@article {pmid40552053,
year = {2025},
author = {Menéndez, E and Brígido, C},
title = {Editorial: Deciphering the root nodule microbiome: implications for legume fitness and stress resilience.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634838},
pmid = {40552053},
issn = {1664-302X},
}

@article {pmid40551765,
year = {2025},
author = {Zhu, J and Giri, K and Lin, Z and Cogan, NO and Jacobs, JL and Smith, KF},
title = {Estimation of ryegrass (Lolium) dry matter yield using genomic prediction considering genotype by environment interaction across south-eastern Australia.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1579376},
pmid = {40551765},
issn = {1664-462X},
abstract = {Genomic Prediction (GP) considering Genotype by Environment (G×E) interactions was, for the first time, used to assess the environment-specific seasonal performance and genetic potential of perennial ryegrass (Lolium perenne L.) in a regional evaluation system across southeastern Australia. The study analysed the Dry Matter Yield (DMY) of 72 base cultivars and endophyte symbiotic effects using multi-harvest, multi-site trial data, and genomic data in a best linear unbiased prediction framework. Spatial analysis corrected for field heterogeneities, while Leave-One-Out Cross Validation assessed predictive ability. Results identified two distinct mega-environments: mainland Australia (AUM) and Tasmania (TAS), with cultivars showing environment-specific adaptation (Base and Bealey in AUM; Platinum and Avalon in TAS) or broad adaptability (Shogun). The G×E-enhanced GP model demonstrated an overall 24.9% improved predictive accuracy (Lin's Concordance Correlation Coefficient, CCC: 0.542) over the Australian industry-standard best linear unbiased estimation model (CCC: 0.434), with genomic information contributing a 12.7% improvement (CCC: from 0.434 to 0.489) and G×E modelling providing an additional 10.8% increase (CCC: from 0.489 to 0.542). Narrow-sense heritability increased from 0.31 to 0.39 with G×E inclusion, while broad-sense heritability remained high in both mega-environments (AUM: 0.73, TAS: 0.74). These findings support informed cultivar selection for the Australian dairy industry and enable genomics-based parental selection in future breeding programs.},
}

@article {pmid40551761,
year = {2025},
author = {Soldek, JN and Ballesteros-Gutiérrez, M and Díaz-Sáez, L and Delgado-Santamaría, I and Palacios, JM and Albareda, M},
title = {Two zinc ABC transporters contribute to Rhizobium leguminosarum symbiosis with Pisum sativum and Lens culinaris.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1598744},
pmid = {40551761},
issn = {1664-462X},
abstract = {The establishment of the rhizobium-legume symbiosis requires adjusting the behavior of both partners to nodule conditions in which transition metals are delivered to the bacteria, as many rhizobial metalloenzymes are essential for bacteroid functions and symbiotic performance. A previous proteomic analysis revealed the existence of a relevant number of proteins differentially expressed in bacteroids induced by Rhizobium leguminosarum bv. viciae (Rlv) UPM791 in pea and lentil nodules. Among these proteins, a metal-binding protein (RLV_3444) component of an ABC-transporter system (RLV_3442-3444) was shown to be overexpressed in pea bacteroids, suggesting that metal provision to the bacteroid is more restrictive in the rhizobium-pea symbiosis. In this work, protein sequence analysis and structural modelling have revealed that RLV_3444 is highly similar to the functionally characterized zinc-binding protein ZniA from Klebsiella pneumoniae, so the host-dependent binding protein was renamed as ZniA and the transporter system as ZniCBA. The genome of Rlv UPM791 also encodes the conserved high-affinity ZnuABC transporter system. We demonstrate that at least one of the two systems must be present for Rlv to grow under zinc-limiting conditions and for optimal symbiotic performance with pea and lentil plants. The three conserved histidine residues present in multiple Zn[2+]-binding proteins have been shown as essential for the function of Rlv ZniA, and in-silico modelling suggests that they might participate in metal coordination. We also demonstrate that both ZniCBA and ZnuA are regulated by zinc in a Zur-dependent manner, consistent with the presence of a Zur box in their regulatory region. The expression patterns revealed that ZniCBA is expressed at lower levels than ZnuA, and its expression increased in a znuA mutant under both free-living and symbiotic conditions. These results, along with the observed increment in the expression of ZniCBA in pea versus lentil bacteroids, suggest that the host-dependent transporter system might play an auxiliary function for zinc uptake under zinc starvation conditions and might play a relevant role in the adaptation of rhizobia to the legume host.},
}

@article {pmid40550998,
year = {2025},
author = {Hu, Y and Liu, Z and Yao, H and Wu, S and Zhang, Q and Pan, S and Shi, S},
title = {Colonization patterns of intestinal pioneering microbiota of different broiler breeds and their effects on composition of intestinal mucosal barrier during early life.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40550998},
issn = {1869-1889},
abstract = {Intestinal pioneering microbiota can affect host growth, development, and health via microbial programming. However, the presence of microbial colonization in the intestine of embryonic chickens, development and colonization patterns of intestinal pioneering microbiota of different broiler breeds and their effects on the composition of intestinal mucosal barrier during early life remain unknown. Arbor Acres (AA) chickens exhibiting high growth efficiency traits and Chinese local Tibetan chickens exhibiting high environmental adaptability traits were used as experimental animals to verify the absence of bacterial colonization and a sterile state in embryonic chickens intestine under normal maternal health. During neonatal early stage, jejunal mucosal structure and barrier function of AA chickens with higher growth efficiency were more conducive to digestion and absorption, corresponding to persistently higher microbial maturity, whereas those of Tibetan chickens with lower growth efficiency were more conducive to stress resistance, corresponding to lower microbial maturity. Colonization patterns of intestinal pioneering microbiota were significantly different between the two breeds. The dominant microbiota of AA chickens, such as Erysipelatoclostridium, Hydrogenoanalobacterium and Shuttleworthia, were related to growth and metabolic functions, whereas those of Tibetan chickens, such as Limosilactobacillus, Ligilactobacillus and Prevotella, were related to immune and anti-stress functions. Transplanting intestinal pioneering microbiota of the donor could transfer the abundance of dominant microbiota to the recipient in a symbiotic state. Growth efficiency and adaptability of transplanted AA chickens improved, accompanied by optimized jejunal mucosal structure and function. However, the growth efficiency of transplanted Tibetan chickens was not affected by the modified microbiota diversity. It was suggested that cross-FMT technology achieved inter-breed complementary advantages of high growth efficiency and high adaptability traits of broilers during neonatal early life; the higher maturity of intestinal pioneering microbiota of the recipient, the more growth efficiency of the recipient would be susceptibly affected by transplanting intestinal pioneering microbiota of the donor.},
}

@article {pmid40550670,
year = {2025},
author = {Nie, Q and Zhang, S and Chen, C and Zou, J and Nie, S},
title = {[Mining and dietary interventions of gut microbiota-derived metabolites].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2275-2289},
doi = {10.13345/j.cjb.240681},
pmid = {40550670},
issn = {1872-2075},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Dysbiosis/microbiology ; *Metabolic Diseases/prevention & control/microbiology/metabolism ; *Diet ; },
abstract = {The intestine is a complex symbiotic system, and the gut microbiota is closely related to host health. Studies have indicated that the gut microbiota influences physiological functions of the host by producing a variety of metabolites, which act as signaling molecules and substrates for metabolic reactions in the host. Dysbiosis of the gut microbiota affects the abundance of gut microbiota-derived metabolites, thereby influencing host health by disrupting signal transduction in multiple organs. Additionally, dietary compounds can shape the gut microbiota, affecting gut microbiota-derived metabolite levels and regulating host metabolism. This article introduces the methods for mining gut microbiota-derived metabolites, reviews the roles of these metabolites in metabolic diseases and related dietary interventions. Which provides a perspective on the prevention and treatment of metabolic diseases by targeting these metabolites, enriching the knowledge on the role of gut microbiota in the regulation of host metabolism.},
}

*Gastrointestinal Microbiome/physiology
Humans
Dysbiosis/microbiology
*Metabolic Diseases/prevention & control/microbiology/metabolism
*Diet

@article {pmid40550427,
year = {2025},
author = {Akber, MA and Cui, Y and Zhang, J and Fang, X},
title = {Genomics of plant-associated fungi: research progress and highlights in forage crops.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112624},
doi = {10.1016/j.plantsci.2025.112624},
pmid = {40550427},
issn = {1873-2259},
abstract = {Plant-associated fungi are fungal groups that exhibit different interactions with plants, such as symbiosis (mycorrhizae), antagonistic (pathogenic) and beneficial (biocontrol), and commensal relationships. Since the publication of the first fungal genome sequence of the rice blast pathogen Magnaporthe grisea in 2005, a new chapter in the genome exploration of plant-associated fungi has been initiated. Research in past decades showed about 1385 sequenced fungal genomes associated with plants. These genomes are linked with grain crops (e.g., wheat, rice), cash crops (e.g., soybean, cotton), and forage crops. The reported fungal functional groups associated with plants include pathogens, endophytes, mycorrhizal fungi, and saprotrophs. Based on our results, among surveyed functional groups, pathogenic fungi were dominant, comprising 96%, followed by endophytes (2%) and other fungi with unclear plant-associated roles (2%). There is no doubt that forage crops support animal nutrition and the sustainability of grasslands. However, only 3.5% of sequenced genomes are associated with forage crops, compared with 67% for food and cash crops. The top 3 host crops with the highest sequenced fungal genomes are wheat (285), rice (178), and apple (94). In this study, we systematically reviewed fundamental information and challenges related to genomics studies of plant-associated fungi to provide a theoretical basis for subsequent research. The results clearly show that only a few studies have focused on sequencing fungi associated with forage crops. Therefore, it is necessary to accelerate genomic research on forage crop-associated fungi. The findings of the current study address critical gaps in genomic knowledge about plant-associated fungi and provide a foundation for future research targeting forage crop fungi.},
}

@article {pmid40549446,
year = {2025},
author = {Gao, K and He, X and Wang, H and Chen, C and Gu, X and Lai, Q and Perez, M and Kojima, S and Amano, K and Sun, J},
title = {Phylogenomic analyses of Pliocardiinae (Bivalvia: Vesicomyidae) update genus-level taxonomy and shed light on trait evolution.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/cla.70001},
pmid = {40549446},
issn = {1096-0031},
support = {LSKJ202203104//Science and Technology Innovation Project of Laoshan Laboratory/ ; ZR2023JQ014//Natural Science Foundation of Shandong Province/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 202241002//Fundamental Research Funds for the Central Universities/ ; tsqn202103036//Young Taishan Scholars Program of Shandong Province/ ; },
abstract = {Vesicomyid clams in the subfamily Pliocardiinae are chemosymbiotic and specific to deep-sea chemosynthetic ecosystems with wide bathymetric and geographic ranges, making them a suitable model to study molecular adaptation and biogeography. Its phylogeny, however, still remains contentious due to limited molecular markers. Here, we elucidate the evolutionary relationships among pliocardiines based on phylogenomics data. By testing a wide range of matrices with methods including maximum likelihood, maximum parsimony, Bayesian inference, and a coalescent approach, we present a robust phylogenomic tree at the genus level supported by AU-test and GLS analyses. We revise the genus-level taxonomy of pliocardiines updating from Johnson et al. (Syst. Biodivers. 2017, 15, 346) synonymising a number of species in the "gigas-group" with Archivesica-also supported by a mitogenome phylogeny. Our fossil-calibrated tree based on the phylogenomic backbone reveals that Pliocardiinae originated earlier than [41.06, 42.00] Ma in the middle Eocene, while its diversification has been concurrent with global climatic cooling events. Ancestral state reconstruction analyses found two independent invasions into the abyssal zone, and a shift from harbouring the Ca. Ruthia symbionts to Ca. Vesicomyosocius symbionts. Our results present a solid backbone for future investigations into molecular adaptation, biogeography and symbiosis in this fascinating group of molluscs.},
}

@article {pmid40548332,
year = {2025},
author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {283},
pmid = {40548332},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).},
}

@article {pmid40548224,
year = {2025},
author = {Tüsüz Önata, E and Özdemir, Ö},
title = {Fecal microbiota transplantation in allergic diseases.},
journal = {World journal of methodology},
volume = {15},
number = {2},
pages = {101430},
pmid = {40548224},
issn = {2222-0682},
abstract = {Microorganisms such as bacteria, fungi, viruses, parasites living in the human intestine constitute the human intestinal microbiota. Dysbiosis refers to compositional and quantitative changes that negatively affect healthy gut microbiota. In recent years, with the demonstration that many diseases are associated with dysbiosis, treatment strategies targeting the correction of dysbiosis in the treatment of these diseases have begun to be investigated. Faecal microbiota transplantation (FMT) is the process of transferring faeces from a healthy donor to another recipient in order to restore the gut microbiota and provide a therapeutic benefit. FMT studies have gained popularity after probiotic, prebiotic, symbiotic studies in the treatment of dysbiosis and related diseases. FMT has emerged as a potential new therapy in the treatment of allergic diseases as it is associated with the maintenance of intestinal microbiota and immunological balance (T helper 1/T helper 2 cells) and thus suppression of allergic responses. In this article, the definition, application, safety and use of FMT in allergic diseases will be discussed with current data.},
}

@article {pmid40548169,
year = {2025},
author = {De Silva, C and Rathor, P and Warkentin, TD and Poudel, HP and Thilakarathna, MS},
title = {Effect of cultivar selection on symbiotic nitrogen fixation and yield traits of pea cultivars in intercropping with wheat.},
journal = {Discover agriculture},
volume = {3},
number = {1},
pages = {93},
pmid = {40548169},
issn = {2731-9598},
abstract = {In recent decades, agricultural practices have shifted from diverse cropping systems to monocropping, leading to soil degradation, nutrient depletion, and reduced biodiversity, which threaten long-term productivity and ecosystem sustainability. This study aimed to explore how legume cultivar selection influences pea (Pisum sativum L.)-wheat (Triticum aestivum L.) intercropping, focusing on symbiotic nitrogen (N) fixation, yield, seed N, and land productivity. A greenhouse experiment was conducted using various pea cultivars that were released in different decades [Century (1960), Trapper (1970), CDC Golden (2002), CDC Amarillo (2012), and CDC Spectrum (2016)] under monocropping and intercropping with wheat to evaluate the yield parameters and symbiotic N fixation capabilities of pea. The old, long-vined pea cultivars (Century and Trapper) had higher seed dry weight (62.9-66.3%), number of pods (82.7-100%) and number of seeds (126.9-163.5%) than the newer, moderate vine length cultivars (CDC Golden, CDC Amarillo and CDC Spectrum) under intercropping. On the other hand, the companion wheat crop had a greater yield (29.8-69.9%) and seed N (31.1-65.5%) when intercropped with the newer pea cultivars. Intercropping enhanced N fixation (0.7-7.5%) in peas across cultivars; however, the older cultivars contributed more to the overall system's N fixation and N carry-over compared to the newer cultivars. While the harvest index, land equivalent ratio (LER), and N-based LER (LERN) of intercropped wheat were not significantly higher than mono-cropped wheat, the increased partial LER and LERN for wheat highlight intercropping benefits. Overall, newer pea cultivars enhanced pea-wheat intercropping by improving productivity and resource efficiency, highlighting the importance of legume cultivar selection in intercropping.},
}

@article {pmid40547945,
year = {2025},
author = {Zeng, J and He, Z and Wang, G and Ma, Y and Zhang, F},
title = {Interaction Between Microbiota and Immunity: Molecular Mechanisms, Biological Functions, Diseases, and New Therapeutic Opportunities.},
journal = {MedComm},
volume = {6},
number = {7},
pages = {e70265},
pmid = {40547945},
issn = {2688-2663},
abstract = {The microbiota is pivotal for our health. It includes different phyla like Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. The interaction between microbiota and immunity shares a bidirectional relationship. The microbiota helps to stimulate immunity development. The immunity influences microbial composition in turn. This interaction is critical for maintaining homeostasis, preventing pathogen invasion, and regulating the immune system. Furthermore, this symbiotic relationship is crucial for maintaining overall health and preventing various diseases. The microbiota-immune system contributes to immune system maturation, while the immune system selects for beneficial microbiota composition, thus enhancing our immunity. This review summarizes the molecular mechanisms and biological functions of the interaction between microbiota and immunity, offering solid evidence for the role of microbiota in immune regulation. Notably, the review categorizes microbiota according to phyla and explains disease associations, molecular effectors, and functional outcomes about the microbiota-immune system. We also introduced three core molecular mechanisms of the microbiota-immune systems. Moreover, we detail the progression from target discovery to clinical trial design for bacterial and immune-related diseases. Finally, we propose four therapeutic strategies for diseases.},
}

@article {pmid40547885,
year = {2025},
author = {Lim, SW and Chou, W and Chen, L},
title = {SankeyNetwork: A clear and concise visualization tool for bibliometric data.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103379},
pmid = {40547885},
issn = {2215-0161},
abstract = {This study proposes a novel framework to overcome the limitations of traditional bibliometric visualizations-such as co-word network charts-by integrating Sankey diagrams with author collaborations and co-word occurrences to better identify key contributors and themes. Analyzing 2252 articles published in the Journal of METHODSX (2020-2024), the study focuses on ten essential metadata elements commonly used in bibliometric evaluations, including country, institution, department, authorship, and keywords. Three complementary approaches are introduced: (1) a summarized performance sheet to present key metrics across entities, (2) Sankey diagrams for streamlined cluster visualization using the Following-Leading Clustering Algorithm (FLCA), and (3) slope graphs to track temporal trends and research bursts. Findings highlight the dominance of the United States, Symbiosis International in India, and author Fengxiang X Han, with the keyword "MODEL" emerging as most frequent. A 2020 article by Wondimagegn Mengist received the highest citation count (370). Slope graphs showed upward trends in four core elements over the past four years. The study concludes that these methods provide clearer insights while reducing visual complexity, and recommends combining performance sheets, Sankey diagrams, and slope graphs in future bibliometric analyses to better detect hotspots and evolving research patterns.•Sankey diagrams to enhance traditional bibliometric visualization methods.•Analyzing 2252 articles from Journal of METHODSX (2020-2024) to highlight author collaborations.•Key insights include the prominence of U.S., and Symbiosis International (India) in author collaborations.},
}

@article {pmid40547299,
year = {2025},
author = {Najafi, M and Çokuysal, B and Rezaee Danesh, Y and Farda, B and Mignini, A and Pellegrini, M},
title = {Evaluation of Funneliformis mosseae inoculation effects on growth, nutrient uptake, and essential oil content in Turkish oregano under drought stress.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19499},
pmid = {40547299},
issn = {2167-8359},
mesh = {*Origanum/microbiology/growth & development/metabolism ; *Oils, Volatile/metabolism/analysis ; *Droughts ; *Mycorrhizae/physiology ; Plant Roots/microbiology/growth & development ; Turkey ; Nutrients/metabolism ; *Glomeromycota/physiology ; Stress, Physiological ; },
abstract = {BACKGROUND: Turkish oregano (Origanum onites L.) is a perennial herb widely recognized for its medicinal, cosmetic, and culinary uses due to its antioxidant and antimicrobial properties. Drought is a significant stressor for crops, particularly affecting O. onites quality and yield. Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with plant roots, enhance plant growth, and improve tolerance to abiotic stresses such as drought.

METHODS: This study investigates the effects of Funneliformis mosseae inoculation on O. onites growth, nutrient content, and essential oil yield under varying drought conditions. A factorial experiment was conducted with eight treatments, consisting of two factors: irrigation levels (100%, 75%, 50%, and 25%) and AMF inoculation (with and without). The experimental design was completely randomized with three replicates.

RESULTS: Results demonstrated that AMF inoculation significantly improved the fresh and dry weight of O. onites compared to non-inoculated controls (+11% and +16%, respectively). Moreover, AMF-inoculated plants showed notable increases in potassium (+7%) and nitrogen (+12%) contents. The essential oil yield was also significantly higher in AMF-inoculated plants (+3%). Increasing water stress levels significantly decreased the number of AMF spores (-47%) and the percentage of fungal colonization (-57%). Nevertheless, under drought stress mycorrhizal inoculation significantly maintained plant biomass and nutrient uptake comparable to full irrigation. The AMF drought tolerance effects were confirmed at 75%, 50%, and 25% irrigation rates.},
}

*Origanum/microbiology/growth & development/metabolism
*Oils, Volatile/metabolism/analysis
*Droughts
*Mycorrhizae/physiology
Plant Roots/microbiology/growth & development
Turkey
Nutrients/metabolism
*Glomeromycota/physiology
Stress, Physiological

@article {pmid40545848,
year = {2025},
author = {Han, K and Ma, X and Li, H and Liu, L and Deng, X and Song, L and Lin, L and Liu, Y and Zhao, Y and Huang, W},
title = {A Biomimetic Copper Silicate-MOF Hybrid for Highly Stable Zn Metal Anode.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2503046},
doi = {10.1002/adma.202503046},
pmid = {40545848},
issn = {1521-4095},
support = {No. 22371043 52472150//National Natural Science Foundation of China/ ; Y07204080K13//Fujian Normal University/ ; },
abstract = {To promote the electrochemical performance of aqueous zinc-ion batteries, various artificial interlayers are developed to mitigate dendrite growth and H2O-induced side reactions of Zn anode. Metal-organic framework (MOF) interlayers show much potential in solving these problems, yet their practical usage is inhibited by their inferior structural stability during cycles. Herein, inspired by the biological mechanism and symbiotic architecture of drosera rotundifolia, this challenge is tackled by constructing a hierarchical hollow CuSiO3-MOF hybrid through in situ MOF conversion. For protecting Zn anode, this biomimetic hybrid offers good structural stability, abundant zincophilic sites, strong desolvation capability, and fast ion migration, which collectively enable highly stable dendrite-free Zn plating/stripping processes and suppress H2O-related side reactions. Consequently, the Zn@CuSiO3-MOF symmetric battery achieves an ultralong lifespan exceeding 3500 h with low voltage hysteresis. Remarkably, it maintains stable cycling behaviors of 1200 and 400 h even under high depths of discharge of 45% and 90%, outperforming the most reported MOF-modified anodes. Moreover, full cells with MnO2 and C@V2O3 cathodes exhibit exceptional cycling performance and rate capability, highlighting the practical applications of Zn@CuSiO3-MOF anode for grid storage and wearable electronics. This bioinspired strategy provides a feasible approach to constructing stable MOF-based hybrid for high-performance Zn anode.},
}

@article {pmid40545786,
year = {2025},
author = {Haq, F and Camuel, A and Carcagno, M and Biondi, EG and Pacquit, V and Deslandes, L and Giraud, E and Mergaert, P},
title = {The rhizobial type III effectors ErnA and Sup3 hijack the SUMOylation pathway to trigger nodule formation in Aeschynomene species.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70334},
pmid = {40545786},
issn = {1469-8137},
support = {ANR-10-INBS-04//Agence Nationale de la Recherche/ ; ANR-11-IDEX-0003-02//Agence Nationale de la Recherche/ ; ANR-20-CE20-0012//Agence Nationale de la Recherche/ ; },
abstract = {Rhizobial type III effectors (T3Es) play a crucial role in the symbiotic relationship between rhizobia and legumes by manipulating host cellular processes to promote nodule formation. Previously, we identified two T3Es, ErnA and Sup3, that trigger nodulation in Aeschynomene spp. in the absence of Nod factors. Here, we further investigate the mode of action of these T3Es during root nodule symbiosis. We employed protein interaction assays, in vitro binding and enzymatic activity assays, mutational analyses, and functional nodulation tests to dissect the roles of ErnA and Sup3 and their interactions with the host Small Ubiquitin-like MOdifier (SUMO) pathway (SUMOylation). We demonstrate that ErnA contains a SUMO-interacting motif (SIM) at its C terminus, which promotes its interaction with SUMO proteins in vitro and in plant nuclei. Additionally, we show that Sup3 possesses a C-terminal SUMO protease domain, which not only interacts with SUMO proteins in vitro and in the nucleus but also exhibits SUMO protease activity. Deletion of the SIM in ErnA or mutation of the catalytic site in Sup3 abolished their ability to trigger nodulation in Aeschynomene indica. These findings suggest that type III secretion system-dependent symbiosis is regulated by posttranslational modification through SUMOylation and that ErnA and Sup3 modulate this SUMOylation pathway to trigger nodulation.},
}

@article {pmid40545364,
year = {2025},
author = {Nakanishi, E and Cornette, R and Shimura, S and Kikawada, T},
title = {Microbiome Associated with Polypedilum sp. (Diptera; Chironomidae), a Midge Adapted to an Extremely Acidic Environment.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24090},
pmid = {40545364},
issn = {1347-4405},
mesh = {Animals ; *Chironomidae/microbiology/physiology/growth & development ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; *Microbiota ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; Japan ; Symbiosis ; DNA, Bacterial/genetics ; Rivers/chemistry ; Acids ; Sequence Analysis, DNA ; },
abstract = {Chironomids (Diptera; Chironomidae), non-biting midges, are a highly diverse family of holometabolous insects, many of which are known for their tolerance to extreme environmental conditions, such as desiccation, pollution, and high acidity. The contribution of microbial symbionts to these adaptations was recently suggested. Therefore, we herein exami-ned the microbiome associated with the larvae of the undescribed acid-tolerant chironomid species, Polypedilum sp., which inhabits the Yukawa River (Gunma, Japan), an environment that is characterized by an extremely low pH (≤2) and high concentrations of heavy metal ions (including arsenic). Amplicon sequencing of the 16S rRNA gene revealed a distinct larval microbiome with a lower alpha diversity value and more enriched and specific bacterial taxa than the surrounding river water and detritus. Full-length 16S rRNA gene sequencing using nanopore long-read technology identified several previously undescribed operational taxonomic units (OTUs), among which OTU_Bacillaceae_Yukawa was consistently present in larvae reared in the laboratory for more than 4 months, suggesting persistent, possibly vertically transmitted, symbiosis. An inferred pathway ana-lysis suggested the contribution of the larval microbiome to host nutritional physiology. The possibly acid-sensitive OTU_Bacillaceae_Yukawa localized to midgut segments, indicating internal pH-buffered niches for microbial survival. These results provide novel insights into the ecology of acid-tolerant chironomids and lay the groundwork for further examinations of holobiont-based stress tolerance.},
}

Animals
*Chironomidae/microbiology/physiology/growth & development
Larva/microbiology
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
*Microbiota
Phylogeny
*Bacteria/classification/genetics/isolation & purification
Japan
Symbiosis
DNA, Bacterial/genetics
Rivers/chemistry
Acids
Sequence Analysis, DNA

@article {pmid40545206,
year = {2025},
author = {Yi, W and Tang, Y and Kawsar, MA and Huang, K and Jin, X and Yu, Z and Mao, F and Zhang, Y},
title = {A novel C1q domain-containing protein from Tridacna crocea exhibits dual functionality in symbiont recognition and immune defense.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110509},
doi = {10.1016/j.fsi.2025.110509},
pmid = {40545206},
issn = {1095-9947},
abstract = {C1q domain-containing (C1qDC) proteins function as versatile pattern recognition receptors that mediate host-microbe interactions through their C-terminal C1q domains. In this study, a novel C1qDC protein named TcC1qDC was characterized from Tridacna crocea, featuring a 690 bp open reading frame encoding 229 amino acids. TcC1qDC exhibited constitutive but tissue-enriched expression, with the highest transcript levels in the outer mantle and hepatopancreas. Functional analyses revealed that recombinant TcC1qDC protein not only binds to symbiotic dinoflagellates but is also predicted to recognize multiple microbial carbohydrates, as demonstrated by molecular docking. Furthermore, this protein also displayed broad-spectrum binding activity against pathogen-associated molecular patterns (lipopolysaccharides, peptidoglycan, lipoteichoic acids, and mannan) and corresponding microorganisms, along with significant microbial agglutination capacity for Gram-negative bacteria, Gram-positive bacteria, and fungi. These findings collectively establish TcC1qDC as a dual-function receptor bridging symbiont recognition and immune defense in giant clams.},
}

@article {pmid40544582,
year = {2025},
author = {Zhuang, W and Feng, X and Li, R and Hu, X},
title = {Molecular phylogeny and taxonomy of three anaerobic ciliates including Bothrostoma aporobustum nov. spec. (Ciliophora, Metopida).},
journal = {European journal of protistology},
volume = {100},
number = {},
pages = {126155},
doi = {10.1016/j.ejop.2025.126155},
pmid = {40544582},
issn = {1618-0429},
abstract = {The order Metopida is a species-rich taxon within the obligate anaerobic ciliate class Armophorea. Metopids have garnered increasing interest due to their potential to shed light on mitochondrial evolution and symbiotic relationship between eukaryotes and prokaryotes. However, the majority of metopid species remain poorly or incompletely studied, largely due to limitations in earlier research methodologies. In this study, three species, Bothrostoma aporobustum nov. spec., Brachonella mitriformis and Planometopus contractus, were examined using a morpho-molecular approach. The new species is distinguished by a short proboscis-shaped snout, an average of 33 somatic kineties, and 21 adoral membranelles. Brachonella mitriformis is characterized by a broad obpyriform body with a narrow and flattened posterior end, an average of 53 somatic kineties and 77 adoral membranelles, and unevenly distributed dikinetids on the preoral dome. Phylogenetic analyses confirmed the validity and monophyly of the genera Bothrostoma and Brachonella, and robustly resolved the phylogenetic position of Brachonella mitriformis. Representatives of geographically distant populations of Planometopus contractus are morphologically highly similar and cluster together with strong support in SSU rRNA gene phylogenies.},
}

@article {pmid40544518,
year = {2025},
author = {Wang, J and Xiong, X and Li, P and Wan, HF and Yang, YH},
title = {Characteristics and Influencing Factors of Rhizosphere Microbial Communities of Tuber himalayense-Corylus heterophylla Ectomycorrhizosphere.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {177-191},
doi = {10.33073/pjm-2025-015},
pmid = {40544518},
issn = {2544-4646},
mesh = {*Mycorrhizae/genetics/classification/growth & development/physiology ; *Rhizosphere ; *Soil Microbiology ; Soil/chemistry ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Seedlings/microbiology/growth & development ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Nitrogen/analysis ; Phylogeny ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; },
abstract = {Microbial diversity plays a crucial role within the plant rhizosphere ecosystem, serving as a pivotal indicator of plant health and stability. In order to explore the correlation between the growth of mycorrhizal seedlings and the nutrition and microbial diversity of the ectomycorrhizosphere, the soil of the ectomycorrhizosphere with different growth conditions was used as the research object, and the ITS1 region and 16S rRNA high-throughput sequencing technology were used to explore the inter-relationship. The findings indicated that the primary phyla within the rhizosphere soil microbial communities of various mycorrhizal seedlings were comparable, although their relative abundances varied. The relative abundance of Tuberaceae in good-growing mycorrhizal seedlings (CHTG) was 17.87% and 15.58% higher than in medium-growing (CHTM) and bad-growing (CHTB), respectively. Comparing the diversity indexes Chao1, Shannon and Simpson, it was found that CHTG had the lowest richness. Redundancy analysis (RDA)/canonical correspondence analysis (CCA) analysis revealed that Tuber was positively correlated with soil pH and negatively correlated with available nitrogen, organic matter, total nitrogen, total phosphorus, total potassium, available potassium, and available phosphorus. Rhizosphere core species analysis showed that symbiotic Ascomycota dominated the rhizosphere soil fungi, and the bacterial community was composed mainly of Proteobacteria. There was a positive correlation between most genera of bacteria and fungi. This study proved that in the bionic cultivation of Tuber himalayense-Corylus heterophylla, the growth of mycorrhizal seedlings can be promoted by adjusting the pH to weakly alkaline and enhancing the advantages of Plectosphaerella in the soil flora, without adding other nutrients, which provides a theoretical basis for the establishment of truffle plantations, soil improvement and ecosystem stability.},
}

*Mycorrhizae/genetics/classification/growth & development/physiology
*Rhizosphere
*Soil Microbiology
Soil/chemistry
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Seedlings/microbiology/growth & development
RNA, Ribosomal, 16S/genetics
Biodiversity
Nitrogen/analysis
Phylogeny
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology

@article {pmid40543842,
year = {2025},
author = {Kato, Y and Watanabe, H},
title = {Crosstalk between environmental factors and sex determination pathway: Insights from lepidopteran insects and cladoceran crustaceans.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101403},
doi = {10.1016/j.cois.2025.101403},
pmid = {40543842},
issn = {2214-5753},
abstract = {Insects exhibit a remarkable diversity of sex-determination systems. Sex-determining mechanisms have been extensively analyzed using the genetic model insects, such as Drosophila melanogaster, revealing that insect sex is determined in a cell-autonomous manner. The sexual identity of each cell is governed by the conserved transcription factor Doublesex, while the regulatory mechanisms controlling its expression are species-specific. In contrast, our understanding of how environmental factors modulate the sex determination pathway remains limited. In this review, we summarize recent discoveries on the crosstalk between environmental factors and sex determination pathways in the lepidopteran insects and the cladoceran crustaceans, which are closely related to insects. We discuss how the symbiotic bacterium Wolbachia hijacks the host WZ/ZZ sex determination pathway in the lepidopteran Ostrinia furnacalis. In addition, we highlight how males that are genetically identical to females are produced in response to environmental stimuli in the cladoceran crustacean Daphnia magna. Based on these findings, we explore the evolutionary, ecological, and applied implications of the molecular mechanisms underlying environmentally influenced sex determination.},
}

@article {pmid40541578,
year = {2025},
author = {Tian, J and Hu, J and Xiong, Y and Deng, X and Fang, Y and Wang, G and Chi, R and Xiao, C},
title = {Metagenomic and metabolomic insights into microalgal-bacterial symbiosis under low carbon-to-nitrogen ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132849},
doi = {10.1016/j.biortech.2025.132849},
pmid = {40541578},
issn = {1873-2976},
abstract = {Microalgal-bacterial symbiotic system (MBSS) is expected to efficiently treat ammonia nitrogen (NH4[+]-N) wastewater at low carbon-to-nitrogen ratio (CNR). In this study, MBSS was constructed and operated at CNRs of 0, 2, and 4 for 36 days, named as L (low CNR), M (medium CNR), and H (high CNR). Microbial interaction mechanisms were explored through metagenomics and non-targeted metabolomics. The average NH4[+]-N removal efficiencies of L, M, and H were 9.2 ± 4.3 %, 33.6 ± 10.9 %, and 51.6 ± 14.1 %, respectively. CNR significantly influenced NH4[+]-N removal. Metagenomics and metabolomics showed that bacteria dominate MBSS, with phylum Pseudomonadota having a large advantage. Addition of simple organic carbon sources may inhibit the generation of complex organic compounds by microalgae, consequently leading to bacteria utilizing simple carbon sources. Certain key microorganisms, genes, and metabolites respond to different CNRs to regulate MBSS performance. This study provides new insights into MBSS nitrogen removal at low CNR.},
}

@article {pmid40541502,
year = {2025},
author = {Jhu, MY and Moura de Souza, VH and Schiessl, K},
title = {From hosts to parasites: hormones driving symbiosis-induced de novo organogenesis.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.05.015},
pmid = {40541502},
issn = {1878-4372},
abstract = {Plants have evolved diverse adaptations in signal perception, hormone regulation, and organ development that enable the formation of specialised structures such as nematode-induced galls, rhizobia-induced nodules, and host-induced parasitic plant haustoria that facilitate both parasitic and mutualistic symbiosis. Despite their differences, these organs share common gene regulatory mechanisms with lateral root development. By comparing their mechanisms of hormonal regulation, we illuminate the shared genetic underpinnings and how plants repurpose vegetative development pathways in response to biotic stimuli. This adaptive retooling positions plants along the symbiotic spectrum from exploited hosts to mutualistic partners and strategic predators. Comparative analysis of the hormonal mechanisms that drive symbiotic organogenesis highlights the plasticity of developmental processes and the interplay between internal signalling and external environmental cues.},
}

@article {pmid40541096,
year = {2025},
author = {Guo, J and Hou, J and Wan, Y and Yang, Z and Li, Y and Zhu, Y and Wang, K and Ding, W},
title = {Integrating thermal vibration and local surface plasmon resonance effect boosted "Symbiotic Co-evolution" for efficient solar evaporation, antimicrobial and antibiotic resistance genes removal.},
journal = {Water research},
volume = {284},
number = {},
pages = {123997},
doi = {10.1016/j.watres.2025.123997},
pmid = {40541096},
issn = {1879-2448},
abstract = {Integrating photocatalytic processes into solar-driven interfacial evaporation technology is an effective approach to combat pollutants threat. However, the challenge lies in synergizing each component to achieve "Symbiotic Co-evolution", which is critical for achieving more with less. Our strategy for the fabrication of hydrogel evaporator (TA-Fe-SA/CoV2O6@Ti3C2Tx evaporator) was integrated by thermal vibration and local surface plasmon resonance (LSPR) effect, achieving efficient degradation and evaporation. On the one hand, the integration of thermal vibration and LSPR effect boosted the heat storage and local heating capacity of evaporator, while reducing equivalent enthalpy for enhancing evaporation. On the other hand, the synergistic effect of thermal vibration and LSPR triggered the efficient electron transfer of CoV2O6@Ti3C2Tx MXene Mott-Schottky heterojunction. As a result, it could achieve nearly 100 % bacteriostatic efficiency and 82 % ARGs removal within 1 hour. Additionally, the rapid generation of vapor and enhanced photothermal conversion strengthened thermal convection formation, accelerating gas release from the reaction system and improving the efficiency of the interfacial photothermal evaporation-photocatalytic process. These results highlighted the feasibility and scientific value of achieving synergy through the deliberate integration of photothermal materials and photothermal-catalysts into SIE technology, providing new perspectives for designing high-performance evaporators.},
}

@article {pmid40540389,
year = {2025},
author = {Huang, YC and Lu, HY and Zhang, L and Olivier, A and Wu, TL and Hsu, CY and LeGrand, C and Zeng, H and Curran, S and Wang, Q and Nannapaneni, R and Zhang, X and Ticó, M and Mariotti, M and Wu, RTY and Combs, GF and Cheng, WH},
title = {Dietary Selenium Deficiency Accelerates the Onset of Aging-Related Gut Microbial Changes in Aged Telomere-Humanized Mice, With Akkermansia muciniphila Being the Most Prominent and Alleviating Selenium Deficiency-Induced Type 2 Diabetes.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70130},
doi = {10.1111/acel.70130},
pmid = {40540389},
issn = {1474-9726},
support = {DK117407/NH/NIH HHS/United States ; 3062-51000-050-00D//Agricultural Research Service/ ; },
abstract = {Previous studies have shown that dietary selenium (Se) deficiency in mice reshapes gut microbiota, exacerbates healthspan deterioration (e.g., type 2 diabetes), and paradoxically activates beneficial longevity pathways. This study demonstrated that dietary Se deficiency accelerated many age-related gut microbial changes in aged telomere-humanized C57BL/6J diabetic mice in a sexually dimorphic manner, with Akkermansia muciniphila showing the greatest enrichment in males. However, dietary Se deficiency did not enrich A. muciniphila in mature or middle-aged male C57BL/6J wild-type mice. Oral gavage of A. muciniphila alleviated Se deficiency-induced type 2 diabetes-like symptoms, reversed mucosal barrier dysfunction and gut inflammation, and resulted in a trend of symbiotic and competitive suppression changes in certain gut bacteria in mature wild-type mice under conventional conditions. The beneficial effects of A. muciniphila appeared to be independent of selenoproteins sensitive to dietary Se deficiency, such as GPX1, SELENOH, and SELENOW, in the liver and muscle. Altogether, these results show that dietary Se deficiency accelerates age-related A. muciniphila enrichment specifically in aged male mice with severe insulin resistance and pancreatic senescence, indicating a potential hormetic response to Se deficiency through reshaped gut microbiota, which alleviates hyperglycemia and partially compensates for healthspan decline.},
}

@article {pmid40540139,
year = {2025},
author = {Su, C and Dong, X and Li, X},
title = {MtLICK1/2: gatekeepers of symbiosis and immunity in Medicago truncatula.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40540139},
issn = {1869-1889},
}

@article {pmid40539942,
year = {2025},
author = {Stewart, JD and Corrales, A and Canteiro, C and Qin, C and Gupta, MM and Otgonsuren, B and Peña-Venegas, CP and Van Nuland, ME and Kohout, P and Větrovský, T and Kokkoris, V and Manley, BF},
title = {Advancing knowledge on the biogeography of arbuscular mycorrhizal fungi to support Sustainable Development Goal 15: Life on Land.},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf055},
pmid = {40539942},
issn = {1574-6968},
support = {024.004.014//Schmidt Family Foundation/ ; 101076062//European Union/ ; CZ.02.01.01/00/22_008/0004597//Ministry of Education, Youth and Sports/ ; },
mesh = {*Mycorrhizae/genetics/classification/physiology ; *Sustainable Development ; Soil Microbiology ; Biodiversity ; Symbiosis ; Plants/microbiology ; Ecosystem ; United Nations ; Phylogeography ; },
abstract = {Arbuscular mycorrhizal (AM) fungi are fundamental to planetary health, enhancing plant nutrient uptake, stabilizing soils, and supporting biodiversity. Due to their prevalence and ecological importance, AM fungi are critical to achieving the environmental targets within the United Nations (UN) Sustainability Development Goals (SDGs) framework, including SDG 15: Life on Land. Despite these fungi engaging in the most widespread and ancient plant-microbe symbiosis, many fundamental aspects of the biogeography of AM fungi remain poorly resolved. This limits our ability to understand and document these fungal species' contributions to preserving terrestrial life on Earth. Using the largest global dataset of AM fungal eDNA sequences, we highlight that > 70% of ecoregions have no available data generated from soil using AM fungal specific metabarcoding. Drawing attention to these severe data gaps can optimize future sampling efforts in key habitats. Filling these gaps and developing a more complete picture on the biogeographic distributions of AM fungal species will help to clarify their contributions to environmental targets.},
}

*Mycorrhizae/genetics/classification/physiology
*Sustainable Development
Soil Microbiology
Biodiversity
Symbiosis
Plants/microbiology
Ecosystem
United Nations
Phylogeography

@article {pmid40538040,
year = {2025},
author = {Yang, DS and Tran, TT and Kazuki, H and Yin, HY and Chou, JY},
title = {Unveiling the Antibacterial Activity Against Staphylococcus aureus of Slime Molds: The Role of Symbiotic Bacteria.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70072},
doi = {10.1002/jobm.70072},
pmid = {40538040},
issn = {1521-4028},
support = {//This study received support from grants provided by the Ministry of Science and Technology (MOST 111-2621-B-018-001 to Jui-Yu Chou). We express our gratitude to the members of the Chou Laboratory for their valuable discussions and insightful comments on the manuscript./ ; },
abstract = {The emergence of multidrug-resistant pathogens has significantly reduced the efficacy of current antimicrobial treatments against bacterial and fungal infections. To combat this challenge, the exploration of novel antimicrobial sources or the development of synthetic antibiotics is imperative. Microbes have emerged as promising natural reservoirs for antimicrobial compounds, with slime molds garnering attention due to their unique bioactive metabolites in recent years. Some of these metabolites demonstrate potent antibiotic properties. This study investigates the inhibitory effects of slime mold extracts on pathogenic bacteria, attributing this activity primarily to symbiotic bacteria associated with the slime molds rather than to the slime mold cells themselves. Furthermore, we demonstrate that this antibacterial effect can be horizontally transferred through bacterial ingestion, enabling recipient slime molds to exhibit antibacterial properties upon extraction. Importantly, slime molds selectively acquire bacteria from their environment to enhance their antibacterial characteristics, a process that appears non-random and persists through sexual cycles. These findings underscore slime molds as valuable reservoirs of antimicrobial agents. Nevertheless, it remains critical to ascertain whether these antimicrobial agents originate solely from symbiotic bacteria or result from complex interactions between these bacteria and their slime mold hosts. Understanding the mechanisms behind this antimicrobial activity not only expands our knowledge of host-microbe interactions but also provides new avenues for bioprospecting novel antibiotics. Investigating how slime molds selectively acquire and retain beneficial bacteria may offer insights into microbial symbiosis that could be leveraged for antimicrobial discovery, potentially addressing the urgent need for alternative treatments against resistant pathogens.},
}

@article {pmid40537475,
year = {2025},
author = {Doyle, JJ and Ren, J and Pawlowski, K and James, EK and Gao, Y},
title = {One versus many independent assemblies of symbiotic nitrogen fixation in flowering plants.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5345},
pmid = {40537475},
issn = {2041-1723},
mesh = {*Nitrogen Fixation/physiology/genetics ; *Symbiosis/physiology ; Phylogeny ; Plant Root Nodulation/genetics ; *Magnoliopsida/microbiology/genetics ; Root Nodules, Plant/microbiology ; Fabaceae/microbiology/genetics ; Mycorrhizae ; },
abstract = {Some species of legumes and nine other flowering plant families form symbioses with bacteria that fix atmospheric nitrogen within specialized plant structures called nodules. How and how often nodulation symbiosis originated has implications for engineering symbiotic nitrogen fixation in non-legume crops. The prevailing hypothesis of a single origin with massive parallel losses has been challenged in a phylogenomic study favoring 16 origins and 10 losses. Nodulation has been assembled once or many times from existing processes (e.g., mycorrhizal symbiosis) and therefore almost nothing about it is truly novel. Because any feature of nodulation can be explained either as divergence from a common origin or as convergence in unrelated taxa, tests are needed that can distinguish whether assembly of homologous components has occurred uniquely or convergently. Much needs to be learned about nodulation symbioses across the proposed independent origins, especially involving the master nodulation transcription factor, Nodule Inception (NIN).},
}

*Nitrogen Fixation/physiology/genetics
*Symbiosis/physiology
Phylogeny
Plant Root Nodulation/genetics
*Magnoliopsida/microbiology/genetics
Root Nodules, Plant/microbiology
Fabaceae/microbiology/genetics
Mycorrhizae

@article {pmid40536527,
year = {2025},
author = {Storb, R and Svriz, M and Aranda, E and Fracchia, S and Spinedi, N and Scervino, JM},
title = {Association between a liverwort and arbuscular mycorrhizal fungi: a promising strategy for the phytoremediation of polycyclic aromatic hydrocarbons.},
journal = {Mycorrhiza},
volume = {35},
number = {4},
pages = {44},
pmid = {40536527},
issn = {1432-1890},
support = {PID2021-123164OB-I00 MCIN/AEI/10.13039/501100011033//ERDF A way of making Europe/ ; PINI 04/B253//Universidad Nacional del Comahue/ ; PICT 00073-2019//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
mesh = {*Mycorrhizae/physiology/metabolism ; Biodegradation, Environmental ; *Hepatophyta/microbiology/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Soil Pollutants/metabolism ; *Glomeromycota/metabolism/physiology ; Symbiosis ; *Anthracenes/metabolism ; Fungi ; },
abstract = {Soil contamination with polycyclic aromatic hydrocarbons (PAHs) represents a major environmental challenge and requires cost-effective and environmentally friendly remediation technologies. Phytoremediation, enhanced by arbuscular mycorrhizal fungi (AMF), is an effective and extensive technique for PAHs remediation, although, its application with non-vascular plants, is largely unexplored. This study investigates the role of the AMF Rhizophagus irregularis in the uptake and bioaccumulation of anthracene in the liverwort Lunularia cruciata under in vitro conditions. The thallus and the AMF were able to absorb and bioaccumulate anthracene in the cell wall and spores, hyphae and arbuscules respectively. Our results indicate that the liverwort-fungus system employs multiple phytoremediation mechanisms, including phytoaccumulation and phytostabilization. At intermediate contamination levels, the fungal symbiont enhanced contaminant accumulation in the plant, whereas at higher contamination levels, this effect diminished, suggesting a potential limitation in fungal-mediated uptake under extreme conditions. These findings highlight the potential of AMF symbiosis in liverworts for developing biological tools for PAHs remediation, emphasizing the dependence on pollutant concentration for the effectiveness of phytoremediation.},
}

*Mycorrhizae/physiology/metabolism
Biodegradation, Environmental
*Hepatophyta/microbiology/metabolism
*Polycyclic Aromatic Hydrocarbons/metabolism
*Soil Pollutants/metabolism
*Glomeromycota/metabolism/physiology
Symbiosis
*Anthracenes/metabolism
Fungi

@article {pmid40502178,
year = {2025},
author = {Tristao Santini, A and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC},
title = {Gut microbiota of Brazilian Melipona stingless bees: dominant members and their localization in different gut regions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40502178},
issn = {2692-8205},
support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; },
abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that are vital for bee health. Two symbionts, Snodgrassella and Gilliamella, are ubiquitous in honeybees and bumblebees. However, their presence varies in the stingless bee clade (Meliponini), a group with pantropical distribution. They are absent or rare in the diverse genus Melipona, indicating a shift in microbiota composition in this lineage. To identify the main members of the Melipona microbiota, we combined newly collected and published data from field-collected individuals of several species. Additionally, we identified the localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides. The dominant microbiota of Melipona species includes members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus, and Bombella. Among these, Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae dominate the ventriculus. The ileum lacks Snodgrassella or Gilliamella but contains a putative new symbiont close to Floricoccus, as well as strains of Bifidobacterium, Lactobacillaceae (including Apilactobacillus), and Bombella. The rectum is dominated by Bifidobacterium and Lactobacillus. In summary, the Melipona microbiota is compositionally distinct but shows spatial organization paralleling that of other eusocial corbiculate bees.},
}

@article {pmid40536287,
year = {2025},
author = {Zhang, Y and Yang, Y and Ma, Y and Wang, D and Wang, X and Zhang, L and Meng, L and Xu, K and Li, X and Shangguan, X and Zheng, X and Li, L and Zang, Z and Kang, G and Li, C},
title = {A Mycorrhiza-Induced Phosphate Transporter TaPT31-7A Regulating Inorganic Phosphate Uptake, Arbuscular Mycorrhiza Symbiosis, and Plant Growth in Wheat.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05299},
pmid = {40536287},
issn = {1520-5118},
abstract = {Phosphate transporters play a key role in improving crop yield. In this study, TaPT31-7A is a high-affinity phosphate transporter strongly induced in arbuscular-mycorrhizal (AM) wheat roots. It restores Pi uptake in yeast mutant MB192 and localizes to the plasma membrane. TaPT31-7A overexpression lines accumulated more shoot and root phosphorus than the wild type under both low- and high-Pi conditions. When inoculated with AM in Pi-deficient soil, these overexpression lines displayed enhanced Pi uptake, higher mycorrhization, and improved growth, ultimately increasing the spikelet number per spike, spike length, 1000-grain weight, grain length, and grain width. Transcriptome and coexpression analyses of TaPT31-7A OE lines and control plants showed altered expression of phosphate-starvation and AM-development genes, while docking and yeast two-hybrid assays confirmed its interaction with PP2C phosphatase TaPP2C12-6A. These results establish TaPT31-7A as a central regulator of Pi uptake, AM symbiosis, and productivity in wheat and highlight its potential for breeding phosphorus-efficient cultivars.},
}

@article {pmid40536173,
year = {2025},
author = {Kazmerski, TM and Kidd, KM and Jain, R and Jathal, I and Stransky, OM and Lee, M and Salyer, RE and Tangpricha, V and Palla, J and Alpern, AN and Lunn, MR and Obedin-Maliver, J and Greenberg, J and Prangley, A and , and Sawicki, GS},
title = {Investigating the Interplay Between Having Cystic Fibrosis and Being a Member of the LGBTQIA+ Community: Protocol for the PRIDE CF Study.},
journal = {Pediatric pulmonology},
volume = {60},
number = {6},
pages = {e71154},
pmid = {40536173},
issn = {1099-0496},
support = {//This study was supported by Cystic Fibrosis Foundation./ ; },
mesh = {Humans ; *Cystic Fibrosis/psychology/epidemiology ; *Sexual and Gender Minorities/psychology/statistics & numerical data ; Male ; Female ; Adolescent ; Adult ; Child ; Young Adult ; Research Design ; },
abstract = {The impact of the intersectional lived experience of having a chronic health condition and identifying as lesbian, gay, bisexual, transgender, queer, intersex, asexual or another sexual or gender minority (LGBTQIA+) on health and wellbeing is largely unknown. In this article, we describe the development and structure of PRIDE CF, an innovative, large-scale epidemiologic study using a mixed-methods team science approach to understand the experiences and health outcomes of people with cystic fibrosis (PwCF) who identify as a gender or sexual minority. Our four separate but symbiotic projects utilize the PRIDE CF cohort (n ~ 300) with the shared goal of better understanding the needs of LGBTQIA+ PwCF. We use a fully decentralized study design to recruit a national group of participants from a small population within a small population and strive to protect participants' confidentiality and privacy. Results will inform intervention development and testing to improve health for this population. This study is the first to comprehensively investigate the long-term impact and experiences of LGBTQIA+ identity on a person with any chronic condition and, thus, can serve as a model for future collaborations outside of cystic fibrosis.},
}

Humans
*Cystic Fibrosis/psychology/epidemiology
*Sexual and Gender Minorities/psychology/statistics & numerical data
Male
Female
Adolescent
Adult
Child
Young Adult
Research Design

@article {pmid40536155,
year = {2025},
author = {Bonfante, P and Genre, A},
title = {The increasingly powerful term mycorrhiza warrants attention.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70324},
pmid = {40536155},
issn = {1469-8137},
}

@article {pmid40536153,
year = {2025},
author = {Xing, Z and Wu, L and Biere, A and Yu, H and Ding, J},
title = {Foliar Herbivory Suppresses Arbuscular Mycorrhizal Colonisation by Weakening Symbiosis Signalling in Root Exudates.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70024},
pmid = {40536153},
issn = {1365-3040},
support = {//This study was supported by National Key R&D Program of China (2024YFF1307500) and National Science Foundation of China (U21A20190, 32301323)./ ; },
abstract = {Foliar insect herbivory could affect arbuscular mycorrhizal fungi (AMF), yet the underlying mechanisms remain understudied. Here, we examined the response of AMF symbiosis signals to foliar herbivory, using six herbaceous plant species and a generalist herbivorous insect. We found AMF colonisation was suppressed by foliar herbivory. After insect attack, plants allocated more biomass to belowground parts and the attack induced defence responses in aboveground parts. Notably, foliar herbivory increased shoot flavonoid concentrations but decreased root flavonoid concentrations. Moreover, quercetin and strigol concentrations in the root exudates were reduced by foliar herbivory. We further tested effect of the root exudates on the in-vitro germination of spores of two common AMF species. Spore germination was lower in treatments with herbivore-induced root exudates than in treatments with no-herbivore root exudates. Moreover, addition of herbivory-modified root exudates reduced AMF colonisation of healthy plants when compared to addition of root exudates from non-herbivory plants. Our results suggest that foliar herbivory weakened symbiosis signalling in root exudates, which could have contributed to the observed lower AMF colonisation following herbivory. Therefore, herbivore-induced symbiosis signalling needs to be considered when studying plant-mediated interactions between foliar herbivores and root microbes.},
}

@article {pmid40534881,
year = {2025},
author = {Mu, Y and Yang, M and Liu, J and Yao, Y and Sun, H and Zhuang, J},
title = {Exosomes in hypoxia: generation, secretion, and physiological roles in cancer progression.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1537313},
pmid = {40534881},
issn = {1664-3224},
mesh = {Humans ; *Exosomes/metabolism ; *Neoplasms/pathology/metabolism ; Tumor Microenvironment ; Disease Progression ; Animals ; *Hypoxia/metabolism ; Signal Transduction ; Cell Hypoxia ; },
abstract = {The hypoxic microenvironment represents a universal hallmark feature of most solid tumors, profoundly shaping cancer progression through multifaceted mechanisms. Acting as nanoscale molecular envoys, exosomes transport oncogenic cargoes (including non-coding RNAs, mutated proteins, and metabolites) to reprogram stromal cells, prime pre-metastatic niches, and establish tumor-host metabolic symbiosis. Their lipid bilayer architecture ensures the protection of labile hypoxia-responsive factors, positioning them as critical amplifiers of intercellular crosstalk within the tumor microenvironment. Despite significant advances, critical gaps persist in understanding the spatiotemporal regulation of exosomal release under hypoxia, particularly the organ-specific variations in hypoxic exosome signatures revealed by single-vesicle analyses. This review synthesizes recent advances in the intricate interplay between hypoxia and exosomes, emphasizing hypoxia-related signaling pathways that directly modulate exosome biogenesis and indirectly activate hypoxia-associated microenvironmental remodeling, alongside their distinct regulatory effects on exosomal cargo composition. Furthermore, it delineates the pivotal role of hypoxia-specific exosomes in driving cancer malignancy, including metastatic dissemination, immune evasion, and therapy resistance. By integrating molecular mechanisms with clinically actionable insights, this work establishes a translational framework for targeting the hypoxic exosome network in precision oncology, offering strategic references for biomarker discovery and therapeutic development.},
}

Humans
*Exosomes/metabolism
*Neoplasms/pathology/metabolism
Tumor Microenvironment
Disease Progression
Animals
*Hypoxia/metabolism
Signal Transduction
Cell Hypoxia

@article {pmid40533170,
year = {2025},
author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25007},
pmid = {40533170},
issn = {1347-4405},
mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; },
abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.},
}

*Bacteria/metabolism/genetics/classification/isolation & purification
*Carbon Cycle
Metagenomics
*Microbial Consortia/genetics
*Ammonia/metabolism
Folic Acid/metabolism/biosynthesis
*Seawater/microbiology
Metagenome
Bioreactors/microbiology
Metabolic Networks and Pathways
Phylogeny
Genome, Bacterial
Wastewater/microbiology
Carbon/metabolism

@article {pmid39989254,
year = {2025},
author = {Coyle, A and O'Hare, L and Ramey, D},
title = {Synapse: A co-designed neurodivergent peer support programme for higher education settings.},
journal = {Autism : the international journal of research and practice},
volume = {29},
number = {7},
pages = {1711-1726},
pmid = {39989254},
issn = {1461-7005},
abstract = {Transitioning to higher education can be challenging for neurodivergent students and they can be particularly vulnerable to experiencing stress in this new environment, resulting in higher levels of non-completion. To address this issue, this study details the co-design of a support programme for neurodivergent students in higher education. It used logic modelling workshop methodology to identify the short-term and long-term outcomes, activities and resources required for implementation. The logic model was produced during a workshop that involved a range of stakeholders, including researchers, neurodivergent and neurotypical students and disability service staff at an Irish university. The qualitative data were analysed through thematic analysis and three key outcomes were generated from the logic modelling process: 'connectedness', 'knowledge and awareness of neurodiversity' and 'empowerment'. The main activities desired by stakeholders included one-to-one mentoring and group-based mentoring, which would allow neurodivergent students to establish new friendships and develop a sense of belonging within the university. The implementation factors identified were providing a dedicated space and mentor pairing. A key finding was that stakeholders did not favour traditional peer mentoring labels of 'mentor' and 'mentee'. Instead, students preferred the development of a symbiotic co-mentoring relationship between peers, with both participants being referred to as 'mentors'.Lay abstractNeurodivergent students may require support with the social aspects of university life. Peer mentoring describes a relationship where a more experienced student helps a less experienced student by providing advice, support and knowledge. It is an effective way to support students' transition to higher education. This study involved a wide range of stakeholders including neurodivergent students, neurotypical students, disability service staff and researchers in the design of a peer mentoring programme called Synapse. A visual representation of the proposed programme (i.e. logic model) was produced during a workshop with the stakeholders. This visual showed the key outcomes or aims of the programme that was agreed upon by the stakeholders. The workshop was audio recorded and the transcripts were analysed to highlight the main conversation themes. Stakeholders stated that neurodivergent students wanted to feel more connected to others at the university to develop a sense of belonging, they also wanted people to learn more about neurodiversity to reduce stigma and finally, they wanted to feel empowered to take control of their lives and have a voice in decision-making. The two preferred activities of the programme were one-to-one and group mentoring. Uniquely, the participants were concerned with traditional terminology around peer mentoring, in particular the terms mentor and mentee, as it inferred an unequal power dynamic in a relationship. The stakeholders believed that students in the Synapse programme should be valued and treated equally, regardless of diagnosis or experience. Therefore, all members of the Synapse programme were paired within a co-mentoring relationship.},
}

@article {pmid40532609,
year = {2025},
author = {Demidova, MA and Vishnyakov, AE and Karagodina, NP and Kotenko, ON and Nekliudova, UA and Bogdanov, EA and Ostrovsky, AN},
title = {Vertical transfer of bacterial symbionts via a placental analogue in the cyclostome bryozoan Patinella verrucaria (Stenolaemata): Ultrastructural and molecular evidence.},
journal = {Zoology (Jena, Germany)},
volume = {171},
number = {},
pages = {126281},
doi = {10.1016/j.zool.2025.126281},
pmid = {40532609},
issn = {1873-2720},
abstract = {Symbiotic associations with prokaryotes are common among marine filter-feeding invertebrates. In the almost exclusively colonial phylum Bryozoa, however, such associations have only been recorded in some species of the order Cheilostomata (class Gymnolaemata). Here we describe for the first time symbiotic bacteria in the colonies, larvae and developing ancestrulae of the bryozoan Patinella verrucaria from the order Cyclostomata (class Stenolaemata) using transmission electron and fluorescent microscopy. Ultrastructural and molecular data suggest the existence of two distinct bacterial species, both from the family Rhodobacteraceae. The presence of bacteria in all three stages of the bryozoan life cycle indicates a vertical transfer of symbionts. Both intracellular and free bacteria were recorded in the colonies, being presumably transported by amoebocytes from autozooids to the colonial incubation chamber. The bacteria are accumulated in the placental analogue and in associated cells surrounding developing embryos and larvae, and are presumably transmitted to the mature ciliated larvae during rupture of the placenta facilitated by the movements of their cilia before and/or during larval release. Thus, the nourishing function of the placenta is complemented by the symbiont transfer, which can be regarded as an example of extension of functions. This is the first example of a placenta providing bacterial infection to the progeny in invertebrates.},
}

@article {pmid40528946,
year = {2025},
author = {Miao, Y and Sun, M and Huo, R and Chen, Y and Xie, J and Dong, T and Zhang, M},
title = {Metagenomics and volatile metabolomics reveal microbial succession and flavor formation mechanisms during fermentation of Novel Pasture-style Laozao.},
journal = {Food chemistry: X},
volume = {28},
number = {},
pages = {102598},
pmid = {40528946},
issn = {2590-1575},
abstract = {Novel Pasture-style Laozao (NPLZ) is a local specialty fermented food with unique flavor and mouthfeel. This study investigated the dynamic changes of physicochemical properties, volatile flavor substances and microbial community succession during the fermentation of NPLZ and revealed their interactions through the joint analysis of metagenomics and volatile metabolomics. Differences in the contents of 52 characteristic flavor substances were the main reasons for the changes in aroma. Saccharomyces cerevisiae, Pseudomonas oryzihabitans, and Pantoea vagans were the dominant microbial communities during fermentation. Under symbiotic conditions, five species including Paenibacillus piri and Methyloversatilis thermotolerans were found to be crucial in influencing microbial community succession. The accumulation of organic acids was identified as the primary environmental factor driving changes in microbial community structure. Through correlation analysis, eight microbial species were identified as core microorganisms affecting flavor differences, and the metabolic networks of key flavor metabolites were reconstructed in conjunction with the KEGG database.},
}

@article {pmid40528245,
year = {2025},
author = {Yang, Q and Zhang, H and Qiu, JW and Huang, D and Zhou, X and Zheng, X},
title = {Symbiotic Symbiodiniaceae mediate coral-associated bacterial communities along a natural thermal gradient.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {72},
pmid = {40528245},
issn = {2524-6372},
support = {2022YFC3102003//National Key Research and Development Program of China/ ; 2020017//he Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 42376110//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; },
abstract = {The coral-associated microbiome plays a vital role in the holobiont, enabling coral adaptation to diverse environments by modulating its composition and mediating interactions among its constituents. However, the responses of coral microbiomes, particularly the interactions between Symbiodiniaceae and bacteria, to environmental changes remain unclear. To fill this knowledge gap, we examined Pocillopora acuta, an environmentally sensitive coral species, collected from three sites along the southeastern coast of Hainan which exhibit moderate environmental differences. We measured the physiological characteristics of Symbiodiniaceae and conducted amplicon sequencing to analyze the structure of Symbiodiniaceae and bacterial communities. Our results revealed that P. acuta in southeastern Hainan maintains stable symbiosis with Symbiodiniaceae sub-clades such as C1, C42.1, C3, D1, D4, and D6, as evidenced by ΔF/Fm' values ranging from 0.45 for P. acuta dominated by Durusdinium (PaD) to 0.6 for counterparts dominated by Cladocopium (PaC). However, the composition of Symbiodiniaceae varied among the three sites, primarily due to differences in the abundance of dominant sub-clades. These variations may reflect adaptations to distinct environmental conditions, which in turn significantly influence the associated bacterial communities. Notably, our results suggest that Symbiodiniaceae may exert a greater regulatory role on the coral-associated bacterial community than environmental differences. Specific bacteria, such as Endozoicomonas and Synechococcus_CC9902, exhibit strong correlations with particular Symbiodiniaceae genera or sub-clades, indicating that the dominant Symbiodiniaceae shape bacterial community dynamics. Despite the observed variations, we identified modular co-occurrence patterns in bacterial networks, with PaC exhibiting a more complex and stable structure. Overall, these results highlight the critical role of various Symbiodiniaceae genera in influencing bacterial community dynamics, emphasizing their importance in maintaining coral health and resilience in the face of changing environmental conditions.},
}

@article {pmid40527464,
year = {2025},
author = {Titelboim, D and Dedman, CJ and Hodgson, RP and Knowles, LS and Liu, X and Lenzi, L and Tudor, J and Vamos, E and Rickaby, REM},
title = {Exogenous diatoms ameliorate thermal bleaching of symbiont bearing benthic foraminifera.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20250596},
pmid = {40527464},
issn = {1471-2954},
support = {/ERC_/European Research Council/International ; //H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {*Foraminifera/physiology ; *Symbiosis ; *Diatoms/physiology ; Temperature ; Hot Temperature ; },
abstract = {Many marine calcifiers engage in obligatory algal symbiosis which is threatened by ocean warming. Large benthic foraminifera are prominent carbonate and sand producers in shallow environments with a wide range of species-specific thermal tolerances assumed to be related to their diverse algal symbionts. We examine two diatom-bearing benthic foraminifera species which differ in their thermal physiological tolerance and symbiont community composition. Our findings demonstrate that the less thermally tolerant host, Amphistegina lobifera Larsen, 1976, 'shuffles' the dominant players of the internal symbiont community with increasing temperature while the more thermally tolerant host Pararotalia calcariformata McCulloch, 1977, is dominated by Arcocellulus cornucervis Medlin, 1990, at all temperatures. Although this diatom species was present in A. lobifera from all treatments, it became more abundant only under the most severe temperature stress. Symbionts were isolated from the thermally tolerant foraminifera P. calcariformata, with only one species of symbiont surviving at 35°C, while the others failed to survive at 32°C. Supplementation of isolated symbionts reduced bleaching of A. lobifera under heat stress suggesting that while increased temperature creates shuffling at the family level, heat tolerance of the holobiont is related to changes at the species level of the symbiont algae.},
}

*Foraminifera/physiology
*Symbiosis
*Diatoms/physiology
Temperature
Hot Temperature

@article {pmid40527262,
year = {2025},
author = {Lynn, KD and Queirós, A and Talbot, E and Mesher, T and Pascoe, C and Quijón, PA},
title = {The disruption of a symbiotic sea anemone by light pollution: Non-linear effects on zooxanthellae and molecular indicators.},
journal = {The Science of the total environment},
volume = {990},
number = {},
pages = {179906},
doi = {10.1016/j.scitotenv.2025.179906},
pmid = {40527262},
issn = {1879-1026},
abstract = {Artificial Light at Night (ALAN) is a pervasive stressor that may affect coastal organisms, particularly sessile forms associated with photosynthetic symbionts. We examined the effects of ALAN upon the symbiotic snakelocks anemone (Anemonia viridis)'s relationship with photosynthetic zooxanthellae, as well as molecular indicators of oxidative stress and metabolism. Anemones were exposed to natural daylight/night or either mild or strong ALAN intensities for four weeks, before quantifying zooxanthellae, superoxide dismutase (SOD) enzymes, and respiration rates. In comparison to natural conditions, anemones exposed to ALAN showed significantly higher and lower zooxanthellae counts, under mild and strong ALAN, respectively. In turn, SOD concentrations were lower and much higher when exposed to mild and strong ALAN, respectively, with no change in respiration rates. Concurrent bleaching suggests that ALAN is harmful to this, and possibly other species associated with symbiotic microalgae. And while we didn't measure heat stress, such bleaching may potentially act synergistically with other larger-scale forms of bleaching associated with rising ocean temperatures.},
}

@article {pmid40524261,
year = {2025},
author = {Leach, WB and Babonis, L and Juliano, CE and Nakanishi, N and Schnitzler, CE and Steinmetz, PRH and Layden, MJ},
title = {Discoveries and innovations in cnidarian biology at Cnidofest 2024.},
journal = {EvoDevo},
volume = {16},
number = {1},
pages = {9},
pmid = {40524261},
issn = {2041-9139},
support = {2436941//NSF/ ; 2436941//NSF/ ; },
abstract = {The third iteration of the Cnidarian Model Systems Meeting (Cnidofest) was held August 14-17th, 2024 at Lehigh University in Bethlehem, PA. The meeting featured presentations from laboratories representing 11 countries, covering a broad range of topics related to cnidarian species. The research highlighted diverse topics, with sessions focused on regeneration, evo-devo, genomics, symbiosis, cell biology, physiology, neurobiology, and development. A notable shift at this meeting was the extent to which established cnidarian model systems have caught up with the classical laboratory models such as Drosophila and vertebrates, with modern genomic, genetic, and molecular tools now routinely applied. In addition, more cnidarian systems are now being developed for functional studies by the community, enhancing our ability to gain fundamental insights into animal biology that are otherwise difficult in the complex bilaterian model systems. Together, the integration of cnidarian and bilaterian model systems provides researchers with a broader toolkit for selecting animal models best suited to address their specific biological questions.},
}

@article {pmid40523202,
year = {2025},
author = {Dal Bó, B and Guo, Y and Mayr, MJ and Pereira, OS and Levin, LA and Orphan, VJ and Goffredi, SK},
title = {Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {26},
pages = {e2501422122},
doi = {10.1073/pnas.2501422122},
pmid = {40523202},
issn = {1091-6490},
support = {OCE-2048481//NSF (NSF)/ ; OCE-2048720//NSF (NSF)/ ; OCE-2048666//NSF (NSF)/ ; },
mesh = {Animals ; *Methane/metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Male ; *Spiders/microbiology/physiology ; Bacteria/metabolism/genetics ; Female ; Methanol/metabolism ; Pacific Ocean ; },
abstract = {Methane seeps harbor uncharacterized animal-microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane- and methanol-oxidizing bacteria on their exoskeleton. δ[13]C tissue isotope values of in situ specimens corroborated methane assimilation (-45‰, on average). Live animal incubations with [13]C-labeled methane and methanol, followed by nanoscale secondary ion mass spectrometry, confirmed that carbon derived from both compounds was actively incorporated into the tissues within five days. Methano- and methylotrophs of the bacterial families Methylomonadaceae, Methylophagaceae and Methylophilaceae were abundant, based on environmental metagenomics and 16S rRNA sequencing, and fluorescence and electron microscopy confirmed dense epibiont aggregations on the sea spider exoskeleton. Egg sacs carried by the males hosted identical microbes suggesting vertical transmission. We propose that these sea spiders farm and feed on methanotrophic and methylotrophic bacteria, expanding the realm of animals known to harness C1 compounds as a carbon source. These findings advance our understanding of the biology of an understudied animal lineage, unlocking some of the unique nutritional links between the microbial and faunal food webs in the oceans.},
}

Animals
*Methane/metabolism
RNA, Ribosomal, 16S/genetics
Symbiosis
Male
*Spiders/microbiology/physiology
Bacteria/metabolism/genetics
Female
Methanol/metabolism
Pacific Ocean

@article {pmid40521991,
year = {2025},
author = {Kulkarni, AS and Carrara, GMP and Jin, J and Laro, J and Peramuna, T and McCall, LI and Garg, N},
title = {Mass spectrometry-based metabolomics approaches to interrogate host-microbiome interactions in mammalian systems.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
pmid = {40521991},
issn = {1460-4752},
support = {R01 GM145649/GM/NIGMS NIH HHS/United States ; R35 GM150870/GM/NIGMS NIH HHS/United States ; },
abstract = {Covering: 2015 to 2025Chemical crosstalk is universal to all life, niche-specific, and essential to thrive. This crosstalk is mediated by a large diversity of molecules, including metal ions, small molecules, polysaccharides, nucleic acids, lipids, and proteins. Among these, specialized small molecules referred to as natural products (NPs) play an important role in microbe-drug/environment interactions, microbe-microbe, and microbe-host interactions. Microbial communication using NPs allows microbes to sense quorum, form biofilms, eliminate competition, establish symbiosis, evade immune attack, and respond to stress. In most cases, the elucidation of small molecule mediators and effectors of microbe-host interactions presents a major challenge due to the relatively low abundance of microbial metabolites in a milieu of host, microbe, and environmental metabolites. Advances in analytical instrumentation, such as mass spectrometers, and both experimental as well as computational methods to analyze data, coupled with the use of model organisms, have enabled fundamental discoveries of mechanisms of small molecule-mediated host-microbe interactions. The focus of this review is to detail the approaches applied in the last decade to disentangle microbiome-derived NPs in human and murine model systems. Select recent findings from diverse biological ecosystems are discussed to inform relevant parallels and potential strategies for research in human health.},
}

@article {pmid40520149,
year = {2025},
author = {Maldonado, M and Pita, L and Hentschel, U and Erpenbeck, D and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {275},
pmid = {40520149},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.},
}

@article {pmid40519728,
year = {2025},
author = {Liu, F and Sun, Y and Wang, J and Zhan, J},
title = {Study on the pathogenesis of idiopathic pediatric acute pancreatitis by combining intestinal microbiome and metabolome.},
journal = {Translational pediatrics},
volume = {14},
number = {5},
pages = {855-870},
pmid = {40519728},
issn = {2224-4344},
abstract = {BACKGROUND: Idiopathic pediatric acute pancreatitis (IPAP) represents a significant health threat to children and adolescents, yet its underlying pathogenesis remains poorly understood, necessitating further research to elucidate its mechanisms. This study aims to explore the roles of intestinal microbiota, short-chain fatty acids (SCFAs), and serum metabolites in the pathogenesis of IPAP, as well as to assess the therapeutic potential of acetic acid intervention in this condition.

METHODS: Fecal and serum samples from 22 cases of IPAP (excluding biliary origin) and 10 healthy controls were collected and analyzed. Intestinal microbial was characterized using 16S ribosomal RNA (16S rRNA) sequencing, while SCFAs and serum metabolites were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Omics analysis was employed to identify microbial-metabolite regulation and regulatory networks and potential disease biomarkers. To evaluate the therapeutic efficacy of acetic acid in acute pancreatitis (AP), AP was induced in animal models by intraperitoneal injection of caerulein (50 µg/kg; once daily for seven days), followed by oral administration of acetic acid (10 mL/kg, once daily) in 4-, 6-, and 8-week models. Pancreatic and ileum tissues were examined for histopathological changes, serum enzymes levels, and intestinal barrier integrity.

RESULTS: The results of 16S rRNA sequencing revealed significant differences in the composition and abundance of intestinal microbial communities between the control (Con) and IPAP groups. Pathogenic bacteria, such as f_Tannerellaceae and c_Bacteroidia, as well as certain symbiotic bacteria, were significantly enriched in the IPAP group. SCFAs metabolome analysis indicated that acetic acid, as a key intermediate metabolite, may play a regulatory role in the pathogenesis of IPAP. The construction of a microbial-metabolite regulatory network demonstrated that microorganisms such as g_Monoglobus and g_Morganella were closely associated with SCFAs, including acetic acid, suggesting that the development of IPAP is influenced by upstream and downstream regulatory mechanisms. Furthermore, significant associations were identified between serum metabolites and gut microbes. For instance, (4E,15E)-bilirubin and creatinine showed significant positive correlations with g_Bacteroides (P<0.01). Similarly, 1,2-ethanediol monoricinoleate was significantly positively correlated with g_Hungatella (P<0.01), while pubescenol and tecastemizole were significantly positively correlated with g_Parabacteroides (P<0.01). Animal experiments demonstrated that pancreatic and intestinal tissue damage was alleviated to varying degrees following treatment. Compared to the disease model group, the acetic acid treatment group exhibited significantly reduced serum levels of D-lactic acid, amylase, and lipase, along with a significantly increased positive staining surface density of intestinal barrier proteins (occludin, claudin-1, and ZO-1).

CONCLUSIONS: Intestinal flora, SCFAs and serum metabolites were significantly altered in IPAP, and the interaction regulated the development of IPAP. Acetic acid can effectively intervene the occurrence of IPAP.},
}

@article {pmid40519530,
year = {2025},
author = {Smith, S and Bongrand, C and Lawhorn, S and Ruby, EG and Septer, AN},
title = {Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf085},
pmid = {40519530},
issn = {2730-6151},
abstract = {The symbiotic relationship between Vibrio (Aliivibrio) fischeri and the Hawaiian bobtail squid, Euprymna scolopes, serves as a key model for understanding host-microbe interactions. Traditional culture-based methods have primarily isolated V. fischeri from the light organs of wild-caught squid, yet culture-independent analyses of this symbiotic microbiome remain limited. This study aims to enhance species-level resolution of bacterial communities associated with E. scolopes using hsp60 amplicon sequencing. We validated our hsp60 sequencing approach using pure cultures and mixed bacterial populations, demonstrating its ability to distinguish V. fischeri from other closely related vibrios and the possibility of using this approach for strain-level diversity with further optimization. This approach was applied to whole-animal juvenile squid exposed to either seawater or a clonal V. fischeri inoculum, as well as ventate samples and light organ cores from wild-caught adults. V. fischeri accounted for the majority of the identifiable taxa for whole-animal juvenile samples and comprised 94%-99% of amplicon sequence variants (ASVs) for adult light organ core samples, confirming that V. fischeri is the dominant, if not sole, symbiont typically associated with E. scolopes light organs. In one ventate sample, V. fischeri comprised 82% of reads, indicating the potential for non-invasive community assessments using this approach. Analysis of non-V. fischeri ASVs revealed that Bradyrhizobium spp. and other members of the Rhodobacterales order are conserved across juvenile and adult samples. These findings provide insight into the presence of additional microbial associations with the squid host tissue outside of the light organ that have not been previously detected through traditional culture methods.},
}

@article {pmid40517925,
year = {2025},
author = {Banerjee, S and Jha, S and Chakraborty, S and Ghosh, S and Sarkar, D and Datta, R and Bhattacharya, SS and Bhattacharyya, P},
title = {Mycorrhiza-assisted phytoremediation of spiked chromium-contaminated soil: Assessing AMF-vetiver symbiosis for Cr accumulation and soil quality enhancement.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122143},
doi = {10.1016/j.envres.2025.122143},
pmid = {40517925},
issn = {1096-0953},
abstract = {Chromium (Cr) is a hazardous pollutant in industrial and mining areas and threatens soil ecosystems. Mycorrhiza-assisted phytoremediation serves as an eco-friendly and effective approach to mitigate Cr contamination from soil. In this investigation, varying Cr dosages (100 mg kg[-1], 500 mg kg[-1], and 1000 mg kg[-1]) were applied into the soil alongside vetiver plants (Chrysopogon zizanioides L.) inoculated with three different AMF species (Claroideoglomus claroideum, Glomus hoi, and Claroideoglomus etunicatum). The results indicated that AMF inoculation enhanced Cr accumulation (1.96 folds, 1.63 folds) in the root tissue of vetiver compared to the control. Among the AMF species, Glomus hoi demonstrated the highest effectiveness in reducing Cr bioavailability (P10: 0.247 mg kg[-1], P11: 1.117 mg kg[-1], and P12: 4.789 mg kg[-1]) in the soil, followed by Claroideoglomus claroideum and Claroideoglomus etunicatum at post-harvest. Additionally, microbial and enzymatic activity improved in the presence of AMF compared to the control, as AMF alleviated Cr-induced stress by stimulating antioxidant activity. AMF enhanced soil glomalin-related proteins and colonization percentage, thereby promoting plant growth. The correlation and principal component analysis depict a positive association between Cr accumulation in vetiver (root and shoot) and the different Cr phases. Interestingly, in the presence of Glomus hoi, the VTF (<1) and VBCF (>1) indicate that this symbiotic association is well-suited for phytoremediation applications. Hence, AMF-assisted phytoremediation emerges as a viable and sustainable approach, offering advantages over other remediation techniques and providing potential solutions for managing soil Cr contamination.},
}

@article {pmid40517638,
year = {2025},
author = {Deng, X and Zhao, D and Li, Y and Li, K and Xia, J and Yu, S and Wang, J and Lin, J},
title = {Arbuscular mycorrhizal fungi confer aluminum toxicity tolerance in Ricinus communis via modulating root metabolic mechanisms and the composition and quantity of root exudates.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110149},
doi = {10.1016/j.plaphy.2025.110149},
pmid = {40517638},
issn = {1873-2690},
abstract = {Aluminum (Al) phytotoxicity is an essential factor that severely threatens plant productivity in acidic soil with pH < 5. Nevertheless, the specific interactions and functional contributions of arbuscular mycorrhizal fungus (AMF) in the adaptability of Ricinus communis to Al stress remain poorly understood. In this study, we investigated the changes in biomass, Al accumulation, antioxidant system, sucrose metabolism, gene expression, and root exudates of R. communis when regulated by AMF (Rhizophagus intraradices, Funneliformis mosseae, and Diversispora versiformis) under Al stress (0-1.2 g kg[-1]). Al detoxification by AMF - R. communis symbiosis was manifested by activating antioxidant levels, sucrose metabolism, thereby alleviating lipid peroxidation (MDA decreased 11.44 %-24.89 %) and increasing plant biomass (10.34 %-33.33 %). Meanwhile, transcriptome analysis revealed 659 differentially expressing genes (DEGs) in AMF-inoculated plants in comparison to non-inoculated plants subjected to Al stress. Furthermore, AMF colonization induced 929 differential metabolites (DAMs) from the perspective of root exudates. The integrating analysis of gene expression and root exudate changes indicating that AMF colonization under Al stress was closely related to ABC transporters, glutathione metabolism, nitrogen metabolism, cyanoamino acid metabolism, starch and sucrose metabolism. Altogether, the result of this study suggest that AMF confer Al tolerance to R. communis via antioxidant activation, sucrose metabolism regulation, and reshaping root exudates and gene networks. The present study provides new insights into the crucial role of AMF in improving Al-tolerance of R. communis.},
}

@article {pmid40516677,
year = {2025},
author = {Li, A and Wang, Z and Shi, C and Li, N and Bai, M and Yao, J and Hrynsphan, D and Qian, H and Hu, S and Wei, J and Chen, J},
title = {Enhanced denitrification performance via biochar-mediated electron shuttling in Pseudomonas guariconensis: mechanistic insights from enzymatic and electrochemical analyses.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126667},
doi = {10.1016/j.envpol.2025.126667},
pmid = {40516677},
issn = {1873-6424},
abstract = {Nitrogen pollution constitutes a critical environmental challenge for aquatic ecosystems, where biological denitrification serves as a critical mechanism for nitrogen removal in wastewater treatment plants (WWTPs). Pseudomonas guariconensis, a key denitrifying bacterium in WWTPs, demonstrates stable symbiotic relationships with organic carbon substrates under operational conditions. This study investigated the biochar-mediated enhancement mechanism of denitrification performance using Pseudomonas guariconensis strain XYH-2. Experimental results revealed that 0.5% (w/w) biochar addition significantly improved denitrification efficiency, elevating NO3[-]-N removal from 39% to 94% within 16 hours while reducing N2O accumulation by 81.7% (from 837 to 153 ppm). Electrochemical characterization and extracellular polymeric substances (EPS) analysis demonstrated biochar's role as an electron shuttle, evidenced by a 48.5% increase in electron transfer system activity (ETSA) and enhanced redox currents. Notably, biochar stimulation elevated the activities of four key denitrifying enzymes: nitrate reductase (NAR, +75.6%), nitrite reductase (NIR, +25.4%), nitric oxide reductase (NOR, +33.3%), and nitrous oxide reductase (N2OR, +159.4%). Structural characterization revealed biochar-induced conformational modifications in N2OR that enhanced substrate binding affinity, particularly explaining the dramatic N2O mitigation. These findings provided mechanistic insights into biochar-bacteria synergism, proposing an effective strategy for optimizing denitrification processes in nitrogen-contaminated wastewater treatment systems.},
}

@article {pmid40516400,
year = {2025},
author = {Ju, X and Sun, H and Ruan, C and Wang, H and Shi, B and Alvarez, PJJ and Yu, P},
title = {Prophage induction and quorum sensing enhance biofilm stability and resistance under ammonia-oxidizing bacteria-mediated oxidative stress.},
journal = {Water research},
volume = {284},
number = {},
pages = {124010},
doi = {10.1016/j.watres.2025.124010},
pmid = {40516400},
issn = {1879-2448},
abstract = {Ammonia-oxidizing bacteria (AOB) and prophage-carrying bacteria are prevalent in water treatment and reuse systems, yet their interactions and implications for biofilm formation and microbial risks remain insufficiently understood. Here, we demonstrate that oxidative stress arising from the metabolism of the AOB Nitrosomonas europaea induces prophage activation in lysogenized Escherichia coli (λ+). This activation triggers cellular lysis, leading to the release of intracellular components (e.g., protein and DNA) and upregulated quorum sensing (QS) followed by biosynthesis and excretion of extracellular polymeric substance (EPS). Integrated transcriptomic and proteomic analysis revealed that the presence of N. europaea significantly upregulated QS- and EPS-related genes by 2.14-2.93 and 2.81-3.11 folds in E. coli (λ+), respectively. Surviving E. coli (λ+) exhibited enhanced prophage-bacterium symbiosis and activated toxin-antitoxin systems, enhancing their resilience to environmental stress. These microbial adaptations markedly increased EPS production, fostering biofilm development and conferring enhanced biofilm resilience to disinfectants and bacterial antibiotic tolerance. Furthermore, metagenomic analysis at the microbial community wide level demonstrated that ammonia addition-driven AOB enrichment stimulated multi-species biofilm formation, promoted bacterium-phage interactions, and increased bacterial antibiotic resistance. Overall, our findings reveal that oxidative stress driven by AOB accelerates biofilm development, an overlooked phenomenon with potential to exacerbate microbial risks.},
}

@article {pmid40516069,
year = {2025},
author = {di Michele, F},
title = {The symbiotic relationship in a case of hysterical psychosis.},
journal = {Psychiatria Danubina},
volume = {37},
number = {1},
pages = {108-109},
pmid = {40516069},
issn = {0353-5053},
}

@article {pmid40515627,
year = {2025},
author = {Hasan, MR and Thapa, A and Kabir, AH},
title = {Iron retention coupled with trade-offs in localized symbiotic effects confers tolerance to combined iron deficiency and drought in soybean.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf263},
pmid = {40515627},
issn = {1460-2431},
abstract = {Iron (Fe) and water availability are closely interlinked, with deficiencies in both adversely affecting soybean growth. However, the strategies employed by soybean to tolerate such conditions remain poorly understood. This study elucidates the interactions of host factors, and microbial associations using multi-omics approaches in Clark (tolerant) and Arisoy (sensitive) genotypes exposed to Fe deficiency and drought. Clark exhibited resilience to stress through sustained osmotic regulation, nutrient uptake, and photosynthetic activity, in contrast to Arisoy. Particularly, Fe retention in Clark, accompanied by the upregulation of ferritin-like proteins, may mitigate oxidative stress by reducing Fenton reactions. Furthermore, higher jasmonic and salicylic acid levels in Clark may contribute to its enhanced stress adaptation compared to Arisoy. RNA-seq analysis revealed 818 and 500 upregulated, along with 931 and 361 downregulated genes, in the roots of Clark and Arisoy, respectively, under stress. We observed the upregulation of symbiotic genes, such as Chalcone-flavonone isomerase 1 and SWEET10, accompanied by increased rhizosphere siderophore and root flavonoid in Clark. This indicates a significant role of microbes in mediating differential stress tolerance in soybean. Particularly, the combined stress led to distinct root and nodule microbiome dynamics, with Clark recruiting beneficial microbes such as Variovorax and Paecilomyces, whereas Arisoy exhibited the opposite pattern. In addition, Clark maintained nodule Bradyrhizobium and tissue nitrogen status, supported by ammonium retention and induction of Ammonium transporter 1 in the roots. Furthermore, in vitro compatibility between V. paradoxus and P. lilacinus suggests a synergistic interaction, with their localized signals benefiting Clark. Remarkably, enriched microbiomes significantly improved growth parameters, accompanied by elevated rhizosphere siderophore in sensitive genotypes under stress. This study is the first to uncover mechanisms of dual stress tolerance in soybean that may offer promising targets for breeding programs and microbiome-based biofertilizer strategies to improve combined stress tolerance in soybean and other legumes.},
}

@article {pmid40515619,
year = {2025},
author = {Ochiai, KK and Goshima, G},
title = {Ruegeria strains promote growth and morphogenesis of the giant coenocytic alga Bryopsis.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf262},
pmid = {40515619},
issn = {1460-2431},
abstract = {An evolutionarily intriguing life form among extant organisms is the giant coenocyte, exemplified by green macroalgae in the order Bryopsidales. In these algae, cell separation does not follow nuclear division, resulting in a body composed of a single multinucleated cell. How a single cell grows to over 10 cm and undergoes characteristic morphogenesis without cell division or differentiation remains poorly understood. Macroalgae are known to associate with numerous microbes, and in some cases, these interactions influence algal cell division and differentiation. Here, we show that specific bacterial strains can promote the growth and morphogenesis of the coenocytic macroalga Bryopsis. Among >100 bacterial isolates obtained from Bryopsis, four strains belonging to the genus Ruegeria were found to accelerate the growth of the main axis and induce side-branch formation when co-cultured with the alga. The same effects were observed using conditioned seawater in which Ruegeria had been pre-cultured and subsequently removed. Seasonal microbiome analysis revealed that cultured Bryopsis associates with hundreds of bacterial species, exhibiting seasonal variations in community composition. However, Ruegeria was one of the few bacterial genera consistently associated with the cultured strain, suggesting a symbiotic relationship. Notably, although Ruegeria was not detected in Bryopsis strains isolated from other regions, its effects on growth and morphogenesis were observed in co-culture experiments. These findings suggest that Bryopsis, like multicellular macroalgae, utilises associated bacteria for growth and development without strict specificity.},
}

@article {pmid40515450,
year = {2025},
author = {Berrios, L},
title = {Is it all about timing? Identifying the symbiosis critical points that govern interactions among bacteria, ectomycorrhizal fungi, and land trees.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70298},
pmid = {40515450},
issn = {1469-8137},
support = {//Stanford Doerr School of Sustainability Discovery Grant/ ; 2109481//Directorate for Biological Sciences/ ; },
abstract = {Tree health and fitness depend on the interactions among soil microbiota across space and time. Recent evidence, for instance, has shown that understanding the individual and interactive lifestyles of bacteria and ectomycorrhizal fungi (EcMF)-two of the most dominant and influential soil microbes in tree microbiomes-enhances our predictions of plant responses and ecosystem functions. The spatial features that shape the coexistence and plasticity of bacteria-EcMF interactions have long been a primary research interest and have therefore revealed key insights in the field. The temporal features of these interactions, however, have received considerably less attention, yet emerging evidence suggests that interactions at a particular time in space may have a disproportionate impact on the stability and outcome of relationships. In light of these observations, I outline bacteria-EcMF-tree interactions across the life cycle of EcMF and highlight the importance of 'symbiosis critical points' across developmental time, providing testable hypotheses and experimental frameworks that aim to advance the field moving forward. Though this viewpoint article focuses on the symbioses among these three organisms, the concepts, hypotheses, and frameworks presented herein extend to diverse multispecies systems.},
}

@article {pmid40514722,
year = {2025},
author = {Zhang, M and Xiao, Y and Song, Q and Li, Z},
title = {Antarctic ice-free terrestrial microbial functional redundancy in core ecological functions and microhabitat-specific microbial taxa and adaptive strategy.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {70},
pmid = {40514722},
issn = {2524-6372},
support = {2022YFC280410//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Although ice-free terrestrial ecosystems in Antarctica cover only limited areas, they harbor diverse and metabolically active microbial communities. These ecosystems encompass distinct microhabitats such as mosses, lichens, and soils, each offering unique ecological niches. However, how different microbial taxa respond to microhabitat heterogeneity, ecological strategies such as functional redundancy and specialization contribute to adaptation in extreme environments remains underexplored. To address these questions, we employed high-throughput 16 S rRNA gene and ITS sequencing in combination with GeoChip-based functional gene profiling to assess the structure and functional potential of microbial communities across moss, lichen and soil microhabitats in Antarctic ice-free terrestrial ecosystem.

RESULTS: Microhabitat type has a greater influence on microbial community structure and function in the ice-free Antarctic terrestrial ecosystem than geographical location. Though all prokaryotic communities were dominated by Pseudomonadota, Nostoc and Endobacter were significantly enriched in the moss and lichen microhabitats, respectively. Meanwhile, all fungal communities were primarily dominated by Ascomycota and Basidiomycota, with Byssoloma and Usnea showing significant enrichment in the moss and lichen microhabitats, respectively. Despite these taxonomic differences, the three microhabitats show similar core ecological functions with widespread microbial functional redundancy. Nevertheless, clear microhabitat-specific functional specialization was suggested. For example, moss microhabitat was enriched in Pyoverdin_pvcC and Zeaxanthin_glucosyltransferase, sdhA, lichen microhabitat harbored higher levels of nhaA, nikC, vacuolar_iron_transport, mttB, glucoamylase, pel_Cdeg, pme_Cdeg, rgh, rgl, while soil microhabitat was enriched in 5f1_ppn and isopullulanase. Notably, genes involved in carotenoid biosynthesis were significantly more abundant in moss and lichen microhabitats than in soil microhabitat, indicating the adaptive capacity of symbiotic microorganisms to mitigate ultraviolet radiation and oxidative stress to protect their hosts.

CONCLUSIONS: Microbial communities associated with distinct microhabitats (i.e. mosses, lichens, and soils) in Antarctic ice-free terrestrial ecosystem exhibit both functional redundancy in core ecological functions and microhabitat-specific specialization in key microbial taxa and adaptive strategy.},
}

@article {pmid40514454,
year = {2025},
author = {Veloso Soares, SP and Jarquín-Díaz, VH and Veiga, MM and Karl, S and Czirják, GÁ and Weyrich, A and Metzger, S and East, ML and Hofer, H and Heitlinger, E and Benhaiem, S and Ferreira, SCM},
title = {Mucosal immune responses and intestinal microbiome associations in wild spotted hyenas (Crocuta crocuta).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {924},
pmid = {40514454},
issn = {2399-3642},
support = {GRAKO 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-Grako 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-Grako 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GRK 2046//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Hyaenidae/microbiology/immunology ; *Immunity, Mucosal ; Feces/microbiology/chemistry ; Female ; Male ; Tanzania ; Bacteria/classification/genetics ; },
abstract = {Little is known about host-gut microbiome interactions within natural populations at the intestinal mucosa, the primary interface. We investigate associations between the intestinal microbiome and mucosal immune measures while controlling for host, social and ecological factors in 199 samples of 158 wild spotted hyenas (Crocuta crocuta) in the Serengeti National Park, Tanzania. We profile the microbiome composition using a multi-amplicon approach and measure faecal immunoglobulin A and mucin. Probabilistic models indicate that both immune measures predicted microbiome similarity among individuals in an age-dependent manner. These associations are the strongest within bacteria, intermediate within parasites, and weakest within fungi communities. Machine learning models accurately predicted both immune measures and identify the taxa driving these associations: symbiotic bacteria reported in humans and laboratory mice, unclassified bacteria, parasitic hookworms and fungi. These findings improve our understanding of the gut microbiome, its drivers, and interactions in wild populations under natural selection.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Hyaenidae/microbiology/immunology
*Immunity, Mucosal
Feces/microbiology/chemistry
Female
Male
Tanzania
Bacteria/classification/genetics

@article {pmid40511412,
year = {2025},
author = {Yan, C and Wang, Y and Guo, Q and Huan, H and Wang, S and Fan, X and Xie, X},
title = {Silencing Arbuscular Mycorrhizal Fungal Gene Using Chitosan Nanoparticle-Mediated dsRNA Delivery System.},
journal = {Bio-protocol},
volume = {15},
number = {11},
pages = {e5326},
pmid = {40511412},
issn = {2331-8325},
abstract = {It has been discovered that many phytopathogenic fungi can absorb exogenous double-stranded RNAs (dsRNAs) to silence target genes, inhibiting fungal growth and pathogenicity for plant protection. In our recent report, the beneficial arbuscular mycorrhizal (AM) fungi are capable of acquiring external naked dsRNAs; however, whether the dsRNAs can be delivered into AM fungi through nanocarriers remains to be investigated. Here, we introduce a simple and advanced method for in vitro synthesizing chitosan (CS)/dsRNA polyplex nanoparticles (PNs) to silence the target gene in the AM fungus Rhizophagus irregularis. This method is straightforward, requiring minimal modifications, and is both efficient and eco-friendly, offering potential for rapid application in elucidating gene functions in AM fungi. Key features • The chitosan can carry the dsRNA derived from the AM fungus Rhizophagus irregularis. • CS/dsRNA polyplex nanoparticles (PNs) can successfully silence the target gene in the AM fungus R. irregularis. • CS/dsRNA PNs can be applied to the characterization of AM fungal genes via the spray-induced gene silencing (SIGS) approach. • This protocol can be applied in asymbiotic and symbiotic cultures of AM fungi. Graphical overview Overview of the chitosan/dsRNA gene silencing procedures.},
}

@article {pmid40510663,
year = {2025},
author = {Zhang, Y and Ma, Y and Ma, X and Li, C},
title = {Temporal changes in arbuscular mycorrhizal fungi communities and their driving factors in Xanthoceras sorbifolium plantations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1579868},
pmid = {40510663},
issn = {1664-302X},
abstract = {Arbuscular mycorrhizal fungi (AMF) communities are influenced by soil nutrients and plant and litter traits during forest ecosystem development. However, the extent to which these factors influence AMF communities in Xanthoceras sorbifolium plantations is unclear. In this study, rhizosphere soil samples were collected from 5-, 13-, 24-, 35-, 47-, and 56-year-old X. sorbifolium plantations. The AMF community was analyzed using Illumina MiSeq sequencing, and AMF spores were isolated and identified by wet sieving. The results showed that X. sorbifolium can establish a symbiotic relationship with AMF at different forest ages. In total, 5,876 AMF amplicon sequence variant (ASVs) were obtained from the soil samples and classified into 1 phylum, 4 classes, 6 orders, 12 families, and 15 genera. Glomus was the dominant genus. In addition, the diversity of AMF communities increased and then decreased with the age of X. sorbifolium, with no significant changes observed between 35-, 47-, and 56-year-old plantations. AMF community variance was primarily determined by soil-specific factors, with soil pH and root C content being the most influential. The results revealed the factors that drive AMF communities during the development of X. sorbifolium and provide valuable information for future conservation and planting management.},
}

@article {pmid40509709,
year = {2025},
author = {Schumacher, JD and Dusek, N and Mendoza-Suárez, M and Geddes, BA},
title = {Adaptation of Plasmid-ID Technology for Evaluation of N2-Fixing Effectiveness and Competitiveness for Root Nodulation in the Sinorhizobium-Medicago System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70118},
doi = {10.1111/1462-2920.70118},
pmid = {40509709},
issn = {1462-2920},
support = {FF-NIA21-0000000061m//Foundation for Food and Agriculture Research/ ; //U.S. Alfalfa Farmer Research Initiative of the National Alfalfa & Forage Alliance/ ; },
mesh = {*Plasmids/genetics ; *Nitrogen Fixation ; *Plant Root Nodulation ; Symbiosis ; *Sinorhizobium/genetics/physiology/metabolism ; Plant Roots/microbiology ; *Medicago sativa/microbiology ; },
abstract = {Maximising the nitrogen fixation occurring in rhizobia-legume associations represents an opportunity to sustainably reduce nitrogen fertiliser inputs in agriculture. High-throughput measurement of symbiotic traits has the potential to accelerate the identification of elite rhizobium/legume associations and enable novel research approaches. Plasmid-ID technology, recently deployed in Rhizobium leguminosarum, facilitates the concurrent assessment of rhizobium nitrogen-fixing effectiveness and competitiveness for root nodulation. This study adapts Plasmid-ID technology to function in Sinorhizobium species that are central models for studying rhizobium-legume associations and form economically important symbioses with alfalfa. New Sino-Plasmid-IDs were developed and tested for stability and their ability to measure competitiveness for root nodulation and nitrogen-fixing effectiveness. Rhizobial competitiveness is measured by identifying strain-specific nucleotide barcodes using next-generation sequencing, whereas effectiveness is measured by GFP fluorescence driven by the synthetic nifH promoter. Sino-Plasmid-IDs allow researchers to efficiently study competitiveness and effectiveness in a multitude of Sinorhizobium strains simultaneously.},
}

*Plasmids/genetics
*Nitrogen Fixation
*Plant Root Nodulation
Symbiosis
*Sinorhizobium/genetics/physiology/metabolism
Plant Roots/microbiology
*Medicago sativa/microbiology

@article {pmid40509355,
year = {2025},
author = {Cazal, CM and Forim, MR and Terezan, AP and Matos, AP and Cunha, GOS and da Silva, MFDGF and Vieira, PC and Pagnocca, FC and Fernandes, JB},
title = {Development of Xanthyletin-Loaded Nanoparticles for the Control of Leucoagaricus gongylophorus.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {11},
pages = {},
pmid = {40509355},
issn = {1420-3049},
support = {//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //National Council for Scientific and Technological Development/ ; //Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
mesh = {*Nanoparticles/chemistry/ultrastructure ; Animals ; *Agaricales/drug effects ; Particle Size ; *Ants/microbiology/drug effects ; *Antifungal Agents/pharmacology/chemistry ; Polyesters/chemistry ; Drug Carriers/chemistry ; Drug Liberation ; },
abstract = {This study describes the development, characterization and in vitro evaluation of poly(ε-caprolactone) (PCL) nanoparticles loaded with xanthyletin for the control of Atta sexdens rubropilosa through the inhibition of its symbiotic fungus Leucoagaricus gongylophorus. Nanoparticles were prepared via interfacial polymer deposition, with formulation NC5 selected based on optimal physicochemical properties. NC5 exhibited an encapsulation efficiency of 98.0%, average particle size of 304 nm and zeta potential of -29.3 mV. Scanning electron microscopy confirmed spherical morphology and the absence of crystalline residues. The formulation remained physically stable for four months at 4 °C. In vitro release showed biphasic behavior, with an initial burst followed by sustained release. Under UV exposure, NC5 enhanced xanthyletin photostability by 15.4-fold compared to the free compound. Fungicidal assays revealed 76% inhibition of fungal growth with NC5, compared to 85% with free xanthyletin. These results support the potential application of xanthyletin-loaded PCL nanoparticles as a stable and controlled delivery system for the biological control of leaf-cutting ants by targeting their fungal mutualist. Further in vivo studies are recommended to assess efficacy under field conditions.},
}

*Nanoparticles/chemistry/ultrastructure
Animals
*Agaricales/drug effects
Particle Size
*Ants/microbiology/drug effects
*Antifungal Agents/pharmacology/chemistry
Polyesters/chemistry
Drug Carriers/chemistry
Drug Liberation

@article {pmid40509088,
year = {2025},
author = {Zheng, T and Liu, Q and Zheng, C and Meng, X and Bai, X and Li, D and Wang, T and Guo, J and Xu, Z and Jie, H},
title = {An Attempted Correlation Between the Fecal Microbial Community of Chinese Forest Musk Deer (Moschus berezovskii) and Differences in Musk Production and Quality.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {11},
pages = {},
pmid = {40509088},
issn = {2076-2615},
support = {82274046, 32470531//National Natural Science Foundation of China/ ; 2024JDKP0219, 2024NSFSC2119//Sichuan Science and Technology Program Grants/ ; 2024jbky-04；2025jbky-009//Basic Scientific Research Fund Project of Chongqing/ ; cstc2021ycjh-bgzxm0201//Chongqing Talent Project/ ; },
abstract = {Musk, a dried secretion from the sac gland near the urethral foramen of adult male forest musk deer (Moschus berezovskii), has significant economic value and is extensively utilized as a valuable component in traditional Chinese medicine. In the practice of forest musk deer breeding, musk with different colors and varying moisture contents is observed during the season when the musk reaches maturity. For many years, researchers have focused mainly on musk composition and symbiotic bacteria. However, the influence of fecal fungi on the production and quality of musk is unknown. In this study, internal transcribed spacer (ITS) analysis was employed to explore the relationships between the fungal composition of musk deer fecal and the quality and production of musk produced by each individual. The results indicate that fungal genera known to cause diseases, such as Colletotrichum and Apiotrichum, are prevalent in the feces of musk deer that produce abnormal musk. Furthermore, the fecal microbiota health index (GMHI) is lower and the intestinal microbiota dysbiosis index (MDI) is greater in musk deer producing white musk than in normal individuals. Additionally, by correlating musk production with fecal fungi, we also found that Dolichousnea and Scolecoleotia were significantly positively correlated with musk production. Moreover, Metschnikowia, Ganodermataceae_gen_Incertae_sedis, Hypoxylon, Neovaginatispora, Didymella, Dothidea, and Trichoderma were negatively correlated with musk production. This study is the first to investigate gut fungi in relation to musk production/quality, establish gut health and fungal dysbiosis links, and identify candidate fungi tightly associated with musk traits. This exploratory approach is critical for exploring uncharted territories like gut fungi in musk deer and musk traits.},
}

@article {pmid40508303,
year = {2025},
author = {Ding, C and Ma, R and Wang, L and Lan, X and Chen, L and Zhu, J and Wang, L},
title = {Fenaminosulf Promotes Growth and Gall Formation in Zizania latifolia Through Modulation of Physiological and Molecular Pathways.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {40508303},
issn = {2223-7747},
support = {LTGN23C150006//Zhejiang Provincial Natural Science Foundation of China/ ; 2021ZDYF10//Primary Research & Development Plan of Lishui/ ; },
abstract = {Zizania latifolia (Jiaobai) is an economically important aquatic crop characterized by unique gall formation through interaction with the smut fungus Ustilago esculenta. Understanding factors influencing this interaction is crucial for cultivation. This study investigates the non-target effects of the fungicide Fenaminosulf (FM) on Z. latifolia's growth, physiology, and underlying molecular pathways. We demonstrate that FM exerts striking concentration-dependent effects, revealing its potential as a modulator of plant development and symbiosis. Physiological measurements showed that a moderate FM concentration (1.25 g/L) promoted key vegetative growth parameters, including plant height and leaf length, while maintaining chlorophyll content, suggesting a potential bio-stimulant effect. In contrast, higher FM concentrations (2.5 g/L and 5 g/L) inhibited vegetative growth but significantly enhanced gall formation, particularly at 2.5 g/L, indicating that FM can redirect plant resources or alter susceptibility to favor the fungal interaction under specific conditions. Transcriptomic analysis provided mechanistic insights, revealing extensive gene expression reprogramming, especially under high FM treatment (5 g/L). Key pathways related to plant-pathogen interaction, phenylpropanoid biosynthesis, and hormone signal transduction were significantly modulated. Notably, FM treatment suppressed key immune-related genes, including Xa21 and PBL19, potentially reducing plant resistance and facilitating gall formation. Hormone signaling analysis revealed inhibition of auxin, cytokinin, brassinosteroid, and jasmonic acid metabolism, indicating a comprehensive molecular recalibration of plant developmental processes. The study provides novel insights into the molecular mechanisms by which FM influences Z. latifolia growth and gall formation. The concentration-dependent effects of FM suggest its potential as a strategic tool for agricultural management, offering a nuanced approach to crop development. These findings contribute to understanding plant-chemical interactions and provide valuable directions for optimizing Z. latifolia cultivation strategies.},
}

@article {pmid40508277,
year = {2025},
author = {Cesari, AB and Paulucci, NS and Dardanelli, MS},
title = {Smart Bioinoculants for Arachis hypogaea: Controlled Release of Bradyrhizobium and the Role of Naringin in Symbiosis Enhancement.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {40508277},
issn = {2223-7747},
support = {11220210100155CO//PIP CONICET/ ; C530-1//PPI Universidad Nacional de Río Cuarto/ ; 696/21//PICT Agencia Nacional de Promoción Científica y Tecnológica/ ; CBA28/22//PICT-O Agencia Nacional de Promoción Científica y Tecnológica/ ; },
abstract = {Peanut (Arachis hypogaea L.) is one of the most important oilseeds crops worldwide. Through symbiosis with the bacterium Bradyrhizobium sp., peanuts can assimilate atmospheric nitrogen, reducing the need for chemical fertilizers. However, this nitrogen fixation process is highly sensitive to environmental factors that can inhibit the early stages of symbiotic interaction. In this study, we propose the encapsulation of Bradyrhizobium sp. SEMIA6144 and the flavonoid naringin (Nar) in alginate beads to improve flavonoid stability and promote nodulation kinetics in peanuts. Three types of beads were synthesized: A (control, SEMIA6144 only); B (SEMIA6144 induced with 10 µM Nar); and C (SEMIA6144 co-entrapped with 1 mM Nar). Although Nar increased cell mortality (2-fold compared to control) and reduced metabolic activity-particularly at 1 mM-cells in beads B and C responded by altering their membrane fatty acid profile (30% and 55.5% of 18:1, respectively) leading to a reduction in saturated fatty acids (5.8% and 13.1% for 16:0 and 18:0 in B; 11.8% and 21.2% in C). Bacterial release kinetics followed a primarily Fickian diffusion model, with minor matrix-bacteria interactions in Nar-treated beads. Notably, bacterial release in peanut root exudates was 6%, 10%, and 11% higher for beads A, B, and C, respectively, compared to release in physiological solutions. Nar-beads enhanced the formation of curved root hairs, promoted bacterial colonization in root hair zones, and stimulated the appearance of rosette-like structures associated with nodule initiation. In conclusion, encapsulating Bradyrhizobium sp. SEMIA6144 with Nar in beads represents a promising strategy to improve symbiotic nitrogen fixation in peanuts.},
}

@article {pmid40508007,
year = {2025},
author = {Zhao, X and Muhammad Aslam, M and Chen, M and Das, D},
title = {Plant-Fungi Mutualism, Alternative Splicing, and Defense Responses: Balancing Symbiosis and Immunity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {11},
pages = {},
pmid = {40508007},
issn = {1422-0067},
support = {2022YFD1700200//National Key Research and Development Program of China/ ; (Natural Science)-ZK[2023]-099//Guizhou Provincial Basic Research Program/ ; 3201452//National Natural Science Foundation of China/ ; 111 Program, D20023//Program of Introducing Talent to Chinese Universities/ ; Qianjiaohe KY (2020)004//Frontiers Science Center for Asymmetric Synthesis and Medicinal Molecules, Department of Ed-ucation, Guizhou Province/ ; AoE/M-403/16, GRF12100318, 12103219, 12103220, 12101722//Hong Kong Research Grant Council/ ; },
mesh = {*Symbiosis/genetics ; *Alternative Splicing ; *Plants/microbiology/genetics/immunology ; *Fungi/physiology ; *Plant Immunity/genetics ; Gene Expression Regulation, Plant ; Plant Diseases/microbiology/immunology/genetics ; },
abstract = {Alternative splicing (AS) is the process of RNA maturation in eukaryotes, which is essential for post-transcriptional regulation. The transcripts produced by AS can encode distinct protein isoforms and contribute to the regulation of eukaryotic growth and development in response to a changing environment, and they are crucial in plant-fungal interactions. Plant-fungal symbiosis is one of the most significant biotic interactions in the biosphere. The symbiotic association of fungi not only improves plant growth and resistance but has potential significance for endangered species conservation and reproduction. Alternative splicing is involved in regulating symbiotic responses to host immune signals, regulating the host-symbiont contact, and initiating signaling during symbiosis. In recent years, mRNAs research has been progressing rapidly, and AS is an important post-transcriptional regulator that requires further investigation. However, while AS has been widely studied in mammalian disease research, very limited studies are available on the regulation of AS in plant-fungal symbiosis and their role in benefiting the interacting partners. In this review, we provide an overview of our existing knowledge about AS in symbiotic plant-fungal relationships and discuss potential hotspots for future investigation to expand our understanding of plant-fungal interactions.},
}

*Symbiosis/genetics
*Alternative Splicing
*Plants/microbiology/genetics/immunology
*Fungi/physiology
*Plant Immunity/genetics
Gene Expression Regulation, Plant
Plant Diseases/microbiology/immunology/genetics

@article {pmid40507152,
year = {2025},
author = {Koller, AM and Săsăran, MO and Mărginean, CO},
title = {The Role of Gut Microbiota in Pediatric Obesity and Metabolic Disorders: Insights from a Comprehensive Review.},
journal = {Nutrients},
volume = {17},
number = {11},
pages = {},
pmid = {40507152},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Pediatric Obesity/microbiology ; Child ; *Metabolic Diseases/microbiology ; Dysbiosis/microbiology ; Adolescent ; Inflammation/microbiology ; Diet, Mediterranean ; },
abstract = {Background: Pediatric obesity represents a multifactorial condition in which gut microbiota dysbiosis, low-grade systemic inflammation, and metabolic dysfunction are intricately connected. Objectives: This systematic review sought to evaluate and integrate current findings regarding the interactions between gut microbial composition, dietary influences, inflammatory status, and metabolic outcomes in obese pediatric populations. Methods: A comprehensive search of PubMed, Scopus, and Web of Science databases was conducted for studies published from January 2010 onward. Eligible studies comprised randomized controlled trials, and cohort, cross-sectional, and longitudinal designs involving individuals aged ≤18 years. Study quality was appraised using the NIH Study Quality Assessment Tool. Results: Sixteen studies fulfilled the inclusion criteria. Dysbiosis was consistently observed among obese children, characterized by alterations in microbial diversity and abundance associated with increased inflammation and adverse metabolic profiles. Dietary interventions, notably symbiotic supplementation and adherence to Mediterranean diet patterns, were associated with favorable modulation of gut microbiota and inflammatory parameters. The majority of studies demonstrated high methodological quality, although minor observational limitations were noted. Conclusions: Gut microbiota dysregulation plays a central role in the development of metabolic and inflammatory complications associated with pediatric obesity. Although dietary and microbiota-modifying strategies show therapeutic promise, their effectiveness must be substantiated through robust, long-term studies.},
}

Humans
*Gastrointestinal Microbiome
*Pediatric Obesity/microbiology
Child
*Metabolic Diseases/microbiology
Dysbiosis/microbiology
Adolescent
Inflammation/microbiology
Diet, Mediterranean

@article {pmid40505561,
year = {2025},
author = {Padhan, A and Paul, B},
title = {Unlocking the potential of red mud: Advanced strategies for economic optimization and sustainable recovery of critical minerals.},
journal = {Journal of environmental management},
volume = {389},
number = {},
pages = {126040},
doi = {10.1016/j.jenvman.2025.126040},
pmid = {40505561},
issn = {1095-8630},
abstract = {Red mud (RM) is a solid by-product generated in large quantities from the Bayer process in alumina refinery industries. The high pH and heavy metal content pose significant environmental challenges for its management and disposal. This comprehensive review highlights RM's potential as a source of valuable raw materials, focusing on both economic and environmental implications. Special attention is given to the recovery of critical minerals such as lithium, titanium, scandium, and rare earth elements (REEs) from RM. The review explores current market trends, recovery methods, and related technical and regulatory challenges. It also discusses the toxicity and environmental concerns of RM disposal, as well as its wide range of applications in the industrial sector. In particular, its use in construction materials such as cement, bricks, and geopolymers while also highlighting its potential in ceramic and catalyst manufacturing. Further, this study reflects economic factors, legal frameworks, and incentives for RM valorization, supported by case studies on its sustainable utilization. Additionally, it also covers health and safety aspects, lifecycle assessments, and future research to improve value added applications and reduce environmental risks. This review uniquely integrates the recovery of critical minerals with sustainable economic strategies, providing a comprehensive framework for the effective utilization of RM in the circular economy.},
}

@article {pmid40505098,
year = {2025},
author = {Jhu, MY and Ledermann, R},
title = {Division of Labour in the Nodule: Plant GluTRs Fuel Heme Biosynthesis for Symbiosis.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf156},
pmid = {40505098},
issn = {1532-298X},
}

@article {pmid40504784,
year = {2025},
author = {Heinen, M and Rovenich, H and Altegoer, F},
title = {The rise of fungal G-protein coupled receptors in pathogenesis and symbiosis.},
journal = {PLoS pathogens},
volume = {21},
number = {6},
pages = {e1013212},
pmid = {40504784},
issn = {1553-7374},
}

@article {pmid40504761,
year = {2025},
author = {Chiriatti, M and Bergamaschi Ganapini, M and Panai, E and Wiederhold, BK and Riva, G},
title = {System 0: Transforming Artificial Intelligence into a Cognitive Extension.},
journal = {Cyberpsychology, behavior and social networking},
volume = {},
number = {},
pages = {},
doi = {10.1089/cyber.2025.0201},
pmid = {40504761},
issn = {2152-2723},
abstract = {This paper introduces "System 0," a conceptual framework for understanding how artificial intelligence functions as a cognitive extension preceding both intuitive (System 1) and deliberative (System 2) thinking processes. As AI systems increasingly shape the informational substrate upon which human cognition operates, they transform from passive tools into active cognitive partners. Building on the Extended Mind hypothesis and Heersmink's criteria for cognitive extension, we argue that AI systems satisfy key conditions for cognitive integration. These include reliability, trust, transparency, individualization, and the ability to enhance and transform human mental functions. However, AI integration creates a paradox: while expanding cognitive capabilities, it may simultaneously constrain thinking through sycophancy and bias amplification. To address these challenges, we propose seven evidence-based frameworks for effective human-AI cognitive integration: Enhanced Cognitive Scaffolding, which promotes progressive autonomy; Symbiotic Division of Cognitive Labor, strategically allocating tasks based on comparative strengths; Dialectical Cognitive Enhancement, countering AI sycophancy through productive epistemic tension; Agentic Transparency and Control, ensuring users understand and direct AI influence; Expertise Democratization, breaking down knowledge silos; Social-Emotional Augmentation, addressing affective dimensions of cognitive work; and Duration-Optimized Integration, managing the evolving human-AI relationship over time. Together, these frameworks provide a comprehensive approach for harnessing AI as a genuine cognitive extension while preserving human agency, critical thinking, and intellectual growth, transforming AI from a replacement for human cognition into a catalyst for enhanced thinking.},
}

@article {pmid40504377,
year = {2025},
author = {Zhang, J and Zhao, Z and Zhu, C and Wang, E and Brunel, B and Li, S and Zheng, Q and Feng, Z and Zhang, H},
title = {Diverse Peanut Bradyrhizobial Communities in Chinese Soils: Insights from Eastern, Central, and Northern Henan Province.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {65},
pmid = {40504377},
issn = {1432-184X},
support = {2024M761756//China Postdoctoral Science Foundation/ ; Yuzutong[2023]No.11//Central Plains Youth Top Talent Project/ ; Sabbatical Year SIP20200726//IPN, Mexico/ ; },
mesh = {*Arachis/microbiology ; China ; *Bradyrhizobium/genetics/classification/isolation & purification ; Phylogeny ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Polymorphism, Restriction Fragment Length ; Symbiosis ; Soil/chemistry ; Root Nodules, Plant/microbiology ; Bacterial Proteins/genetics ; },
abstract = {Henan province is a major peanut-producing area in China, but research on rhizobia nodulating peanut have been limited to southern Henan, which accounts for only less than half of the province. A collection of 212 strains of peanut rhizobia was obtained from six field sites in eastern, central, and northern Henan, Central China, by using peanut as a trap host under glasshouse conditions. PCR-RFLP analysis of ribosomal IGS sequences classified the 212 strains into 28 distinct types. Phylogenetic analyses of the 16S rRNA, atpD, gyrB, dnaK, and rpoB genes from 30 representative strains of the 28 IGS types identified revealed the presence of Bradyrhizobium. liaoningense, B. yuanmingense, B. zhengyangense, and two novel Bradyrhizobium genospecies. This composition differs from the peanut rhizobia community found in southern Henan. B. liaoningense was the dominant species, covering 49% of the total isolates across the field sites, while B. zhengyangense accounting for 27%, B. yuanmingense for 7% and the two novel Bradyrhizobium genospecies for 17%. Phylogenetic analysis showed that the symbiosis-related nodC and nifH gene sequences clustered into six groups: three associated exclusively with the peanut host (symbiovar arachidis and two unnamed group), three originating from other legume hosts (sv. glycinearum, cajani and retamae). Through the principal component analysis (PCA) between IGS types or species and soil physicochemical properties and environmental factors, it showed that IGS types 1, 3, 5, 8, 9, 12, 14, 15, 18, and 21 positively correlated with AveTmax, AveTmin, AN and AP. IGS types 4, 11, 16, 17, 20, 25, and 26 were positively associated with Alt, AvePrecp, and pH. IGS types 2, 7, 10, 22, 24, and 27 correlated with AP, while remaining types exhibited correlations with OM. In addition, B. yuanmingense, B. liaoningense, and Bradyrhizobium genosp. I positively affected by AveTmax, AP, AN, and AK. Bradyrhizobium genosp. II positively correlated with AK, AN, and OM while B. zhengyangense mainly affected by AvePrecp and pH. The alkaline soil pH in this study differs greatly from the acid soils in southern Henan, explaining the inconsistency between the species of peanut rhizobia detected in southern Henan and the rest of the province. The symbiotic effect assay demonstrated that all representative strains successfully formed nodules and exhibited a significant increase in symbiotic efficiency. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature and drought. It conducted a comprehensive collection of peanut rhizobia in eastern, central, and northern Henan province, identifying two putative novel Bradyrhizobium species and isolating rhizobial strains with high symbiotic efficiency and robust stress tolerance. This study is a necessary basic for the producing and application of peanut rhizobial inoculant in this main agricultural province.},
}

*Arachis/microbiology
China
*Bradyrhizobium/genetics/classification/isolation & purification
Phylogeny
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Polymorphism, Restriction Fragment Length
Symbiosis
Soil/chemistry
Root Nodules, Plant/microbiology
Bacterial Proteins/genetics

@article {pmid40504144,
year = {2025},
author = {Sun, X and Li, H and Chen, ZB and Liu, BQ and Li, CQ and Zhao, ZY and Li, XY and Luan, JB},
title = {Hamiltonella symbionts benefit whitefly fertilization by regulating the maternal protein Tudor-mediated piRNA pathway.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {24},
pages = {e2427053122},
doi = {10.1073/pnas.2427053122},
pmid = {40504144},
issn = {1091-6490},
support = {32225042//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Hemiptera/microbiology/physiology/genetics ; *Symbiosis ; Female ; *RNA, Small Interfering/genetics/metabolism ; *Insect Proteins/metabolism/genetics ; *Fertilization/physiology ; Ovary/metabolism ; Adenosine Triphosphate/metabolism ; Piwi-Interacting RNA ; },
abstract = {Although it is widely recognized that nutritional symbionts can manipulate host reproduction, the underlying molecular and cellular mechanisms are largely unclear. The facultative symbiont Hamiltonella in bacteriocyte induces female-biased sex ratio of whiteflies. Here, we demonstrate that a maternal gene tudor (tud) and its encoded protein have lower expression levels in ovaries of Hamiltonella-cured whiteflies. Tud family proteins can interlink the various stages of biosynthesis of PIWI-interacting RNA (piRNA), a class of small noncoding RNAs. We find that Hamiltonella affects the abundance of a piRNA through the maternal gene tud, thereby regulating the expression of the vacuolar (H+)-ATPase H subunit (VATPH), which is the switch of activity of the vacuolar (H+)-ATPase that plays a crucial role in maintaining the homeostasis of intracellular energy and supporting mitochondrial respiration. This regulation adjusts the ATP level in ovaries of whiteflies. The ATP level shapes the F-actin pattern in ovaries and eggs of whiteflies, ultimately manipulating whitefly fertilization. Silencing tud inhibited whitefly fertilization by impairing ATP levels and F-actin patterns in ovaries and eggs. This study reveals that symbiont and maternal protein associations can regulate host fertilization by piRNA biosynthesis.},
}

Animals
*Hemiptera/microbiology/physiology/genetics
*Symbiosis
Female
*RNA, Small Interfering/genetics/metabolism
*Insect Proteins/metabolism/genetics
*Fertilization/physiology
Ovary/metabolism
Adenosine Triphosphate/metabolism
Piwi-Interacting RNA

@article {pmid40503882,
year = {2025},
author = {Jonas, L and Lee, Y-Y and Bachvaroff, T and Hill, RT and Li, Y},
title = {Two novel Patescibacteria: Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov., both associated with microalgae optimized for carbon dioxide sequestration from flue gas.},
journal = {mBio},
volume = {},
number = {},
pages = {e0123125},
doi = {10.1128/mbio.01231-25},
pmid = {40503882},
issn = {2150-7511},
abstract = {The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%-10% CO2. Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.IMPORTANCETo our knowledge, this is the first report of Patescibacteria as dominant bacteria associated with microalgae or within a biologically mediated carbon capture system. Two novel Patescibacteria were found in two ecologically distinct microalgal cultures (one freshwater strain and one marine) regardless of whether the cultures were bubbled with air, 5% CO2, or 10% CO2. This unexpected and unprecedented dominance led to long-read sequencing and the assembly of high-quality metagenomes for both Patescibacteria, as well as five other bacteria in the system. The discovery of two novel species belonging to two novel genera, one novel family, and one novel order has enabled us to fill in gaps of a major, uncharacterized branch within the bacterial tree of life. Additionally, the extreme gene loss found in both Patescibacteria, Phycocordibacter aenigmaticus and Minusculum obligatum, contributes knowledge to a rapidly advancing body of research on the scavenging metabolic nature of this enigmatic and largely unclassified phylum.},
}

@article {pmid40501974,
year = {2025},
author = {Jacobs, J and Mirchandani, C and Seligmann, WE and Sacco, S and Escalona, M and Green, RE and Russell, SL},
title = {Wolbachia induces host cell identity changes and determines symbiotic fate in Drosophila.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.05.658111},
pmid = {40501974},
issn = {2692-8205},
abstract = {UNLABELLED: Many host-associated bacteria influence the differentiation of their eukaryotic host cells. The association between Wolbachia pipientis and Drosophila melanogaster offers a model for understanding how host-microbe gene expression co-evolves. Using Wolbachia -infected Drosophila cell lines, we show that the w Mel strain alters host cell states, inducing novel gene expression programs that diverge from known cell types. Transcriptomic co-expression network analysis identified gene expression modules specific to each cell type and infection state, and revealed that w Mel tailors its gene expression to host context. In macrophage-like host cells, w Mel expresses pathogenic effectors, whereas in neuron-like cells, w Mel upregulates metabolic genes. Micro-C chromatin contact data revealed that many of these infection-induced changes are epigenetically encoded, with w Mel infection conferring reduced chromatin contacts and widespread transcriptional derepression in D. melanogaster . These findings show that the nature of Wolbachia symbiosis-mutualistic or pathogenic-emerges from host cell environments and suggest new paths for engineering host-specific microbial phenotypes.

IN BRIEF: Wolbachia pipientis reprograms Drosophila cell identity by reshaping host gene expression and chromatin in a cell type-specific manner. Infected cells adopt novel states tailored to w Mel strain gene expression, enabling either mutualism or pathogenesis. These findings advance Wolbachia engineering for targeted host cell interactions and symbiont-driven phenotypes.},
}

@article {pmid40501112,
year = {2025},
author = {Bytnerowicz, TA and Griffin, KL and Menge, DNL},
title = {Time lags in the regulation of symbiotic nitrogen fixation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70295},
pmid = {40501112},
issn = {1469-8137},
support = {DEB-1457650//National Science Foundation/ ; IOS-2129542//National Science Foundation/ ; Stengl-Wyer Scholars Program//University of Texas at Austin/ ; FP91781501-0/EPA/EPA/United States ; },
abstract = {Theory has shown that time lags in the regulation of symbiotic nitrogen (N) fixation (SNF) can be important to the competitive dynamics and ecosystem consequences of N-fixing trees, but measurements of these time lags are lacking. Here, we used a novel method to measure SNF in seedlings of four N-fixing tree species that represent tropical and temperate origins and actinorhizal and rhizobial symbiotic associations, each grown under warm and cold temperature regimes. We added N to previously N-poor pots to induce downregulation and flushed N out of previously N-rich pots to induce upregulation. It took 31-51 d for SNF to decline by 95%, with faster downregulation in temperate species and at warm temperatures. Upregulation by 95% took 108-138 d in total, including 21-57 d after SNF was first detectable. SNF started earlier in rhizobial symbioses, but increased faster once it started in actinorhizal symbioses. These results suggest that time lags in regulating SNF represent a significant constraint on facultative SNF and can lead to large losses of available N from ecosystems, providing a resolution to the paradox of sustained N richness.},
}

@article {pmid40500556,
year = {2025},
author = {Shi, D and Liu, L and Zhang, D and Zheng, Y and Hu, W and Wu, P and Hao, X and Liu, H and Gao, J and Li, J and Wu, Z and Li, S and Wang, H},
title = {One-step Radiosynthesis and Preclinical Evaluation of Molecular Tracer [[18]F]FEtO-CHC Targeting Monocarboxylate Transporters for PET Imaging in Tumor-bearing Mice.},
journal = {Molecular imaging and biology},
volume = {},
number = {},
pages = {},
pmid = {40500556},
issn = {1860-2002},
support = {81471695//National Natural Science Foundation of China/ ; 82027804//National Natural Science Foundation of China/ ; 82001873//National Natural Science Foundation of China/ ; },
abstract = {PURPOSE: Monocarboxylate transporters (MCTs) play a pivotal role in tumor metabolic symbiosis, acid resistance, and metastatic progression. Herein, we report the development of [[18]F]FEtO-CHC, a novel MCTs-targeted positron emission tomography (PET) radiotracer, and systematically evaluate its potential for non-invasive tumor imaging.

PROCEDURES: The radiosynthesis of [[18]F]FEtO-CHC and its non-radioactive analog was achieved through optimized precursor synthesis and fluorination protocols. Comprehensive in vitro characterization encompassed: radiochemical purity and stability assessments, cellular uptake kinetics and inhibition assays in MCT-expressing BxPC3 (pancreatic) and 4T1 (breast) cancer models, biodistribution and dynamic micro-PET/CT imaging in tumor-bearing murine models.

RESULTS: [[18]F]FEtO-CHC, a CHC-derived radioligand, was synthesized via streamlined one-step radiosynthesis with 52.08 ± 6.74% decay-corrected yield (n=7), >99% radiochemical purity, and excellent stability. Cellular studies demonstrated MCTs-dependent uptake with significant suppression (>70%) by α-CHC competition. In vivo pharmacokinetics revealed favorable metabolic stability with dual hepatorenal clearance. Tumor uptake correlated with MCT expression levels, as confirmed by immunohistochemistry.

CONCLUSIONS: This study establishes an efficient one-step radiosynthetic approach for [[18]F]FEtO-CHC production and validates its specificity as a MCT-targeted PET probe, offering potential utility in tumor imaging with further structural optimization.},
}

@article {pmid40500257,
year = {2025},
author = {Pérez, J and Picioreanu, C},
title = {Diffusion-based mechanism explains spatial organization in cross-feeding biofilms.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {102},
pmid = {40500257},
issn = {2055-5008},
support = {PID2021-126102OB-I00//Ministerio de Ciencia e Innovación/ ; ORIGEN PID2021-126102OB-I00//European Regional Development Fund/ ; },
mesh = {*Biofilms/growth & development ; Diffusion ; Models, Biological ; Anaerobiosis ; Aerobiosis ; *Bacteria/metabolism/growth & development ; Models, Theoretical ; },
abstract = {Complex symbiotic interactions were claimed for explaining spatial organization of microbial species in cross-feeding biofilms. Here however, a distinct mechanism is proposed, called diffusion-based enhanced microbial organization (DEMO). An accepted mathematical model based on one-dimensional balances with diffusion-reaction of substrates and convection of multiple microbial types in a cross-feeding biofilm was used to describe emerging microbial distributions. The model allowed isolation of the effects of diffusion from other factors (kinetics, stoichiometry, specific symbiotic interactions), pointing to a possible mechanism for stratification in anaerobic biofilms. The secondary degrader consuming waste metabolite from a primary degrader was retained in anaerobic biofilms in an apparent growth yield disproportion. However, diffusion of an intermediate substrate can be responsible for this disproportion, even in longer food chains. This microbial distribution was not observed in independent feeding. In aerobic biofilms, this mechanism remains inactive, explaining the preference for full oxidation of organic matter in aerobic degradation.},
}

*Biofilms/growth & development
Diffusion
Models, Biological
Anaerobiosis
Aerobiosis
*Bacteria/metabolism/growth & development
Models, Theoretical

@article {pmid40500053,
year = {2025},
author = {Deng, SJ and Tu, L and Li, L and Hu, JP and Li, JL and Tang, JX and Zhang, MC and Zhu, GD and Cao, J},
title = {A symbiotic bacterium regulates the detoxification metabolism of deltamethrin in Aedes albopictus.},
journal = {Pesticide biochemistry and physiology},
volume = {212},
number = {},
pages = {106445},
doi = {10.1016/j.pestbp.2025.106445},
pmid = {40500053},
issn = {1095-9939},
mesh = {Animals ; *Pyrethrins/metabolism/pharmacology ; *Aedes/microbiology/metabolism/drug effects ; *Nitriles/metabolism/pharmacology ; *Insecticides/metabolism/pharmacology ; Symbiosis ; *Serratia marcescens/physiology/genetics/metabolism ; Insecticide Resistance ; Inactivation, Metabolic ; Glutathione Transferase/metabolism/genetics ; Insect Proteins/metabolism/genetics ; },
abstract = {The mosquito Aedes albopictus is an important vector of dengue, chikungunya, and Zika; and is a globally distributed invasive mosquito with increasing resistance to insecticides, thereby posing a serious risk to global public health. Symbiotic gut bacteria have been shown to be related to insecticide resistance, but knowledge is still limited for A. albopictus. Here, we explored the role of Serratia marcescens, a gut symbiotic bacterium, in the resistance of A. albopictus to the insecticide deltamethrin. Using 16S-rRNA sequencing we found that S. marcescens was significantly enriched in A. albopictus after deltamethrin exposure, and that resistance increased after S. marcescens enrichment. The enzymatic activities of mixed-function oxidase (MFO) and glutathione S-transferase (GST), two important detoxification enzymes, were higher in the bacteria-enriched mosquitoes. The expressions of ABCG4 and GSTD1, two genes related to detoxification metabolism, were up-regulated following S. marcescens infection and after deltamethrin exposure, as assayed using RNA-seq. The up-regulation of these two genes was most significant in midgut and Malpighian tubules. Our results suggest that S. marcescens infection could enhance deltamethrin resistance in A. albopictus by increasing detoxification metabolism; of interest for designing more efficient mosquito control measures.},
}

Animals
*Pyrethrins/metabolism/pharmacology
*Aedes/microbiology/metabolism/drug effects
*Nitriles/metabolism/pharmacology
*Insecticides/metabolism/pharmacology
Symbiosis
*Serratia marcescens/physiology/genetics/metabolism
Insecticide Resistance
Inactivation, Metabolic
Glutathione Transferase/metabolism/genetics
Insect Proteins/metabolism/genetics

@article {pmid40498450,
year = {2025},
author = {Teyssier, E and Grat, S and Landry, D and Ouradou, M and Rich, MK and Fort, S and Keller, J and Lefebvre, B and Delaux, PM and Mbengue, M},
title = {A plant Lysin Motif Receptor-Like Kinase plays an ancestral function in mycorrhiza.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {24},
pages = {e2426063122},
doi = {10.1073/pnas.2426063122},
pmid = {40498450},
issn = {1091-6490},
support = {OPP1172165//Bill and Melinda Gates Foundation (GF)/ ; OPP1172165//Foreign, Commonwealth and Development Office (FCDO)/ ; 101001675//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; ANR-17-EURE-0003//LABoratoires d'EXcellence ARCANE (Labex ARCANE)/ ; ANR-15-IDEX-02//Glyc@Alps/ ; CARN-025-01//Institut Carnot PolyNat (PolyNat)/ ; ANR-10-LABX-41//Laboratoire d'Excellence TULIP (Labex TULIP)/ ; ANR-18-EURE-0019//École Universitaire de Recherche (EUR) - TULIP-GS/ ; },
mesh = {*Mycorrhizae/genetics/physiology/metabolism ; Symbiosis ; *Marchantia/genetics/microbiology/enzymology ; *Plant Proteins/metabolism/genetics ; *Protein Kinases/metabolism/genetics ; Glomeromycota ; Phylogeny ; },
abstract = {Arbuscular mycorrhiza (AM) with soilborne Glomeromycota fungi was pivotal in the conquest of land by plants almost half a billion years ago. In flowering plants, it is hypothesized that AM is initiated by the perception of AM fungi-derived chito- and lipochito-oligosaccharides (COs/LCOs) in the host via Lysin Motif Receptor-Like Kinases (LysM-RLKs). However, it remains uncertain whether plant perception of these molecules is a prerequisite for AM establishment and for its origin. Here, we made use of the reduced LysM-RLK complement present in the liverwort Marchantia paleacea to assess the conservation of the role played by this class of receptors during AM and in CO/LCO perception. Our reverse genetic approach demonstrates the critical function of a single LysM-RLK, MpaLYKa, in AM formation, thereby supporting an ancestral function for this receptor in symbiosis. Binding studies, cytosolic calcium variation recordings and genome-wide transcriptomics indicate that another LysM-RLK of M. paleacea, MpaLYR, is also required for triggering a response to COs and tested LCOs, despite being dispensable for AM formation. Collectively, our results demonstrate that the perception of symbionts by LysM-RLK is an ancestral feature in land plants, and suggest the existence of yet-uncharacterized AM fungi signals.},
}

*Mycorrhizae/genetics/physiology/metabolism
Symbiosis
*Marchantia/genetics/microbiology/enzymology
*Plant Proteins/metabolism/genetics
*Protein Kinases/metabolism/genetics
Glomeromycota
Phylogeny

@article {pmid40497987,
year = {2025},
author = {Kamalabadi Farahani, M and Bahar, A and Tahmasebi, H and Oksenych, V and Jahantigh, M},
title = {Microbial Metabolite Effects on Vasculogenic Mimicry in Metastatic Cancers.},
journal = {Cells},
volume = {14},
number = {11},
pages = {},
pmid = {40497987},
issn = {2073-4409},
mesh = {Humans ; *Neoplasms/pathology/microbiology/blood supply/metabolism ; Neoplasm Metastasis ; *Neovascularization, Pathologic/pathology/microbiology ; Tumor Microenvironment ; Animals ; *Microbiota ; },
abstract = {Aggressive cancer cells can form new, functional blood vessel-like structures independently of endothelial cells, known as vasculogenic mimicry (VM), instead of the usual tumor blood vessel formation process. However, the symbiotic relationship between microbial communities and human cells ensures the upkeep of cellular metabolism and the functionality of the immune system and metastatic cancers. This interaction typically happens through the generation and management of hormonal intermediates, metabolites, secondary metabolites, proteins, and toxins. A disturbance in the balance between the host and microbiota can alter the dynamics of their relationship, creating a conducive environment for the development of diseases, such as cancers. This review aims to synthesize the initial evidence on the molecular processes governing the interactions between GM and cancer development and emphasize microbial metabolites' effects on vasculogenic mimicry. Some microbial metabolites could also contribute to developing interactions between microbes and the tumor microenvironment. While numerous obstacles persist, GM's immense significance and complete capability in shaping tailored anticancer plans cannot be exaggerated, highlighting the need to investigate a holistic method that includes microbial modulation therapy in cancer management.},
}

Humans
*Neoplasms/pathology/microbiology/blood supply/metabolism
Neoplasm Metastasis
*Neovascularization, Pathologic/pathology/microbiology
Tumor Microenvironment
Animals
*Microbiota

@article {pmid40497665,
year = {2025},
author = {Chen, C and Dunn, DW and Shi, L and Wang, R and Wang, RW},
title = {Parasites and investment to host inflorescences in a fig tree-fig wasp mutualism.},
journal = {Ecology},
volume = {106},
number = {6},
pages = {e70123},
doi = {10.1002/ecy.70123},
pmid = {40497665},
issn = {1939-9170},
support = {31760105//National Natural Science Foundation of China (NSFC)/ ; 31901105//National Natural Science Foundation of China (NSFC)/ ; 32160239//National Natural Science Foundation of China (NSFC)/ ; 32070453//National Natural Science Foundation of China (NSFC)/ ; 2023D61//Yunnan University of Finance and Economics/ ; U2102221//NSFC-Yunnan United Fund/ ; },
mesh = {Animals ; *Wasps/physiology ; *Ficus/parasitology/physiology ; *Symbiosis ; *Flowers/parasitology/physiology ; Pollination ; Female ; Host-Parasite Interactions ; },
abstract = {Most mutualisms are parasitized by third-party species that inflict costs to the mutualists. How such parasites affect mechanisms that help maintain mutualism stability is poorly understood, even in well-studied systems. Angiosperm plants tend to invest most resources in tissue that yields high net benefits. In mutualisms with plant hosts, reduction in such investment can function as a key stability-promoting mechanism, such as in fig-wasp mutualisms. Here, uncooperative symbiont wasps that fail to pollinate incur "sanctions" via reduced host investment to unpollinated figs, realized via fig abortion, killing all wasp offspring, or via elevated offspring mortality within unaborted figs. We experimentally exposed host Ficus racemosa figs to parasitic wasps Sycophaga fusca, which convert fig flowers into offspring without benefitting host trees, with or without uncooperative (pollen-free) or cooperative (pollen-laden) symbiont pollinator wasps Ceratosolen fusciceps. Pollen-free C. fusciceps were still able to convert fig flower ovaries into wasp offspring, whereas those naturally pollen laden were prevented from reproducing by experimental manipulation. Independent of the effects of pollination and reproduction by pollinators, increased exposure to S. fusca parasites resulted in reduced rates of fig abortion and gall failure in unaborted figs. Although S. fusca convert flower ovaries that could otherwise become beneficial pollinator offspring or fig seeds into parasite offspring, figs with intermediate levels of parasite exposure received high levels of investment. Our results suggest that S. fusca parasite oviposition/larval activities can result in host trees boosting investment to figs, even when this may counter the tree's interests. We suggest that oviposition/larval activity by these parasites may mimic the biochemical pathways of pollinator gall formation and seed production.},
}

Animals
*Wasps/physiology
*Ficus/parasitology/physiology
*Symbiosis
*Flowers/parasitology/physiology
Pollination
Female
Host-Parasite Interactions

@article {pmid40497339,
year = {2025},
author = {Dou, Q and Yang, J and Zhang, L and Fan, R and Peng, Y},
title = {Bridge-Mediated Electron Transfer: Bioinspired Redox Communication for Sustained Nitrite-Independent Anaerobic Ammonium Oxidation.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c04107},
pmid = {40497339},
issn = {1520-5126},
abstract = {The lack of nitrite (NO2[-]) in real wastewater severely limits the sustainable nitrogen removal of anaerobic ammonium oxidation (anammox). Although microbial extracellular electron transfer (EET) provides a new approach for NO2[-]-independent anammox, the slow electron transfer at the microbe-material interface hinders its engineering application. Herein, this study proposes a strategy to enhance the electrical contact between microorganisms and insoluble acceptors through conductive bridging materials (e.g., Fe2O3 nanoparticles encapsulated by flavin-rich extracellular polymeric substances). Results showed that the interface between anammox bacteria (AMX1) and Fe2O3 exhibited a high electron flux (6.86 mA·cm[-2]), considerably higher than all reports to date, achieving stable ammonium (NH4[+]) removal of approximately 97.90% and operating continuously for over 150 days. Building on the efficient EET, Fe2O3 was further triggered into Fe[2+]/Fe[3+] redox signaling for microbial metabolic coordination. Specifically, Fe[2+] signals channeled reducing power into coenzyme A/biotin synthesis in symbiotic bacteria (VER2) and fed back to the carbon fixation enzyme (FC = 1.1-fold) of AMX1 through chemotaxis migration and cross-feeding, while Fe[2+] was reconverted to Fe[3+]. The Fe[3+] signals induced gene expression (Log2FC > 0) of EET-associated proteins and simultaneously facilitated the conversion of electricity to critical chemical energy, accelerating the autotrophic growth of AMX1. In this way, anammox bacteria not only survived but also thrived in NO2[-]-limited environments, with relative abundance increasing by 127.22% to sustain NH4[+] removal. This study offers a novel solution to the NO2[-] supply challenge in wastewater treatment, advancing industry toward carbon neutrality goals.},
}

@article {pmid40496994,
year = {2025},
author = {Chen, J and Cao, J and Guo, B and Han, M and Feng, Z and Tang, J and Mo, X and Wang, J and Yang, Q and Pei, Y and Kuzyakov, Y and Ding, J and Makita, N and Yang, X and Zhang, H and Zhao, Y and Kong, D},
title = {Increased dependence on mycorrhizal fungi for nutrient acquisition under carbon limitation by tree girdling.},
journal = {Plant diversity},
volume = {47},
number = {3},
pages = {466-478},
pmid = {40496994},
issn = {2468-2659},
abstract = {Nutrient acquisition through symbiotic ectomycorrhizal fungi is carbon (C) costly but fundamental for plant growth, community, and ecosystem functioning. Here, we examined the functions of roots and mycorrhiza with respect to nutrient uptake after artificially inducing C limitation-seven months after girdling of an ectomycorrhizal tree, Pinus taeda. Root physiological activity (measured as root nitrogen content and root exudation) declined after girdling and was accompanied with 110% and 340% increases in mycorrhizal colonization and extramatrical hyphal length, respectively. Fungi colonizing roots switched to a community characterized by higher C efficiency (lower C cost) of nutrient acquisition (CENA, the amount of nutrient acquisition per unit C cost) and lower network complexity, indicating a tradeoff between CENA and stability of the fungal community. Root transcriptome analysis suggested a shift in metabolic pathways from a tricarboxylic acid cycle decomposition of carbohydrate to lipid biosynthesis to maintain closer associations with mycorrhiza for nutrient cycling after the girdling. By integrating multi-level evidence, including root transcriptome, fungal composition, and network complexity data, we demonstrate an increased dependence on mycorrhiza for nutrient acquisition under the C limitation condition, which is likely due to a shift to fungal community with higher CENA at the cost of lower stability.},
}

@article {pmid40495375,
year = {2025},
author = {Fattar, N and Louni, M and Buysse, M and Floriano, AM and Bertaux, J and Cantereau, A and Rivero, A and Bruley, M and McCoy, KD and Delafont, V and Boulanger, N and Vavre, F and Bouchon, D and Duron, O},
title = {Evolutionary Convergence of Nutritional Symbionts in Ticks.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70120},
pmid = {40495375},
issn = {1758-2229},
support = {ANR- 20-CE34-0002//Agence Nationale de la Recherche/ ; ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche/ ; ANR-21-CE02-0002//Agence Nationale de la Recherche/ ; //Université de Montpellier, KIM RIVE, MUSE/ ; //Région Occitanie Pyrénées-Méditerranée, RIVOC/ ; },
mesh = {Animals ; *Symbiosis ; *Ticks/microbiology/physiology ; *Coxiella/genetics/physiology/metabolism ; *Francisella/genetics/physiology/metabolism ; *Biological Evolution ; Phylogeny ; Heme/biosynthesis ; *Bacteria/genetics/classification/metabolism ; },
abstract = {Symbiosis with bacteria is essential for the survival of animals with an obligate blood-feeding lifestyle. In ticks, two distinct bacterial lineages, Coxiella-like and Francisella-like endosymbionts, have independently evolved into nutritional symbionts, converging on a key biochemical function for the tick's survival and growth: the production of three B vitamins. In this study, we carried out comparative analyses across multiple tick species and characterised remarkable similarities in their tissue localisation, particularly in organs important for nutrient metabolism and maternal transmission to progeny. In these organs, both symbionts colonise similar intracellular niches, residing within membrane-bound, replicative vacuoles that occupy a substantial part of the cytoplasm of tick cells. Despite extensive genomic reduction, both symbionts have retained pathways for the biosynthesis of B vitamins and, in some cases, chorismate, a precursor used for the production of serotonin by ticks. However, differences exist: while Coxiella-like endosymbionts lack the ability to synthesise heme, Francisella-like endosymbionts possess a complete heme biosynthesis pathway and may potentially provide ticks with this essential cofactor. Overall, these phenotypic and genomic characteristics reveal a broad convergence among symbiotic interactions across major tick families, highlighting the essential role of symbiosis in tick nutrition, feeding behaviour, blood intake and subsequently in pathogen transmission.},
}

Animals
*Symbiosis
*Ticks/microbiology/physiology
*Coxiella/genetics/physiology/metabolism
*Francisella/genetics/physiology/metabolism
*Biological Evolution
Phylogeny
Heme/biosynthesis
*Bacteria/genetics/classification/metabolism

@article {pmid40494677,
year = {2025},
author = {Gao, JP and Chiu, CH and Oldroyd, GED},
title = {Unlocking the role of NSP1 and NSP2: nutrient-responsive regulators in nodulation.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.05.008},
pmid = {40494677},
issn = {1878-4372},
abstract = {Symbiotic nitrogen fixation represents a crucial yet energy-demanding strategy for legumes to survive in nutrient-poor soils. We highlight the multifaceted roles of NSP1 and NSP2 in this symbiosis and propose their function as 'nutrient-responsive regulators', integrating environmental signals, physiological status, and nutrient availability, to ensure nodulation occurs only under favorable conditions.},
}

@article {pmid40494494,
year = {2025},
author = {María, CM and José V, D and Adrián, PR and Enrique, QM and Natalia, GM},
title = {Transcriptome analyses reveal Beauveria bassiana endophyte induced disruption of aphid physiology.},
journal = {Journal of invertebrate pathology},
volume = {212},
number = {},
pages = {108377},
doi = {10.1016/j.jip.2025.108377},
pmid = {40494494},
issn = {1096-0805},
abstract = {Some strains of entomopathogenic fungi are known to colonize crops endophytically, providing systemic protection against insect pests. This colonization has been revealed to reduce aphid survival and reproductive potential. Understanding the molecular mechanisms underlying these effects could provide insight into what occurs to aphids when they feed on endophytically colonized plants. In this study, an RNA sequencing (RNA-Seq) was conducted for transcriptome analyses of the melon aphid Aphis gossypii and its symbiotic bacteria after feeding on Beauveria bassiana endophytically colonized melon plants. The fungal colonization triggers significant alterations in the aphid transcriptome, reflecting molecular responses to fungal propagules and/or plant-induced systemic resistance. Key changes include the up-regulation of genes involved in host plant recognition by the aphid pest, immune system activation, energy production, and defense mechanisms such as toxin adaptation, detoxification, and cell death markers. Genes associated with escape responses, including alarm pheromone production and wing bud differentiation, were also up-regulated. In contrast, down-regulated genes point to disruptions in homeostasis and neuronal function, further impacting aphid physiology and its symbiotic relationship with Buchnera. These molecular perturbations likely underlie the lethal and sublethal effects observed in aphids feeding on B. bassiana-colonized plants. This study identifies critical pathways involved in aphid-fungal-plant interactions, offering valuable insights into the potential of endophytic entomopathogenic fungi for aphid pest management.},
}

@article {pmid40494311,
year = {2025},
author = {van Galen, LG and Corrales, A and Truong, C and van den Hoogen, J and Kumar, S and Manley, BF and Stewart, JD and Kohout, P and Baldrian, P and Větrovský, T and Crowther, TW and Kiers, ET and Van Nuland, ME},
title = {The biogeography and conservation of Earth's 'dark' ectomycorrhizal fungi.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R563-R574},
doi = {10.1016/j.cub.2025.03.079},
pmid = {40494311},
issn = {1879-0445},
mesh = {*Mycorrhizae/physiology/classification/genetics ; *Biodiversity ; *Conservation of Natural Resources ; *Soil Microbiology ; Mycobiome ; Phylogeography ; Earth, Planet ; Symbiosis ; },
abstract = {Breakthroughs in DNA sequencing have upended our understanding of fungal diversity. Only ∼155,000 of the 2-3 million fungal species on the planet have been formally described and named, and 'dark taxa' - species known only from sequences - represent the vast majority of species within the fungal kingdom. The International Code of Nomenclature requires physical type specimens to officially recognize new fungal species, making it difficult to name dark taxa. This is a significant problem for conservation because, without names, species cannot be recognized for environmental and legal protection. Symbiotic ectomycorrhizal (EcM) fungi play a particularly important role in forest carbon drawdown, but at present we have little understanding of how many EcM fungal species exist, or where to prioritize research activities to survey and describe EcM fungal lineages. In this review, we use global soil metabarcoding databases (GlobalFungi and the Global Soil Mycobiome consortium) to evaluate current estimates of the total number of EcM fungal species on Earth, outline the current state of undescribed EcM dark taxa, and identify priority regions for future dark taxa exploration. The metabarcoding databases include up to 219,730 EcM fungal operational taxonomic units (OTUs) detected from almost 39,500 samples. Using Chao richness estimates corrected for extrapolating species numbers from metabarcoding datasets, we predict that the global diversity of EcM fungi could be ∼25,500-55,500 species. Dark taxa - those that do not match species-level identities - account for 79-83% of OTUs. Oceania contains the highest percentage of dark taxa (87%), and Europe the lowest (78%). Priority 'darkspots' for future research occur predominantly in tropical regions, but also in selected temperate forests at both southern and northern latitudes. We propose concrete steps to reduce the prevalence of EcM darkspots, including performing targeted field surveys, barcoding fungaria voucher specimens, and developing new ways to describe and conserve fungal taxa from DNA alone.},
}

*Mycorrhizae/physiology/classification/genetics
*Biodiversity
*Conservation of Natural Resources
*Soil Microbiology
Mycobiome
Phylogeography
Earth, Planet
Symbiosis

@article {pmid40494298,
year = {2025},
author = {Martin, F and Tan, H},
title = {Saprotrophy-to-symbiosis continuum in fungi.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R469-R475},
doi = {10.1016/j.cub.2025.01.032},
pmid = {40494298},
issn = {1879-0445},
mesh = {*Symbiosis/physiology ; *Fungi/physiology/genetics ; Biological Evolution ; Ecosystem ; },
abstract = {Fungi are one of the most diverse and ecologically important groups of organisms on Earth. They exhibit remarkable diversity in their ecological roles, ranging from decomposers to mutualistic symbionts to parasites. They have a wide array of lifestyles, which reflect their diverse ecological roles and evolutionary adaptations to marine, aquatic, and terrestrial ecosystems. Fungi are osmotrophs that grow as filaments of cells (hyphae) into their food, secrete digestive enzymes across their cells' chitinous walls, and absorb dissolved nutrients. The classification of fungal lifestyles is primarily based on how they obtain nutrients, with the major modes of nutrition being saprotrophy, parasitism, mutualism and commensalism. Here, we briefly explore these various lifestyles, illustrating their significance in ecosystems and their relationships with other organisms, and then discuss how comparative genomics provides novel insights into their evolutionary trajectories.},
}

*Symbiosis/physiology
*Fungi/physiology/genetics
Biological Evolution
Ecosystem

@article {pmid40494297,
year = {2025},
author = {Hibbett, D and Nagy, LG and Nilsson, RH},
title = {Fungal diversity, evolution, and classification.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R463-R469},
doi = {10.1016/j.cub.2025.01.053},
pmid = {40494297},
issn = {1879-0445},
mesh = {*Fungi/classification/genetics ; Phylogeny ; *Biodiversity ; *Biological Evolution ; },
abstract = {Fungi include mushrooms, molds, lichens, yeasts, and zoosporic forms that occur as free-living or symbiotic organisms in every ecosystem on Earth. About 155,000 species of Fungi have been described, and possibly millions more remain to be named. Recent focus on aquatic habitats has illuminated major groups near the boundary between Fungi and protists. Fungal systematists have made remarkable progress toward resolving the major branches of the phylogeny, although some deep nodes have proven recalcitrant. Fungal taxonomists steadily describe about 3,000 new species per year, and fungal molecular ecologists routinely detect many thousands of unidentifiable 'dark fungi' through metagenomic analyses. To assemble the complete fungal tree of life, it will be necessary to connect the main branches of the phylogeny to information on all described species and integrate the vast and rapidly growing corpus of dark fungi.},
}

*Fungi/classification/genetics
Phylogeny
*Biodiversity
*Biological Evolution

@article {pmid40494295,
year = {2025},
author = {Chen, KH and Darnajoux, R and Magain, N},
title = {Fungi-cyanobacteria associations.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R456-R458},
doi = {10.1016/j.cub.2025.03.058},
pmid = {40494295},
issn = {1879-0445},
mesh = {*Symbiosis ; *Cyanobacteria/physiology ; *Fungi/physiology ; },
abstract = {In this quick guide, Chen et al. introduce the various symbiotic interactions that are found between fungi and cyanobacteria, as seen for example in the cyanolichens.},
}

*Symbiosis
*Cyanobacteria/physiology
*Fungi/physiology

@article {pmid40493490,
year = {2025},
author = {Risser, DD},
title = {Motility in Filamentous Cyanobacteria.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-051024-033328},
pmid = {40493490},
issn = {1545-3251},
abstract = {Filamentous cyanobacteria are multicellular organisms that perform oxygenic photosynthesis and frequently exhibit surface motility. This review discusses the underlying mechanism facilitating motility in these organisms, with a focus on recent molecular and genetic studies. While previous explanations for this motility have proposed exotic mechanisms, the current data indicate that all filamentous cyanobacteria produce a similar motility-associated extracellular polysaccharide (EPS) or slime essential for movement and employ a type IV pilus (T4P) motor to power motility. The (a) regulation of the motor to facilitate coordinated polarity and phototaxis and (b) possible bidirectional feedback between the T4P and motility-associated polysaccharide are discussed as well. Finally, the role of motility in promoting diverse biological phenomena, including dispersal, phototaxis, biofilm formation, granulation, and symbiosis, is explored.},
}

@article {pmid40492833,
year = {2025},
author = {Henry, R and Gurney, J and Armen, S and Barrett, CD and Gavitt, B and Van, P and Lammers, D and McClellan, J and Schreiber, M},
title = {The Joint Trauma System: A critical lifeline facing an uncertain future.},
journal = {The journal of trauma and acute care surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/TA.0000000000004688},
pmid = {40492833},
issn = {2163-0763},
abstract = {ABSTRACT: The Joint Trauma System (JTS) has become a cornerstone of modern trauma care, revolutionizing battlefield treatment and saving countless lives through standardized, evidence-based protocols. Its development and success are rooted in lessons learned from the wars in Iraq and Afghanistan, where fragmented systems were transformed into cohesive, high-performing networks. The JTS has influenced not only military but also civilian trauma care, fostering a symbiotic relationship that advances innovation across both sectors. Despite its proven effectiveness, a growing movement within the US military questions its relevance during peacetime, threatening its existence. This article examines the history, impact, and future of the JTS while emphasizing the critical need for civilian advocacy to preserve its role as a key enabler of military readiness and trauma care innovation.

LEVEL OF EVIDENCE: Expert Opinion; Level V.},
}

@article {pmid40492740,
year = {2025},
author = {Green, EA and Klepacki, I and Klassen, JL},
title = {Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals high niche overlap leading to co-exclusion.},
journal = {mBio},
volume = {},
number = {},
pages = {e0089325},
doi = {10.1128/mbio.00893-25},
pmid = {40492740},
issn = {2150-7511},
abstract = {UNLABELLED: Two mollicute species belonging to the Mesoplasma and Spiroplasma genera have been detected in several species of fungus-growing ants using molecular methods. However, their ecological roles remain largely inferred from metagenomic data. To better understand their diversity and specialization, we cultured both of these Mesoplasma and Spiroplasma symbionts from the fungus-growing ant Trachymyrmex septentrionalis, providing the first isolated mollicutes from any fungus-growing ant species. The genomes of our isolates and related metagenome-assembled genomes (MAGs) from T. septentrionalis fungus gardens comprise two unique phylogenetic lineages compared to previously described Mesoplasma and Spiroplasma species, and from related MAGs previously sequenced from the leaf-cutting ant Acromyrmex echinatior. This suggests that the T. septentrionalis symbionts comprise undescribed species that can exclude each other from a niche that is largely shared between them. Mesoplasma genomes and MAGs also demonstrate regional specificity with their T. septentrionalis ant hosts. Both Mesoplasma and Spiroplasma strains from T. septentrionalis can catabolize glucose and fructose; both sugars are common in the ant's diet. Similarly, both these Mesoplasma and Spiroplasma can catabolize arginine, but only Mesoplasma can catabolize N-acetylglucosamine; both could produce ammonia for the ants or fungus garden. Based on our genomic and phenotypic analyses, we describe these T. septentrionalis symbionts as Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov., providing insight into their genomic and phenotypic diversity and cultures to facilitate future studies of how these common but poorly understood members of the fungus-growing ant symbiosis separately colonize different ant colonies despite having highly overlapping niches.

IMPORTANCE: Fungus-growing ants partner with multiple microbial symbionts to obtain food and remain free from disease. Of these symbionts, those inhabiting the ant gut remain the least understood and are known only from environmental surveys. Such surveys can infer potential functions of gut symbionts, but cultures are required to experimentally validate these hypotheses. Here, we describe the first cultures of the ant gut symbionts of the fungus-growing ant Trachymyrmex septentrionalis, using comparative genomics and phenotypic experiments to describe them as two novel species: Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov. This genomic analysis suggests that these species are highly specialized to T. septentrionalis and are distinct from related environmental data generated from the related ant species Acromyrmex echinatior, implying substantial host specificity. Our phenotypic experiments and genomic reconstructions highlight the highly overlapping niches and likely costs and benefits of these symbionts to their ant host, setting the stage for further experimentation.},
}

@article {pmid40491555,
year = {2025},
author = {Cheng, H and Li, H and Li, Z and Wang, Y and Liu, L and Wang, J and Ma, X and Tan, B},
title = {The role of glycosylated mucins in maintaining intestinal homeostasis and gut health.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {439-446},
pmid = {40491555},
issn = {2405-6383},
abstract = {The intestinal mucus barrier is a crucial component of the host's innate defense system, playing a vital role in regulating intestinal microecology and maintaining intestinal homeostasis. Glycosylated mucins, the core components of this barrier, are essential for preserving its integrity by preventing bacterial degradation. Additionally, mucins significantly contribute to establishing a balanced symbiotic relationship between the host and microbes. These mucins have the potential to mitigate intestinal epithelial damage by capturing and transporting cell debris and pathogenic bacteria. Meanwhile, certain bacteria help maintain the equilibrium and stability of the gut microbiome by degrading glycosylated mucins to utilize the carbohydrate chains, thus affecting the cytokine expression to regulate the synthesis and secretion of specific glycans. Investigating the complex connections between the mucus barrier and mucin glycosylation holds great promise for advancing our understanding of gastrointestinal disease mechanisms, paving the way for innovative prevention and treatment strategies.},
}

@article {pmid40488931,
year = {2025},
author = {Zhang, Y and Wang, SW and Li, NQ and Jin, Q and Anbazhakan, R and Dai, YF and Xiang, ZX and Gao, JY},
title = {Ecological specificity of fungi on seedling establishment in Dendrobium huoshanense: a narrow distributed medicinal orchid.},
journal = {Mycorrhiza},
volume = {35},
number = {3},
pages = {41},
pmid = {40488931},
issn = {1432-1890},
support = {Grant No. 202304BP090006//The project of innovation guidance & science and technology enterprise cultivation plan of Yunnan Provincial Department of Science and Technology/ ; },
}

@article {pmid40488710,
year = {2025},
author = {Williams, JP and Macdonald, M and Watts, PA and Peckler, BF},
title = {Comparative Evaluation of Blue Phantom and SCOBY-Based Models for Ultrasound-Guided Intravenous Cannulation Training.},
journal = {Simulation in healthcare : journal of the Society for Simulation in Healthcare},
volume = {},
number = {},
pages = {},
pmid = {40488710},
issn = {1559-713X},
abstract = {INTRODUCTION: Ultrasound-guided intravenous (USIV) cannulation is a common alternative when IV access cannot otherwise be obtained. Many hospitals teach this skill with the commercial CAE Blue Phantom gelatinous training blocks. However, their cost is a barrier. This has led to experimentation with creative alternatives. Recent studies have trialed SCOBY (Symbiotic Culture of Bacteria and Yeast) in the production of training models for medical procedures. SCOBY is a biofilm-like structure appearing as a thick, rubbery film. We aimed to develop a 2-vessel SCOBY-based model and compare its effectiveness for teaching USIV against the Phantom.

METHODS: Participants, 23 emergency medicine clinicians, performed USIV on each model and completed a pre- and post-procedure questionnaire.

RESULTS: Seventy-four percent of participants indicated that the SCOBY model more closely resembled the clinical reality of human tissue compared with 13% for the Phantom. SCOBY provided an improved visual appearance, physical touch, feel of the procedure, and appearance of "subdermal tissues" on ultrasound compared to the Phantom.

CONCLUSION: These results suggest a promising future for SCOBY as a cost-effective alternative to teaching clinical skills.},
}

@article {pmid40488530,
year = {2025},
author = {Gao, H and Zhuang, D and Zhou, H and Su, Q and Hu, X and Wang, Y and Bao, W and Zhu, L},
title = {A comprehensive analysis of human gut microbial biosynthesis gene clusters unveiling the dominant role of Paenibacillus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0061025},
doi = {10.1128/msystems.00610-25},
pmid = {40488530},
issn = {2379-5077},
abstract = {The secondary metabolites produced by the gut microbiota serve as crucial signaling molecules and substrates for gastrointestinal metabolic reactions, thereby playing a pivotal role in human physiological and pathological processes. In this study, we explore the complex symbiotic relationship between the gut microbiota and the human host by systematically annotating the biosynthetic gene clusters (BGCs) across 4,744 human gut microbiota genomes, sourced from the Unified Human Gastrointestinal Genome database. Our comprehensive analysis compares the differential biosynthetic potentials of microbiota from diverse continents and phyla while also elucidating the biosynthetic profiles of gut archaea. Notably, our findings identify Paenibacillus as a dominant genus within the human gut microbiota, characterized by its extensive biosynthetic capacity. This study presents the first global atlas of BGCs within the human gut microbiome, offering valuable insights into gut-derived secondary metabolic pathways and their intricate interactions with host physiology. These results lay the groundwork for future investigations into the microbiota's role in health and disease, underscoring the importance of understanding microbiota-derived metabolites in microbiology and gastroenterology.IMPORTANCEThis study provides a comprehensive analysis of biosynthetic gene clusters in the human gut microbiome, revealing a vast diversity of natural products with potential therapeutic applications. We identified Paenibacillus as a key genus with exceptional biosynthetic capabilities, including the production of leinamycin, a potent anticancer compound previously thought to be exclusive to Streptomyces. The findings highlight the gut microbiome as a rich, untapped resource for novel drug discovery, particularly in cancer therapy and immune modulation.},
}

@article {pmid40488491,
year = {2025},
author = {Franco, MEE and Nickerson, MN and Bowen, BP and Louie, K and Northen, TR and U'Ren, JM},
title = {Hyperdiverse, bioactive, and interaction-specific metabolites produced only in co-culture suggest diverse competitors may fuel secondary metabolism of xylarialean fungi.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0046825},
doi = {10.1128/msystems.00468-25},
pmid = {40488491},
issn = {2379-5077},
abstract = {Xylariales is one of the largest and most ecologically diverse fungal orders that is well-known for its chemical diversity. Enhanced secondary metabolism of Xylariales taxa is associated with increased gene duplication and horizontal gene transfer (HGT) of biosynthetic gene clusters (BGCs), especially in generalist taxa with both greater saprotrophic abilities and broader host ranges as foliar endophytic symbionts. Thus, one hypothesis for BGC diversification among more generalist fungi is that diverse competitive interactions-in both their free-living and symbiotic life stages with many hosts-may exert selective pressure for HGT and a diverse metabolic repertoire. Here, we used untargeted metabolomics to examine how competition (pairwise co-cultures) between seven xylarialean fungi influenced their metabolite production. Of the >9,000 total features detected, 6,115 and 2,071 were over-represented in co-cultures vs monocultures, respectively. For each strain, each additional co-culture interaction resulted in an 11- to 14-fold increase in metabolite richness compared to monocultures, reflecting the limited amount of metabolite overlap among different co-culture combinations. Phylogenetic relatedness and BGC content did not impact the diversity of metabolites produced in co-culture; however, co-cultures between more ecologically distinct fungi elicited the strongest metabolic response. Overall, the diversity, specificity, and putative bioactivity of metabolites over-represented in co-culture support the role of widespread and diverse competitive fungal interactions to drive xylarialean metabolic diversification. Additionally, as fungal-produced plant hormones were only detected in co-culture, our results reveal the potential for in planta interactions among fungal endophytes to influence the host plant.IMPORTANCESaprotrophic and endophytic xylarialean fungi are among the most prolific producers of bioactive secondary metabolites, with numerous industrial uses as antibiotics, pharmaceuticals, and insecticidal toxins. Fungal secondary metabolites are typically encoded in biosynthetic gene clusters (sets of physically clustered genes), but the products of most clusters are unknown as the genes are not active in typical culture conditions. Co-cultures can help to "turn on" fungal secondary metabolite production, yet factors that can influence co-culture outcomes are largely unknown. Here, we used untargeted metabolomics to assess how differences in genomic content, ecology, and phylogenetic relatedness among seven diverse xylarialean fungal strains impact metabolic production in co-culture. As expected, co-culturing significantly increased metabolite diversity, as well as the abundance of putatively bioactive metabolites. Each new pairwise combination produced different metabolites, indicative of strain-specific responses to competitors. This new information will enable further characterization of the immense biotechnological potential of xylarialean fungi.},
}

@article {pmid40488407,
year = {2025},
author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B},
title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf119},
pmid = {40488407},
issn = {1751-7370},
abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.},
}