expression patterns analogous to those of the four NIN genes, while GmRKD4/13 also display abnormally high expression in root nodules. Therefore, there are at least eight RWP-RK genes that are specifically expressed or highly expressed in root nodules. Co-expression and functional enrichment analyses of transcriptome data further revealed the expression patterns of eight nodule-specific/highly expressed genes of NLPs and RKDs in soybean can be divided into those associated with early development and late maturation. Integrating ATAC-seq data, we further constructed a potential regulatory network of eight nodule-specific/highly expressed genes and their co-expressed transcription factors. In summary, our study elucidates the evolutionary expansion and expression divergence of NLPs and RKDs across plants, providing insights into dissecting the transcriptional regulatory network underlying soybean root nodule development and adaptive evolution of plant gene families.},
}

@article {pmid41741520,
year = {2026},
author = {Valadez-Ingersoll, M and Bodnar, CA and Feng, EX and Wong, A and Gilmore, TD and Davies, SW},
title = {Symbiotic state affects microbiome recovery in a facultatively symbiotic cnidarian.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38684-4},
pmid = {41741520},
issn = {2045-2322},
support = {NRT DGE 1735087//National Science Foundation/ ; IOS-1937650//National Science Foundation/ ; },
abstract = {Cnidarian holobionts consist of host cells, algal symbionts, and a complex microbiome residing in and on host tissue and algal symbionts. To investigate interactions among these three partners, we used antibiotics to deplete the microbiome of the facultatively symbiotic sea anemone Exaiptasia pallida (Aiptasia) in both symbiotic and aposymbiotic states and profiled 16S bacterial communities throughout recovery. We assessed host molecular response to microbiome depletion and recovery using RNA-seq and Western blotting of immune transcription factor NF-κB. 16S results demonstrate that, following depletion, symbiotic Aiptasia readily reestablished bacterial communities similar to control anemones. However, aposymbiotic Aiptasia microbiomes failed to reestablish control-level microbiomes even after seven days of recovery, highlighting differences between symbiotic states. Specifically, Endozoicomonadaceae reestablished to control levels in symbiotic, but not aposymbiotic, Aiptasia, suggesting a close physical association between Endozoicomonadaceae and algal symbionts. Molecular analyses showed that, during antibiotic recovery, host immune system gene expression was downregulated, but NF-κB protein levels increased, suggesting mechanisms for microbiome reestablishment following disruption. This study demonstrates the dynamics of microbiome recovery and how microbiome community members influence host gene expression in a cnidarian, providing a foundation for future research involving pairwise interactions between microorganisms and hosts.},
}

@article {pmid41741418,
year = {2026},
author = {Qiu, Y and Zhao, Y and Wang, B and Xu, X and He, T and Zhang, K and Bai, T and Li, Z and Ye, C and Gillespie, C and Wang, X and Zhao, Y and Guo, L and Qian, K and Chen, H and Cao, X and Wu, S and Guo, L and Tisdale, R and Woodley, A and Garcia, K and Zhu, W and Liu, L and Wang, Y and Zhang, Y and Hu, S},
title = {Root traits and mycorrhizal fungi mediate reactive N and warming impacts on soil organic carbon.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69301-7},
pmid = {41741418},
issn = {2041-1723},
abstract = {Plant roots and arbuscular mycorrhizal fungi (AMF) form a ubiquitous symbiosis in terrestrial ecosystems and critically affect soil organic carbon (SOC) dynamics. However, how roots and AMF mediate the impact of reactive nitrogen (Nr) and climate warming on SOC remains unclear. Using a multi-year Nr addition and simulated warming experiment in a semi-arid grassland, we show that Nr input and warming alter SOC by reshaping plant communities and inducing multidimensional tradeoffs among fine-root traits and AMF communities. Stable isotope ([13]C) tracing revealed that Nr- and warming-induced changes in roots and AMF reduced C input belowground, and mineral-associated organic C and microbial necromass in soil, while stimulating organic C decomposition. Nr input also increased soil N:P ratios and shifted AMF communities toward taxa with finer extraradical hyphae, weakening SOC protection. Together, these findings highlight root-AMF interactions as critical regulators and improve predictions of long-term SOC dynamics under future climate change.},
}

@article {pmid41740703,
year = {2026},
author = {Garrigós, M and Jiménez-Peñuela, J and Saavedra, I and Veiga, J and García-López, MJ and Garrido, M and Ruiz-López, MJ and Figuerola, J and Moreno-Indias, I and Martínez-de la Puente, J},
title = {Interactions between urbanization, malaria infection and avian cloacal microbiome.},
journal = {Environmental research},
volume = {297},
number = {},
pages = {124073},
doi = {10.1016/j.envres.2026.124073},
pmid = {41740703},
issn = {1096-0953},
abstract = {Urbanization, a major component of global change, has drastically modified the landscape, and is generally associated with biodiversity loss. Pollutants and low-quality food resources, among other urban stressors, can alter the physiology of urban-dwelling birds, ultimately affecting their interactions with other organisms, including pathogens and symbiotic microorganisms. The house sparrow (Passer domesticus) is one of the most common passerine species closely associated with anthropized environments. Here, we explored the association between the level of habitat urbanization, avian malaria infection (Plasmodium and Haemoproteus are grouped together in this study) and their combined effects on the composition of the cloacal microbiome of wild house sparrows. Urban birds showed a lower parasite prevalence than those from natural and rural habitats. In addition, the association between avian malaria infection and avian cloacal bacterial-microbiome composition depended on the habitat type. In natural habitats, infected birds showed a nearly significant increase in bacterial richness and significant differences in the relative abundance of various taxa, compared to uninfected individuals. In contrast, infection status was not associated with any microbiome parameter in birds from rural and urban habitats. In conclusion, habitat type is associated with avian malaria prevalence in house sparrows and may modulate the relationship between parasite infection and the bacterial composition of avian cloacal microbiome.},
}

@article {pmid41740024,
year = {2026},
author = {Prosdocimi, F and Garbin, M and Dondero, F},
title = {From natural theology to the extended synthesis: Historical milestones and conceptual expansions in evolutionary biology.},
journal = {Genetics and molecular biology},
volume = {49},
number = {suppl 2},
pages = {e20250179},
pmid = {41740024},
issn = {1415-4757},
abstract = {This article explores the historical development of evolutionary biology-from Natural Theology to the Modern Synthesis (MS)-and the ongoing debate around the Extended Evolutionary Synthesis (EES). Over the past 2,500 years, evolutionary thinking has emerged from the interplay between empirical discoveries and dominant philosophical paradigms. Beginning with Aristotle and Saint Augustine, we trace how Darwin and Wallace introduced a scientific framework grounded in natural mechanisms. In the early 20th century, the MS unified Mendelian genetics and Darwinian selection, forming a gene-centered model of evolution focused on mutations and population dynamics. In recent decades, discoveries in epigenetics, phenotypic plasticity, symbiosis, niche construction, and cultural inheritance have challenged the explanatory scope of MS. The EES seeks to incorporate these processes not by discarding Darwinian principles, but by reinterpreting them through a systems biology lens. This mostly represents a conceptual shift in focus: from linear, gene-driven causality to multilevel, reciprocal, and environmentally embedded dynamics. While gaining traction, the EES has been criticized for its lack of formal models and predictive frameworks, remaining a contested proposal. Ultimately, evolutionary biology continues to evolve as a powerful scientific tradition, driven by humanity's enduring quest to understand the origins and evolution of life on Earth.},
}

@article {pmid41739865,
year = {2026},
author = {Ramos, RJ and Richards, BL and Schultz, PA and Bever, JD},
title = {Host plant phylogeny predicts arbuscular mycorrhizal fungal communities, but plant life history and fungal genetic change predict feedback.},
journal = {PLoS biology},
volume = {24},
number = {2},
pages = {e3003304},
pmid = {41739865},
issn = {1545-7885},
mesh = {*Mycorrhizae/genetics/physiology ; Phylogeny ; Symbiosis/genetics ; *Plants/microbiology/genetics ; Mycobiome/genetics ; Grassland ; Plant Roots/microbiology ; },
abstract = {Symbioses exert strong influence on host phenotypes; however, benefits from symbionts can increase or degrade over time. Understanding the context-dependence of reinforcing or degrading dynamics is pivotal to predicting stability of symbiotic benefits. Host phylogenetic relationships and host life history traits are two candidate axes that have been proposed to structure symbioses. However, the relative influence of host evolutionary history and life history on symbiont composition, and whether changes in symbiont composition translate into stronger mutualistic benefits is unknown. We tested the influence of plant phylogenetic relationships and plant life history on the composition of arbuscular mycorrhizal (AM) fungi, perhaps the most ancestral and influential of plant symbionts, and then tested whether AM fungal differentiation resulted in improved mutualism as expected from coadaptation. We constructed mycobiomes composed of seven AM fungal isolates derived from tallgrass prairie and grew them for two growing seasons with 38 grassland plant species. We found that host phylogenetic structure was a significant predictor of the composition of AM fungal communities and the genetic composition of AM fungal species, patterns consistent with phylosymbiosis. However, the phylogenetic structure of AM fungi failed to translate to improved benefits to their host. While AM fungi generally improved plant growth and mycorrhizal feedback was generally positive, the strength of feedback was not predicted by plant phylogenetic distance. The composition of the AM fungal community and genetic composition within AM fungal species were also significantly influenced by plant life history and feedbacks between early and late successional species were generally positive. Interestingly, positive mycorrhizal feedback was predicted by changes in genetic composition of the two most abundant AM fungal species, not by changes in species composition. Positive mycorrhizal feedbacks across life history can mediate plant species turnover during succession and suggests that consideration of mycorrhizal dynamics could improve ecosystem restoration.},
}

*Mycorrhizae/genetics/physiology
Phylogeny
Symbiosis/genetics
*Plants/microbiology/genetics
Mycobiome/genetics
Grassland
Plant Roots/microbiology

@article {pmid41739059,
year = {2026},
author = {Ding, H and Luo, Y and Wang, J and Zhang, Z and Feng, H and Xu, L and Zhou, Y},
title = {Ectomycorrhizal and Dark Septate Endophytic Fungi Synergistically Enhance Salt Tolerance of Pinus tabulaeformis via Antioxidant Defense and Ion Homeostasis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag054},
pmid = {41739059},
issn = {1365-2672},
abstract = {AIMS: Plant root symbiotic fungi, ectomycorrhizal fungi (ECMFs) and dark septate endophytes (DSEs), increase host salt tolerance, but their combined effects remain unclear. This study aimed to evaluate the effects of these fungi isolated from Pinus tabulaeformis on seedling growth and physiology under NaCl stress, and clarify the pathways of their synergistic improvement of P. tabulaeformis salt tolerance.

METHODS AND RESULTS: Two experiments were performed: (1) An in vitro assay tested the salt tolerance of two ectomycorrhizal fungi (ECMF: Suillus granulatus, Pisolithus tinctorius) and two dark septate endophytes (DSEs: Pseudopyrenochaeta sp., Pleotrichocladium opacum) at NaCl concentrations of 0, 0.1, 0.2, 0.4 and 0.6 mol·L-1; (2) A pot experiment evaluated Pinus tabulaeformis seedlings inoculated with single/mixed fungi under soil NaCl stress (0, 1, 2, 3 g·kg-1). Fungal biomass and most antioxidant/osmoregulatory traits peaked at moderate NaCl levels in vitro, except for Pleotrichocladium opacum (Po), where superoxide dismutase (SOD), peroxidase (POD), and soluble protein contents increased with rising NaCl concentration. In the pot experiment, inoculated seedlings exhibited improved plant height, biomass, root development, antioxidant enzyme activities, and osmolyte accumulation under salt stress, along with reduced malondialdehyde (MDA) content, Na+ accumulation, and Na+/K+ ratios, compared with uninoculated controls. Mixed inoculation of ECMF and DSEs showed synergistic effects on most growth and stress resistance indicators relative to single inoculation.

CONCLUSIONS: The results highlight the potential of ECMF and DSE to increase P. tabulaeformis salt tolerance via growth promotion, antioxidant defense, and ion homeostasis, with combined inoculation offering synergistic benefits for saline soil restoration.},
}

@article {pmid41738934,
year = {2026},
author = {Sexauer, M and Markmann, K},
title = {The roots of nodules: a shared genetic infrastructure of root lateral organs suggests a common origin.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag088},
pmid = {41738934},
issn = {1460-2431},
abstract = {Nitrogen (N)-fixing root nodule symbiosis (RNS) is founded on a blend of genes borrowed from pre-existing processes. Infection and intracellular uptake of bacterial symbionts have long been associated with fungal accommodation in arbuscular mycorrhiza as putative genetic origin. This review focuses on the second key feature of RNS, the nodule organ. It investigates evidence for its genetic origin in lateral root and, more globally, lateral organ formation, and pinpoints a set of common organogenesis (COR) genes. The transcription factor gene NODULE INCEPTION (NIN) is discussed as a mediator of both infection and organogenesis, bridging both processes and harbouring the molecular key to an evolutionarily successful N-fixing association between Eurosid nodulators and bacterial microbionts. Comparing the hormonal and genetic mediators of lateral root and nodule priming, initiation and primordium formation, we scrutinize parallels and differences along their respective developmental trajectories. The transcription factors LOB-DOMAIN PROTEIN (LBD) 16 and SCARECROW (SCR)/SHORTROOT (SHR) are highlighted as mediators of both lateral root and nodule formation. Their roles as both recipients and activators of regulatory activity in either of these organs are analysed in the light of recent findings. Finally, we summarize and integrate novel insights on LIGHT DEPENDENT SHORT HYPOCOTYLS (LSH) 1/2 as master regulators of nodule versus root identity.},
}

@article {pmid41738909,
year = {2026},
author = {Schäfer, NM and Krol, E and Paczia, N and Farmani, N and Becker, A},
title = {CHASE-independent cytokinin perception triggers 3',5'-cAMP signaling in Sinorhizobium meliloti.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0058525},
doi = {10.1128/jb.00585-25},
pmid = {41738909},
issn = {1098-5530},
abstract = {The Medicago sativa-Sinorhizobium meliloti symbiotic plant-microbe interaction, which results in the formation of nitrogen-fixing root nodules, is subject to sophisticated genetic and metabolic regulation by both partners. S. meliloti is capable of inhibiting secondary plant infections via an adenosine 3',5'-cyclic adenosine monophosphate (cAMP)-dependent regulatory pathway that depends on CHASE2 domain adenylate/guanylate cyclases (AC/GCs). This pathway likely responds to a plant signal of protein nature. Plant cytokinins (CKs) are adenine derivative phytohormones that control many aspects of plant development, including the symbiotic nodule formation. Classical CK receptors in plants and bacteria contain a CHASE domain. In our study, we present a novel, CK-dependent cAMP signaling pathway, specifically mediated by the AC/GC CyaB, which lacks any known receptor domains. The plant CKs N[6](Δ[2]isopentenyl)-adenine (iP), trans-zeatin, kinetin, and 6-benzylaminopurine all promoted CyaB-dependent increase in cAMP levels detected through a genetic reporter construct. Among these four CKs, iP exerted the strongest effect. Metabolic profiling confirmed the CyaB-dependent accumulation of cAMP in S. meliloti cells, cultured in the presence of iP. The first enzyme in the terpenoid biosynthetic pathway, 1-deoxyxylulose-5-phosphate synthase Dxs, was identified as a CyaB interaction partner and is proposed to mediate the CK perception. CyaB homologs from closely related members of the Rhizobiaceae were able to interact with Dxs and to mediate cAMP signaling in response to iP.IMPORTANCESymbiotic interactions between nitrogen-fixing bacteria and leguminous plants are important for agriculture, ecological sustainability, and human nutrition. Maintaining an optimal number of symbiotic infections per plant is crucial for efficient symbiosis. Previous studies have shown that S. meliloti 3',5'-cyclic adenosine monophosphate (cAMP) signaling mediates the inhibition of secondary symbiotic infections of Medicago plants. We discovered a molecular mechanism that allows the symbiotic bacterium Sinorhizobium meliloti to respond to the Medicago plant adenosine derivative phytohormones named cytokinins (CKs) via cAMP signaling. This mechanism is mediated by the adenylate/guanylate cyclase CyaB. CyaB lacks any sensory domains and may perceive the CKs via its interaction partner deoxyxylulose-5-phosphate synthase Dxs.},
}

@article {pmid41737676,
year = {2026},
author = {Hauer, MA and Klier, KM and Langwig, MV and Anantharaman, K and Beinart, RA},
title = {Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag022},
pmid = {41737676},
issn = {2730-6151},
abstract = {Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts through the oxidation of chemical reductants in vent fluids. Hydrothermal vents also support unique viral communities that often exhibit high host-specificity and frequently integrate into host genomes as prophages; however, little is known about the role of viruses in influencing the chemosynthetic symbionts of vent foundation fauna. Here, we present a comprehensive examination of contemporary lysogenic and lytic bacteriophage infections, auxiliary metabolic genes (AMGs), and CRISPR spacers associated with the intracellular bacterial endosymbionts of snails and mussels at hydrothermal vents in the Lau Basin (Tonga). Our investigation of contemporary phage infection among bacterial symbiont species and across distant vent locations indicated that each symbiont species interacts with different phage species across a large geographic range. Surprisingly, prophages were absent from almost all symbiont genomes, suggesting that phage interactions with intracellular symbionts may differ from free-living microbes at vents. Altogether, these findings suggest that chemosynthetic symbionts primarily interact with species-specific phages via lytic infections, which may ultimately be important to the composition and dynamics of symbiont populations.},
}

@article {pmid41735472,
year = {2026},
author = {England, H and Oakley, CA and Herdean, A and Hughes, DJ and Songsomboon, K and Matthews, JL and Camp, EF},
title = {Manganese supplementation enhances cnidarian-dinoflagellate symbiosis under thermal stress.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09748-y},
pmid = {41735472},
issn = {2399-3642},
abstract = {Manganese (Mn) is an essential trace element for all photosynthetic life, playing an integral role in their photosystems, metabolism, and antioxidant activity. For corals, most studies focus on the potential toxicity of Mn at high concentrations (e.g. >700 µg L[-1]). However, there has been less exploration on beneficial, biologically relevant levels of Mn. Combining promtomics, ICP, and PAM fluorometry, we evaluate how Mn supplementation at increasing concentrations (0.5, 4.8, 11.4, 15.6 µg L[-1]) alters the physiology and proteome of the model cnidarian, Exaiptasia diaphana, when subjected to ambient (26 ˚C) and elevated (32 ˚C) temperatures. We demonstrate that Mn from 4.8 to 15.6 µg L[-1] mitigates thermal stress to E. diaphana, resulting in reduced photochemical damage and symbiont expulsion. Derived photobiology and proteomics data contributes to a mechanistic model for how Mn reduces thermal susceptibility, supporting the viability of Mn additions to enhance the protective capacities of photosynthetic cnidarians during heatwaves.},
}

@article {pmid41735439,
year = {2026},
author = {Khan, S and Mathur, A},
title = {Genome Insight and factorial design to elucidate the regulation of the tryptophan-mediated IAA biosynthetic pathway in an endophyte.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40546-y},
pmid = {41735439},
issn = {2045-2322},
abstract = {Endophytes are microorganisms that colonize plants, often via commensal or symbiotic associations, and regulate plant growth and metabolism. Such organisms are usually suitable alternatives to therapeuticallly relevant, bioactive, and commercially essential metabolites, particularly under optimized bioprocess conditions. The current study highlights the key research challenge of maximizing the production of Indole-3-Acetic Acid (IAA), a compound difficult to isolate from the plant due to low yield, by elucidating the genetic composition of an isolated endophyte and determining the biosynthetic pathway using the KEGG pathway. Moreover, deciphering the functional genomic and refining production optimization remain significant challenges. The whole-genome sequencing of the endophytic bacterium Bacillus cereus SKAM2 (Strain SKAM2) revealed a genome size of 5.6 Mb, a GC content of 36%, multiple tryptophan-dependent and tryptophan-independent pathways. Furthermore, the IAA biosynthetic pathways pave the way for process-optimization studies. The influence of various abiotic parameters and media supplements on IAA production in both intra- and extracellular media was compared, using a full-factorial design of experiments (DOE). The results showed the highest yield in the extracellular fraction, a 3.81-fold increase, exceeding the intracellular IAA yield. The results highlight the strong potential of strain SKAM2 as a microbial platform for sustainable IAA production.},
}

@article {pmid41733340,
year = {2026},
author = {Huang, X and Dong, X and Li, C and Xie, J and Sun, Y and Hu, Y and Xia, L and Tu, Q and Zhang, Y and Hu, S},
title = {XopA: a novel type III secretion system effector in Xenorhabdus that modulates host cell responses through apoptosis, autophagy, and immune evasion.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0387125},
doi = {10.1128/spectrum.03871-25},
pmid = {41733340},
issn = {2165-0497},
abstract = {UNLABELLED: The type III secretion system (T3SS) of bacterial pathogens plays an essential role in infection and colonization processes. T3S effectors (T3SEs) are pivotal in mediating these interactions and their mechanisms of action. This study delves into the functional mechanisms of XopA, the first T3SE identified in the bacterium Xenorhabdus, which belongs to the YopJ family. XopA demonstrates cytotoxicity akin to other YopJ family members and possesses virulence determinants capable of inducing both apoptosis and autophagy. Notably, our findings reveal a complex regulatory network between XopA-induced apoptosis and autophagy. Moreover, XopA modulates the host cell's global and inflammatory responses by targeting tubulin, thereby affecting cytoskeletal dynamics and the secretion of extracellular vesicles (EVs). The acetylation activity characteristic of the YopJ family effectors is significantly altered in HeLa cells upon XopA action, highlighting its role in post-translational modifications. Collectively, this study elucidates the multifaceted functional mechanisms of XopA, which will undoubtedly be beneficial for a better understanding of the molecular mechanisms of Xenorhabdus pathogenesis.

IMPORTANCE: This study reports the groundbreaking discovery of XopA as the first type III secretion system effectors (T3SE) identified in Xenorhabdus bacteria. By demonstrating its unique ability to concurrently induce host cell apoptosis and autophagy, execute lysine acetyltransferase activity to suppress inflammatory signaling, and disrupt cytoskeletal dynamics to inhibit extracellular vesicle secretion, this work reveals a sophisticated multifunctional virulence mechanism. These findings significantly advance our understanding of bacterial pathogenesis, providing crucial insights into how T3SEs manipulate host cell processes and evade immune responses, thereby establishing a new frontier in host-pathogen interaction research.},
}

@article {pmid41733235,
year = {2026},
author = {Li, K and Chen, K and Hao, H and Zhang, K and Brunel, B and Zhou, W and Zhang, J},
title = {Native bradyrhizobia for soybean: genetic and functional diversity in Heihe soils, a major production zone of Heilongjiang, China.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag026},
pmid = {41733235},
issn = {1472-765X},
abstract = {Soybean (Glycine max) forms symbiotic nitrogen fixation with rhizobia, and compatible, efficient rhizobia in soils are vital for its sustainable production. This study analyzed the distribution and traits of native soybean-associated rhizobia in soils from Heihe, Heilongjiang Province, to identify strains with high symbiotic nitrogen fixation efficiency and environmental adaptability, and select candidates for local microbial inoculants to boost sustainable soybean production. Seventy-four rhizobial isolates were obtained from three Heilongjiang sampling sites using a local soybean variety, and characterized genetically and symbiotically. PCR-RFLP of IGS DNA grouped them into 9 genotypes. Multilocus sequence analysis (16S rRNA, recA, atpD, gyrB genes) placed representative strains into three known species (Bradyrhizobium japonicum, B. diazoefficiens, B. ottawaense) and an uncharacterized Bradyrhizobium group (64%, dominant). Phylogeny of nodC/nifH markers showed affiliation with symbiovar glycinearum. All strains nodulated soybean with symbiotic efficiency (67-88%); about half enhanced plant biomass. Three strains (DG28, GCZ12, SH16) showing superior symbiotic efficiency. Representative strains had varied tolerance to alkalinity, high temperature, and PEG-induced drought. Strain SH16 combined high efficiency and stress tolerance. These results provide promising candidates for local soybean inoculant development.},
}

@article {pmid41731702,
year = {2026},
author = {Bonnot, C and Morin, E and Da Silva Machado, E and Veneault-Fourrey, C and Kohler, A and Martin, F},
title = {Poplar CLE peptides promoting ectomycorrhizal symbiosis identified through genome-wide analysis of responsive small secreted peptides.},
journal = {Plant physiology},
volume = {200},
number = {3},
pages = {},
doi = {10.1093/plphys/kiag071},
pmid = {41731702},
issn = {1532-2548},
support = {ANR-11-LABX-0002-01//Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems/ ; },
mesh = {*Populus/genetics/microbiology/metabolism ; *Symbiosis/genetics ; *Mycorrhizae/physiology ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; *Peptides/metabolism/genetics ; *Quercus/genetics/microbiology ; Genome, Plant ; Plant Roots/microbiology/genetics ; },
abstract = {Plant small secreted peptides (SSPs) are involved in numerous developmental processes and adaptive plant responses. These include root development, immunity, and symbiotic relationships in herbaceous plants; three processes crucial for establishing functional ectomycorrhizal associations in trees. While fungal SSPs involved in ectomycorrhizal establishment have been identified, the role of plant SSPs remains largely unexplored. Although thousands of SSPs have been predicted in plant genomes, their small size and high sequence divergence hinder accurate automated annotation. To address this issue, we combined de novo gene prediction with a family-specific motif search to identify 1,053 SSPs from 21 symbiosis-related families in the genomes of two ectomycorrhizal (ECM) tree species: poplar (Populus trichocarpa) and English oak (Quercus robur). Nearly half of these SSPs, which included signaling, antimicrobial, and peptidase inhibitor peptides, were transcriptionally regulated during ectomycorrhizal symbiosis with various fungal partners, implying that SSPs involved in ECM symbiosis support a diversity of functions. Five ectomycorrhizal-responsive CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides from poplar enhanced ectomycorrhizal root formation in functional assays. These peptides, which belong to CLE clades associated with meristematic activity, are phylogenetically distinct from CLEs involved in the autoregulation of arbuscular mycorrhizal and rhizobial symbioses, indicating that poplar co-opted a distinct set of SSPs for ECM development. The activity of these peptides did not increase lateral root number but inhibited adventitious and lateral root growth, suggesting their role in promoting ectomycorrhizal root organogenesis. Our results expand the understanding of host tree contributions to ectomycorrhizal development and identify a set of candidate SSPs for future functional studies, thereby highlighting a previously uncharacterized layer of regulation in tree-fungi mutualism.},
}

*Populus/genetics/microbiology/metabolism
*Symbiosis/genetics
*Mycorrhizae/physiology
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
*Peptides/metabolism/genetics
*Quercus/genetics/microbiology
Genome, Plant
Plant Roots/microbiology/genetics

@article {pmid41731187,
year = {2026},
author = {Yang, Z and Xi, H and Huo, J and Zhang, Q and Pan, J and Liu, Y and Feng, H},
title = {Drivers of ectomycorrhizal fungi in a subalpine mixed forest: the roles of host plants and edaphic factors.},
journal = {Mycorrhiza},
volume = {36},
number = {2},
pages = {},
pmid = {41731187},
issn = {1432-1890},
support = {U21A20186//the National Natural Science Foundation of China/ ; 32171579//the National Natural Science Foundation of China/ ; 32371592//the National Natural Science Foundation of China/ ; 23JRRA1029//the Natural Science Foundation of Gansu Province/ ; 23JRRA1034//the Natural Science Foundation of Gansu Province/ ; },
}

@article {pmid41731135,
year = {2026},
author = {De La Cruz, HJ and Marro, N and Caccia, M and Žďárská, K and Janoušková, M},
title = {Competitive dynamics of arbuscular mycorrhizal fungi as depending on fungal traits and host plant species.},
journal = {Mycorrhiza},
volume = {36},
number = {2},
pages = {},
pmid = {41731135},
issn = {1432-1890},
abstract = {UNLABELLED: Arbuscular mycorrhizal fungi (AMF) are ubiquitous root-associated symbionts, but competitive interactions among coexisting taxa remain poorly understood. The variation in colonization and resource-acquisition strategies drive competition, shaping the relative abundances of AMF within their communities and mycorrhiza functioning. However, the factors that determine the competitive outcomes have received limited experimental attention. We hypothesized that AMF abundances, competitive responses, and contributions to plant growth would vary according to fungal traits and host plant species. Three AMF isolates of contrasting growth and competitive abilities, each representing one AMF species, were mono- and co-inoculated under six host plant species. Fungal abundance, root colonization (RC), and mycorrhizal growth response (MGR) were measured at early and late stages of the symbiosis. Fungal competitive responses depended on the isolate’s root colonization strategy in monoculture and mycorrhizal stage. The fast-colonizing isolate dominated initially, while slower-growing isolates displayed different temporal patterns, either declining or maintaining their abundance over time. Our findings suggest competitive outcomes among AMF that were asymmetric at early stages but became more symmetric later. The host plant species importantly modulated the dominance of the fast root-colonizer. MGR was positively associated with total AMF abundance and RC, yet the most abundant isolate did not necessarily provide the greatest growth benefits to the host plant. Our results suggest that maintaining a diversity of AMF functional types, rather than introducing a single highly competitive isolate, is favourable to the establishment of stable and efficient plant-AMF associations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00572-026-01254-7.},
}

@article {pmid41731102,
year = {2026},
author = {Jiang, P and Li, X and Wang, Z and Li, S and Huang, Y and Li, YX and Chen, Y and Sun, X},
title = {COL3A1[high] cancer-associated fibroblasts orchestrate metabolic and immune microenvironments to confer chemoresistance in breast cancer.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01338-9},
pmid = {41731102},
issn = {2397-768X},
support = {TJYXZDXK-3-003A//Tianjin Key Medical Discipline Construction Project/ ; 2023ZD0502200//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82403430//National Natural Science Foundation of China/ ; 2023-BSBA-207//Technology Program Joint Fund of Liaoning Province/ ; 2024-ZLKF-09//Oncology Project of Liaoning Cancer Hospital/ ; },
abstract = {Chemoresistance remains a critical challenge in breast cancer (BC) treatment. By integrating multi-omics (single-cell, spatial, and bulk transcriptomics) with clinical validation, we identified a specific COL3A[high] CAF subset that drives BC chemoresistance. Mechanistically, these CAFs undergo lipid metabolic reprogramming, secreting excess oleic acid via SCD. This oleic acid binds to ENO1 on tumor cells, activating the PI3K/Akt pathway and inhibiting chemotherapy-induced apoptosis. Simultaneously, COL3A[high] CAFs orchestrate an immunosuppressive niche by recruiting regulatory T cells and impairing cytotoxic CD8[+] T cells. Our findings establish COL3A[high] CAFs as key mediators of resistance through metabolic symbiosis and immune evasion. The strong correlation between COL3A[high] CAF abundance and clinical poor response highlights their potential as both predictive biomarkers and therapeutic targets to overcome chemoresistance in BC patients.},
}

@article {pmid41728996,
year = {2026},
author = {Li, Z and Zhang, H and Wei, T and He, L and Wang, Y},
title = {Anoxia-adapted cyanobacteria in a marine blue hole.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0257625},
doi = {10.1128/aem.02576-25},
pmid = {41728996},
issn = {1098-5336},
abstract = {Vertical transmission of marine particles brings ocean surface cyanobacteria into the deep ocean, where heterotrophic cyanobacterial lineages probably evolve to adapt to new environments even in oxygen-depleted zones. At present, active cyanobacteria have rarely been reported in dark and anoxic water columns in the deep sea. In this study, we recovered three metagenome-assembled genomes of cyanobacteria from the Yongle blue hole located in the South China Sea, two of which were actively transcribed in a dark, anoxic environment at 250 m depth, through integrated metagenomic and metatranscriptomic analyses of water samples from 21 stratified depths collected using in situ microbial fixation and filtration. These anoxia-adapted cyanobacteria were phylogenetically approximate to the sponge cyanobacterial symbionts, while the genomic features showed similarities with both free-living and sponge symbiotic counterparts. They exhibit genomic features shared with symbiotic lineages, including loss of substrate utilization, biosynthesis pathways, DNA repair, and circadian regulation. Conversely, they retain selected metabolic characteristics of free-living lineages, including phenylalanine biosynthesis and phosphoserine metabolism. Additionally, the discovery of taurine transport proteins in the genomes suggests the potential for organic sulfur uptake from the environment. Altogether, these findings reveal a distinct genomic configuration in cyanobacteria inhabiting a permanently dark and anoxic marine system, characterized by the retention of oxygen-dependent metabolic potential alongside sustained transcriptional suppression under in situ conditions. This study provides new insights into the ecological persistence and evolutionary adaptation of cyanobacteria under long-term oxygen limitation.IMPORTANCEWe report metabolically active cyanobacteria thriving in darkness and oxygen deprivation at 250 m depth in the ocean. Genomics results show these microbes share evolutionary roots with sponge cyanobacterial symbionts but developed unique adaptations for anoxic and sulfidic environments. Strikingly, they retain photosynthesis genes as genomic remnants (with no detected transcription) while losing genes critical for environmental stress responses, including DNA repair, osmotic regulation, and circadian control, suggesting a potential evolutionary connection to symbiotic relatives. Crucially, they maintain metabolic autonomy via phenylalanine biosynthesis and light-independent serine biosynthesis, exhibiting traits absent in most symbionts. This demonstrates how cyanobacteria adapt to anoxic environments through targeted genome reduction, revealing novel survival strategies in oxygen-depleted oceans and providing a research case for microbial resilience during marine deoxygenation.},
}

@article {pmid41728346,
year = {2026},
author = {Kage, A and Kanaya, HJ},
title = {Long-term behavioral tracking of Paramecium bursaria.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {41728346},
issn = {2578-9430},
abstract = {The ciliate protozoan Paramecium exhibits complex behaviors in response to environmental cues. Here we report a method that enables long-term observation (over 24 hours) of Paramecium with a simple experimental procedure. We observed the behavior of Paramecium bursaria , a species of Paramecium harboring symbiotic green algae, in gas-permeable chambers, where they exhibited light-dependent changes in behavior. We found that, in the 12-hour light-dark (LD) cycles, P. bursaria responds to both the dark-to-light and the light-to-dark transitions in different manners. This method provides a way to evaluate the long-term changes in the behaviors of Paramecium and other protists.},
}

@article {pmid41726958,
year = {2026},
author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.12.705600},
pmid = {41726958},
issn = {2692-8205},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid41726154,
year = {2026},
author = {Martin, FM and Morin, E and Kuo, A and Miquel, I and Labbé, J and Tacon, FL and Fauchery, L and Kohler, A and Andreopoulos, W and Copeland, A and Sun, H and Salamov, A and Lipzen, A and Han, J and LaButti, K and Tritt, A and Barry, K and Grigoriev, IV},
title = {Draft Genomes of Geographically Distinct Strains and Progeny of the Ectomycorrhizal Basidiomycete Laccaria bicolor.},
journal = {Journal of genomics},
volume = {14},
number = {},
pages = {10-17},
pmid = {41726154},
issn = {1839-9940},
abstract = {The ectomycorrhizal fungus Laccaria bicolor is a key symbiotic mutualist in forest ecosystems, where it enhances nutrient uptake and promotes the growth of host trees. Here, we present genome assemblies of 14 geographically distinct strains and progeny of L. bicolor, providing new insights into the intraspecific genomic diversity. Pangenome analysis revealed substantial variation in assembly size (42-96 Mbp), gene content (16,084-26,800 genes), and single nucleotide polymorphism (SNP) density (0.04-12.08 SNPs/kb). This variation likely reflects genuine biological differences among strains adapted to diverse environmental conditions, although differences in assembly quality and repeat content may also play a role. These genomic resources, comprising draft genome assemblies with comprehensive annotations, will facilitate comparative studies of the genetic diversity and functional traits underlying the ecological success of this model ectomycorrhizal fungus.},
}

@article {pmid41725065,
year = {2026},
author = {Wang, TY and Lv, C and Zhang, LL and Ma, ZY and Zhang, Q and Zhang, Y and Guan, NC and Huang, YZ and Luan, JB},
title = {Autophagy mediated symbiont elimination for the management of the whitefly Bemisia tabaci.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70597},
pmid = {41725065},
issn = {1526-4998},
support = {JYTTD2024001//Basic Research Project of Department of Education, Liaoning Province/ ; },
abstract = {BACKGROUND: Symbionts influence the biological and ecological traits of host insects. Regulating the insect-microbe symbiosis represents new strategies for pest control. We previously demonstrated that autophagy induction regulates the abundance of bacteriocyte symbionts in the whitefly Bemisia tabaci MEAM1.

RESULTS: This study further investigated whether autophagy induction via silencing the Target of Rapamycin (TOR) pathway genes (LST8 and TOR) using the plant-mediated gene silencing technology can repress the symbiont abundance and fitness of another invasive whitefly B. tabaci MED. We found that whitefly LST8 and TOR genes can be silenced by virus induced gene silencing approach. LST8 and TOR gene silencing significantly up-regulated the expression of autophagy marker gene Atg8 and led to reduction in the abundance of the symbionts Portiera, Hamiltonella, and Rickettsia in whiteflies. This reduction in symbiont titers led to increased mortality and decreased fecundity in whiteflies.

CONCLUSION: These findings underscore the potential of manipulating autophagy to disrupt symbiotic abundance as a novel and environmentally friendly strategy for pest management. Our study also suggests that disruption of intracellular symbiosis via insect immunity modulation is feasible for the management of sap-sucking insect pests. © 2026 Society of Chemical Industry.},
}

@article {pmid41722740,
year = {2026},
author = {Shen, H and Chen, J and Zheng, W and Cao, Y and Du, T and Wu, W},
title = {Topical application of Clostridium butyricum by an anaerobic hydrogel for accelerated diabetic wound healing through selective bacteria inhibition and ROS scavenging.},
journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V},
volume = {},
number = {},
pages = {115027},
doi = {10.1016/j.ejpb.2026.115027},
pmid = {41722740},
issn = {1873-3441},
abstract = {Selective inhibition of harmful bacteria without affecting skin symbiotic probiotics and selective scavenging of highly toxic reactive oxygen species (ROS) such as hydroxyl radicals (•OH) and peroxynitrite anions (ONOO[-]) are new requirements for more precise treatment of diabetic ulcer wounds. Achieving either is challenging, simultaneous achievement remains unreported. Clostridium butyricum (C. butyricum) inherently offers selective antibacterial action and produces hydrogen, specifically scavenging •OH and ONOO[-], showing great potential for diabetic wound treatment. However, as an anaerobic bacterium, its anaerobic nature limits topical application in normoxic environments on the skin. To overcome this, we developed a novel hydrogel creating an internal anaerobic microenvironment via the oxygen-depleting reaction between vanillin and laccase. Serving as a carrier, this hydrogel ensures internalized C. butyricum maintains activity in normoxia, enabling effective dual functions: selective bacterial inhibition and selective ROS scavenging. In vivo studies demonstrate the significant efficacy of this C. butyricum-loaded hydrogel in promoting diabetic wound healing. This work pioneers the topical therapeutic use of C. butyricum for wound treatment.},
}