@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},
doi = {10.1126/sciadv.adw8163},
pmid = {41779834},
issn = {2375-2548},
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.},
}

@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},
}

@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 = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70084-0},
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)/ ; },
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.},
}

@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 {pmid41634568,
year = {2026},
author = {Zhu, M and Su, L and Shang, N and Su, S and Jiang, F and He, Y and Zhou, X and Zhao, Y and Wei, X},
title = {The phosphate-solubilizing capacity of Rhizobium tropici LNP6 and its growth-promoting effects on Ormosia hosiei seedlings.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {41634568},
issn = {1471-2229},
support = {Qian Ke He Platform Talents - CXTD [2023]006//Innovative talent team project of seedling breeding and plantation cultivation for precious tree species in Guizhou/ ; Qian Ke He [2016] 5661//Guizhou Province "Hundred" Talents Training Plan Project/ ; },
abstract = {UNLABELLED: Globally, available phosphorus is generally scarce in terrestrial soils, despite the abundance of potential phosphorus sources. Therefore, isolating and utilizing microbial strains with both phosphate-solubilizing and nitrogen-fixing capabilities is crucial for enhancing the environmental adaptability and growth performance of woody leguminous plants in phosphorus-deficient conditions. This study employs the highly efficient plant growth-promoting strain Rhizobium tropici LNP6, which was isolated from the root nodules of Ormosia hosiei and verified through re-inoculation screening, to explore its phosphorus solubilization mechanisms and evaluate its growth-promoting effects in soils with three different phosphorus sources. The results indicated that strain LNP6 is capable of solubilizing both insoluble organic and inorganic phosphorus. Analysis of its metabolites revealed that the strain exerts its phosphorus-solubilizing function through the production of organic acids and the secretion of phosphatases. The pot experiment demonstrated that LNP6 significantly accelerated the release of available nutrients in the seedling rhizosphere soil through two pathways: symbiotic nitrogen fixation and free-state phosphate solubilization. This enhancement resulted in a substantial improvement in the uptake efficiency of N, P, K by O.hosiei seedlings, thereby robustly promoting seedling growth and biomass accumulation. The greatest promoting effect was observed following the application of Calcium phytate under low-phosphorus conditions. This study establishes a theoretical foundation for the development of nitrogen and phosphorus-efficient microbial agents for O. hosiei, which is essential for alleviating the impacts of soil phosphorus deficiency on its growth.

GRAPHICAL ABSTRACT: The phosphate-solubilizing capacity of Rhizobium tropici LNP6 and its growth-promoting effects. [Image: see text]},
}

@article {pmid41776290,
year = {2024},
author = {Lai, J and Zhang, Y and Zhao, C and Wang, J and Yan, Y and Chen, M and Ji, L and Guo, J and Han, B and Shi, Y and Zhang, J and Chen, Y and Feng, Q and Yang, W},
title = {Multi-expert ensemble ECG diagnostic algorithm using mutually exclusive-symbiotic correlation between 254 hierarchical multiple labels.},
journal = {NPJ cardiovascular health},
volume = {1},
number = {1},
pages = {},
pmid = {41776290},
issn = {2948-2836},
support = {no.2018YFC2001203//National Key R&D Program of China/ ; no. 2020B1212060039//Key Laboratory of Medical Image Processing of Guangdong Provincial/ ; },
abstract = {Electrocardiograms (ECGs) are a cheap and convenient means of assessing heart health and provide an important basis for diagnosis and treatment by cardiologists. However, existing intelligent ECG diagnostic approaches can only detect up to several tens of ECG terms, which barely cover the most common arrhythmias. Thus, further diagnosis is required by cardiologists in clinical settings. This paper describes the development of a multi-expert ensemble learning model that can recognize 254 ECG terms. Based on data from 191,804 wearable 12-lead ECGs, mutually exclusive-symbiotic correlations between hierarchical multiple labels are applied at the loss level to improve the diagnostic performance of the model and make its predictions more reasonable while alleviating the difficulty of class imbalance. The model achieves an average area under the receiver operating characteristics curve of 0.973 and 0.956 on offline and online test sets, respectively. We select 130 terms from the 254 available for clinical settings by considering the classification performance and clinical significance, providing real-time and comprehensive ancillary support for the public.},
}

@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},
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.},
}

@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},
doi = {10.1002/jobm.70156},
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/ ; },
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.},
}

@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},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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},
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.},
}

@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 {pmid41629792,
year = {2026},
author = {Yuan, G and Chai, S and Huang, Y and Tao, C and Li, M and Dai, Q and Wang, Y and Wang, Y and Jiang, H and Luo, Y and Jiang, Q and Wei, X and Zeng, D and Fu, C and Liang, Y},
title = {Comparison and structure of fungal diversity in roots and rhizosphere soils of wild and reintroduced populations of three Paphiopedilum species.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41629792},
issn = {1471-2164},
support = {X2025106020244//Guangxi Normal University's Provincial Training Program of Innovation and Entrepreneurship for Undergraduates/ ; 2022YFF1300700//National Key R&D Program Project of China/ ; Guike24010014//Guangxi Key R&D Program Project/ ; 32160096//National Natural Science Foundation of China/ ; 2025GXNSFAA069252//Guangxi Natural Science Foundation/ ; XNK202305//Guangxi new agricultural science research and practice project/ ; YCSW2025223//Innovation Project of Guangxi Graduate Education/ ; },
abstract = {UNLABELLED: Mycorrhizal fungi play critical roles in the seed germination and the growth of orchid plants. The investigation of fungi, especially mycorrhizal fungi, associated with orchid roots is important for both the protection and sustainable utilization of the plants. The Paphiopedilum orchid genus is severely endangered, and thus analysis of the composition and diversity of rhizosphere mycorrhizal fungi in wild and reintroduced Paphiopedilum species is beneficial for protecting wild Paphiopedilum resources and significant for the large-scale reintroduction and cultivation of Paphiopedilum. Here, high-throughput sequencing (HTS) was used to analyze the species and composition of mycorrhizal fungi in the roots and rhizosphere soils of wild and reintroduced populations of Paphiopedilum dianthum, Paphiopedilum hirsutissimum, and Paphiopedilum micranthum. The clustering of operational taxonomic units (OTUs) and determination of diversity indices showed significant differences between the fungal communities associated with the roots and rhizosphere soils of these three species of Paphiopedilum, with markedly fewer OTUs associated with the roots (3465) than the rhizosphere (5221). The numbers of mycorrhizal fungi in the roots (226) of these three species of Paphiopedilum were also less than in the rhizosphere (259). P. micranthum showed the greatest diversity of associated fungi compared to the two other species. The dominant fungal taxa associated with these orchids included Sebacina (Basidiomycota) and Tulasnella (Basidiomycota). Among these, Tulasnella and Sebacina are well-known orchid mycorrhizal fungi (OMF) that form essential symbiotic structures. These findings provide a reference for the reintroduction, protection, and resource development of the Paphiopedilum species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12572-7.},
}

@article {pmid41405424,
year = {2026},
author = {Travers-Cook, TJ and Gonzalez-Gonzalez, E and Jokela, J and King, KC and Knight, S and Buser, CC},
title = {Evidence for toxin-encoding coinfections driving intransitive dynamics between allelopathic phenotypes in natural yeast populations.},
journal = {Journal of evolutionary biology},
volume = {39},
number = {3},
pages = {404-411},
doi = {10.1093/jeb/voaf150},
pmid = {41405424},
issn = {1420-9101},
support = {ETH-23 20-1//ETH Zurich/ ; },
abstract = {Competitive intransitivity, or non-hierarchical competitive interactions, such as those exemplified by the rock-paper-scissors game where no single competitor wins outright, has been proposed as a key mechanism for maintaining biodiversity; however, empirical evidence supporting the importance of intransitivity remains limited. Natural populations of Saccharomyces cerevisiae often include strains harboring totivirus-satellite coinfections that encode a lethal toxic glycoprotein capable of eliminating competing yeast strains. Killer strains are sparsely distributed in natural populations, despite their assumed competitive advantage. Yeast isolates occasionally exhibit toxin resistance, but it remains untested whether they can outcompete and replace killer strains. Similarly, the persistence of toxin-susceptible yeast is not well understood-particularly whether they can invade resistant populations in the absence of killers, thereby completing an intransitive loop. In a multi-year collection of yeast isolates from vineyards across New Zealand, we observed a near-complete disappearance of a previously common killer yeast genotype of S. cerevisiae over consecutive years. Using space-time-shift competition assays, we demonstrate that strains sympatric to this killer genotype were universally toxin-resistant, unlike the allopatric strains that were frequently eliminated in competition assays. Furthermore, the extinction of the focal killer genotype appears to have enabled the emergence of toxin-susceptible competitors in sites formerly occupied by the killer genotype. Our findings suggest that the competitive advantage of toxin production is evident in natural populations but appears to be eroded when resistance evolves in competitors of the focal killer genotype. We suggest that such killer-resistant-susceptible polymorphisms are being maintained by evolutionary dynamics akin to rock-paper-scissors-like intransitivity, driven by the invasion of susceptible strains after costly resistance has driven killer strains to extinction in natural populations, all being driven by toxin-encoding coinfections.},
}

@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/ ; },
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.},
}

@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 = {},
number = {},
pages = {},
pmid = {41760926},
issn = {2058-5276},
support = {JPMJER1902//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; 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)/ ; 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)/ ; },
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.},
}

@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},
doi = {10.1371/journal.pone.0336145},
pmid = {41758921},
issn = {1932-6203},
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.},
}

@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 = {},
doi = {10.3390/plants15040543},
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 = {},
doi = {10.3390/microorganisms14020455},
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 = {},
doi = {10.3390/microorganisms14020380},
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 = {},
doi = {10.3390/life16020287},
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 = {},
doi = {10.3390/molecules31040693},
pmid = {41752469},
issn = {1420-3049},
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.},
}

@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 = {},
doi = {10.3390/ijms27042031},
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/ ; },
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.},
}

@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 = {},
doi = {10.3390/ani16040610},
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 = {},
doi = {10.3390/biom16020334},
pmid = {41750402},
issn = {2218-273X},
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.},
}

@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 = {},
doi = {10.3390/biology15040363},
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 = {},
doi = {10.3390/biology15040314},
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 = {},
doi = {10.3390/biology15040311},
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 = {},
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},
doi = {10.1590/1678-4685-GMB-2025-0179},
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},
doi = {10.1371/journal.pbio.3003304},
pmid = {41739865},
issn = {1545-7885},
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.},
}

@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 {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 {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 = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag071},
pmid = {41731702},
issn = {1532-2548},
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.},
}

@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 {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.},
}

@article {pmid41722168,
year = {2026},
author = {Lange, K and Ferrier-Pagès, C and Canestrier, L and Rottier Henry, C and Marcus Do Noscimiento, MI and Béraud, E},
title = {Survival at a cost: Corals endure microplastic and nanoplastic pollution by sacrificing energy reserves.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119436},
doi = {10.1016/j.marpolbul.2026.119436},
pmid = {41722168},
issn = {1879-3363},
abstract = {Plastic pollution poses an increasing threat to coral reef ecosystems, yet the physiological impacts of small-sized microplastics (MPs; ∅ 2.1 μm) and nanoplastics (NPs; ∅ 30 nm) at low mass concentrations (MPs: 5.25 × 10[-4] mg L[-1]; NPs: 2.4 × 10[-2] mg L[-1]) comparable to those found in situ (<0.01 mg L[-1]) remain largely unknown. In this study, the effects of chronic exposure to MPs and NPs on two symbiotic scleractinian coral species, Stylophora pistillata and Turbinaria reniformis, were investigated over 5 and 10 weeks under controlled laboratory conditions. We evaluated symbiont physiology, photosynthetic performance, respiration, and energy reserve content of the holobiont. The results show that S. pistillata was highly sensitive to MPs, with progressive bleaching, reduced photosynthesis, and significant depletion of lipids, proteins, and carbohydrates. Despite transient metabolic adaptations after 5 weeks, prolonged exposure resulted in physiological decline. In contrast, T. reniformis maintained stable symbiotic parameters, but still exhibited a reduction in net photosynthesis and energy reserves, indicating sublethal physiological costs. NPs elicited milder and delayed effects in both species, with significant effects in S. pistillata occurring only after 10 weeks, possibly due to the low NP mass concentration used. Species-specific responses were likely influenced by differences in morphology, polyp size, heterotrophic capacity, and the dominant Symbiodiniaceae clade. These findings demonstrate that low mass concentrations of plastics can nonetheless disrupt coral physiology and energy balance over time. This can affect coral fitness and their resilience to additional stressors such as ocean warming.},
}

@article {pmid41720786,
year = {2026},
author = {Yao, Y and Han, B and Bodegom, PMV and Dong, X and Zhong, Y and Niu, S and Chen, X and Li, Z},
title = {Plant traits explain variation in symbiotic nitrogen fixation responses to global nitrogen enrichment: a meta-analysis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69876-1},
pmid = {41720786},
issn = {2041-1723},
abstract = {Anthropogenic nitrogen enrichment is widely expected to suppress symbiotic nitrogen fixation in terrestrial ecosystems. Nevertheless, observed symbiotic nitrogen fixation responses remain incompletely explained by exogenous nitrogen inputs, climate, and edaphic factors. In this meta-analysis, we integrate 908 globally distributed field measurements to identify the key predictors that improve simulation of symbiotic nitrogen fixation responses to nitrogen enrichment. On average, symbiotic nitrogen fixation declines by 33.0% upon nitrogen enrichment, with the reduction being more pronounced in non-croplands than croplands. Models considering only environmental factors overestimate symbiotic nitrogen fixation decline relative to observations. The better performance of plant traits like plant growth and biomass allocation (shoot:root ratio) partially buffer symbiotic nitrogen fixation suppression under nitrogen enrichment. Integrating both environmental factors and plant performance traits improves predictive accuracy of symbiotic nitrogen fixation responses by 42.7% and brings the simulated symbiotic nitrogen fixation reductions into close agreement with observations. The alterations in plant performance traits are thus critical for explaining variability in terrestrial symbiotic nitrogen fixation responses, and incorporating plant trait dynamics in Earth System Models can quantitatively partition the compensatory symbiotic nitrogen fixation supported by nitrogen-fixing plant growth from the direct negative impact of nitrogen inputs.},
}

@article {pmid41719980,
year = {2026},
author = {Xu, Y and Ke, J and Zhang, Y and Chen, X and Wang, Y},
title = {Harnessing AMF-plant-microbe systems for heavy metal remediation.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119885},
doi = {10.1016/j.ecoenv.2026.119885},
pmid = {41719980},
issn = {1090-2414},
abstract = {Soil heavy metal pollution poses a global environmental threat, demanding effective and sustainable remediation strategies. Arbuscular mycorrhizal fungi (AMF) play a multifaceted role in enhancing the remediation of heavy metal (HM)-contaminated soils through extensive hyphal networks that interact with plant roots and soil microbiota. AMF hyphae and their exudates, such as glomalin, directly immobilize metal ions and reduce bioavailability by modifying soil properties (e.g., pH). Furthermore, AMF reshape the rhizosphere microbiome by enriching metal-tolerant bacteria (e.g., Pseudomonas, Bacillus) and fostering synergistic microbial communities via cross-kingdom signaling. Within plants, AMF symbiosis-especially with hyperaccumulators-optimizes root architecture, enhances nutrient and water uptake, stimulates biomass production, and regulates key physiological and molecular responses. These include bolstering antioxidant defenses, maintaining photosynthetic efficiency, and upregulating genes involved in metal transport, compartmentalization, and stress signaling. Field studies confirm the potential of AMF-hyperaccumulator systems in metal extraction and stabilization. However, transitioning from controlled experiments to field applications remains challenging due to the complexity of multipartite interactions and a lack of predictive frameworks. This review critically integrates interdisciplinary insights into a forward-looking perspective, emphasizing the need to shift from empirical approaches to an intelligent, predictive design paradigm. We propose leveraging machine learning to decode interactions among AMF genotypes, plant phenotypes, microbial consortia, and soil properties, enabling the rational design of efficient remediation systems. Ultimately, overcoming barriers to field implementation requires integrating robust science with advanced engineering and supportive policy frameworks.},
}

@article {pmid41717118,
year = {2026},
author = {Wu, J and Chen, K and Sheng, L and Han, H and Li, J and Guo, Z and Gong, S and Wang, H and Chen, L and Zhang, Z and Gao, F},
title = {Spatiotemporal dynamics of rhizosphere microbial communities under different mulching methods in spring maize.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1732283},
pmid = {41717118},
issn = {1664-462X},
abstract = {INTRODUCTION: Plastic film mulching is a critical practice in arid agroecosystems, yet its spatiotemporal impacts on the rhizosphere microbiome remain poorly understood.

METHODS: Here, we investigated how no-mulching (CK), on-film hole sowing (UPM), and film-side planting (FPM) shape the bacterial and fungal communities in the maize rhizosphere across developmental stages (V12 and R6) and soil depths (10, 20, and 30 cm).

RESULTS: Concurrently, both mulching strategies increased maize yield relative to CK, with FPM ultimately outperforming UPM (19.05% vs. 6.24%). Amplicon sequencing showed that mulching strongly structured the rhizosphere microbiome with clear spatiotemporal variation. Bacterial and fungal communities exhibited contrasting patterns: bacteria responded mainly in topsoil at V12 and across all depths by R6, whereas fungi responded across the soil profile at V12, with responses weakening with depth at R6. Mulching-particularly UPM-reduced key taxa, including the nitrifying genus Nitrospira and symbiotic Glomeromycota. Correlation analyses revealed significant associations between these taxonomic shifts and maize yield components, consistent with Nitrospira's preference for aerobic conditions. Functional predictions suggested UPM favored communities with higher representation of anaerobic decomposition pathways, whereas FPM supported greater potential for aerobic heterotrophy and nitrogen-related processes.

DISCUSSION: Although microbial shifts were correlated with yield components, yield increases were likely dominated by the direct physical effects of mulching. Overall, distinct mulching strategies generated divergent rhizosphere trajectories, with FPM potentially offering a more sustainable option for dryland maize production.},
}

@article {pmid41717113,
year = {2026},
author = {Sultan, Y and Ullah, I and Paľove-Balang, P and Mukhtiar, A and Mudasir, M and Bačovčinová, M and Kemešyte, V and Liatukiene, A and Petrauskas, G and Norkevičienė, E},
title = {Factors affecting the genetic diversity of Lotus corniculatus in the Hemi-boreal zone of Baltic States and their agronomical implications.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1748495},
pmid = {41717113},
issn = {1664-462X},
abstract = {Bird's-foot trefoil (BFT) is an underutilized perennial legume of increasing importance for sustainable agriculture in Europe, particularly within the Hemi-boreal zone of the Baltic states. It is a resistant, symbiosis-forming, and abiotic stress resistance making it a nitrogen-fixing soil, high potential of biodiversity conservation, pasture restoration, and low input farming systems. Yet, molecular genetic investigations of BFT with systematic investigations populations, of Lithuania, of Latvia, and of Estonia, are practically non-existent, to develop a critical knowledge gap in the agricultural development of the region and conservation planning. This gap is filled by this review through (1) synthesizing global evidence on BFT genetic diversity, population structure, adaptive traits, and characteristics revealed by molecular markers; (2) surveying the little information on the same already available distribution, habitat diversity, and ecotypic variation of the Baltic region; (3) the critical assessment of the applicability of the findings of neighboring European, Transcaucasian, and Central Asian races to Baltic Hemi-boreal states; and (4) setting out a research framework and future research priorities in Baltics-specific genetic studies. We point out the action of ecological gradients, climatic anthropogenic activities, pressures, and biotic interactions on population differentiation and adaptability based on research of the neighboring lands and ecological zones. By directly filling in the existing gap of lack of Baltic-specific molecular data, our analysis creates a level of cognition, which is a synthesis of global comprehension research and a knowledge road map of addressing gaps of knowledge that are critical. The findings underscore that BFT needs genetic diversity to be able to persist despite alteration. Hemi-boreal status and satisfaction of European Union biodiversity and agriculture sustainability goals. Local genetic resources will be tapped through the collection of customized germplasm, which will be molecularly characterized and bred according to their specific ecotype. This approach is essential for developing robust forage systems and supporting productive grassland restoration in the Baltic States. The findings underscore that genetic diversity in BFT is essential for its persistence under changing Hemi-boreal conditions and for meeting European Union biodiversity and agriculture sustainability goals. High genetic diversity provides the adaptive foundation necessary for breeding stress-tolerant cultivars, enhancing nitrogen fixation efficiency, and maintaining ecosystem resilience under climate variability and evolving agricultural practices. The conservation of local genetic resources, molecular characterization, and breeding of ecotypes will be crucial for utilizing these resources to develop resilient forage systems and promote efficient grassland recovery in the Baltic States, where baseline genetic diversity data remains limited.},
}

@article {pmid41717090,
year = {2025},
author = {Karunarathna, SC and Tibpromma, S and Karunarathna, BS and Dai, DQ and Kumla, J and Lu, W and Perera, RH and Wang, M and Priyadarshani, TDC and Hapuarachchi, KK and Suwannarach, N},
title = {Mushrooms in climate change mitigation: a comprehensive review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727022},
pmid = {41717090},
issn = {1664-302X},
abstract = {Mushroom-forming basidiomycetes are increasingly recognized for their significant potential to remediate polluted environments and mitigate climate change. This review synthesizes evidence positioning mushroom-forming basidiomycetes at the nexus of ecological resilience and a sustainable bioeconomy, highlighting their dual roles in environmental repair and green innovation. Ectomycorrhizal (ECM species) enhance carbon acquisition by plants and long-term soil carbon sequestration; ECM-dominant forests stockpile upto 70% more below-ground carbon than their non-mycorrhizal counterparts. Saprotrophic fungi drive lignocellulose degradation, nutrient cycling, and the stabilization of soil organic matter. Basidiomycetes also play a crucial role in mycoremediation by degrading recalcitrant contaminants (pesticides, hydrocarbons) and immobilizing heavy metals. Furthermore, mycelium-based biomaterials are being developed as green-technology alternatives to plastics and synthetic foams, reflecting the growing commercialization of fungal biotechnology, as evidenced by the global mycelium material industry projected to exceed USD 5 billion by 2032. The intersection of ecological function and economic value positions mushrooms at the forefront of the circular bioeconomy. However, challenges remain, including production scalability, environmental sensitivity, and economic viability. Addressing these challenges through interdisciplinary research could unlock the full potential of fungi as nature-based climate solutions.},
}

@article {pmid41716666,
year = {2026},
author = {Tuo, Y and Chu, H and Wang, L and Qi, Z and Hu, J and Zhang, B and Li, Y and Li, X},
title = {Three new species and two new records of Hydnum (Hydnaceae, Cantharellales) from the Dabie Mountains, China.},
journal = {MycoKeys},
volume = {128},
number = {},
pages = {167-195},
pmid = {41716666},
issn = {1314-4049},
abstract = {Hydnum (Hydnaceae, Cantharellales), one of the edible ectomycorrhizal fungi, is characterized by a spine-bearing hymenophore. It is widely distributed in temperate regions and forms stable symbiotic relationships with Fagaceae and Pinaceae. During a survey of macrofungi in the Dabie Mountains region of China, ten specimens of Hydnum were collected. Based on morphological characteristics and phylogenetic analysis using three genetic markers (ITS + nrLSU + tef1-α), three new species (H. luteoalbum, H. albodentum, and H. albotomentosum) were identified and described, and two species newly recorded from the Dabie Mountains (H. berkeleyanum and H. pallidomarginatum) were reported. H. luteoalbum is distinguished by a white pileus covered with white tomentum, dagger-shaped or sword-like spines, and broadly ellipsoid basidiospores. H. albodentum is characterized by a pale brown pileus and subelliptical basidiospores (8.0-8.5 × 6.0-7.0 μm; av. Q = 1.17). H. albotomentosum features smaller basidiocarps, extremely short spines (0.5-2 mm), and globose to subglobose basidiospores. This study enriches the known taxonomic diversity of Hydnum and provides a dichotomous key to the species of Hydnum in China to facilitate species identification.},
}

@article {pmid41716576,
year = {2026},
author = {Yuan, X and Li, H and Yu, X and Ji, Z},
title = {Genetic Adaptation of Mesorhizobium Symbionts Associated With Caragana in Northern China Deserts.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73134},
pmid = {41716576},
issn = {2045-7758},
abstract = {Caragana, a keystone leguminous species dominating arid semi-fixed deserts in northern China, forms specialized symbiotic nitrogen-fixing partnerships with Mesorhizobium, which are indispensable for sustaining ecosystem function globally. However, the roles of membrane transporters and nucleotide repair genes in conferring survival advantages to desert-dwelling Mesorhizobium across desert environments remained poorly elucidated. Therefore, a total of 68 representative Mesorhizobium strains associated with Caragana, isolated from five geographically distant areas (A to E) in the desert belt of northern China, were investigated to elucidate the pivotal roles of three membrane transporters (cysW, exoY, idhA) and two nucleotide repair genes (mutS, uvrC) in microbial adaptation to environmental stress. Phylogenetic analysis results revealed that strains assigned to the same genospecies primarily clustered by genetic lineage rather than geographic origin, with stronger intralineage sequence cohesion observed relative to interregional divergence. Notably, phylogenetic trees of membrane transporter genes, nucleotide repair genes, and core genes showed high topological congruence, underscoring their concerted evolutionary dynamics and shared selective pressures. Furthermore, consistent nucleotide diversity (π), low πN/πS ratios (<< 1.0) and genetic distance (Dxy) across populations indicated that purifying selection predominated in membrane transporters and nucleotide repair genes. Elevated recombination impact (r/m) and frequency (ρ/θ) revealed that homogenizing gene flow, rather than mutation, was the primary driver of population differentiation enabling rapid adaptation to desert environments.},
}

@article {pmid41716420,
year = {2026},
author = {Liao, J and Zhou, Z and Lv, Y and Zhang, Y and Liu, S and Tang, H and Qv, F and Wang, S and Yang, L and Lu, Y and Yang, Z and Xie, X and Shao, M},
title = {Pathogenesis and intervention strategies for metabolic dysfunction-associated fatty liver disease from the perspective of the gut-microbiota-liver axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1667180},
pmid = {41716420},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver/metabolism/pathology ; Animals ; *Non-alcoholic Fatty Liver Disease/therapy/microbiology/metabolism/etiology ; Probiotics/therapeutic use ; },
abstract = {Trillions of microorganisms in the human gut are important regulators of health, and the gut and liver have a symbiotic relationship with them. The study found that there is bidirectional communication of substances and signals between the gut and liver, and the gut microbiota is an important medium for mediating bidirectional communication in the gut-liver axis. During metabolic dysfunction-associated fatty liver disease (MAFLD) development, the gut microbiota and its metabolites change to different degrees and affect MAFLD pathogenesis through the gut-liver axis. However, the bidirectional communication mechanism between the gut and liver in MAFLD remains unexplored, and further investigation in this domain is warranted. In this review, we summarize the role of the gut-liver axis in the pathogenesis of MAFLD and explore potential therapeutic strategies targeting intestinal microecology (such as probiotic intervention and phage therapy) to provide a theoretical basis for the precise prevention and treatment of MAFLD.},
}

Humans
*Gastrointestinal Microbiome
*Liver/metabolism/pathology
Animals
*Non-alcoholic Fatty Liver Disease/therapy/microbiology/metabolism/etiology
Probiotics/therapeutic use

@article {pmid41716122,
year = {2026},
author = {Bibi, AC and Ioannidis, P and Spilianakis, C and Vasilarou, M and Bazakos, C and Pavlidis, P and Kalantidis, K},
title = {High-Quality Genome Assembly and Annotation of Ceratonia siliqua Provide Insights Into the Secondary Loss of Symbiotic Nitrogen Fixation.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70803},
doi = {10.1111/ppl.70803},
pmid = {41716122},
issn = {1399-3054},
support = {OP 402//Region of Crete/ ; MIS: 5163923//Hellenic Foundation for Research and Innovation/ ; },
mesh = {*Nitrogen Fixation/genetics/physiology ; *Fabaceae/genetics/physiology ; *Genome, Plant/genetics ; *Symbiosis/genetics ; Molecular Sequence Annotation ; Retroelements/genetics ; Phylogeny ; },
abstract = {The carob tree (Ceratonia siliqua L.), an evergreen legume native to West Asia and long cultivated throughout the Mediterranean basin, is valued for its drought tolerance, nutritious pods, and ecological value. Despite its economic and environmental importance, genomic resources for this species have been limited. Here, we present a high-quality, chromosome-scale genome assembly of C. siliqua, generated using PacBio HiFi long-read and Hi-C sequencing technologies. The final assembly spans 501.39 Mb, organized into 12 pseudomolecules, with a scaffold N50 of 39.58 Mb. Genome annotation identified 30,295 protein-coding gene models, with 99.5% completeness according to conserved single-copy orthologs. Repetitive elements account for 52.2% of the genome, primarily long terminal repeat (LTR) retrotransposons of the Gypsy and Copia families. Comparative orthology analysis with 24 other plant genomes revealed conserved gene content and a substantial number of species-specific genes in C. siliqua. Demographic inference using the PSMC model indicated historical population size fluctuations, with convergence in effective population size between Cretan and Moroccan populations approximately 50,000 years ago. Notably, we investigated the potential for symbiotic nitrogen fixation, a trait ancestral to legumes. Genomic evidence suggests pseudogenization of key nodulation genes (NIN and RPG), consistent with ecological observations of the absence of root nodules. These results support the hypothesis of a secondary loss of nodulation in C. siliqua. This genome provides a valuable resource for evolutionary, ecological, and agricultural studies, particularly for understanding legume adaptation to Mediterranean climates and the molecular basis of symbiotic regression.},
}

*Nitrogen Fixation/genetics/physiology
*Fabaceae/genetics/physiology
*Genome, Plant/genetics
*Symbiosis/genetics
Molecular Sequence Annotation
Retroelements/genetics
Phylogeny

@article {pmid41715139,
year = {2026},
author = {Bajerlein, D and Zduniak, P and Wyszyńska, A and Baraniak, E and Przewoźny, M and Grzegorczyk, T and Urbański, A},
title = {Males have a greater mite burden than females, and size does not matter: species- and sex-specific infestation patterns of mites (Uropodina) on burying beetles (Nicrophorus spp.).},
journal = {Frontiers in zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12983-026-00601-w},
pmid = {41715139},
issn = {1742-9994},
support = {No. OR.271.3.9.215//the National Forest Holding "The State Forests", Poland/ ; },
abstract = {BACKGROUND: Phoretic mites and their carriers represent a dynamic system shaped by ecological and evolutionary processes. In highly specific phoresy, which involves long-term or permanent associations, profound consequences for phoretics, including cospeciation or the transition to phoretic parasitism, can occur. Mites within the complex of cryptic species of Uroobovella nova are carried exclusively on burying beetles (Nicrophorus spp.). Nevertheless, compared with the Poecilochirus mite-Nicrophorus system, this type of interaction remains poorly understood. In this study, we investigated whether different species of burying beetles play the same role in the local dispersal of U. nova deutonymphs. To achieve this, we compared the infestation patterns of deutonymphs among field-collected beetle species, while accounting for sex and body size.

RESULTS: Our results revealed species-specific patterns in deutonymph infestations, with Nicrophorus vespillo being the most frequently infested species, followed by N. humator and N. interruptus. Furthermore, Nicrophorus vespillo and N. humator hosted the greatest number of deutonymphs, whereas in N. interruptus, the number of carried mites was significantly lower. The infestation pattern of U. nova demonstrated significant sexual bias, with males exhibiting higher mite prevalence and intensity than females. Interestingly, the variation in host body size was not a significant predictor of U. nova infestation. Although more mites were attached to the anterior than to the posterior parts of the beetle body in all the examined species, species- and sex-specific patterns in the distribution of deutonymphs were evident.

CONCLUSIONS: Species-specific infestation patterns indicate that, at the local scale, individual burying beetle species play different roles in the dispersal of U. nova mites. Sex-specific infestation patterns suggest that biological differences between females and males may be key determinants of deutonymph infestations. Body size does not drive the prevalence, intensity, or distribution of deutonymphs. The assumption that larger hosts carry more symbionts does not hold universally in ecology.},
}

@article {pmid41713736,
year = {2026},
author = {He, S and Fu, L and Shi, Y and Shi, W and Zhang, S and Gao, Z and Li, X},
title = {Root exudate-mediated nutrient exchange in the rhizosphere: multi-element networks, dynamic regulation, and implications for sustainable agriculture.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.02.039},
pmid = {41713736},
issn = {2090-1224},
abstract = {BACKGROUND: Over hundreds of millions of years of co-evolution, plants and microbes have co-optimized nutrient exchange strategies at the rhizosphere-the core interface for chemical communication-leading to highly diverse and sophisticated patterns. Although recent studies have partially clarified the mechanisms underlying carbon-nitrogen, carbon-phosphorus, and other nutrient exchange processes between plant roots and microbes, a systematic understanding of these nutrient exchange strategies remains insufficient.

AIM OF REVIEW: This review synthesizes recent research findings on root metabolites and plant-microbe nutrient exchange, analyzes the collaborative mechanisms of key nutrient elements (nitrogen, phosphorus, potassium) in the rhizosphere, explores the dynamic response characteristics of multi-element interaction networks to stresses such as drought, salinity and pathogens, and discusses the implications of these processes for plant environmental adaptability. Additionally, it summarizes advanced technologies applied in rhizosphere nutrient research and outlines future research directions, thereby providing a theoretical basis for understanding the functional mechanisms of rhizosphere ecosystems and promoting the development of sustainable agriculture.

Root exudates act as both chemical signals for cross-kingdom communication and metabolic resources. Via root exudate-mediated carbon allocation mechanisms, plants and microbes construct multidimensional interaction networks in the rhizosphere. These networks involve both macronutrients (nitrogen, phosphorus, potassium) and micronutrients (sulfur, iron, zinc), with synergistic regulation between elements. The co-evolved nutrient exchange strategies are highly diverse and precise. They not only regulate nutrient exchange via element interaction networks but also dynamically adjust to plant growth stages, soil conditions, and stresses (e.g., drought, salinity, pathogens). This dynamic adjustment helps plants overcome soil nutrient limitations, thereby enhancing their adaptability to complex environments.},
}

@article {pmid41713632,
year = {2026},
author = {Yu, XZ and Liu, ZY},
title = {Advances in response mechanisms of fish to ammonia stress: A review.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110487},
doi = {10.1016/j.cbpc.2026.110487},
pmid = {41713632},
issn = {1532-0456},
abstract = {Ammonia stress has emerged as a critical challenge in global aquaculture, driving extensive research into fish response mechanisms spanning physiological, molecular, and ecological dimensions. This review synthesizes advances in understanding multi-tiered adaptations, including branchial ammonia excretion, urea/glutamine conversion pathways, and microbial symbiosis-mediated detoxification. Key findings highlight species-specific strategies: teleosts prioritize oxidative stress mitigation via Nrf2/glutathione redox regulation, while ureogenic species enhance urea cycle enzyme activities. Microbial communities in aquatic ecosystems further modulate ammonia dynamics through nitrification and denitrification processes. Current mitigation approaches ranging from bioaugmentation and photocatalytic oxidation to dietary antioxidants like probiotics and polyphenols demonstrate efficacy but face limitations in scalability and ecological compatibility. Emerging technologies such as CRISPR-edited ammonia-tolerant strains, real-time water quality monitoring, and circular bioeconomy models (e.g., algal bioconversion of effluents) may represent paradigm-shifting solutions. Future research must integrate multi-omics platforms with ecological modeling to decode evolutionary trade-offs between detoxification energetics and growth performance, ultimately enabling precision aquaculture systems that harmonize productivity with environmental resilience. This comprehensive analysis not only refines theoretical frameworks for ammonia toxicity but also contributes to developing effective strategies for sustainable aquaculture management and addressing the ongoing challenge of ammonia pollution.},
}

@article {pmid41711653,
year = {2026},
author = {Usai Satta, P and Astegiano, M and Pasta, A and Romano, A and Ciprandi, G and Brandimarte, G},
title = {The SymbioCare initiative: management of irritable bowel syndrome, comparison between Italian gastroenterologists and general practitioners.},
journal = {Minerva gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5985.25.03987-7},
pmid = {41711653},
issn = {2724-5365},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common medical condition characterized by different phenotypes. Diarrhea is usually prevalent in IBS patients, but constipation and meteorism are also common. Pharmacological therapies do not modify the IBS natural history. Thus, food supplements are used in clinical practice. The present Italian educational activity investigated the characteristics of IBS patients and compared the attitudes of gastroenterologists (GEs) and general practitioners (GPs).

METHODS: Fifty-three gastroenterologists and 42 GPs enrolled 2442 IBS patients. This initiative consisted of two distance learning sessions and a field training session. Demographic and clinical parameters, tests, and treatments (including past/ongoing and current) were collected.

RESULTS: Mean age (46 years), female gender, and IBS with diarrhea were prevalent and consistent with literature data. Roma IV criteria were scarcely adopted by GPs. Patients managed by GEs were more complex than patients followed by GPs. GEs prescribed more appropriate diagnostic tests than GPs. Food supplements were commonly used both alone or combined with drugs, mainly by GPs. Symbiotic use was associated with less cramping pain, tension pain, and meteorism than other food supplements. An impressive increase in symbiotic prescriptions occurred during the field training.

CONCLUSIONS: This real-world experience described the main characteristics of IBS patients, highlighted the differences between GEs and GPs, and reinforced the importance of educational programs in updating the medical class.},
}