@article {pmid40733334,
year = {2025},
author = {Radi, H and Koufan, M and Belkoura, I and Koussa, T and Mazri, MA},
title = {In Vitro Mycorrhization for Plant Propagation and Enhanced Resilience to Environmental Stress: A Review.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733334},
issn = {2223-7747},
abstract = {Arbuscular mycorrhizal fungi (AMF) play a key role in enhancing plant stress tolerance, nutrient uptake, and overall health, making them essential for sustainable agriculture. Their multifaceted contributions to the rhizosphere-through biofertilization, bioprotection, and biostimulation-have led to growing interest in their application. In recent years, in vitro mycorrhization has emerged as a promising approach for the rapid propagation of economically and ecologically important plant species, offering improved agronomic and physiological traits as well as increased resilience to environmental stressors. However, challenges remain in achieving consistent AMF-plant symbiosis under in vitro conditions across diverse species. This review highlights the potential of in vitro mycorrhization as a controlled system for investigating AMF interactions and their impact on plant development. Various in vitro mycorrhization systems are described and discussed, along with their applications in the mass production of AMF propagules and mycorrhizal plants, and their role in enhancing the acclimatization of micropropagated plantlets to ex vitro conditions. The role of in vitro mycorrhization as an effective tissue culture approach that integrates plant propagation with enhanced resilience to environmental stress is emphasized. The factors influencing the success of in vitro mycorrhization and strategies for the large-scale production of AMF propagules and mycorrhizal plants are explored. Although research in this area is still limited, existing studies underscore the potential of in vitro mycorrhization to enhance plant tolerance to abiotic and biotic stresses-an increasingly urgent goal in the context of climate change and global food security.},
}

@article {pmid40732484,
year = {2025},
author = {Ahangar, MN and Farhat, ZA and Sivanathan, A},
title = {AI Trustworthiness in Manufacturing: Challenges, Toolkits, and the Path to Industry 5.0.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {14},
pages = {},
pmid = {40732484},
issn = {1424-8220},
support = {123456789//Innovate Uk/ ; },
abstract = {The integration of Artificial Intelligence (AI) into manufacturing is transforming the industry by advancing predictive maintenance, quality control, and supply chain optimisation, while also driving the shift from Industry 4.0 towards a more human-centric and sustainable vision. This emerging paradigm, known as Industry 5.0, emphasises resilience, ethical innovation, and the symbiosis between humans and intelligent systems, with AI playing a central enabling role. However, challenges such as the "black box" nature of AI models, data biases, ethical concerns, and the lack of robust frameworks for trustworthiness hinder its widespread adoption. This paper provides a comprehensive survey of AI trustworthiness in the manufacturing industry, examining the evolution of industrial paradigms, identifying key barriers to AI adoption, and examining principles such as transparency, fairness, robustness, and accountability. It offers a detailed summary of existing toolkits and methodologies for explainability, bias mitigation, and robustness, which are essential for fostering trust in AI systems. Additionally, this paper examines challenges throughout the AI pipeline, from data collection to model deployment, and concludes with recommendations and research questions aimed at addressing these issues. By offering actionable insights, this study aims to guide researchers, practitioners, and policymakers in developing ethical and reliable AI systems that align with the principles of Industry 5.0, ensuring both technological advancement and societal value.},
}

@article {pmid40732102,
year = {2025},
author = {Liu, Y and Ren, J and Yu, B and Liu, S and Cao, X},
title = {Metagenomic and Metabolomic Perspectives on the Drought Tolerance of Broomcorn Millet (Panicum miliaceum L.).},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071593},
pmid = {40732102},
issn = {2076-2607},
support = {YDZJSX2022A044//the Central Guiding Local Science and Technology Development Funds/ ; CARS-06-14.5-A16//the earmarked fund for CARS/ ; 2025CYJSTX03-23//the earmarked fund for Modern Agro-Industry Technology Research System/ ; },
abstract = {Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop's drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants.},
}

@article {pmid40732090,
year = {2025},
author = {da Silva, IA and de Andrade, JLS and Barbosa, FLA and Almeida, MS and Araújo, MLH and de Souza, AJ and Araujo, ASF and Pereira, APA and Garcia, KGV},
title = {Co-Application of Seaweed Extract (Solieria filiformis) and Silicon: Effect on Sporulation, Mycorrhizal Colonization, and Initial Growth of Mimosa caesalpiniaefolia.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071581},
pmid = {40732090},
issn = {2076-2607},
abstract = {Seaweed extracts (SEs) and silicon (Si) are known to enhance plant growth under adverse conditions. However, their combined effects on arbuscular mycorrhizal fungi (AMF) are not yet fully understood. This study evaluated the effect of the co-application of an SE and Si on the AMF spore abundance, mycorrhizal colonization, and early growth of Mimosa caesalpiniaefolia. Plants were grown in a greenhouse for 70 days in soil with or without an SE (Solieria filiformis) and three Si levels (0, 150, and 300 mg kg[-1]). Growth parameters, AMF spore abundance, mycorrhizal colonization, and plant/soil chemical composition were assessed. SE and Si increased the plant height, stem diameter, number of leaves, and shoot dry mass, while higher Si levels reduced the root dry mass and length. Mycorrhizal colonization was highest (64%) at 150 mg kg[-1] Si with SE, whereas AMF spore abundance decreased as Si increased. SE and 300 mg kg[-1] Si raised the Si levels in the shoot, while root Si increased only at 300 mg kg[-1] Si. Shoot Na increased at 300 mg kg[-1] Si without SE, whereas K was highest at 150 mg kg[-1] Si with SE. The soil pH, electrical conductivity, and Na increased at 300 mg kg[-1] Si, while K and P decreased at this level without SE. These findings indicate that SE and Si co-application benefits early growth and may modulate mycorrhizal symbiosis, highlighting the importance of proper management to maximize plant and soil benefits.},
}

@article {pmid40732061,
year = {2025},
author = {Alahmari, AN and Hassoubah, SA and Alaidaroos, BA and Al-Hejin, AM and Bataweel, NM and Farsi, RM and Algothmi, KM and Alshammari, NM and Ashour, ATK},
title = {Antimicrobial Metabolites Isolated from Some Marine Bacteria Associated with Callyspongia crassa Sponge of the Red Sea.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071552},
pmid = {40732061},
issn = {2076-2607},
abstract = {The Red Sea is rich in symbiotic microorganisms that have been identified as sources of bioactive compounds with antimicrobial, antifungal, and antioxidant properties. In this study, we aimed to explore the potential of marine sponge-associated bacteria as sources of antibacterial compounds, emphasizing their significance in combating antibiotic resistance (AMR). The crude extracts of Micrococcus, Bacillus, and Staphylococcus saprophyticus exhibited significant antibacterial activity, with inhibition zones measuring 12 mm and 14 mm against Escherichia coli, Staphylococcus aureus, Candida albicans, and other infectious strains. The DPPH assay showed that the bacterial isolates AN3 and AN6 exhibited notable antioxidant activity at a concentration of 100 mg/mL. To characterize the chemical constituents responsible for the observed bioactivity, a GC-MS analysis was performed on ethyl acetate extracts of the potent strains. The analysis identified a range of antimicrobial compounds, including straight-chain alkanes (e.g., Tetradecane), cyclic structures (e.g., Cyclopropane derivatives), and phenolic compounds, all of which are known to disrupt microbial membranes or interfere with metabolic pathways. The bioprospecting and large-scale production of these compounds are challenging. In conclusion, this study underscores the potential for marine bacteria associated with sponges from the Red Sea to be a source of bioactive compounds with therapeutic relevance.},
}

@article {pmid40732002,
year = {2025},
author = {Jin, Y and Chen, Z and Malik, K and Li, C},
title = {Achnatherum inebrians Bacterial Communities Associated with Epichloë gansuensis Endophyte Infection Under Low-Concentration Urea Treatment: Links to Plant Growth and Root Metabolite.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071493},
pmid = {40732002},
issn = {2076-2607},
support = {32201445, 2021M701525, 2024M761243, 22JR5RA434, 22ZSCQD01, 22JR5RA532, lzujbky-2022-kb02, lzujbky-2023-49 and [2021]794.//the National Science Foundation of China , the China Postdoctoral Science Foundation, Gansu Province Outstanding Doctoral Students Project , Intellectual Property Plan (Targeted Organization) Project of Gansu Administration for Market Regulation, Gansu Pr/ ; },
abstract = {Despite chemical exchange often serving as the first step in plant-microbe interactions, the specialized chemical metabolites produced by grass-Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte-infected plants (E+) and Epichloë endophyte-free plants (E-) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E- groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO3[-]-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E- plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E- plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E- plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth.},
}

@article {pmid40731996,
year = {2025},
author = {Asimakis, E and Galiatsatos, I and Apostolopoulou, G and Savvidou, EC and Balatsos, G and Karras, V and Evangelou, V and Dionyssopoulou, E and Augustinos, A and Papadopoulos, NT and Michaelakis, A and Stathopoulou, P and Tsiamis, G},
title = {The Symbiotic Bacterial Profile of Laboratory-Reared and Field-Caught Aedes albopictus Mosquitoes from Greece.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071486},
pmid = {40731996},
issn = {2076-2607},
support = {«moSquITo»: Innovative approaches for monitoring and management of the Asian tiger mosquito with emphasis on the Sterile Insect Technique (ΤΑΕΔΚ06173)//National Recovery and Resilience Plan, "Greece 2.0" & EU Funding - Next Generation EU/ ; },
abstract = {The Asian tiger mosquito Aedes albopictus is a highly invasive species capable of transmitting human pathogens. For population management, the sterile insect technique (SIT) is considered an effective and sustainable alternative to conventional methods, such as insecticides and reducing or eliminating breeding sites. The use of symbiotic bacteria to improve the application of SIT or design combined SIT/incompatible insect technique (IIT) approaches is currently considered. In this context, exploring the microbiota of local mosquito populations is crucial for identifying interesting components. This study employed 16S rRNA sequencing and microbiological methods to characterize the diversity of laboratory and wild Ae. albopictus in Greece. Differences were recorded between wild and lab-reared mosquitoes, with laboratory samples exhibiting higher diversity. Laboratory treatment, sex, and developmental stage also resulted in variations between communities. Populations reared in the same facility developed mostly similar bacterial profiles. Two geographically distant wild populations displayed similar bacterial profiles, characterized by seasonal changes in the relative abundance of Pantoea and Zymobacter. Wolbachia was dominant in most groups (63.7% relative abundance), especially in field-caught mosquitoes. It was identified with two strains, wAlbA (21.5%) and wAlbB (42.2%). Other frequent taxa included Elizabethkingia, Asaia, and Serratia. Blood feeding favored an increase in Serratia abundance. Various Enterobacter, Klebsiella, Aeromonas, and Acinetobacter strains were isolated from larval and adult mosquito extracts and could be further characterized as diet supplements. These findings suggest that the microbiota of local populations is highly variable due to multiple factors. However, they retain core elements shared across populations that may exhibit valuable nutritional or functional roles and could be exploited to improve SIT processes.},
}

@article {pmid40731987,
year = {2025},
author = {Zhu, F and Liu, Y and Wu, C and Li, K and Hu, Y and Liu, W and Yu, S and Li, M and Dong, X and Yu, H},
title = {Microbial Corrosion Behavior of L245 Pipeline Steel in the Presence of Iron-Oxidizing Bacteria and Shewanella algae.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071476},
pmid = {40731987},
issn = {2076-2607},
abstract = {Microbiologically influenced corrosion (MIC) poses significant challenges in oilfield water injection environments, leading to substantial socioeconomic losses. L245 steel, a low-alloy steel widely used in oil and gas pipelines due to its excellent mechanical properties and cost-effectiveness, remains highly vulnerable to MIC during long-term service. This study uses surface characterization and electrochemical techniques to investigate the corrosion behavior of L245 pipeline steel under short-cycle conditions in a symbiotic environment of iron-oxidizing bacteria (IOB) and Shewanella algae (S. algae). Key findings revealed that localized corrosion of L245 steel was markedly exacerbated under coexisting IOB and S. algae conditions compared to monoculture systems. However, the uniform corrosion rate under symbiosis fell between the rates observed in the individual IOB and S. algae systems. Mechanistically, the enhanced corrosion under symbiotic conditions was attributed to the synergistic electron transfer interaction: IOB exploited electron carriers secreted by S. algae during extracellular electron transfer (EET), which amplified the microbial consortium's capacity to harvest electrons from the steel substrate. These results emphasize the critical role of interspecies electron exchange in accelerating localized degradation of carbon steel under complex microbial consortia, with implications for developing targeted mitigation strategies in industrial pipelines exposed to similar microbiological environments.},
}

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071468},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731227,
year = {2025},
author = {Chen, CY and Chang, YH and Leong, YK and Chang, JS},
title = {Application of algae-bacteria symbiosis system for ammonia nitrogen wastewater treatment.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.06.011},
pmid = {40731227},
issn = {1347-4421},
abstract = {In industrial processes, the primary sources of ammonia nitrogen emissions are organic matter and nitrogen-containing chemicals. When released directly into the environment, these nitrogen compounds elevate aquatic toxicity and reduce dissolved oxygen levels, significantly affecting aquatic ecosystems. This review introduces both traditional and novel ammonia nitrogen wastewater treatment technologies. Traditional methods include physical, chemical, and biological processes. The focus of this review is on novel ammonia nitrogen wastewater treatment technology based on algae-bacteria symbiosis systems. The review discusses key environmental factors influencing the algae-bacteria symbiosis system, such as temperature, light intensity, carbon dioxide concentration, and bioflocculation. Furthermore, it presents innovative large-scale algae-bacteria symbiosis system designed to achieve high carbon dioxide removal efficiency while effectively treating ammonia nitrogen wastewater with low energy consumption. This review aims to provide valuable insights that support the future development of efficient and commercially viable novel technologies for treating ammonia-nitrogen wastewater.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
doi = {10.1073/pnas.2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40729385,
year = {2025},
author = {Chen, P and Geng, H and Ma, B and Zhang, Y and Zhu, Z and Li, M and Chen, S and Wang, X and Sun, C},
title = {Integrating spatial omics and single-cell mass spectrometry imaging reveals tumor-host metabolic interplay in hepatocellular carcinoma.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2505789122},
doi = {10.1073/pnas.2505789122},
pmid = {40729385},
issn = {1091-6490},
support = {82404587//the National Natural Science Foundation of China/ ; 82273888//the National Natural Science Foundation of China/ ; tsqn202403096//the Taishan Scholars Program of Shandong Province/ ; tstp20221138//the Taishan Scholar Progarm of Shandong Province/ ; 2024QZJH04//the Youth Excellent Talents Program of Qilu University of Technology (Shandong Academy of Sciences)/ ; },
mesh = {*Carcinoma, Hepatocellular/metabolism/pathology/diagnostic imaging ; *Liver Neoplasms/metabolism/pathology/diagnostic imaging ; Humans ; Tumor Microenvironment ; Single-Cell Analysis/methods ; Cancer-Associated Fibroblasts/metabolism/pathology ; Mass Spectrometry/methods ; Macrophages/metabolism ; Glycolysis ; Metabolomics/methods ; Cell Communication ; Cell Line, Tumor ; },
abstract = {Metabolic crosstalk among diverse cellular populations contributes to shaping a competitive and symbiotic tumor microenvironment (TME) to influence cancer progression and immune responses, highlighting vulnerabilities that can be exploited for cancer therapy. Using a spatial multiomics platform to study the cell-specific metabolic spectrum in hepatocellular carcinoma (HCC), we map the metabolic interactions between different cells in the HCC TME and identify a unique tumor-immune-cancer-associated fibroblast (CAF) "interface" zone, where cell-cell interactions are enhanced and accompanied by significant upregulation of lactic acid and long-chain polyunsaturated fatty acids. Further combining single-cell mass spectrometry imaging of patient-derived tumor organoids, cocultured CAFs, and macrophages, we demonstrate that CAFs increase glycolysis and secrete lactic acid to the surrounding microenvironment to drive immunosuppressive macrophage M2 polarization. These findings facilitate the understanding of cancer-associated metabolic interactions in complex TME and provide clues for targeted clinical therapies.},
}

*Carcinoma, Hepatocellular/metabolism/pathology/diagnostic imaging
*Liver Neoplasms/metabolism/pathology/diagnostic imaging
Humans
Tumor Microenvironment
Single-Cell Analysis/methods
Cancer-Associated Fibroblasts/metabolism/pathology
Mass Spectrometry/methods
Macrophages/metabolism
Glycolysis
Metabolomics/methods
Cell Communication
Cell Line, Tumor

@article {pmid40728918,
year = {2025},
author = {Vannette, RL and Williams, NM and Peterson, SS and Martin, AN},
title = {Pollen diet, more than geographic distance, shapes provision microbiome composition in two species of cavity-nesting bees.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf067},
pmid = {40728918},
issn = {1574-6941},
abstract = {The microbial composition of stored food can influence its stability and determine the microbial species consumed by the organism feeding on it. Many bee species store nectar and pollen in provisions constructed to feed developing offspring. Yet whether microbial composition is determined by the pollen types within provisions, variation between bee species at the same nesting sites, or geographic distance was unclear. Here, we sampled two species of co-occurring cavity nesting bees in the genus Osmia at 13 sites in California and examined the composition of pollen, fungi and bacteria in provisions. Pollen composition explained 15% of variation in bacterial composition and ∼30% of variation in fungal composition, whereas spatial distance among sites explained minimal additional variation. Symbiotic microbe genera Ascosphaera, Sodalis and Wolbachia showed contrasting patterns of association with pollen composition, suggesting distinct acquisition and transmission routes for each. Comparing provisions from both bee species comprised of the same pollens points to environmental acquisition rather than bee species as a key factor shaping the early stages of the bee microbiome in Osmia. The patterns we observed also contrast with Apilactobacillus-dominated provision microbiome in other solitary bee species, suggesting variable mechanisms of microbial assembly in stored food among bee species.},
}

@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}

@article {pmid40726432,
year = {2025},
author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T},
title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e01707},
doi = {10.1002/advs.202501707},
pmid = {40726432},
issn = {2198-3844},
support = {2021YFA1301201//National Key R&D Program of China/ ; 2021YFA0805400//National Key R&D Program of China/ ; 2024YFA1307004//National Key R&D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; },
abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.},
}

@article {pmid40725467,
year = {2025},
author = {Ye, S and Wei, X and Chen, J and Luo, S and Jiang, T and Yang, J and Zheng, R and Chen, S},
title = {Research on Key Genes for Flowering of Bambusaoldhamii Under Introduced Cultivation Conditions.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
pmid = {40725467},
issn = {2073-4425},
support = {2021YFD2200501301//National Key Research and Development Program of China during the 14th Five-Year Plan Period, "Geographical Differentiation of Biomass Formation in Bambusaoldhamii Germplasm"/ ; },
mesh = {*Flowers/genetics/growth & development ; Gene Expression Regulation, Plant ; Transcriptome/genetics ; *Plant Proteins/genetics ; Gene Regulatory Networks ; Gene Expression Profiling ; Genes, Plant ; *Bambusa/genetics/growth & development ; *Poaceae/genetics/growth & development ; },
abstract = {BACKGROUND: Bambusaoldhamii is an important economic bamboo species. However, flowering occurred after its introduction and cultivation, resulting in damage to the economy of bamboo forests. Currently, the molecular mechanism of flowering induced by introduction stress is still unclear. This study systematically explored the key genes and regulatory pathways of flowering in Bambusaoldhamii under introduction stress through field experiments combined with transcriptome sequencing and weighted gene co-expression network analysis (WGCNA), with the aim of providing a basis for flower-resistant cultivation and molecular breeding of bamboo.

RESULTS: The study conducted transcriptome sequencing on flowering and non-flowering Bambusaoldhamii bamboo introduced from Youxi, Fujian Province for 2 years, constructed a reference transcriptome containing 213,747 Unigenes, and screened out 36,800-42,980 significantly differentially expressed genes (FDR < 0.05). The results indicated that the photosensitive gene CRY and the temperature response gene COR413-PM were significantly upregulated in the flowering group; the expression level of the heavy metal detoxification gene MT3 increased by 27.77 times, combined with the upregulation of the symbiotic signaling gene NIN. WGCNA analysis showed that the expression level of the flower meristem determination gene AP1/CAL/FUL in the flowering group was 90.38 times that of the control group. Moreover, its expression is regulated by the cascade synergy of CRY-HRE/RAP2-12-COR413-PM signals.

CONCLUSIONS: This study clarifies for the first time that the stress of introducing Bambusaoldhamii species activates the triad pathways of photo-temperature signal perception (CRY/COR413-PM), heavy metal detoxification (MT3), and symbiotic regulation (NIN), collaboratively driving the AP1/CAL/FUL gene expression network and ultimately triggering the flowering process.},
}

*Flowers/genetics/growth & development
Gene Expression Regulation, Plant
Transcriptome/genetics
*Plant Proteins/genetics
Gene Regulatory Networks
Gene Expression Profiling
Genes, Plant
*Bambusa/genetics/growth & development
*Poaceae/genetics/growth & development

@article {pmid40725341,
year = {2025},
author = {López-Hernández, MG and Rincón-Rosales, R and Rincón-Molina, CI and Manzano-Gómez, LA and Gen-Jiménez, A and Maldonado-Gómez, JC and Rincón-Molina, FA},
title = {Diversity and Functional Potential of Gut Bacteria Associated with the Insect Arsenura armida (Lepidoptera: Saturniidae).},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725341},
issn = {2075-4450},
support = {19337.24-P and 19414.24-P//Tecnológico Nacional de México/ ; },
abstract = {Insects are often associated with diverse microorganisms that enhance their metabolism and nutrient assimilation. These microorganisms, residing in the insect's gut, play a crucial role in breaking down complex molecules into simpler compounds essential for the host's growth. This study investigates the diversity and functional potential of symbiotic bacteria in the gut of Arsenura armida (Lepidoptera: Saturniidae) larvae, an edible insect from southeastern Mexico, using culture-dependent and metagenomic approaches. Bacterial strains were isolated from different gut sections (foregut, midgut, and hindgut) and cultured on general-purpose media. Isolates were identified through 16S rRNA gene sequencing and genomic fingerprinting. Metagenomics revealed the bacterial community structure and diversity, along with their functional potential. A total of 96 bacterial strains were isolated, predominantly Gram-negative bacilli. Rapidly growing colonies exhibited enzymatic activity, cellulose degradation, and sugar production. Phylogenetic analysis identified eight genera, including Acinetobacter, Bacillus, Enterobacter, Pseudomonas, and others, with significant cellulose-degrading capabilities. Metagenomics confirmed Bacillota as the most abundant phylum. These complementary methods revealed abundant symbiotic bacteria with key metabolic roles in A. armida, offering promising biotechnological applications in enzymatic bioconversion and cellulose degradation.},
}

@article {pmid40725334,
year = {2025},
author = {Gao, H and Yin, XJ and Fan, ZH and Gu, XH and Su, ZQ and Luo, BR and Qiu, BL and Zhang, LH},
title = {Effects of Endosymbionts on the Nutritional Physiology and Biological Characteristics of Whitefly Bemisia tabaci.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725334},
issn = {2075-4450},
support = {Grant No.KJQN202400533//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; Grant No.23XLB031//Chongqing Normal University Foundation/ ; CSTB2024TIAD-KPX0015//Chongqing Technological Innovation and Application Development Project/ ; },
abstract = {Insects and their endosymbionts have a close mutualistic relationship. However, the precise nature of the bacterial endosymbiont-mediated interaction between host plants and whitefly Bemisia tabaci MEAM1 is still unclear. In the present study, six populations of Bemisia tabaci MEAM1 sharing the same genetic background were established by rearing insects for ten generations on different host plants, including poinsettia, cabbage, cotton, tomato, and tobacco, and an additional population was reared on cotton and treated with antibiotics. The physiological and nutritional traits of the insects were found to be dependent on the host plant on which they had been reared. Systematic analysis was conducted on the endosymbiont titers, the amino acid molecules and contents, as well as developmental and oviposition changes in the MEAM1 populations reared on each host plant tested. The results indicate that B. tabaci contained the primary symbiont Portiera and the secondary symbionts Hamiltonella and Rickettsia. In addition, the titer of endosymbiotic bacteria in females is higher than that in males. Among the MEAM1 populations reared on each host plant, the variation pattern of Portiera titer generally corresponded with changes in biological characteristics (body length, weight and fecundity) and AA contents. This suggests that changes in the amino acid contents and biological characteristics of different B. tabaci populations may be due to changes in the Portiera content and the differences in the nutrition of the host plants themselves. Our findings were further confirmed by the reduction in Portiera with antibiotic treatment. The amino acids, body size, body weight, and fecundity of B. tabaci were all reduced with the decrease in the Portiera titer after antibiotic treatment. In summary, our research revealed that host plants can affect the content of symbiotic bacteria, particularly Portiera, and subsequently affect the nutrition (i.e., the essential amino acids content) of host insects, thus changing their biological characteristics.},
}

@article {pmid40725318,
year = {2025},
author = {Prieto, SV and Dho, M and Orrù, B and Gonella, E and Alma, A},
title = {Symbiont-Targeted Control of Halyomorpha halys Does Not Affect Local Insect Diversity in a Hazelnut Orchard.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725318},
issn = {2075-4450},
support = {//Regione Piemonte/ ; },
abstract = {Harmless crop-associated insect communities are a fundamental part of the agroecosystem. Their potential as a reservoir of natural enemies of pests has encouraged their conservation through the development of low-impact pest management programs. The brown marmorated stink bug, Halyomorpha halys, represents a serious threat to Italian hazelnut production. Laboratory and field experiments confirmed the susceptibility of this pest to the disruption of the obligated symbiotic interaction with gut bacteria, paving the way for the development of the symbiont-targeted control strategy. Here we present the results of a three-year field assessment of symbiont-targeted control in a hazelnut orchard in northwestern Italy. The use of a biocomplex to disrupt symbiont acquisition by H. halys nymphs was compared to the use of lambda-cyhalothrin insecticide. The effects on the local entomofauna were assessed, as were the trend of H. halys population and the damage caused by stink bugs to harvested hazelnuts. The insecticide consistently reduced the insect diversity in the field, while the anti-symbiont biocomplex had no effect. However, the control of the H. halys population and the stink bug-induced damage to hazelnuts varied over the years in the field plot submitted to the symbiont-targeted approach. Our results indicate that the symbiont-targeted control does not interfere with local insect communities. Key aspects for improving the effectiveness of this tactic are discussed.},
}

@article {pmid40725284,
year = {2025},
author = {Wang, Y and Zhang, Y and Li, R and Li, Y and Cha, M and Yi, X},
title = {Host Plant Dependence of the Symbiotic Microbiome of the Gall-Inducing Wasp Trichagalma acutissimae.},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725284},
issn = {2075-4450},
support = {ZR2024MC092//Natural Science Foundation of Shandong Province/ ; },
abstract = {Symbiotic bacteria play a pivotal role in the biology and ecology of herbivorous insects, affecting host growth and adaptation. However, the effects of host identity on the symbiotic microbiota of gall-inducing insects remain less explored. In this study, we utilized high-throughput sequencing to investigate the effects of different oak hosts on the structure and diversity of the symbiotic microbial community in the asexual larvae of the gall-inducing wasp Trichagalma acutissimae. Host plant species significantly altered the alpha and beta diversity of symbiotic microbiota of T. acutissimae. At the phylum level, Proteobacteria was the predominant microflora in both groups, with significantly higher abundance in larvae parasitizing Quercus acutissima than in those parasitizing Q. variabilis. Pseudomonas, which has been identified as responsible for tannin decomposition, was the most dominant genus in T. acutissimae larvae infesting both hosts. LEfSe analysis revealed substantial differences in the symbiotic microbial communities between the two hosts while also highlighting some commonalities. Functional prediction analysis indicated no significant difference in the functional roles of symbiotic bacteria between larvae infesting the two hosts. These findings suggest that the symbiotic microbiome of T. acutissimae larvae is influenced by host plant species, yet different microbial compositions may perform similar functions, implying the potential role of symbiotic microbiota in the adaptation to high-tannin oak leaves. This research enhances our understanding of the symbiotic relationship between forest pests and their associated microbes.},
}

@article {pmid40725114,
year = {2025},
author = {Wilgan, R},
title = {Phylogenetic Determinants Behind the Ecological Traits of Relic Tree Family Juglandaceae, Their Root-Associated Symbionts, and Response to Climate Change.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40725114},
issn = {1422-0067},
support = {N.A.//Institute of Dendrology Polish Academy of Sciences/ ; 2020/37/N/NZ8/01403//National Science Center/ ; },
mesh = {*Symbiosis ; *Phylogeny ; *Plant Roots/microbiology/genetics ; *Mycorrhizae/physiology/genetics ; *Climate Change ; *Trees/microbiology/genetics ; },
abstract = {Dual mycorrhizal symbiosis, i.e., the association with both arbuscular and ectomycorrhizal fungal symbionts, is an ambiguous phenomenon concurrently considered as common among various genetic lineages of trees and a result of bias in data analyses. Recent studies have shown that the ability to form dual mycorrhizal associations is a distinguishing factor for the continental-scale invasion of alien tree species. However, the phylogenetic mechanisms that drive it remain unclear. In this study, all the evidence on root-associated symbionts of Juglandaceae from South and North America, Asia, and Europe was combined and re-analysed following current knowledge and modern molecular-based identification methods. The Juglandaceae family was revealed to represent a specific pattern of symbiotic interactions that are rare among deciduous trees and absent among conifers. Closely related phylogenetic lineages of trees usually share the same type of symbiosis, but Juglandaceae contains several possible ones concurrently. The hyperdiversity of root symbionts of Juglandaceae, unlike other tree families, was concurrently found in Central and North America, Asia, and Europe, indicating its phylogenetic determinants, which endured geographical isolation. However, for many Juglandaceae, including the invasive Juglans and Pterocarya species, this was never studied or was studied only with outdated methods. Further molecular research on root symbionts of Juglandaceae, providing long sequences and high taxonomic resolutions, is required to explain their ecological roles.},
}

*Symbiosis
*Phylogeny
*Plant Roots/microbiology/genetics
*Mycorrhizae/physiology/genetics
*Climate Change
*Trees/microbiology/genetics

@article {pmid40724547,
year = {2025},
author = {Golaz, D and Bürgi, L and Egli, M and Bigler, L and Pessi, G},
title = {The Siderophore Phymabactin Facilitates the Growth of the Legume Symbiont Paraburkholderia phymatum in Aluminium-Rich Martian Soil.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {40724547},
issn = {2075-1729},
support = {310030_215282/SNSF_/Swiss National Science Foundation/Switzerland ; 4000144510//prodex/ ; },
abstract = {Beneficial interactions between nitrogen-fixing soil bacteria and legumes offer a solution to increase crop yield on Earth and potentially in future Martian colonies. Paraburkholderia phymatum is a nitrogen-fixing beta-rhizobium, which enters symbiosis with more than 50 legumes and can survive in acidic or aluminium-rich soils. In a previous RNA-sequencing study, we showed that the beta-rhizobium P. phymatum grows well in simulated microgravity and identified phymabactin as the only siderophore produced by this strain. Here, the growth of the beta-rhizobium P. phymatum was assessed in Martian simulant soil using Enhanced Mojave Mars Simulant 2 (MMS-2), which contains a high amount of iron (18.4 percent by weight) and aluminium (13.1 percent by weight). While P. phymatum wild-type's growth was not affected by exposure to MMS-2, a mutant strain impaired in siderophore biosynthesis (ΔphmJK) grew less than P. phymatum wild-type on gradient plates in the presence of a high concentration of MMS-2 or aluminium. This result suggests that the P. phymatum siderophore phymabactin alleviates aluminium-induced heavy metal stress. Ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) showed that phymabactin can bind to aluminium more efficiently than iron. These results not only deepen our understanding of the behaviour of rhizobia in simulated extraterrestrial environments but also provide new insights into the potential use of P. phymatum for bioremediation of aluminium-rich soils and the multiple roles of the siderophore phymabactin.},
}

@article {pmid40724335,
year = {2025},
author = {Cánovas, BM and Pérez-Novas, I and García-Viguera, C and Domínguez-Perles, R and Medina, S},
title = {Assessment of Winery By-Products as Ingredients as a Base of "3S" (Safe, Salubrious, and Sustainable) Fermented Beverages Rich in Bioactive Anthocyanins.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40724335},
issn = {2304-8158},
support = {PRTR-C17.I1//Ministerio de Ciencia e Innovación/ ; PID2023-148254OB-C21 (FERMISANO) funded by MICIU/AEI/10.13039/501100011033 and by "ERDF/EU"//Ministerio de Ciencia, Innovación y Universidades/ ; 22300/FPI/23//Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia/ ; },
abstract = {Oenological residues may cause environmental pollution when processing does not significantly reduce volume and/or harmful conditions. The lack of proper valorisation alternatives entails high disposal costs and resource inefficiency that jeopardise the sustainability and competitiveness of the industry. Interestingly, wine by-products are underappreciated sources of multipurpose bioactive compounds, such as anthocyanins, associated with health benefits. Alternatively, transforming oenological by-products into valuable co-products will promote sustainability and thus, create new business opportunities. In this context, the present study has assessed the applicability of winery by-products (grape pomace and wine lees) as ingredients to develop new functional kombucha-analogous beverages "3S" (safe, salubrious, and sustainable) by the Symbiotic Culture of Bacteria and Yeast (SCOBY). Concerning the main results, during the kombucha's development, the fermentation reactions modified the physicochemical parameters of the beverages, namely pH, total soluble solids, acetic acid, ethanol, and sugars, which remained stable throughout the monitored shelf-life period considered (21 days). The fermented beverages obtained exhibited high anthocyanin concentration, especially when using wine lees as an ingredient (up to 5.60 mg/L at the end of the aerobic fermentation period (10 days)) compared with the alternative beverages produced using grape pomace (1.69 mg/L). These findings demonstrated that using winery by-products for the development of new "3S" fermented beverages would provide a dietary source of bioactive compounds (mainly anthocyanins), further supporting new valorisation chances and thus contributing to the competitiveness and sustainability of the winery industries. This study opens a new avenue for cross-industry innovation, merging fermentation traditions with a new eco-friendly production of functional beverages that contribute to transforming oenological residues into valuable co-products.},
}

@article {pmid40723480,
year = {2025},
author = {Zhou, C and Ding, F},
title = {Analysis of the Alterations in Symbiotic Microbiota and Their Correlation with Intestinal Metabolites in Rainbow Trout (Oncorhynchus mykiss) Under Heat Stress Conditions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {14},
pages = {},
pmid = {40723480},
issn = {2076-2615},
abstract = {Global warming represents one of the most pressing environmental challenges to cold-water fish farming. Heat stress markedly alters the mucosal symbiotic microbiota and intestinal microbial metabolites in fish, posing substantial barriers to the healthy artificial breeding of rainbow trout (Oncorhynchus mykiss). However, the relationship between mucosal commensal microbiota, intestinal metabolites, and host environmental adaptability under heat stress remains poorly understood. In this study, rainbow trout reared at optimal temperature (16 °C) served as controls, while those exposed to maximum tolerated temperature (24 °C, 21 d) comprised the heat stress group. Using 16S rRNA amplicon sequencing and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS), we analysed the mucosal commensal microbiota-including gastrointestinal digesta, gastrointestinal mucosa, skin mucus, and gill mucosa-and intestinal metabolites of rainbow trout under heat stress conditions to explore adaptive and regulatory mechanisms. Analysis of microbial composition and diversity revealed that heat stress exerted the greatest impact on the diversity of gill and skin mucus microbiota, followed by gastrointestinal digesta, with relatively minor effects on the gastrointestinal mucosa. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were predominant in the stomach, intestine, and surface mucosa. At the genus level, Acinetobacter showed the greatest increase in abundance in skin and gill mucosa under heat stress, while Enterobacteriaceae exhibited the most pronounced increase in intestinal digesta, gastric digesta, and gastric mucosa. Differential metabolites in the intestinal digesta under heat stress were predominantly enriched in pathways associated with amino acid metabolism, particularly tryptophan metabolism. This study provides a comprehensive characterisation of microbiota and metabolic profile alterations in rainbow trout under heat stress condition, offering a theoretical foundation for understanding the response mechanisms of fish commensal microbiota to thermal stress.},
}

@article {pmid40723436,
year = {2025},
author = {Maimaitiyiming, M and Huang, Y and Jia, L and Wu, M and Chen, Z},
title = {Epichloë Endophyte Alters Bacterial Nitrogen-Cycling Gene Abundance in the Rhizosphere Soil of Perennial Ryegrass.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723436},
issn = {2079-7737},
support = {2014CB138702//National Basic Research Program of China/ ; 32201445//National Science Foundation of China/ ; 2021M701525//China Postdoctoral Science Foundation/ ; IRT17R50//Program for Changjiang Scholars and Innovative Research Team in University, China/ ; 22JR5RA532//Gansu Provincial Youth Science and Technology Fund Program/ ; 22JR5RA434//Gansu Province Outstanding Doctoral Students Project/ ; B12002//111 Project (B12002)/ ; },
abstract = {Perennial ryegrass (Lolium perenne), an important forage and turfgrass species, can establish a mutualistic symbiosis with the fungal endophyte Epichloë festucae var. lolii. Although the physiological and ecological impacts of endophyte infection on ryegrass have been extensively investigated, the response of the soil microbial community and nitrogen-cycling gene to this relationship has received much less attention. The present study emphasized abundance and diversity variation in the AOB-amoA, nirK and nosZ functional genes in the rhizosphere soil of the endophyte-ryegrass symbiosis following litter addition. We sampled four times: at T0 (prior to first litter addition), T1 (post 120 d of 1st litter addition), T2 (post 120 d of 2nd litter addition) and T3 (post 120 d of 3rd litter addition) times. Real-time fluorescence quantitative PCR (qPCR) and PCR amplification and sequencing were used to characterize the abundance and diversity of the AOB-amoA, nirK and nosZ genes in rhizosphere soils of endophyte-infected (E+) plants and endophyte-free (E-) plants. A significant enhancement of total Phosphorus (P), Soil Organic Carbon (SOC), Ammonium ion (NH4[+]) and Nitrate ion (NO3[-]) contents in the rhizosphere soil was recorded in endophyte-infected plants at different sampling times compared to endophyte-free plants (p ≤ 0.05). The absolute abundance of the AOB-amoA gene at T0 and T1 times was higher, as was the absolute abundance of the nosZ gene at T0, T1 and T3 times in the E+ plant rhizophere soils relative to E- plant rhizosphere soils. A significant change in relative abundance of the AOB-amoA and nosZ genes in the host rhizophere soils of endophyte-infected plants at T1 and T3 times was observed. The experiment failed to show any significant alteration in abundance and diversity of the nirK gene, and diversity of the AOB-amoA and nosZ genes. Analysis of the abundance and diversity of the nirK gene indicated that changes in soil properties accounted for approximately 70.38% of the variation along the first axis and 16.69% along the second axis, and soil NH4[+] (p = 0.002, 50.4%) and soil C/P ratio (p = 0.012, 15.8%) had a strong effect. The changes in community abundance and diversity of the AOB-amoA and nosZ genes were mainly related to soil pH, N/P ratio and NH4[+] content. The results demonstrate that the existence of tripartite interactions among the foliar endophyte E. festucae var. Lolii, L. perenne and soil nitrogen-cycling gene has important implications for reducing soil losses on N.},
}

@article {pmid40723404,
year = {2025},
author = {Fan, Y and Tian, M and Hu, D and Xiong, Y},
title = {Exploring the Biocultural Nexus of Gastrodia elata in Zhaotong: A Pathway to Ecological Conservation and Economic Growth.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723404},
issn = {2079-7737},
support = {81960654//the National Natural Science Foundation of China/ ; 101520250000030//the Yunnan Minzu University Talent Introduction Program/ ; },
abstract = {Gastrodia elata, known as Tianma in Chinese, is a valuable medicinal and nutritional resource. The favorable climate of Zhaotong City, Yunnan Province, China, facilitates its growth and nurtures rich biocultural diversity associated with Tianma in the region. Local people not only cultivate Tianma as a traditional crop but have also developed a series of traditional knowledge related to its cultivation, processing, medicinal use, and culinary applications. In this study, field surveys employing ethnobotanical methods were conducted in Yiliang County, Zhaotong City, from August 2020 to May 2024, focusing on Tianma. A total of 114 key informants participated in semi-structured interviews. The survey documented 23 species (and forms) from seven families related to Tianma cultivation. Among them, there were five Gastrodia resource taxa, including one original species, and four forms. These 23 species served as either target cultivated species, symbiotic fungi (promoting early-stage Gastrodia germination), or fungus-cultivating wood. The Fagaceae family, with 10 species, was the most dominant, as its dense, starch-rich wood decomposes slowly, providing Armillaria with a long-term, stable nutrient substrate. The cultural importance (CI) statistics revealed that Castanea mollissima, G. elata, G. elata f. flavida, G. elata f. glauca, G. elata f. viridis, and Xuehong Tianma (unknown form) exhibited relatively high CI values, indicating their crucial cultural significance and substantial value within the local community. In local communities, traditionally processed dried Tianma tubers are mainly used to treat cardiovascular diseases and also serve as a culinary ingredient, with its young shoots and tubers incorporated into dishes such as cold salads and stewed chicken. To protect the essential ecological conditions for Tianma, the local government has implemented forest conservation measures. The sustainable development of the Tianma industry has alleviated poverty, protected biodiversity, and promoted local economic growth. As a distinctive plateau specialty of Zhaotong, Tianma exemplifies how biocultural diversity contributes to ecosystem services and human well-being. This study underscores the importance of biocultural diversity in ecological conservation and the promotion of human welfare.},
}

@article {pmid40721058,
year = {2025},
author = {Gerlin, L and Gaget, K and Lapetoule, G and Quivet, Y and Baa-Puyoulet, P and Rahioui, I and Lopes, MR and Da Silva, P and Calevro, F and Charles, H},
title = {Quantifying supply and demand in the pea aphid-Buchnera symbiosis reveals the metabolic Achilles' heels of this interaction.},
journal = {Metabolic engineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymben.2025.07.011},
pmid = {40721058},
issn = {1096-7184},
abstract = {Many herbivorous insects feed on unbalanced diets and rely on bacterial endosymbionts to meet all their nutritional needs. This is the case for the pea aphid (Acyrthosiphon pisum), a plant pest whose remarkable growth and reproductive capacities cannot be sustained by its sole nutritional resource, the plant phloem sap, and which relies on a symbiotic relationship maintained over millions of years with the intracellular bacterium Buchnera aphidicola for the biosynthesis of amino acids and vitamins. Exploiting original experimental data and metabolic reconstructions, we have built a quantitative genome-scale metabolic model of B. aphidicola and used it to quantify amino acid exchanges between the bacterium and its host. We found metabolites that can rewire pathways, influencing the balance between selfish (growth-focused) and mutualist (amino acid synthesis) behavior. Among the products synthesized by Buchnera, phenylalanine, tyrosine and leucine are the main matter sinks and consume more than 60% of imported glucose and serine. Finally, we compared the predicted bacterial supply to the aphid demand in amino acids. We found that the pea aphid may efficiently regulate its symbiont population density depending on its metabolic requirements, but that embryos are quantitatively not self-sustaining, with embryonic bacteria supply falling short of demand by 50%. Overall, our study highlights candidate compounds and pathways to target for destabilizing this symbiosis or predicting its resilience to environmental or nutritional perturbations.},
}

@article {pmid40719630,
year = {2025},
author = {Kelleher, LA and Ramalho, MO},
title = {Impact of rising temperatures on the bacterial communities of Aphaenogaster ants.},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.062145},
pmid = {40719630},
issn = {2046-6390},
abstract = {Studies have shown that biodiversity will be impacted by global climate change, with the effect on ants just beginning to be documented. However, this influence on ant symbiotic bacterial communities remains understudied. Aphaenogaster Mayr, 1853, are seed dispersing ants in deciduous forests and their bacterial communities have just been uncovered; however, much is unknown. We aim to determine the impact that warming temperatures will have on Aphaenogaster survival and on their bacterial communities. Ants from four colonies were collected from West Chester, Pennsylvania, USA and entire colonies were subjected to a control temperature (22 °C). After 6-12 months the same colonies were subjected to an experimental temperature (32 °C). DNA was then extracted from ants of all development stages and the 16S rRNA gene was amplified and sequenced following the NGS amplicon approach. The findings revealed that Aphaenogaster ant mortality rates increased, and their symbiotic bacterial communities changed in warmer temperatures. This resulted in a decrease in the presence of Wolbachia spp. and an increase in the presence of Corynebacterium sp. This study reveals important information about the impact of warming temperature on Aphaenogaster ants, and we suggested methods to help protect these ants and other insects in the future.},
}

@article {pmid40716373,
year = {2025},
author = {Liu, Z and Lei, J and Yang, R and Cheng, L and Du, Y and Zhang, Y and Wang, J and Liu, Y},
title = {An artificial intelligence modeling framework based on microbial community structure prediction enhances the pollutant removal efficiency of the algae-bacteria granular sludge system.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126648},
doi = {10.1016/j.jenvman.2025.126648},
pmid = {40716373},
issn = {1095-8630},
abstract = {Algae-bacteria granular sludge (ABGS) technology is a new energy-saving and low-carbon water treatment technology based on the algae-bacteria symbiotic system. However, due to its complex internal microbial system, the regulation mechanism of ABGS is unclear. To address this issue, the present study constructed a two-stage optimal control model for the ABGS system, which includes prediction of microbial community structure and planning of pollutant removal efficiency. This model enabled intelligent optimization of the system's pollutant removal efficiency through the regulation of operational parameters. In the first stage, seven machine learning (ML) algorithms were compared to predict the succession process of microbial community structure under the different conditions (R[2] > 0.94). In the second stage, six ML algorithms were compared to predict the pollutant removal efficiency of the ABGS system, combining regulatory indicators and microbial community structure (R[2] > 0.94). Finally, the non-dominated sorting genetic algorithm was used to integrate the prediction models of the two stages, and the microbial community structure was selectively shaped to enhance the removal efficiency of any two of the carbon, nitrogen, and phosphorus pollutants in the ABGS system (removal rate >90 %). The results of this study provided a universally applicable and quantitative intelligent guidance model for the performance optimization of ABGS technology and other biological systems.},
}

@article {pmid40718908,
year = {2025},
author = {Sun, G and Zhang, Y and Jin, C and Jia, Y},
title = {Ultrasound-CT Symbiosis in Pediatric Lung Abscess Volume Tracking.},
journal = {Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/jum.70015},
pmid = {40718908},
issn = {1550-9613},
}

@article {pmid40717827,
year = {2024},
author = {Hui, F and Lin, YT and Perez, M and Qiu, JW and Sun, Y},
title = {A New Species of Natsushima (Annelida: Chrysopetalidae) Living in the Mantle Cavity of a Deep-Sea Solemyid Clam.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e41},
pmid = {40717827},
issn = {1810-522X},
abstract = {Natsushima is a genus of deep-sea Chrysopetalidae (Annelida) characterized by numerous bifurcate chaetae. It is poorly known, with three species living in the mantle cavity of bivalves in chemosynthetic habitats. Here we describe Natsushima nanhaiensis n. sp. based on an integrative morphological and molecular phylogenetic analysis of specimens collected from the Haima cold seep in the South China Sea. Morphologically, the new species can be distinguished from its congeneric species by the shape and number of the neuropodial hooks and bifurcate chaetae, the shape of the parapodia, and the long dorsal cirri. Sequence comparison and phylogenetic analysis based on the mitochondrial COI and 16S rRNA gene sequences supported the placement of Natsushima nanhaiensis n. sp. in Natsushima and its status as a distinct species. We also present a key to species of Natsushima and discuss their biogeography.},
}

@article {pmid40717644,
year = {2025},
author = {Gobetti, A and Cornacchia, G and Tomasoni, G and Ramorino, G},
title = {The environmental benefits of industrial symbiosis: A case study on substituting sand with steel slag as filler in epoxy mortar.},
journal = {Waste management & research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA},
volume = {},
number = {},
pages = {734242X251350543},
doi = {10.1177/0734242X251350543},
pmid = {40717644},
issn = {1096-3669},
abstract = {Electric arc furnace (EAF) slag, a by-product of steelmaking commonly utilized as artificial aggregate, still faces significant landfilling despite extensive reuse. This study explores sustainable alternatives to minimize landfilling by investigating the environmental benefits of incorporating EAF slag as filler in epoxy mortar, as a substitute for a natural material such as river sand. Experimental results demonstrate that slag-filled mortar exhibits comparable or superior mechanical performance to sand-filled mortar, making it a technically feasible substitute. Moreover, the heavy metals leaching of slag, which is one of the major concerns about the reuse of this material, is reduced thanks to the incorporation into the polymeric matrix, ensuring a safe reuse. To quantify these sustainability benefits, a comparative life cycle assessment is conducted for two scenarios involving the production of a functional unit of 1 m[2] of epoxy mortar, typically applied in epoxy screeds, using sand or slag at equal volume fraction. Scenario 1 encompasses slag landfilling and sand extraction, while scenario 2 involves slag reuse as a filler, avoiding landfilling and sand extraction. Life cycle impact assessment using the Environmental Footprint 3.0 method reveals across-the-board reductions. The majority of analyzed impact categories experience a reduction of over 90% attributed to the avoidance of slag disposal and landfill inertization. Overall, reusing slag as an epoxy filler presents significant sustainability benefits compared to disposal, promoting the adoption of this industrial symbiosis application.},
}

@article {pmid40717481,
year = {2025},
author = {Larkin, J and Kassam, R and Crow, W and Hajihassani, A},
title = {Exploring the diversity of turfgrass-associated entomopathogenic nematodes and their symbiotic bacteria for root-knot and sting nematode biocontrol.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70077},
pmid = {40717481},
issn = {1526-4998},
support = {//US Department of agriculture/ ; 2022-51102-38143//Methyl Bromide Transitions Program/ ; },
abstract = {BACKGROUND: Symbiotic bacteria from the genera Xenorhabdus and Photorhabdus associated with Steinernema and Heterorhabditis entomopathogenic nematodes (EPNs), respectively, show nematicidal properties against plant-parasitic nematodes. This study investigated the diversity of EPNs in Floridian turfgrass systems and the effect of secondary metabolites of their symbiotic bacteria against grass root-knot (Meloidogyne graminis) and sting (Belonolaimus longicaudatus) nematodes, major pests in turfgrass systems.

RESULTS: Six isolates of H. indica, four of S. glaseri, and two of S. diaprepesi were isolated and identified molecularly from three turfgrass locations. Additionally, their symbiotic bacteria, X. poinarii, X. griffiniae, X. doucetiae, X. indica, P. akhurstii and P. luminescens were isolated and molecularly identified. Nematicidal efficacy of bacterial secondary metabolites (crude extracts) was tested against M. graminis and B. longicaudatus nematodes in vitro. Bioassays demonstrated a concentration-dependent increase in nematode mortality. The isolates X. poinarii 733 and X. griffiniae 1050 exhibited high mortality against M. graminis after 24, 48 and 72 h of exposure at 25% concentration (>87%) (P < 0.05). In addition to these isolates, two others, P. akhurstii 846 and P. luminescens 1189, exhibited high mortality (44-100%) against B. longicaudatus after 72 h at 25%, 50% and 100% concentrations (P < 0.05).

CONCLUSION: These findings indicate that Florida turfgrass soils harbor a high diversity of EPNs and associated bacteria. Furthermore, our results suggest for the first time that Xenorhabdus and Photorhabdus-derived secondary metabolites offer a promising biocontrol approach for managing M. graminis and B. longicaudatus. © 2025 Society of Chemical Industry.},
}

@article {pmid40714542,
year = {2025},
author = {Cáceres-Mago, K and Salazar, MJ and Becerra, AG},
title = {Glomalin-related soil protein produced by arbuscular mycorrhizal fungi: its role in Pb stabilization at heavily contaminated sites.},
journal = {Chemosphere},
volume = {385},
number = {},
pages = {144589},
doi = {10.1016/j.chemosphere.2025.144589},
pmid = {40714542},
issn = {1879-1298},
abstract = {Glomalin-related soil protein (GRSP), produced by arbuscular mycorrhizal fungi (AMF), plays a key role in stabilizing potentially toxic elements. This study evaluated the impact of Pb contamination on GRSP content in rhizosphere soil and its contribution to Pb binding at heavily contaminated sites. AMF colonization, spore density, and AMF species richness and diversity were also assessed. Additionally, methodological tests were conducted to evaluate the suitability of protocols for quantifying the amount of Pb bound to GRSP. Soil and root samples were collected from three dominant plant species at 20 locations near an abandoned Pb smelter, along with three uncontaminated locations. A Pb concentration gradient (149.28-77,588.77 mg kg[-1]) was identified. GRSP, classified into easily extractable (EE-GRSP: 0.46-1.75 mg g[-1]) and total (T-GRSP: 1.22-3.89 mg g[-1]), was detected at all sites. GRSP content was not directly affected by Pb contamination, but showed a positive association with AMF richness and diversity. The abundance of the morphospecies Acaulospora rehmii, A. scrobiculata, Entrophospora infrequens, Funneliformis geosporus, and Racocetra fulgida correlated positively with T-GRSP. Reliable quantification of Pb bound to GRSP required protein precipitation followed by dialysis. Pb bound to T-GRSP (2.03-548.54 mg g[-1]) increased with soil Pb, while the percentage of soil Pb retained by GRSP decreased (23.13-1.04 %). Nevertheless, the same amount of T-GRSP bound 77 times more Pb in the most contaminated location compared to the least. Therefore, enhancing the GRSP pool, particularly through AMF morphospecies related to higher GRSP content, may be a key strategy for AMF-assisted phytoremediation.},
}

@article {pmid40713930,
year = {2025},
author = {Escudero-Leyva, E and Belle, M and DadkhahTehrani, A and Culver, JN and Araya-Salas, M and Kutza, JP and Goldson, N and Chavarría, M and Chaverri, P},
title = {Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {95},
pmid = {40713930},
issn = {2524-6372},
support = {IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; IOS-2321265//National Science Foundation/ ; },
abstract = {BACKGROUND: Endohyphal microbial communities, composed of bacteria and viruses residing within fungal hyphae, play important roles in shaping fungal phenotypes, host interactions, and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity, secondary metabolism, and adaptability, much remains unknown about their diversity and host specificity. Even less is known about endohyphal viruses, whose ecological roles and evolutionary dynamics are poorly understood. This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses.

RESULTS: We analyzed 19 fungal isolates spanning eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales). Bacterial communities were highly diverse and showed significant phylogenetic signal, with core taxa-such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales-shared across hosts. Several bacterial groups were associated with specific fungal orders, suggesting host specialization: Moraxellales, Sphingomonadales, and Streptosporangiaceae in Amphisphaeriales; Enterobacterales, Hyphomicrobiales, and Micrococcales in Glomerellales; and Cytophagales in Diaporthales. In contrast, viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae. No core viral taxa were detected in metatranscriptomic data, and only a few reads of double-stranded RNA viruses were found.

CONCLUSIONS: Overall, our results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts, with dsDNA viruses dominating the endohyphal virome. These findings provide new insights into the ecological and evolutionary dynamics of fungal-associated microbiota. Future work expanding taxonomic reference databases and exploring the functional roles of these microbial symbionts will be essential to understanding their contributions to fungal biology, host interactions, and broader ecosystem processes.},
}

@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}

@article {pmid40712336,
year = {2025},
author = {Thirunavukkarasu, S and Rajendran, P and Hwang, JS},
title = {Adaptations of Xenograpsus testudinatus to shallow hydrothermal vent environments in the western Pacific: A comprehensive review.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118467},
doi = {10.1016/j.marpolbul.2025.118467},
pmid = {40712336},
issn = {1879-3363},
abstract = {The grapsoid crab Xenograpsus testudinatus, Ng et al. (2000) inhabits unique ecosystems of active shallow-water hydrothermal vents of the western Pacific volcanic rises as the dominant vent metazoan. This species provides a valuable model to explore population expansion, evolutionary ecology, metabolic regulation, genetic adaptation, and meta-population dynamics. A comprehensive literature review revealed that X. testudinatus, a dominant vent metazoan, has evolved robust metabolic strategies driven by mechanisms of acid-base regulation, allowing it to preserve its eco-physiological balance under extreme conditions. The species' physiology and metabolism are intricately linked to symbiotic relationships with beneficial microbiomes, which play a crucial role in its adaptive strategies. The genetic masterpiece of the genomic constitution of vent crabs showed extreme sulfur toxic tolerance through a specified genetic mechanism to H2S detoxification through epithelial and pillar cells of the gill filaments. Furthermore, the isotopic analyses of δ[13]C and δ1[5]N values suggest extensive ingestion of dead zooplankton with microbes forming marine snow in the shallow vents, facilitating a highly efficient recycling trophic system. The overall review highlights critical advancements in our understanding of the eco-physiology, symbiotic relationships, and evolutionary adaptations of marine organisms thriving in one of the earth's most extreme environments.},
}

@article {pmid40711997,
year = {2025},
author = {Hansen, AK and Percy, DM and Mao, S and Degnan, PH},
title = {Effect of oceanic islands on an insect symbiont genome in transition to a host-restricted lifestyle.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf153},
pmid = {40711997},
issn = {1759-6653},
abstract = {Islands offer unique opportunities to study adaptive radiations and their impacts on host genome evolution. In Hawaiian Pariaconus psyllids, all species harbor the ancient nutritional symbiont Carsonella, while only free-living and open-gall species on younger islands host a second stable co-symbiont, Makana. In contrast, a third co-symbiont, Malihini, appears to be in an early-stage of host restriction and genome degradation, making it a valuable model for understanding symbiont evolution during island radiations. Here, we examine Malihini genome evolution across multiple Pariaconus lineages using 16S rRNA sequencing, metagenomics, phylogenetic reconstruction, and microscopy. We find that Malihini is co-diversifying with its hosts on the oldest island Kaua'i (kamua group; open- and closed-gall makers) and on the younger islands only in free-living species (bicoloratus group). Comparison of five Malihini genomes-including three newly assembled in this study-shows ongoing genome reduction from a large-genome ancestor (>3,900 protein-coding genes), likely driven by relaxed selection, vertical transmission bottlenecks, and island dispersal over the past 5-million-years. On Kaua'i, the galling psyllids appear to depend more heavily on co-symbiont (Malihini) for the biosynthesis of amino acids and B-vitamins than galling species on younger islands-especially closed-gall species, which only have Carsonella. Surprisingly, free-living psyllids on younger islands with all three symbionts, show metabolic reliance similar to Kaua'i gall-makers. Together, our results demonstrate that island biogeography and host plant ecology shape symbiont losses and co-diversification patterns. Malihini represents an early-stage of symbiont genome degradation during host restriction, in sharp contrast to its more stable co-residents, Carsonella and Makana.},
}

@article {pmid40711302,
year = {2025},
author = {Yu, Y and Jin, F and Wang, L and Cheng, J and Pan, S},
title = {Role of Gut Microbiota and Metabolite Remodeling on the Development and Management of Rheumatoid Arthritis: A Narrative Review.},
journal = {Veterinary sciences},
volume = {12},
number = {7},
pages = {},
pmid = {40711302},
issn = {2306-7381},
support = {32072809//National Natural Science Foundation of China/ ; BK20211119//Natural Science Foundation of Jiangsu Province/ ; G2023014067L//National Foreign Experts Project (High-end Foreign Experts Introduction Programs of Ministry of Science and Technology)/ ; 22-R-17//Open Fund of Meat Processing Key Laboratory of Sichuan Province/ ; SJCX23_2016//Research and Practice Innovation Plan for Postgraduates in Jiangsu Province/ ; 202411117163Y//Innovation and Entrepreneurship Training Program for College Students of Higher Education In-stitutions in Jiangsu Province/ ; SBJC23007//Special Project of Cross-cooperation of Northern Jiangsu People's Hospital/ ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease that has a serious impact on both human health and animal production. The gut microbiota is a large and complex symbiotic ecosystem in animals, and the imbalance of gut microbiota is closely related to the pathogenesis of numerous diseases, including RA. The interactions among the gut microbiota, intestinal barrier, and immune system play key roles in maintaining intestinal homeostasis and affecting the development of RA. Regulating intestinal flora and metabolites provides new ideas for the prevention and treatment of RA. Probiotics can regulate the balance of intestinal flora and metabolites, improve the immune environment, and provide novel therapeutic strategies against RA. In order to summarize the role of gut microbiota and metabolite remodeling in the development and management of RA, this review will elaborate on the role of intestinal flora imbalance in the pathogenesis of RA and assess prospective therapeutic approaches that target the gut flora. Understanding the interaction among intestinal flora, metabolites, and RA will help to clarify the pathogenesis of RA and develop innovative and personalized therapeutic interventions against chronic autoimmune diseases.},
}

@article {pmid40709927,
year = {2025},
author = {De Santiago, A and Barnes, SJ and Pereira, TJ and Marcelino-Barros, M and Bik, HM and Thrash, JC},
title = {Complete genome sequences of two Pseudoalteromonas undina strains isolated from a marine nematode (Oncholaimidae) collected at Tybee Island.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0041925},
doi = {10.1128/mra.00419-25},
pmid = {40709927},
issn = {2576-098X},
abstract = {Pseudoalteromonas is known to form symbiotic relationships with various marine invertebrates, but association with nematodes has not been well-explored. Here, we report the genome sequences of two Pseudoalteromonas strains isolated from a predatory marine nematode (Oncholaimidae) collected from Tybee Island, GA, that will facilitate the study of nematode-bacterial interactions.},
}

@article {pmid40708922,
year = {2025},
author = {Long, XN and Zhang, XK and Wu, Y and Tang, SS and Zheng, TX and Chen, D and Cao, GH and Zhou, XH and He, S},
title = {Diversity and functional roles of endophytic and rhizospheric microorganisms in Ophioglossum vulgatum L.: implications for bioactive compound synthesis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1618667},
pmid = {40708922},
issn = {1664-302X},
abstract = {BACKGROUND: Ophioglossum vulgatum L. is a widely utilized medicinal plant, with the entire plant being used for medicinal purposes. This study systematically characterized the endophytic and rhizospheric community structure, taxonomic diversity, and symbiotic networks within distinct compartments of O. vulgatum, while evaluating their potential associations with the accumulation of pharmacologically active metabolites.

METHODS: Endophytic and rhizospheric community profiling was conducted via Illumina sequencing, while bioactive compounds were identified using UPLC-ESI-MS/MS.

RESULTS: Roots and leaves harbored beneficial bacteria (e.g., Methylobacterium, Streptomyces, Sphingomonas, and Flavobacterium). Dominant fungi included Archaeorhizomyces (rhizosphere soil) and Homophron (roots/leaves). Dark septate endophytes (DSEs; e.g., Cladosporium, Cladophialophora, and Chaetomium) were abundant across rhizosphere soil, roots, and leaves. Alpha/beta diversity analyses showed higher microbial richness in rhizosphere soil than in plant tissues. Functional predictions (PICRUSt2/FUNGuild) linked endophytic and rhizospheric bacteria to metabolism, human diseases, and biological systems. Network analysis highlighted Basidiomycota as keystone taxa, with modular community structure. Functional predictions revealed that endophytic and rhizospheric microorganisms were associated with critical metabolic pathways, particularly in the biosynthesis of flavonoids and alkaloids (primary bioactive compounds). LEFSe analyses highlighted compartment-specific biomarkers: Acidobacteria, Basidiomycota, and Ascomycota were enriched in distinct zones (rhizosphere, roots, and leaves), with Actinobacteria exhibiting highly significant correlations (P < 0.01) with flavonoids, lipids, and quinones, while Acidobacteria, Basidiomycota, and Ascomycota were strongly linked to steroids and tannins (P < 0.05).

CONCLUSION: The diversity and abundance of microbial communities in O. vulgatum exhibited tissue-specific and rhizosphere-dependent variations, with distinct patterns strongly correlating to bioactive compound accumulation. Notably, biomarker taxa including Actinobacteria, Acidobacteria, Basidiomycota, and Ascomycota demonstrated robust microbe-metabolite interactions, suggesting their critical regulatory role in biosynthesis pathways. These findings establish endophytic-rhizospheric microbiota as key biosynthetic modulators, proposing innovative approaches for enhancing phytochemical production through targeted microbial community manipulation.},
}

@article {pmid40708921,
year = {2025},
author = {Umanzor, EF and Kelly, SE and Ravenscraft, A and Matsuura, Y and Hunter, MS},
title = {The facultative intracellular symbiont Lariskella is neutral for lifetime fitness and spreads through cytoplasmic incompatibility in the leaffooted bug, Leptoglossus zonatus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595917},
pmid = {40708921},
issn = {1664-302X},
abstract = {The maternally-inherited, intracellular bacterium Lariskella (Alphaproteobacteria: Midichloreaceae) has been widely detected in arthropods including true bugs, beetles, a wasp, a moth, and pathogen-vectoring fleas and ticks. Despite its prevalence, its role in the biology of its hosts has been unknown. We set out to determine the role of this symbiont in the leaffooted bug, Leptoglossus zonatus (Hempitera: Coreidae). To examine the effects of Lariskella on bug performance and reproduction as well as in possible interactions with the bug's obligate nutritional symbiont, Caballeronia, bugs were reared in a factorial experiment with both Lariskella and Caballeronia positive and negative treatments. Lifetime survival analysis (~120 days) showed significant developmental delays and decrease in survival for bugs that lacked Caballeronia, and Caballeronia-free bugs did not reproduce. However, among the Caballeronia carrying treatments, there were no significant differences in lifetime survival or reproduction in treatments with and without Lariskella, suggesting this symbiont is neutral for overall bug fitness. To test for reproductive manipulation, crossing among Lariskella-positive and negative individuals was performed. When Lariskella-negative females were mated with Lariskella positive males, fewer eggs survived early embryogenesis, consistent with a cytoplasmic incompatibility (CI) phenotype. Wild L. zonatus from California and Arizona showed high but not fixed Lariskella infection rates. Within individuals, Lariskella titer was low during early development (1st-3rd instar), followed by an increase that coincided with development of reproductive tissues. Our results reveal Lariskella to be among a growing number of microbial symbionts that cause CI, a phenotype that increases the relative fitness of females harboring the symbiont. Understanding the mechanism of how Lariskella manipulates reproduction can provide insights into the evolution of reproductive manipulators and may eventually provide tools for management of hosts of Lariskella, including pathogen-vectoring ticks and fleas.},
}

@article {pmid40708668,
year = {2025},
author = {Beavers, KM and Gutierrez-Andrade, D and Van Buren, EW and Emery, MA and Brandt, ME and Apprill, A and Mydlarz, LD},
title = {Machine learning reveals distinct gene expression signatures across tissue states in stony coral tissue loss disease.},
journal = {Royal Society open science},
volume = {12},
number = {7},
pages = {241993},
pmid = {40708668},
issn = {2054-5703},
abstract = {Stony coral tissue loss disease (SCTLD) has rapidly degraded Caribbean reefs, compounding climate-related stressors and threatening ecosystem stability. Effective intervention requires understanding the mechanisms driving disease progression and resistance. Here, we apply a supervised machine learning approach-support vector machine recursive feature elimination-combined with differential gene expression analysis to describe SCTLD in the reef-building coral Montastraea cavernosa and its dominant algal endosymbiont, Cladocopium goreaui. We analyse three tissue types: apparently healthy tissue on apparently healthy colonies, apparently healthy tissue on SCTLD-affected colonies and lesion tissue on SCTLD-affected colonies. This approach identifies genes with high classification accuracy and reveals processes associated with SCTLD resistance, such as immune regulation and lipid biosynthesis, as well as processes involved in disease progression, such as inflammation, cytoskeletal disruption and symbiosis breakdown. Our findings support evidence that SCTLD induces dysbiosis between the coral host and Symbiodiniaceae and describe the metabolic and immune shifts that occur as the holobiont transitions from healthy to diseased. This supervised machine learning methodology offers a novel approach to accurately assess the health states of endangered coral species, with potential applications in guiding targeted restoration efforts and informing early disease intervention strategies.},
}

@article {pmid40708654,
year = {2025},
author = {Bulaj, G and Forero, M and Huntsman, DD},
title = {Biophilic design, neuroarchitecture and therapeutic home environments: harnessing medicinal properties of intentionally-designed spaces to enhance digital health outcomes.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1610259},
pmid = {40708654},
issn = {2296-858X},
abstract = {Digital health technologies (DHT) support patient-centered care by delivering behavioral, educational, self-efficacy and self-management interventions. Yet, multifactorial chronic diseases are shaped by complex interactions between genetics, environment and behavior, embodied in social and commercial determinants of health. Given that people in the United States spend on average 18 h per day at home, the impact of home environment on a person's health is underutilized in medicine. Herein, we discuss opportunities to improve therapy outcomes through bridging digital interventions with intentionally-designed restorative and multisensory environments that simultaneously foster physiological and emotional homeostasis. Harnessing positive effects of biophilic design, neuroarchitecture and therapeutic home environments can enhance the effectiveness of digital interventions, including digital therapeutics (DTx), wearables and drug + digital combination therapies that utilize "prescription drug use-related software" (PDURS) framework. Real-world barriers to advance these solutions include a lack of public awareness about connections between the built environment, health and wellbeing, the knowledge gap in long-term clinical outcomes of biophilic interventions, and a limited funding for advancing "biophilic design as an adjunctive therapy" applications. In conclusion, creating digital health ecosystems that favor symbiosis between digital health interventions and enriched environments can promote sustained behavior change, elevate precision care and improve value-based healthcare outcomes.},
}

@article {pmid40708584,
year = {2025},
author = {Jin, C and Kambara, K and Fujino, K and Shimura, H},
title = {Transcriptomic and protein-protein interaction network analyses of the molecular mechanisms underlying the mycorrhizal interaction in Cypripedium macranthos var. rebunense.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1597154},
pmid = {40708584},
issn = {1664-462X},
abstract = {INTRODUCTION: Orchid mycorrhizal (OM) symbiosis plays an essential role in orchid seed germination and development, but its molecular mechanisms remain largely unexplored.

METHODS: To comprehensively analyze gene expression associated with early fungal colonization, transcriptome analysis of Cypripedium macranthos var. rebunense was performed using mycorrhizal tissues prepared by inoculating seedling plants with a fungus that exhibited different mycorrhizal interaction properties among subcultures.

RESULTS: Colonization with the mycorrhizal fungus induced an increased expression of orchid genes encoding enzymes involved in cell wall synthesis, degradation, and modification, as well as those encoding transporters of sugars, amino acids, nucleic acids, and other nitrogen-containing compounds. Enrichment analysis focusing on genes associated with protein-protein interactions (PPI) suggested a potential role of lectin domain-containing receptor-like kinases (LecRLKs) in the recognition of fungal colonization and the induction of cell wall-modifying enzymes and nutrient transporters required for mycorrhizal formation. Kinase genes such as MAPKKK and serine/threonine protein kinase were upregulated in tissues exhibiting continued peloton formation, whereas these genes exhibited no changes in tissues showing no peloton formation four weeks after inoculation.

DISCUSSION: These results suggest that the continuous phosphorylation signaling cascade plays a crucial role in the regulatory pathway for maintaining mycorrhizal interactions between Cypripedium and its mycorrhizal fungus.},
}

@article {pmid40708289,
year = {2025},
author = {Zheng, Z and Cai, M and Liu, H and Li, X and Xu, H and Mysore, KS and Wen, J and Staehelin, C and Downie, JA and Kong, F and Xie, F},
title = {RinRK1's extracellular domain acts as a host-specific gatekeeper for rhizobial infection in Medicago truncatula.},
journal = {The Plant journal : for cell and molecular biology},
volume = {123},
number = {2},
pages = {e70340},
doi = {10.1111/tpj.70340},
pmid = {40708289},
issn = {1365-313X},
support = {2023ZD0406905//STI 2030-Major Projects/ ; YSBR-011//CAS Project for Young Scientists in Basic Research/ ; 21XD1403900//the Program of Shanghai Academic/Technology Research Leader/ ; 21ZR1471100//the Shanghai Natural Science Fund/ ; },
mesh = {*Medicago truncatula/microbiology/genetics/metabolism ; *Plant Proteins/metabolism/genetics ; *Sinorhizobium meliloti/physiology ; Plant Root Nodulation ; Symbiosis ; Protein Domains ; Root Nodules, Plant/microbiology/metabolism ; Host Specificity ; },
abstract = {Legume nodulation by nitrogen-fixing rhizobia displays strict host specificity, primarily determined by rhizobial nodulation factors (NFs). While the kinase domain of NF receptors in Lotus japonicus suffices for nodule organogenesis, their extracellular domains govern rhizobial infection. In Sinorhizobium meliloti, specific NF modifications (nodL-dependent acetylation and nodF-dependent N-linked C16:2 acyl chains) are critical for infecting certain Medicago truncatula ecotypes, with LYK2bis essential for nodL-mediated infection. However, how NF receptors discern NF modifications to enable rhizobial infection remains unknown. Here, we demonstrate that M. truncatula RinRK1 (MtRinRK1) interacts with NF receptors and is indispensable for root hair infection of ecotype R108 by S. meliloti nodF nodL mutant producing modified NFs. Notably, a screen of 50 M. truncatula natural variants revealed only R108 forms functional nodules with S. meliloti nodF nodL, and we pinpointed three residues in MtRinRK1 extracellular domains essential for this infection. Despite homology with L. japonicus RinRK1 (LjRinRK1), these proteins are functionally non-interchangeable, with their extracellular domains acting as host-specific determinants. Our findings establish RinRK1 as a core regulator of NF-dependent host specificity in rhizobia infection.},
}

*Medicago truncatula/microbiology/genetics/metabolism
*Plant Proteins/metabolism/genetics
*Sinorhizobium meliloti/physiology
Plant Root Nodulation
Symbiosis
Protein Domains
Root Nodules, Plant/microbiology/metabolism
Host Specificity

@article {pmid40708129,
year = {2025},
author = {Vitale, E and Feuerborn, TR and Walls, M},
title = {Human-Dog Symbiosis and Ecological Dynamics in the Arctic.},
journal = {Evolutionary anthropology},
volume = {34},
number = {3},
pages = {e70009},
doi = {10.1002/evan.70009},
pmid = {40708129},
issn = {1520-6505},
mesh = {Animals ; Arctic Regions ; Humans ; *Symbiosis ; Dogs/physiology ; *Inuit ; Archaeology ; Anthropology, Physical ; },
abstract = {Since the Late Pleistocene, humans and dogs have coevolved in the Arctic, forming a symbiotic relationship essential to survival, mobility, and adaptation. Archeological evidence shows dogs were used as traction animals by the Early Holocene, ultimately facilitating Inuit expansion and shaping Arctic settlement patterns. Despite recent declines in sled dog populations due to colonial factors, climate change, and cultural shifts, dogs remain central to Inuit identity. This paper frames the human-dog cooperation as a dynamic system of mutual learning, or enskilment, where both species acquire shared skills through collaboration. Tools like harnesses and whips serve as communicative devices within this system. Drawing on archeological and contemporary Inuit practices, the study highlights how embodied knowledge and animal agency contribute to ecological resilience. By viewing the Arctic as a co-managed landscape shaped by human-dog cooperation, the paper challenges static views of adaptation and underscores the enduring significance of this interspecies relationship.},
}

Animals
Arctic Regions
Humans
*Symbiosis
Dogs/physiology
*Inuit
Archaeology
Anthropology, Physical

@article {pmid40707117,
year = {2025},
author = {Stock, ML and Heerema, RJ and Randall, JJ and Romero-Olivares, AL and Belteton, SA and Velasco-Cruz, C and Pietrasiak, N},
title = {Uncovering the morphological and phylogenetic diversity of mushrooms in pecan orchards in the Southwestern United States.},
journal = {Fungal biology},
volume = {129},
number = {5},
pages = {101608},
doi = {10.1016/j.funbio.2025.101608},
pmid = {40707117},
issn = {1878-6146},
mesh = {*Phylogeny ; *Carya/microbiology ; *Agaricales/classification/genetics/isolation & purification/cytology ; Southwestern United States ; Mycorrhizae/classification/genetics/isolation & purification ; *Biodiversity ; Soil Microbiology ; },
abstract = {Symbiotic relationships between pecan tree roots and mycorrhizal fungi may enhance drought and salt tolerance, nutrient absorption, and disease resistance in pecan (Carya illinoinensis (Wangenh.) K. Koch) orchards of the arid Southwestern United States. Saprotrophic fungi contribute to orchard ecosystem health by breaking down organic matter and enriching soil quality. However, we currently have limited, mostly anecdotal knowledge on mushroom-forming fungi in Southwestern pecan orchards, and studies in other regions primarily focus on ectomycorrhizal fungi. This study provides a novel mycological survey of mushroom-forming fungi (both ectomycorrhizal and saprotrophic) in pecan orchards across New Mexico, Arizona, West Texas, and California. In collaboration with pecan producers, sporocarps from 31 different fungal taxa were collected for morphological, phylogenetic, and ecological analyses. UNITE and NCBI databases aided in taxon identification to construct a maximum-likelihood phylogenetic tree. Common ectomycorrhizal taxa included Scleroderma species, Pisolithus tinctorius, and Tuber lyonii.Saprotrophs included Chlorophyllum molybdites, the regionally-unique Agaricus deserticola, and others. Logistic regression revealed bare soil and tree row location as significant predictors for mycorrhizal fungi presence. This study offers an inaugural characterization of mushroom-forming fungal communities in Southwestern pecan orchards and highlights their potential roles in enhancing orchard ecosystem health and resilience.},
}

*Phylogeny
*Carya/microbiology
*Agaricales/classification/genetics/isolation & purification/cytology
Southwestern United States
Mycorrhizae/classification/genetics/isolation & purification
*Biodiversity
Soil Microbiology

@article {pmid40706114,
year = {2025},
author = {Sheng, L and Ke, S and Jiao, W and Li, Z and Zheng, Y and Tao, S and Hu, X and Fan, Z and Zhang, F and Wu, S},
title = {Sugar-inducible promoters mitigate the fitness cost of engineered Serratia marcescens in the control of Monochamus alternatus.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128282},
doi = {10.1016/j.micres.2025.128282},
pmid = {40706114},
issn = {1618-0623},
abstract = {Pine wilt disease is a devastating disorder of pine trees, vectored and transmitted by Monochamus alternatus Hope. However, vector control strategies for this disease are hampered by the resistance mechanisms of the pathogen, which hinders the long-term survival of control agents in nature. Serratia marcescens, isolated from Pinus massoniana and the gut of M. alternatus, was selected as the carrier strain for engineered bacteria in this study owing to its symbiotic nature. To realize the possibility of the long-term survival of transgenic bacteria in the gut of M. alternatus and the wild, four sugar-inducible promoters were used to construct transgenic strains. The S. marcescens strains with sugar-inducible promoters exhibited higher fitness than the constitutive strain expressing the Cry3Aa-T toxin, while maintaining a growth curve similar to that of the wild-type strain. The conditional expression of the Cry3Aa-T toxin in S. marcescens was triggered by the presence of sugar, and the lactose-induced transgenic symbiotic strain significantly reduced the survival rate of M. alternatus. Thus, this strategy may enable the engineered bacteria to effectively colonize and spread in the wild, indicating a feasible and sustainable vector control approach against M. alternatus.},
}

@article {pmid40705360,
year = {2025},
author = {Feierabend, M and Töpfer, N},
title = {In silico encounters: Harnessing metabolic modelling to understand plant-microbe interactions.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf030},
pmid = {40705360},
issn = {1574-6976},
abstract = {Understanding plant-microbe interactions is vital for developing sustainable agricultural practices and mitigating the consequences of climate change on food security. Plant-microbe interactions can improve nutrient acquisition, reduce dependency on chemical fertilizers, affect plant health, growth, and yield, and impact plants' resistance to biotic and abiotic stresses. These interactions are largely driven by metabolic exchanges and can thus be understood through metabolic network modelling. Recent developments in genomics, metagenomics, phenotyping, and synthetic biology now enable researchers to harness the potential of metabolic modelling at the genome scale. Here, we review studies that utilize genome-scale metabolic modelling to study plant-microbe interactions in symbiotic, pathogenic, and microbial community systems. This review catalogues how metabolic modelling has advanced our understanding of the plant host and its associated microorganisms as a holobiont. We showcase how these models can contextualize heterogeneous datasets and serve as valuable tools to dissect and quantify underlying mechanisms. Finally, we consider studies that employ metabolic models as a testbed for in silico design of synthetic microbial communities with predefined traits. We conclude by discussing broader implications of the presented studies, future perspectives, and outstanding challenges.},
}

@article {pmid40705355,
year = {2025},
author = {Mathieson, OL and Schultz, DL and Hunter, MS and Kleiner, M and Schmitz-Esser, S and Doremus, MR},
title = {The ecology, evolution and physiology of Cardinium: a widespread heritable endosymbiont of invertebrates.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf031},
pmid = {40705355},
issn = {1574-6976},
abstract = {Candidatus Cardinium hertigii (Cardinium) are maternally-transmitted obligate intracellular endosymbiotic bacteria found in a wide range of invertebrate hosts, including arthropods and nematodes. Infection with Cardinium has substantial consequences for host biology, with many strains manipulating host reproduction to favor symbiont transmission by (i) feminizing male hosts, (ii) altering host sex allocation, (iii) inducing parthenogenesis, or (iv) causing cytoplasmic incompatibility. Other Cardinium strains can confer benefits to their host or alter host behavior. Cardinium-modified host phenotypes can result in selective sweeps of cytological elements through host populations and potentially reinforce host speciation. Cardinium has potential for applications in controlling arthropod pest species and arthropod-vectored disease transmission, although much remains to be explored regarding Cardinium physiology and host interactions. In this review, we provide an overview of Cardinium evolution and host distribution. We describe the various host phenotypes associated with Cardinium and how biological and environmental factors influence these symbioses. We also provide an overview of Cardinium metabolism, physiology and potential mechanisms for interactions with hosts based on recent studies using genomics and transcriptomics. Finally, we discuss new methodologies and directions for Cardinium research, including improving our understanding of Cardinium physiology, response to environmental stress, and potential for controlling arthropod pest populations.},
}

@article {pmid40705231,
year = {2025},
author = {Ting, TY and Lee, WJ and Goh, HH},
title = {Molecular Genetics and Probiotic Mechanisms of Saccharomyces cerevisiae var. boulardii.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40705231},
issn = {1867-1314},
support = {FRGS/1/2024/STG01/UKM/02/05//Ministry of Higher Education, Malaysia/ ; GUP-2024-092//Universiti Kebangsaan Malaysia/ ; },
abstract = {Saccharomyces cerevisiae var. boulardii (Sb) is a S. cerevisiae (Sc) strain that has been widely used in the treatment of gastrointestinal diseases due to its unique probiotic properties. The key genomic differences that distinguish Sb from Sc include the tetrasomy of chromosome XII, the absence of intact transposon-yeast (Ty) elements, and variations in the copy number of specific genes. These genomic variations may contribute to enhanced thermotolerance, increased acid resistance, and elevated acetate production, collectively supporting its probiotic functions. The probiotic mechanisms of Sb are mediated through luminal actions, mucosal actions, and trophic effects. Its luminal activity involves neutralizing pathogen toxins via the secretion of proteins and inhibiting pathogen growth through the production of short-chain fatty acids (SCFAs). Additionally, Sb modulates gut microbiota composition by fostering symbiotic relationships, thereby increasing the abundance of beneficial microbes and SCFA levels to promote gut health. The mucosal action of Sb promotes anti-inflammatory responses by regulating the nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) pathways. Meanwhile, its trophic effects, driven by polyamine production, enhance the function of intestinal epithelial cells. Recent findings further suggest that Sb may serve as a potential adjuvant therapy for brain disorders by modulating the gut-brain axis (GBA) to attenuate neuroinflammation. With continued multidisciplinary research, Sb is well-positioned to advance the biotherapeutic landscape. This review aims to synthesize recent advances in the genetics and probiotic mechanisms of Sb, with particular emphasis on its modulatory effects on the GBA.},
}

@article {pmid40705181,
year = {2025},
author = {Mir, R and Javid, J and Ullah, MF and Alrdahe, S and Altedlawi, IA and Mustafa, SK and Jalal, MM and Altayar, MA and Albalawi, AD and Abunab, MK and Alanazi, HS and Barnawi, J and Algehainy, NA and Altemani, FH and Tayeb, FJ},
title = {Metabolic reprogramming and functional crosstalk within the tumor microenvironment (TME) and A Multi-omics anticancer approach.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {9},
pages = {373},
pmid = {40705181},
issn = {1559-131X},
mesh = {Humans ; *Tumor Microenvironment/physiology ; *Neoplasms/metabolism/pathology/genetics ; *Metabolomics/methods ; Proteomics/methods ; Genomics/methods ; Animals ; Metabolic Networks and Pathways ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Tumors are characterized by a complex interplay of various cell types, each contributing to the unique metabolic landscape of the tumor microenvironment (TME). The key metabolic interactions explored within the TME include nutrient competition, symbiotic nutrient exchange, and the role of metabolites as signaling messengers. Metabolic flexibility allows cancer cells to survive and proliferate even under harsh conditions, such as hypoxia and nutrient deprivation. Recent advances highlight that tumors possess inherent metabolic heterogeneity, underpinning the intricate web of intra- and extra- tumoral metabolic connections. Harnessing the power of multi-omics approaches offers unprecedented insights into this metabolic diversity, paving the way for innovative therapeutic strategies targeting the metabolic crosstalk within the tumor microenvironment. Multi-omics approaches, integrating genomics, transcriptomics, proteomics, and metabolomics data, provide a comprehensive view of tumor metabolism. This holistic approach allows for the identification of key metabolic pathways and regulatory networks that drive tumor progression, as well as potential vulnerabilities that can be exploited for therapeutic intervention. In this review, we discuss the metabolic symphony within the TME, the intricacies of tumor metabolism through multi-omics methodologies, and the prospects of devising innovative and effective cancer therapeutic strategies.},
}

Humans
*Tumor Microenvironment/physiology
*Neoplasms/metabolism/pathology/genetics
*Metabolomics/methods
Proteomics/methods
Genomics/methods
Animals
Metabolic Networks and Pathways
Metabolic Reprogramming
Multiomics

@article {pmid40703972,
year = {2025},
author = {Muñoz, I and García-Raso, JE and Cuesta, JA},
title = {A New Varunid Subfamily (Decapoda, Brachyura, Grapsoidea, Varunidae) for Crabs From European and West African Waters, With the Description of Two New Genera and Two New Species.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71712},
pmid = {40703972},
issn = {2045-7758},
abstract = {The subfamily Asthenognathinae is currently composed of a single genus, Asthenognathus Stimpson, 1858, with three species, A. inaequipes Stimpson, 1858, A. hexagonus Rathbun, 1909 (both from the Indo-West Pacific), and A. atlanticus Monod, 1933 (European and West Tropical African waters). All Asthenognathus species are difficult to collect due to their small size and symbiotic lifestyle with fossorial organisms. The examination of specimens of A. atlanticus from European and West African waters deposited in scientific collections shows significant morphological and molecular differences with the Indo-West Pacific species, which makes the creation of a new subfamily (Schubartinae n. subf.) and two new genera necessary. The identity of A. atlanticus, the only species found along the East Atlantic and Mediterranean waters, is clarified, and a new genus, Dudekemus n. gen., is established for this species, Dudekemus atlanticus (Monod, 1933) n. gen., n. comb. This study also describes another new genus, Schubartus n. gen., based on morphological differences and genetic data. These two new genera can be distinguished from Asthenognathus by the carapace proportions and differences in the structures of the male pleonal somites, pereiopods and endostome. In addition, two new species distributed in Guinea-Bissau and Mauritania, Schubartus mauritanicus n. gen., sp. nov., and S. ngankeeae n. gen., n. sp., are described. A key for species of the subfamilies Asthenognathinae and Schubartinae n.subf. is provided.},
}

@article {pmid40703634,
year = {2025},
author = {Kauai, F and Wybouw, N},
title = {Reciprocal Host-Wolbachia Interactions Shape Infection Persistence Upon Loss of Cytoplasmic Incompatibility in Haplodiploids.},
journal = {Evolutionary applications},
volume = {18},
number = {7},
pages = {e70138},
pmid = {40703634},
issn = {1752-4571},
abstract = {Maternally transmitted symbionts such as Wolbachia spread within host populations by mediating reproductive phenotypes. Cytoplasmic incompatibility (CI) is a reproductive phenotype that interferes with embryonal development when infected males fertilize uninfected females. Wolbachia-based pest control relies on strong CI to suppress or replace pest populations. Host genetic background determines CI strength, and host suppressors that cause weak CI threaten the efficacy of Wolbachia-based pest control programs. In haplodiploids, CI embryos either die (Female Mortality, FM-CI) or develop into uninfected males (Male Development, MD-CI). The reciprocal spread of host suppressors and infection, as well as the interaction with the two CI outcomes in haplodiploids, remains poorly understood. The contribution of sex allocation distortion (Sd), an independent Wolbachia-mediated reproductive phenotype that causes a female-biased sex ratio, to infection persistence in haplodiploids is also poorly understood, especially with imperfect maternal transmission. To address these issues, we developed individual-based simulations and validated this computational tool by tracking Wolbachia spread in experimental Tetranychus urticae populations and by contrasting infection dynamics with deterministic mathematical models. Within ⁓14 host generations, we found that deterministic models inflate infection frequencies relative to simulations by ⁓8.1% and overestimate the driving potential of CI, particularly under low initial infection frequencies. Compared to MD-CI, we show that FM-CI strongly extends infection persistence when nuclear suppressors are segregating in the population. We also quantify how maternal transmission modulates the reciprocal spread of suppressors and infection. Upon loss of CI, we show that hypomorphic expression of Sd (~5%) is sufficient for a stable persistence of infection. We derive a mathematical expression that approximates the stable polymorphic infection frequencies that can be maintained by Sd. Collectively, our results advance our understanding of how symbiosis with CI-inducing Wolbachia and haplodiploid hosts might evolve and inform CI-based pest control programs of potential future risks.},
}

@article {pmid40703233,
year = {2025},
author = {Wang, X and Ma, J and Fang, C and Zhu, J and Wang, S and Yang, Z},
title = {Soil types create different rhizosphere ecosystems and profoundly affect the growth characteristics of ratoon sugarcane.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541329},
pmid = {40703233},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere ecological factors play a crucial role in the soil feedback function of ratoon sugarcane. However, limited information exists regarding the differences and relationships among these factors across various soil types (sandy, loam, and clay) and their impact on sugarcane growth and yield characteristics. This study aims to address this knowledge gap by investigating the rhizosphere ecological dynamics of ratoon sugarcane in different soil types.

METHODS: A combination of biochemical experiments and high-throughput sequencing was employed to analyze the rhizosphere ecological factors of ratoon sugarcane. The study examined biochemical function- and enzymatic activity-related factors in the rhizosphere soil, as well as the microbial community composition and their relationships with sugarcane growth and yield characteristics.

RESULTS: Biochemical function- and enzymatic activity-related factors in the rhizosphere soil were generally positively correlated with each other and with sugarcane growth characteristics. For instance, soil respiration and soil catalase activity showed significant positive correlations with theoretical sugarcane yield (correlation coefficients of 0.773, p < 0.05 and 0.863, p < 0.01, respectively). Symbiotic relationships were observed between the rhizosphere soil microbial and root system endophyte communities. Functional differences in microbial communities among different soil types were significant (p < 0.05), indicating that soil type strongly influences the functional expression of rhizosphere soil microbial communities. The abundance of bacteria and fungi in the ratoon sugarcane rhizosphere soil was negatively and positively correlated with most soil biochemical functions, respectively. Additionally, correlations existed between the abundance of endophytic bacteria and fungi in the root system and sugarcane yield. Eleven soil biochemical and functional factors were positively correlated with theoretical sugarcane yield and theoretical sugar yield indicators.

DISCUSSION: Our findings suggest that different feedback directions and correlation strengths exist between sugarcane growth characteristics and various ecological factors in their rhizosphere across different soil types and spatial scales. These results provide insights into the complex interactions between sugarcane and its rhizosphere environment, highlighting the importance of soil type in shaping these interactions. The study offers guidance for improving soil microbial community structure to enhance sugarcane growth and yield, serving as a valuable reference for soil management in sugarcane fields.},
}

@article {pmid40702084,
year = {2025},
author = {Liu, J and Ye, W and Wang, D and Zhang, H and Wang, J and Li, D},
title = {Comparative transcriptome analysis reveals the potential mechanism of seed germination promoted by trametenolic acid in Gastrodia elata Blume.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26869},
pmid = {40702084},
issn = {2045-2322},
mesh = {*Germination/drug effects/genetics ; *Gastrodia/genetics/drug effects/growth & development ; *Seeds/genetics/drug effects/growth & development ; Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; *Transcriptome ; Symbiosis ; Armillaria ; },
abstract = {Gastrodia elata Blume (GEB) is a potential medicinal and edible plant with several active components and pharmacological activity that has a high application value in medicine and the food business. However, in natural conditions, GEB seed has a very low germination rate and depends on two specific fungi, germinal and nutritive fungi, to complete the germination process and growth. Armillaria mellea, while acting as a nutrient supplier, actually inhibits the germination of GEB seeds. Mycena strains, as the main germinating fungi, can facilitate germination but cannot support the subsequent growth and development of GEB. It requires symbiotic interactions with Mycena and Armillaria mellea to obtain nutrients for its complex life cycle. Our previous studies have shown that trametenolic acid (TA) can effectively promote seed germination of GEB. The aim of this study was to use transcriptome sequencing to further understand the potential mechanism of seed germination triggered by TA in GEB, in order to lay the groundwork for developing a new germination-growth system for GEB with Armillaria mellea. The untreated symbiotic group (Group A0) did not germinate in the seed germination test. The high-dose TA-treated symbiotic group (Group B), the low-dose TA-treated symbiotic group (Group C), and the non-symbiotic untreated germination group (Group A) had germination rates of 85.01, 61.18 and 27.39%, respectively. This indicates that TA treatment can induce symbiosis with Armillaria mellea in GEB seeds and significantly increase germination rates. Transcriptome sequencing (RNA-seq) of Groups A, B, and C identified 86,843 annotated genes. There were more down-regulated genes than up-regulated genes, with 3912, 2518, and 814 differentially expressed genes (DEGs) between B and A, C and A, and B and C, respectively. The DEGs were mainly involved in DNA transcription factors, cell wall actions, plant-pathogen interactions, phenylpropanoid biosynthesis, phytohormone signal transduction, and starch-sucrose metabolism pathways. Six genes were confirmed using qRT-PCR: Down-regulated genes in the lignin biosynthesis pathway include MYB4 and 4CL, while GA20ox1 in the gibberellin biosynthesis pathway was also down-regulated. Up-regulated genes in the plant-pathogen interaction pathway are AIB and WRKY51, with MYB44 in the lignin biosynthesis pathway showing up-regulation. The transcriptomics results supported these expression patterns. Lignin, GA, and abscisic acid (ABA) levels were analyzed in GEB protocorms to understand how TA promotes germination. Results showed that groups B and C had lower lignin and ABA levels, but higher GA levels compared to group A. The study revealed that certain genes play a crucial role in promoting GEB seed germination through TA, by regulating gene expression to alter lignin content and hormone levels, breaking seed dormancy, facilitating seed-fungus interactions, and promoting symbiotic relationships with Armillaria mellea. TA modulates the expression of genes involved in lignin biosynthesis and hormone signaling, leading to an increase in GA content and a decrease in ABA and lignin content. This helps seeds break dormancy and promote germination. Additionally, TA can enhance GEB's defense response against fungi by regulating plant-pathogen interaction genes. It also improves the interactions between GEB and Armillaria mellea, overcoming the technical challenges associated with using Armillaria mellea as a germinating fungus. This establishes a new symbiotic germination-growth system between Armillaria mellea and GEB, laying the foundation for further research on the molecular mechanisms of GEB seed germination.},
}

*Germination/drug effects/genetics
*Gastrodia/genetics/drug effects/growth & development
*Seeds/genetics/drug effects/growth & development
Gene Expression Profiling
Gene Expression Regulation, Plant/drug effects
*Transcriptome
Symbiosis
Armillaria

@article {pmid40702032,
year = {2025},
author = {Jia, B and Li, S and Lin, H and Chen, D and Zhang, J},
title = {Quantitative sources identification of gas emissions in mined-out area of coal seams in the Huanglong coalfield of the Ordos Basin, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26731},
pmid = {40702032},
issn = {2045-2322},
abstract = {This study integrates different geochemical analyses (chemical compositions, carbon isotopes) and a physical mixing model to quantitatively identify gas sources and migration mechanisms in the Nanchuan No.2 coal mine. Results reveal distinct isotopic signatures: gases from mine-out area exhibit intermediate δC1 values (- 55.1‰ to - 49.6‰) between coal-seam methane (avg. δ[13]C1 = - 61.0‰) and Yanchang oil-type gas (avg. δ[13]C1 = - 49.7‰), indicating mixed origins. The mixing model quantifies oil-type gas contributions to goaf emissions as 74.3% (methane) and 75.5% (ethane), dominated by vertical migration from Triassic Yanchang Formation source rocks through mining-induced fractures. Low coal-seam gas content (avg. 0.97 m[3]/t) further supports external hydrocarbon influx. Structural heterogeneity in oil-type gas distribution correlates with spatial variations in contribution ratios (52.7-100%). Mining disturbances disrupt caprock integrity, creating pressure-relief pathways that drive gas migration via fracture networks. This work establishes a framework for optimizing gas control strategies in coal-oil-gas symbiotic systems, emphasizing the critical role of isotopic tracing in hazard mitigation.},
}

@article {pmid40701417,
year = {2025},
author = {Qin, L and Lin, Z and Kong, W and Xu, Y and Xie, J and Chen, S and Xiong, J and Wang, Y and Zhu, H and Wang, S},
title = {Resilience of microalgal-bacterial biofilm for saline wastewater treatment under sulfamethoxazole stress: Insights from microbial physiological and ecological responses.},
journal = {Bioresource technology},
volume = {436},
number = {},
pages = {133019},
doi = {10.1016/j.biortech.2025.133019},
pmid = {40701417},
issn = {1873-2976},
abstract = {The emerging antibiotics in mariculture wastewater has challenged conventional biological treatment processes, but the impact of sulfamethoxazole (SMX) on saline microalgal-bacterial symbiotic systems and the underlying microbial response mechanisms remain unclear. This study investigated the resilience of a microalgal-bacterial symbiotic moving bed biofilm reactor (MBS-MBBR) treating saline wastewater under SMX stress, focusing on nitrogen removal performance, microbial physiological activities, and ecological interactions. The ammonia removal efficiency remained stable (>99.0%) at 0.1-1 mg/L SMX but decreased to 62.3% at 5 mg/L SMX. Elevated SMX inhibited microbial respiration, but enhanced extracellular polymer substances synthesis and intracellular antioxidant activities. Microbial community analysis revealed that 0.1-1 mg/L SMX promoted the enrichment of denitrifer (Denitromonas), while 5 mg/L SMX suppressed nitrifiers (Nitrosomonas, Nitrospira). SMX exhibited differential impacts to distinct nitrogen metabolic functions. Furthermore, microalgal-bacterial consortia exhibited enhanced cooperative interactions under SMX stress. This study provides theoretical support to stabilize engineering mariculture wastewater treatment processes.},
}

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

@article {pmid40701150,
year = {2025},
author = {Cho, HS and Yoo, JS and Song, X and Goh, B and Diallo, A and Lee, J and Son, S and Hwang, YS and Park, SB and Oh, SF and Kasper, DL},
title = {Structure of gut microbial glycolipid modulates host inflammatory response.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.016},
pmid = {40701150},
issn = {1097-4172},
abstract = {Commensals are constantly shaping the host's immunological landscape. Lipopolysaccharides found in gram-negative microbes have a terminal lipid A in their outer membrane. Here, we report that structural variations in symbiotic lipid A lead to divergent immune responses with each lipid A structure, eliciting effects distinct from those induced by classical lipid A. Certain lipid A structures can induce a sustained interferon (IFN)-β response orchestrated by Cdc42-facilitated Toll-like receptor 4 (TLR4) endocytosis and lipid droplet (LD) formation. This lipid A-directed IFN-β response is paramount for colon RORγt[+] regulatory T cell (Treg) induction while simultaneously suppressing colonic TH17 cells and controlling gut inflammation. Intriguingly, the quantitatively dominant penta-acylated lipid A species in Bacteroidetes fails to elicit an IFN-β response. Instead, a less abundant tetra-acylated lipid A species sustainably induces IFN-β, thereby contributing to RORγt[+] Treg homeostasis. Nuances in symbiont lipid A structure contribute to maintaining potent regulation of Tregs to maintain a healthy endobiotic balance.},
}

@article {pmid40700644,
year = {2025},
author = {Marqués-Gálvez, JE and de Freitas Pereira, M and Nehls, U and Ruytinx, J and Barry, K and Peter, M and Martin, F and Grigoriev, IV and Veneault-Fourrey, C and Kohler, A},
title = {Comparative transcriptomics uncovers poplar and fungal genetic determinants of ectomycorrhizal compatibility.},
journal = {The Plant journal : for cell and molecular biology},
volume = {123},
number = {2},
pages = {e70352},
pmid = {40700644},
issn = {1365-313X},
support = {ANR-11-LABX-0002-01//Laboratory of Excellence ARBRE/ ; CoFUND-FP7-267196//Agreenskills Marie Sklodowska Curie/ ; DE-AC02-05CH11231//Office of Science of the U.S. Department of Energy/ ; DE-AC05-589 00OR22725//Plant Microbe Interfaces Scientific Focus Area/ ; //NextGenerationEU/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Populus/microbiology/genetics ; Symbiosis/genetics ; *Transcriptome ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; },
abstract = {Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ectomycorrhiza (ECM) first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de novo tree and fungal transcriptional datasets. We identified co-expressed genes enabling ECM symbiosis at early and mature stages of the interaction. These sets of genes can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defenses and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases, and the downregulation of plant cell wall remodeling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene regulation, but also its temporal scale and dynamics seem to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway and nutrient transporters was also studied, revealing constitutive levels of expression and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility, and serve as a data-rich transcriptomic resource to open new research questions in the field.},
}

*Mycorrhizae/genetics/physiology
*Populus/microbiology/genetics
Symbiosis/genetics
*Transcriptome
Gene Expression Regulation, Plant
Gene Expression Profiling
Plant Proteins/genetics/metabolism

@article {pmid40700049,
year = {2025},
author = {Suksavate, W and Ngernsaengsaruay, C and Nipitwattanaphon, M and Hasin, S and Phosri, C and Voraphab, I and Sakolrak, B and Choosa-Nga, P and Nakpong, L and Khunkrai, R and Bunlerlerd, K and Kaewgrajang, T},
title = {Effect of climate change on truffle (Tuber species) distribution and host plant interactions in Thailand.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/00275514.2025.2522020},
pmid = {40700049},
issn = {1557-2536},
abstract = {Climate change is an important driver of shifts in species' geographic distributions, including those of several truffle species. Understanding these shifts is essential for effective conservation and sustainable ecosystem management. This study aimed to identify suitable habitats for three Tuber species discovered in Thailand-Tuber lannaense, T. thailandicum, and T. magnatum-and project their future distributions under climate change scenarios. Using MaxEnt modeling and presence-only occurrence data, we predicted current and future suitable habitats under two climate scenarios: SSP1-2.6 (low emissions) and SSP5-8.5 (high emissions) for the year 2050. Annual precipitation (bio12) and mean diurnal range (bio02) were the most influential environmental variables for three Tuber species and their host plants. Currently, suitable habitats for Tuber species and their host trees (Betula alnoides and Carpinus londoniana) are concentrated in mountainous areas of northern and northeastern Thailand, covering approximately 6000 km[2]. By 2050, under both SSP1-2.6 and SSP5-8.5 scenarios, the shared suitable habitat between truffles and their host plants is projected to be completely lost (100%). Carpinus londoniana is expected to lose nearly 100% of its suitable habitat under SSP1-2.6 and retain only 37 km[2] under SSP5-8.5, whereas B. alnoides shows potential for southward range expansion despite some habitat loss. These findings underscore the urgent need for targeted conservation strategies to preserve Thai Tuber species and their symbiotic hosts under changing climatic conditions.},
}

@article {pmid40699806,
year = {2025},
author = {Lin, W and Shang, JX and Li, XY and Zhou, XF and Zhao, LQ},
title = {Nitric Oxide Regulates Multiple Signal Pathways in Plants via Protein S-Nitrosylation.},
journal = {Current issues in molecular biology},
volume = {47},
number = {6},
pages = {},
doi = {10.3390/cimb47060407},
pmid = {40699806},
issn = {1467-3045},
support = {DR2024017//Hebei Normal University for Nationalities/ ; },
abstract = {Nitric oxide (NO) can perform its physiological role through protein S-nitrosylation, a redox-based post-translational modification (PTM). This review details the specific molecular mechanisms and current detection technologies of S-nitrosylation. It also comprehensively synthesizes emerging evidence of S-nitrosylation roles in plant biological processes, including growth and development, immune signaling, stress responses and symbiotic nitrogen fixation. Furthermore, the review analyzes research progress on the crosstalk between S-nitrosylation and other protein PTMs. Finally, unresolved issues such as the spatio-temporal resolution of SNO-proteome mapping and standardized protocols for reproducibility are pointed out. In summary, this work proposes a roadmap for future research.},
}

@article {pmid40698186,
year = {2025},
author = {Lukács, AF and Herczeg, G and Kovács, GM},
title = {Effects of dark septate endophytic fungi on the performance of non-mycorrhizal cabbage plants under normal and low water conditions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593265},
pmid = {40698186},
issn = {1664-302X},
abstract = {Drought, a major consequence of global environmental change, poses a serious threat to both natural and agricultural ecosystems. Root-associated fungi, particularly the widely distributed dark septate endophytes (DSE), are key components of the plant microbiome and can influence host plant performance in various ways. We conducted two manipulative experiments using two model DSE species from a semiarid habitat to investigate their effects on a non-mycorrhizal host plant (cabbage) under both normal and reduced water supply conditions. The positive effects of Periconia were limited-it not only increased root biomass but also reduced water potential and soil moisture under normal watering conditions. In contrast, Cadophora significantly increased shoot biomass (by up to 50%) and root biomass in one experiment. However, this was also associated with a decline in plant water potential, particularly at the cost of reduced plant water status, and their effects varied on the same host. Interestingly, autoclaved inoculum, also had positive effects on plant growth. Our findings highlight the potential role of symbiotic DSE fungi in mitigating drought stress and suggest their promise as biotechnological tools for addressing the increasing challenges posed by drought.},
}

@article {pmid40696756,
year = {2025},
author = {Peretz, T and Cattan-Tsaushu, E and Conti, C and Rosental, B and Steindler, L and Avrani, S},
title = {Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70155},
doi = {10.1111/1462-2920.70155},
pmid = {40696756},
issn = {1462-2920},
support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; 1386/20//Israel Science Foundation/ ; },
mesh = {Animals ; *Symbiosis ; *Bacteriophages/genetics/isolation & purification/physiology ; *Porifera/microbiology/virology ; *Synechococcus/virology/physiology/genetics ; Prophages/genetics ; *Cyanobacteria/virology ; Genome, Viral ; },
abstract = {Sponges are sessile animals that play crucial roles in marine ecosystems by facilitating nutrient cycling, enhancing biodiversity, and structuring benthic habitats. Microbial symbionts, including cyanobacteria, are vital to sponges, aiding in nutrient cycling, metabolism, and defence. However, due to the sponge's ability to concentrate phages from seawater, extracellular sponge symbionts are particularly vulnerable to phage infection. By contrast, little is known about the susceptibility of intracellular sponge symbionts to phage predation. Here, we present evidence that Candidatus Synechococcus feldmannii, a facultative, horizontally transmitted cyanobacterial endosymbiont of the sponge Petrosia ficiformis, is susceptible to cyanophages. We analysed four Ca. S. feldmannii genomes and found evidence for phage interactions in two, including CRISPR spacers matching sipho- and T4-like cyanophages. One genome harboured a prophage region resembling freshwater cyanobacterial prophages, featuring conserved regions associated with Type VI secretion systems, similar to Wolbachia endosymbionts prophages. Additionally, we developed a method for isolating cyanophages directly from purified sponge bacteriocytes (specialised sponge cells harbouring symbionts) and identified nine T4-like cyanophages with less than 60% similarity to known relatives. Collectively, our findings indicate that Ca. S. feldmannii is susceptible to cyanophages and suggest potential functional parallels between phages infecting endosymbionts across different animal hosts.},
}

Animals
*Symbiosis
*Bacteriophages/genetics/isolation & purification/physiology
*Porifera/microbiology/virology
*Synechococcus/virology/physiology/genetics
Prophages/genetics
*Cyanobacteria/virology
Genome, Viral

@article {pmid40696482,
year = {2025},
author = {Thaqi, SK and Hensel, N and Vitow, N and Baum, C and Streb, LM and Kublik, S and Leinweber, P and Panten, K and Schloter, M and Schulz, S},
title = {Non-rhizobial endophyte recruitment and diversity in Pisum sativum are strongly shaped by phosphorus fertilizer form.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {92},
pmid = {40696482},
issn = {2524-6372},
support = {031B1061B//German Federal Ministry of Education and Research (BMBF); InnoSoilPhos/ ; 031B1061A//German Federal Ministry of Education and Research (BMBF); InnoSoilPhos/ ; 031B0509E//German Federal Ministry of Education and Research (BMBF); InnoSoilPhos/ ; },
abstract = {BACKGROUND: Non-rhizobial endophytes (NREs) support plant health and nodule function by enhancing symbiotic interactions and nitrogen fixation. However, their recruitment dynamics under fertilizers of varying phosphorus solubility remain poorly understood. This study investigated how four P fertilization treatments-no phosphorus (P0), bone char (BC), surface-modified bone char plus (BC[plus]), and triple superphosphate (TSP)-with increasing solubility influence microbial recruitment and diversity in Pisum sativum, leading to differences in plant-available phosphorus across bulk soil, rhizosphere, roots, and nodules.

RESULTS: Using 16S rRNA amplicon sequencing, we found that nodule-associated microbial communities were primarily recruited from unknown sources, likely seeds, followed by roots, especially under BC[plus]. Phosphorus solubility of treatments significantly influenced recruitment patterns, with solubility further shaping microbial diversity. BC[plus] recruited beneficial taxa like Beijerinckiaceae and Flavobacteriaceae, which are associated with nitrogen fixation and biocontrol. In contrast, the highly soluble TSP treatment expanded recruitment from the rhizosphere, reflecting less stringent environmental filtering and promoting taxa like Steroidobacteraceae and Blastocatellaceae, known for nutrient cycling and pathogen suppression. In the absence of P fertilization (P0), recruitment relied heavily on seeds and roots, with arbuscular mycorrhizal fungi colonization prioritized over nodulation. Notably, TSP supported significantly more nodules with greater microbial diversity, potentially enhanced by NREs.

CONCLUSIONS: Phosphorus solubility of the applied fertilizers strongly influences NRE recruitment dynamics in P. sativum. Seeds and roots act as primary reservoirs, while highly soluble fertilizers promote broader recruitment from the rhizosphere and increase microbial diversity in nodules. These results underscore the importance of the fertilization form in modulating NRE recruitment.},
}

@article {pmid40695816,
year = {2025},
author = {Xu, X and Wang, Q and Sun, T and Gao, H and Gu, R and Yang, J and Zhou, J and Fu, P and Wen, H and Yang, G},
title = {Structural basis for the activity regulation of Medicago calcium channel CNGC15.},
journal = {Cell discovery},
volume = {11},
number = {1},
pages = {63},
pmid = {40695816},
issn = {2056-5968},
support = {32422038//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Cyclic nucleotide-gated ion channels (CNGCs) in plants mediate Ca[2+] influx in response to environmental changes. Among numerous plant CNGCs, Medicago truncatula CNGC15a/b/c (MtCNGC15) is localized to the nuclear envelope. The opening and closing cycle of MtCNGC15 is tightly associated with the Ca[2+] oscillation in symbiosis. However, the molecular mechanism underlying MtCNGC15 activity regulation remains unclear. In this study, we present the structures of MtCNGC15 in its apo form and in the presence of CaM. The apo MtCNGC15b exhibits a flexible cytoplasmic domain (CPD), whereas binding of the MtCaM inhibits Ca[2+] currents and stabilizes the highly dynamic CPD. Furthermore, the activity of MtCNGC15b seems to be independent of cGMP. The hypothetical binding pocket for cGMP is occupied by an arginine residue. These findings elucidate the structural basis for the activity regulation of nuclear localized MtCNGC15.},
}

@article {pmid40694858,
year = {2025},
author = {diCenzo, GC and Gutmanis, SM and Esme, O and Moulin, L},
title = {Re-evaluation of the nodulation capacity of Sphingomonas sediminicola DSM 18106T indicates that this strain is not capable of inducing root nodule formation on Pisum sativum (pea).},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0100},
pmid = {40694858},
issn = {1480-3275},
abstract = {Rhizobia are soil-dwelling proteobacteria that can enter into symbiotic nitrogen-fixing relationships with compatible leguminous plants. Taxonomically, rhizobia are divided into alpha-rhizobia, which belong to the class Alpharoteobacteria, and beta-rhizobia, which belong to the class Betaproteobacteria. To date, all bona fide alpha-rhizobia belong to the order Hyphomicrobiales. However, a recent study suggested that Sphingomonas sediminicola DSM 18106T is also a rhizobium and is capable of nodulating pea plants (Pisum sativum), which would expand the known taxonomic distribution of alpha-rhizobia to include the order Sphingomonadales. Here, we attempted to replicate the results of that previous study. Resequencing and computational analysis of the genome of S. sediminicola DSM 18106T failed to identify genes encoding proteins involved in legume nodulation or nitrogen fixation. In addition, experimental plant assays indicated that S. sediminicola DSM 18106T is unable to nodulate the two cultivars of pea tested in our study, unlike the rhizobium Rhizobium johnstonii 3841T. Taken together, and in contrast to the previous study, these results suggest that S. sediminicola DSM 18106T is not capable of inducing root nodule formation on pea, meaning that the taxonomic distribution of all known alpha-rhizobia remains limited to the class Hyphomicrobiales.},
}

@article {pmid40694187,
year = {2025},
author = {Singh, A and Mandal, PK and Reddy, PM},
title = {Transgene expression and root hair deformation of transgenic rice plants harbouring legume-specific Nod factor receptor genes in the presence and absence of nitrogen when inoculated with Sinorhizobium meliloti.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {744},
pmid = {40694187},
issn = {1573-4978},
support = {NRRI/ Incentivizing Research/ BNF / Revised Sanction Order (2023-24)//Indian Council of Agricultural Research/ ; },
mesh = {*Sinorhizobium meliloti/physiology ; *Oryza/genetics/microbiology/metabolism ; Plants, Genetically Modified/genetics/microbiology ; *Plant Roots/genetics/microbiology/metabolism ; *Nitrogen/metabolism ; Symbiosis/genetics ; Plant Proteins/genetics/metabolism ; *Fabaceae/genetics/metabolism/microbiology ; Gene Expression Regulation, Plant ; Transgenes/genetics ; Nitrogen Fixation ; },
abstract = {BACKGROUND: Nitrogen-fixing symbiosis is an effect of crosstalk between legumes and rhizobia, mediated by Nod factors (NF) recognized by legume-specific nod factor (NF) receptors. Developing this symbiotic capability in cereal crops like rice is a promising strategy to reduce dependency on synthetic nitrogen fertilizers, but it is neither simple nor easy. To find whether legume-specific Nod Factor receptor genes are expressed in rice and whether they can change root hair morphology.

METHODS AND RESULTS: We developed transgenic rice plants harbouring two NF receptor genes, a co-receptor gene and two NF binding proteins: MtLYK3, MtNFP, MtDMI2, LjLNP, and MtSYMREM1. When transgenic rice roots were inoculated with fluorescent Sinorhizobium meliloti (S. meliloti), colonization of bacteria was observed on the root surface. Still, it was reduced significantly in the presence of nitrogen in the media. Gene expression of all the five transgenes in the S.meliloti inoculated roots increased to 3.5 fold. Root hair deformation was also observed when transgenic rice roots were treated with purified SmNod Factor (SmNF), and the presence of nitrogen in the medium reduced the root hair deformation percentage.

CONCLUSIONS: This study suggested that rice could interact with S. meliloti for colonization and gene expression and also could perceive the NF signal to deform root hair when the legume-specific NF receptor genes along with co-receptor gene and two NF binding proteins were present in the rice plant. This is an initial indication that rice roots can behave like a symbiotic legume if appropriate genes are transferred to it.},
}

*Sinorhizobium meliloti/physiology
*Oryza/genetics/microbiology/metabolism
Plants, Genetically Modified/genetics/microbiology
*Plant Roots/genetics/microbiology/metabolism
*Nitrogen/metabolism
Symbiosis/genetics
Plant Proteins/genetics/metabolism
*Fabaceae/genetics/metabolism/microbiology
Gene Expression Regulation, Plant
Transgenes/genetics
Nitrogen Fixation

@article {pmid40693735,
year = {2025},
author = {Wu, Z and Sun, Y and Yang, J and Liu, Z and Niu, Y and Zhang, X},
title = {Gene expression and regulatory networks provide new insights into the similarity between nitrogen fixing and arbuscular mycorrhizal symbioses.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf082},
pmid = {40693735},
issn = {1471-9053},
abstract = {Although the evolutionarily younger nitrogen-fixing symbioses (NFS) occurring between plants and rhizobia are predominantly confined to legume species, they exhibit a series of highly conserved characteristics in common with the more ancestral arbuscular mycorrhizal symbiosis (AMS). A growing number of symbiosis-regulated genes have been characterized through either genetic analysis or phylogenomic profiling. However, the underlying similarities and specificities of the transcription regulatory machinery in AMS and NFS remain largely unclarified. Here, we systematically profiled the gene expression changes in three legume species, namely Medicago truncatula, Glycine max, and Lotus japonicus, during AMS and NFS. Additionally, we investigated gene expression changes in three non-legume plants, Solanum lycopersicum, Zea mays, and Oryza sativa, during AMS. We identified thousands of genes that were activated by AMS or NFS in their respective host plants. Through comparative genomics analysis, we systematically explored the conservation and specificity of genes responsive to AMS or NFS. Employing M. truncatula and G. max as illustrative cases, we harnessed the XGboost machine-learning model to construct co-expression-based gene regulatory networks for AMS and NFS within these two species. Through this approach, we successfully illuminated the similarities and unique features of the two symbiotic types at the gene regulatory network level. Further, utilizing known symbiosis genes as queries, we pinpointed a multitude of genes that are intimately associated with AMS and NFS. Overall, via in-depth gene expression profiling and regulatory network analysis, our results indicate that, while NFS in legumes has regulatory circuits similar to those of AMS, there exist certain symbiosis type-specific molecular components.},
}

@article {pmid40692024,
year = {2025},
author = {Zhao, Z and Duan, X and Zhang, T and Bi, S and Noor, Z and Guo, S and Wei, Z and Zhang, Y and Qin, Y and Ma, H and Pan, Y and Yu, Z and Li, J and Zhang, Y},
title = {Adapting to Hypo-Salinity: Molecular Mechanisms in Giant Clams and Symbionts with Implications for Coral Reef Resilience Under Climate Change.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122385},
doi = {10.1016/j.envres.2025.122385},
pmid = {40692024},
issn = {1096-0953},
abstract = {Typhoon climates and extreme rainy seasons drive changes in seawater salinity and quality, threatening coral reef ecosystems. As key contributors to coral reef ecosystems, giant clams face major survival pressures from salinity fluctuations and heat waves. Understanding their salinity adaptation and recovery strategies is thus critical for the long-term conservation and sustainable management of coral reefs. Here, we integrated physiological and meta-transcriptomic analyses to investigate responses of Tridacna crocea to hypo-saline conditions (20 ppt, 27 ppt) and subsequent recovery at 34 ppt. Hypo-salinity significantly reduced growth and survival, with only 69% survival at 20 ppt, while elevated sodium-potassium pump (NKA) activity was observed, facilitating ion balance maintenance. Meta-transcriptomic analysis revealed downregulated genes related to antioxidants (GGT1), ABC transporters (ABCB11, ABCA12), and fatty acid metabolism (ACAA1), alongside upregulated genes involved in amino acid metabolism (AGXT2, ALDH4A1). Symbionts exhibited decreased photosystem II (PSII) activity, reactive oxygen species (ROS) accumulation, and expulsion. Notably, partial recovery was achieved under 27 ppt hypo-salinity, whereas 20 ppt induced irreversible damage. Collectively, T. crocea copes with hypo-saline stress through coordinated regulation of ion transport, amino acid metabolism, and symbiont functionality, with 27 ppt potentially emerging as a critical threshold for recoverable adaptation. These findings provide valuable mechanistic insights to inform coral reef conservation strategies under global climate change.},
}

@article {pmid40691718,
year = {2025},
author = {Ikram, RMA and Wang, M and Moayedi, H and Ahmadi Dehrashid, A and Gharibi, S and Han, JC},
title = {Application of smart technologies for predicting soil erosion patterns.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26479},
pmid = {40691718},
issn = {2045-2322},
abstract = {Soil is a critical natural resource, and accurate erosion susceptibility assessment is vital for the optimal management and development of soil resources. Erosion susceptibility assessment is necessary for long-term conservation plans, but the process can be expensive and time-consuming over large areas. It is imperative to examine the impact of water-induced erosion on cultivated lands, as it can cause significant damage. This study evaluates the effectiveness of four data-driven approaches (biogeography-based optimization, earthworm optimization algorithm, symbiotic organisms search, and whale optimization algorithm) combined with artificial neural network models for the assessment of erosion susceptibility. The examined criteria include 14 geographic and environmental criteria, and the data used in a ratio of 70 to 30 for training and testing operations. And its results were measured by AUC values. The evaluation of AUC accuracy indices revealed compelling results. Specifically, in the case of SOS-MLP, the highest AUC values were observed, reaching 0.9973 for test data and 0.9296 for train data. Conversely, for WOA-MLP, the AUC values obtained were slightly lower but still notable, registering at 0.9809 for test data and 0.959 for train data. These values were also calculated for BBO-MLP (0.999 and 0.9327) and EWA-MLP (0.9304 and 0.9296) in the training and testing phases, respectively. Results showed that all four methods could successfully evaluate erosion susceptibility according to AUC values greater than 0.92, especially the BBO-MLP with the highest AUC values. Therefore, the findings of this study have shown that the combined optimization algorithms and Machine Learning used in this research have a suitable ability to optimize the artificial neural network and are very useful for identifying areas sensitive to erosion.},
}

@article {pmid40691349,
year = {2025},
author = {Nobu, MK},
title = {A model 'organism' split to uncover microbial symbiosis.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40691349},
issn = {1740-1534},
}

@article {pmid40690270,
year = {2025},
author = {Kemlein, M and Peters, L and Schulenburg, H and Obeng, N},
title = {Maintenance and loss of microbe-mediated protection in the absence of pathogens.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf090},
pmid = {40690270},
issn = {1420-9101},
abstract = {Protective microbes are known for their service to hosts. While they allow hosts to survive infection, microbes, too, benefit from successful inhibition of incoming pathogens. Under constant pathogen exposure, protective symbionts should thus be selected for. Yet, it is less clear if, and how, microbe-mediated protection is maintained in symbionts in the absence of pathogen pressure. Addressing the stability of protective symbiosis during bacterial adaptation to healthy hosts, we studied microbe-mediated protection of Pseudomonas lurida MYb11 against pathogenic Bacillus thuringiensis Bt247 in its natural host Caenorhabditis elegans MY316. Specifically, we assessed host protection and in vitro inhibition of the pathogen for a collection of derived MYb11 isolates, which were previously evolved during serial passaging in healthy C. elegans hosts. We found that all evolved MYb11 isolates continued to inhibit the pathogen in vitro, while most, albeit not all, continued to protect hosts. We focused on two of these isolates, MT5 and MT11, one with and one without protection, and found that intact protection is associated with high symbiont colonization and resulting lower pathogen proportions. In sum, our study dissects the stability of a natural protective symbiosis and suggests that high colonization ability ensures microbe-mediated protection, even if microbes adapt to host association in the absence of pathogen selection.},
}

@article {pmid40690090,
year = {2025},
author = {Lin, YC and Huang, YM and Huang, YL and Liu, SL and He, SH and Zhou, LW and Chen, CC},
title = {New species and new records of Trechispora (Trechisporales, Basidiomycota) from Taiwan.},
journal = {Botanical studies},
volume = {66},
number = {1},
pages = {21},
pmid = {40690090},
issn = {1817-406X},
support = {NSTC 112-2621-B-178-002-MY3//National Science and Technology Council/ ; 113-7.2.6--02//Forestry and Nature Conservation Agency of the Ministry of Agriculture (TW)/ ; },
abstract = {BACKGROUND: Trechispora (Hydnodontaceae) comprises a diverse group of wood- and soil-inhabiting fungi, primarily functioning as saprotrophs, with some species forming symbiotic associations with plants and animals. Despite the recognition of over 100 species worldwide, its diversity in Taiwan remains understudied. This study presents the first comprehensive taxonomic revision of Trechispora in Taiwan, integrating morphological and phylogenetic analyses based on sequence data from the nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 (ITS) region and the nuc 28S rDNA (28S).

RESULTS: We describe four new species (Trechispora acerosa, T. floralis, T. formosana, and T. orchidophila) and report seven newly recorded species for Taiwan (T. crystallina, T. dentata, T. latehypha, T. mollusca, T. odontioidea, T. subsinensis, and T. wenshanensis). T. sinensis is synonymized under T. odontioidea. Morphological and phylogenetic analyses support their taxonomic placements, and an identification key to accepted Trechispora species in Taiwan is provided.

CONCLUSION: This study expands the known diversity of Trechispora in Taiwan to 17 species, highlighting their ecological significance and potential interactions with plants in Taiwan's forest ecosystems.},
}

@article {pmid40688685,
year = {2025},
author = {Zhang, Y and Du, Y and Mu, Z and Islam, W and Zeng, F and Gonzalez, NCT and Zhang, Z},
title = {Impact of seasonal changes on root-associated microbial communities among phreatophytes of three basins in desert ecosystem.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1554879},
pmid = {40688685},
issn = {1664-462X},
abstract = {Seasons often alter climate conditions and affect nutrient cycling by altering plant physiology and microbial dynamics. Plant growth and health depend on a symbiotic relationship with root microbes, however, the root-associated microbiota is key to plant evolution and ecosystem function. Seasonal changes in root-associated microbiome diversity and composition of desert plants are vital for understanding plant adaptation in desert ecosystems. We employed high-throughput sequencing to investigate the seasonal dynamics of root-associated microbial communities, including the root endosphere (RE), rhizosphere soil (RS), and bulk soil (BS), across three basins in Xinjiang, China: Turpan, Tarim, and Dzungaria. Proteobacteria dominated bacterial communities in different seasons, while Ascomycota prevailed in fungi. The spring and summer conditions favor greater microbial differentiation. The RE, RS, and BS bacterial communities in May (spring) showed a noticeable absence of highly connected nodes within and between modules. However, the opposite trend was observed in July (summer) and September (autumn). The community assembly of root-associated microbiome (bacteria and fungi) in different seasons primarily followed a random process. Random forest analysis found that seasonal variations in RE bacterial communities were primarily influenced by scattered radiation, while fungal communities were mainly affected by soil available potassium. Environmental factors affect the BS bacterial community more than the fungal community across different seasons. A structural equation model revealed temperature and precipitation's direct effects on microbial communities, mediated by soil and root nutrient availability. Soil pH and EC predominantly affected root bacterial communities, not fungal communities. The fungal community within the RE was found to be directly influenced by seasonal shifts, whereas the RS fungal community composition was significantly impacted by changes in precipitation patterns driven by seasonal variation. The climate seems to be a crucial factor in influencing the dynamic of the root microbiome in desert plants, surpassing the influence of soil and root nutrient availability. This study underscores seasonal root-associated microbiome variations and their important roles in desert ecosystem functions.},
}

@article {pmid40687751,
year = {2025},
author = {Olaranont, Y and Stewart, AB and Songnuan, W and Traiperm, P},
title = {Analysis of ergot alkaloid gene expression and ergine levels in different parts of Ipomoea asarifolia.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19692},
pmid = {40687751},
issn = {2167-8359},
mesh = {*Ergot Alkaloids/metabolism/biosynthesis/genetics ; *Ipomoea/genetics/metabolism ; Plant Leaves/metabolism/genetics/chemistry ; *Gene Expression Regulation, Plant ; Seeds/metabolism/genetics ; Plant Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Ergot alkaloids are renowned for their pharmacological significance and were historically attributed to fungal symbioses with cereal crops and grasses. Recent research uncovered a symbiotic relationship between the fungus Periglandula ipomoea and Ipomoea asarifolia (Convolvulaceae), revealing a new source for ergot alkaloid synthesis. While past studies have emphasized the storage of both the fungus and alkaloids in leaves and seeds, recent work has found they also occur in other plant parts. This study aimed to examine expression of the dmaW gene, which plays a crucial role in ergot alkaloid biosynthesis, and to quantify ergot alkaloid levels across various organs and growth stages of I. asarifolia.

RESULTS: Our findings revealed the highest levels of dmaW gene expression in young seeds and young leaves, whereas the highest ergine concentrations were found in mature leaves followed by young leaves. In light of previous studies, we propose three hypotheses to reconcile these conflicting results: the possibility of an inefficient ergot alkaloid biosynthesis pathway, the possibility that different types of ergot alkaloids are produced, and the existence of an ergot alkaloid translocation system within the plant. Furthermore, ergine concentration and ergot alkaloid biosynthesis gene expression were detected in stems, roots, and flowers, indicating that ergot alkaloids are produced and accumulated in all studied parts of I. asarifolia, rather than being solely confined to the leaves and seeds, as previously reported.

CONCLUSIONS: Overall, our study reveals that ergot alkaloids are produced and accumulated in most parts of I. asarifolia, suggesting a plant-wide biosynthesis and potential transport system, challenging the previous belief that biosynthesis was confined to glandular trichomes on leaves.},
}

*Ergot Alkaloids/metabolism/biosynthesis/genetics
*Ipomoea/genetics/metabolism
Plant Leaves/metabolism/genetics/chemistry
*Gene Expression Regulation, Plant
Seeds/metabolism/genetics
Plant Proteins/genetics/metabolism

@article {pmid40686107,
year = {2025},
author = {Wang, EJ and Zhang, YL and Ma, XH and Gong, HQ and Xi, SY and Zhang, GS and Jin, L},
title = {[Research progress on interactions between medicinal plants and microorganisms].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {12},
pages = {3267-3280},
doi = {10.19540/j.cnki.cjcmm.20250314.103},
pmid = {40686107},
issn = {1001-5302},
mesh = {*Plants, Medicinal/microbiology/growth & development/metabolism ; *Bacteria/metabolism/genetics ; Symbiosis ; },
abstract = {The interactions between microorganisms and medicinal plants are crucial to the quality improvement of medicinal plants. Medicinal plants attract microorganisms to colonize by secreting specific compounds and provide niche and nutrient support for these microorganisms, with a symbiotic network formed. These microorganisms grow in the rhizosphere, phyllosphere, and endophytic tissues of plants and significantly improve the growth performance and medicinal component accumulation of medicinal plants by promoting nutrient uptake, enhancing disease resistance, and regulating the synthesis of secondary metabolites. Microorganisms are also widely used in the ecological planting of medicinal plants, and the growth conditions of medicinal plants are optimized by simulating the microbial effects in the natural environment. The interactions between microorganisms and medicinal plants not only significantly improve the yield and quality of medicinal plants but also enhance their geoherbalism, which is in line with the concept of green agriculture and eco-friendly development. This study reviewed the research results on the interactions between medicinal plants and microorganisms in recent years and focused on the analysis of the great potential of microorganisms in optimizing the growth environment of medicinal plants, regulating the accumulation of secondary metabolites, inducing systemic resistance, and promoting the ecological planting of medicinal plants. It provides a scientific basis for the research on the interactions between medicinal plants and microorganisms, the research and development of microbial agents, and the application of microorganisms in the ecological planting of medicinal plants and is of great significance for the quality improvement of medicinal plants and the green and sustainable development of TCM resources.},
}

*Plants, Medicinal/microbiology/growth & development/metabolism
*Bacteria/metabolism/genetics
Symbiosis

@article {pmid40684582,
year = {2025},
author = {Rajabifar, N and Alemi, MH and Rostami, A and Zarrintaj, P and Zare, Y and Munir, MT and Shahrousvand, M and Rhee, KY and Nazockdast, H},
title = {3D printing of hydrogel nanocomposites: A symbiotic union for advanced biomedical applications.},
journal = {Advances in colloid and interface science},
volume = {344},
number = {},
pages = {103602},
doi = {10.1016/j.cis.2025.103602},
pmid = {40684582},
issn = {1873-3727},
abstract = {Hydrogels have emerged as thriving materials for developing biomedical devices due to their biocompatibility and hydrophilic nature, encompassing various fields from biomedical engineering and pharmaceuticals to wound care and tissue scaffolding. Nevertheless, traditional hydrogels are beset with poor mechanical strength, limited controlled release of medicines, and irreversible chain breakage, all of which compromise their efficacy in practice. The desirable performance of hydrogels can be notably lifted upon incorporating nanomaterials, yielding tunable functions for devising next-generation biocompatible structures. Despite the alluring prospects offered by hydrogel nanocomposites, the processing of these materials is still in its infancy and remains full of challenges to produce personalized, tangible items. Herein, we endeavor to bridge the gap between hydrogel nanocomposites for biomedical applications with additive manufacturing processing, providing a useful guideline for comparing and selecting viable three-dimensional (3D) printing approaches. We review the background of synthesizing hydrogel nanocomposites along with the key concepts toward biomedical applications, featuring a survey on the recent reports on 3D printing of hydrogel nanocomposites for developing customized tissues, drug delivery, bioadhesives, wound dressing, and biosensors.},
}

@article {pmid40683892,
year = {2025},
author = {Zhao, L and Ji, CY and Murray, JD and Liu, CW},
title = {A legume cellulase required for rhizobial infection and colonization in root nodule symbiosis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6663},
pmid = {40683892},
issn = {2041-1723},
mesh = {*Symbiosis/physiology ; *Root Nodules, Plant/microbiology/enzymology ; *Cellulase/metabolism/genetics ; *Medicago truncatula/microbiology/enzymology/genetics ; *Rhizobium/physiology ; *Plant Proteins/metabolism/genetics ; Nitrogen Fixation ; Cell Wall/metabolism ; Mutation ; },
abstract = {In root nodule symbiosis, the accommodation of rhizobia in legumes necessitates extensive plant cell wall remodeling to build infection threads (ITs) for rhizobia travelling into nodules, and to subsequently release rhizobia from ITs to form nitrogen fixing symbiosomes. The molecular and cellular mechanisms underlying these processes are obscure. Here we report that Medicago truncatula Glycoside Hydrolase 9C2 (GH9C2) is required for both rhizobial infection and nodule colonization. The gh9c2-1 mutant exhibits incompetent nodules with disorganized ITs and defective rhizobial release, likely due to cellulose accumulation. GH9C2 localizes to IT wall and rhizobial release sites, and cellulase activity is indispensable for GH9C2 function. CBM49 domain of GH9C2 is required for rhizobial infection but not for rhizobial release. Furthermore, GH9C1and NPL act synergistically with GH9C2 in rhizobial infection. Our finding reveals transient IT-derived structures, the rhizobial release foci and uncovers a mechanism mediated by host cellulases for the symbiotic colonization by rhizobia.},
}

*Symbiosis/physiology
*Root Nodules, Plant/microbiology/enzymology
*Cellulase/metabolism/genetics
*Medicago truncatula/microbiology/enzymology/genetics
*Rhizobium/physiology
*Plant Proteins/metabolism/genetics
Nitrogen Fixation
Cell Wall/metabolism
Mutation

@article {pmid40683195,
year = {2025},
author = {Younis, C and Camp, EF and Raina, JB and Cresswell, T and Gissi, F},
title = {Effects of selenium on the model cnidarian Exaiptasia diaphana and its symbiotic algae.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {287},
number = {},
pages = {107495},
doi = {10.1016/j.aquatox.2025.107495},
pmid = {40683195},
issn = {1879-1514},
abstract = {Characterising toxicity thresholds for coral reefs is essential for understanding and safeguarding these ecosystems. Coral reefs are highly sensitive to environmental changes, including pollutants and increased trace element concentrations. Corals and other cnidarians form symbiotic associations with photosynthetic algae (Symbiodiniaceae) allowing for diverse nutrient acquisition methods and effective nutrient transformation and recycling between the host animal and their Symbiodiniaceae. Selenium (Se), an essential element, supports crucial physiological functions in marine taxa but it can become toxic at elevated concentrations. Currently, Se exposure thresholds for cnidarians and Symbiodiniaceae remain unknown. To assess the impact of high inorganic Se concentrations on cnidarians and Symbiodiniaceae, we conducted toxicity tests using the model sea anemone, Exaiptasia diaphana, exposing individuals to Se-enriched seawater using Na2SeO3 (76 - 1100 µg Se/L) for 96 h. Mortality occurred in the highest concentration of Se (1100 µg/L) for all replicates, but 100 % survival was recorded in all lower concentrations, including 570 µg/L. This latter concentration exceeded environmentally relevant levels, negating the need to acquire more refined mortality data. In addition, decreases in oral disk and reduced tentacle length at higher Se exposures indicated potential sublethal effects and physiological stress where E. diaphana exposed to concentrations ranging from 245- 570 µg/L decreasing in size by ∼15-20 %. These findings contribute to our understanding of cnidarian physiology and stress responses, highlighting the importance of trace elements in coral reef environments. This knowledge is crucial for developing effective management strategies to protect and preserve vital ecosystems in the face of environmental challenges.},
}

@article {pmid40682706,
year = {2025},
author = {Lin, PR and Deng, LJ and Zhang, HZ and Liu, L and Liu, TH and Lu, DC and Du, ZJ},
title = {Zhengella sedimenti sp. nov. and Phycobacter sedimenti sp. nov., two novel bacteria isolated from coastal sediment with genomic and metabolic analysis.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {117},
pmid = {40682706},
issn = {1572-9699},
support = {ZR2023QC197//the Science Foundation for Youths of Shandong Province/ ; 2022FY101100//the Science and Technology Fundamental Resources Investigation Program/ ; 92351301//the National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; China ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Genome, Bacterial ; Phospholipids/analysis ; Sequence Analysis, DNA ; Genomics ; Seawater/microbiology ; },
abstract = {In this study, two novel Gram-stain-negative bacterial strains, K97[T] and ZM62[T], were isolated from sediment samples collected along the coast of Weihai, China, and described using polyphasic taxonomic techniques. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain K97[T] exhibited the highest sequence similarity (98.34%) with Phycobacter azelaicus F10[T] within the genus Phycobacter, followed by Pseudooceanicola marinus AZO-C[T] (97.14%) and Phaeobacter italicus LMG24365[T] (96.85%). Strain ZM62[T] exhibited the highest sequence similarity (98.53%) with Zhengella mangrovi X9-2-2[T] within the genus Zhengella, followed by Phyllobacterium myrsinacearum NBRC 100019[T] (96.49%) and Oricola thermophila MEBiC13590[T] (96.35%). The respiratory quinone was Q-10 for both strains. The major fatty acid in both strains K97[T] and ZM62[T] is Summed Feature 8 (C18:1ω6c/C18:1ω7c). The main polar lipids for strain K97[T] included diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), while for strain ZM62[T], the main polar lipids included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). Based on the polyphasic taxonomic data, strain K97[T] is proposed as a novel species within the genus Phycobacter, for which the name Phycobacter sedimenti is proposed, and the type strain is K97[T] (= KCTC 8365[T] = MCCC 1H01460[T]). Strain ZM62[T] is proposed as a novel species within the genus Zhengella, for which the name Zhengella sedimenti is proposed, and the type strain is ZM62[T] (= KCTC 8813[T] = MCCC 1H01495[T]). Additionally, genomic and metabolic analyses revealed that the genus Phycobacter possesses DMSP synthesis and metabolism genes and a complete CMP-KDO pathway, indicating potential symbiosis with algae. Metabolic analysis of strain ZM62[T] indicates its potential role in the degradation of xenobiotic compounds, supported by the presence of annotated pathways for aminobenzoate (ko00627) and toluene (ko00623) degradation.},
}

*Geologic Sediments/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Fatty Acids/analysis
China
DNA, Bacterial/genetics
Base Composition
Bacterial Typing Techniques
Genome, Bacterial
Phospholipids/analysis
Sequence Analysis, DNA
Genomics
Seawater/microbiology

@article {pmid40682559,
year = {2025},
author = {Yuan, Z and Zhang, Y and Zhang, X and Wang, L and Ling, G and Zhang, P},
title = {Microalgae and Bioactive Substances Therein: Unveiling Therapeutic Promise against Inflammatory Bowel Disease.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04341},
pmid = {40682559},
issn = {1520-5118},
abstract = {Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), represents a chronic and recurrent inflammatory ailment of the intestines. It strikes a harsh blow to patients' quality of life. Currently, there is a dearth of effective treatments for IBD, which causes patients to endure significant distress. Thus, it is of utmost urgency to formulate a treatment plan for IBD that is safe, effective, and affordable. In recent years, natural products have increasingly become a new strategy to alleviate IBD due to their safety and effectiveness. Among many natural products, microalgae have attracted extensive attention from researchers, owing to their abundance in a diverse range of bioactive constituents, such as polysaccharides, phycocyanin, and carotenoids. Microalgae and the bioactive compounds within them can effectively alleviate IBD. Their potential application value is discussed as they are expected to be new strategies concerning the prevention and treatment of this disease. In retrospect, we start from the pathogenesis of IBD, and combining with the deep therapeutic mechanism of microalgae-derived active ingredients, this article expounds on its broad prospects in the treatment of IBD. Meanwhile, the positive effects of microalgae as biological carriers and symbiotic components on the treatment of IBD were summarized.},
}

@article {pmid40682492,
year = {2025},
author = {Milasan, LH and Finta, O},
title = {"Rising Like Phoenix From the Ashes": An Arts-Based Qualitative Study of Mental Health Resilience and Recovery in Romania.},
journal = {Qualitative health research},
volume = {},
number = {},
pages = {10497323251355120},
doi = {10.1177/10497323251355120},
pmid = {40682492},
issn = {1049-7323},
abstract = {The philosophy underpinning mental health care has undergone a shift from a biomedical, deficit model to a recovery-oriented, strengths-based approach prioritizing individual abilities, experiences, and skills. Within this context, it is paramount to understand how resilience is experienced by people living with mental distress, and the role it plays in the recovery process. This arts-based qualitative study aims to explore the meanings and experiences of resilience as part of the recovery journey of nine mental health service users from a community day center in Romania. In Romania, the mental health system and research into mental distress and recovery have been traditionally guided by a biomedical approach. This is the first study conducted from the perspective of people living with mental distress in Romania, revealing the experiential and conceptual complexities of resilience in their recovery. Thematic analysis of data generated through ten creative workshops, a focus group, and art-elicited semi-structured interviews revealed four key themes of resilience intertwined with participants' experiences of recovery: re(dis)covering the authentic self, symbiosis with the day center, navigating conflicts (with self, society, and the psychiatric system), and leaving the past behind. The insights from participants' verbal contributions triangulated with their artwork provided a deeper understanding of resilience within the cultural context of Romania. The findings add to an increasing body of evidence that informs the reformation of mental health practices in line with the perspectives on resilience held by people experiencing mental distress.},
}

@article {pmid40682111,
year = {2025},
author = {Chen, Y and Jiang, W and Wu, P and Liu, Y and Ma, Y and Ren, H and Jin, X and Jiang, J and Zhang, R and Li, H and Feng, L and Zhou, X},
title = {Probiotic efficacy of Cetobacterium somerae (CGMCC No. 28843): promoting intestinal digestion, absorption, and structural integrity in juvenile grass carp (Ctenopharyngodon idella).},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {103},
pmid = {40682111},
issn = {1674-9782},
abstract = {BACKGROUND: Cetobacterium somerae, a symbiotic microorganism resident in various fish intestines, is recognized for its beneficial effects on fish gut health. However, the mechanisms underlying the effects of C. somerae on gut health remain unclear. In this experiment, we investigated the influence of C. somerae (CGMCC No.28843) on the growth performance, intestinal digestive and absorptive capacity, and intestinal structural integrity of juvenile grass carp (Ctenopharyngodon idella) and explored its potential mechanisms.

METHODS: A cohort of 2,160 juvenile grass carp with an initial mean body weight of 11.30 ± 0.01 g were randomly allocated into 6 treatment groups, each comprising 6 replicates (60 fish per replicate). The experimental diets were supplemented with C. somerae at graded levels of 0.00 (control), 0.68 × 10⁹, 1.35 × 10⁹, 2.04 × 10⁹, 2.70 × 10⁹, and 3.40 × 10⁹ cells/kg feed. Following a 10-week experimental period, biological samples were collected for subsequent analyses.

RESULTS: Dietary supplementation with C. somerae at 1.35 × 10⁹ cells/kg significantly enhanced growth performance, intestinal development, and nutrient retention rate in juvenile grass carp (P < 0.05). The treatment resulted in increased intestinal acetic acid concentration and enhanced activities of digestive enzymes and brush border enzymes (P < 0.05). Furthermore, it reduced intestinal permeability (P < 0.05), preserved tight junctions (TJ) ultrastructural integrity, and increased the expression of TJ and adherens junctions (AJ) biomarkers at both protein and transcriptional levels (P < 0.05). Mechanistically, these effects may be correlated with enhanced antioxidant capacity and coordinated modulation of the RhoA/ROCK, Sirt1, and PI3K/AKT signaling pathways. The appropriate supplementation levels, based on weight gain rate, feed conversion ratio, the activity of serum diamine oxidase and the content of lipopolysaccharide, were 1.27 × 10⁹, 1.27 × 10⁹, 1.34 × 10⁹ and 1.34 × 10⁹ cells/kg, respectively.

CONCLUSIONS: C. somerae improved intestinal digestive and absorptive capacity of juvenile grass carp, maintained intestinal structural integrity, and thus promoted their growth and development. This work demonstrates the potential of C. somerae as a probiotic for aquatic animals and provides a theoretical basis for its utilization in aquaculture.},
}

@article {pmid40681981,
year = {2025},
author = {El-Sharkawy, HHA and Rashad, YM and El-Blasy, SSA and Amin, BH and Youssef, MAA and Hafez, M and Abd-ElGawad, A and Bourouah, M and Elsherbiny, EA and Yousef, SA},
title = {Mycorrhizal symbiosis and application of vitamin B3-treated Trichoderma Harzianum HE24 additively trigger immunity responses in faba bean plants against Rhizoctonia root rot and promote the plant growth and yield.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {926},
pmid = {40681981},
issn = {1471-2229},
abstract = {BACKGROUND: Faba bean is a valuable legume crop, known for its high nutritional value and nitrogen fixing ability. Rhizoctonia root rot of faba bean, caused by Rhizoctonia solani, severely affects the plant growth and yield. This study aimed to evaluate the effect of symbiosis with arbuscular mycorrhizal fungi (AMF) and application of vitamin B3-treated Trichoderma harzianum HE24 on plant immune responses against Rhizoctonia root rot under greenhouse conditions.

RESULTS: Results revealed that symbiosis with AMF and the application of vitamin B3-treated T. harzianum HE24 significantly upregulated the defense-related genes CHI II (50.2-fold), PAL1 (13.3-fold), and HQT (37.0-fold). Additionally, this combined treatment led to an increment in the enzymatic activity of peroxidase and polyphenol oxidase recording 23.7 and 14.6-unit min[−1]g[−1] fresh weight, respectivly. Furthermore, the phenolic content in faba bean plants was enhanced (1402.3 mg/g fresh weight) suggesting a strong activation of the plant’s biochemical defense mechanisms and metabolic activities. Rhizoctonia root rot severity in faba bean plants was reduced by 80.4% following this treatment. Moreover, the results demonstrated that AMF symbiosis notably improved plant growth, photosynthetic content, and yield, compared to the infected control, leading to enhanced overall plant performance and disease resistance.

CONCLUSIONS: These findings suggest that the additive interaction between AMF and vitamin B3-treated T. harzianum HE24 provides an effective, eco-friendly alternative for managing root rot of faba bean.},
}

@article {pmid40681704,
year = {2025},
author = {Liu, S and Chu, H and Xie, Y and Wu, F and Mu, F and Wei, J and Ni, N and Wang, C and Zhang, J and Chen, M and Li, J and Yu, F and Fu, H and Wang, S and Tian, C and Wang, Z and Gao, YQ},
title = {Assisting and accelerating NMR assignment with restrained structure prediction.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1067},
pmid = {40681704},
issn = {2399-3642},
mesh = {*Proteins/chemistry ; Protein Conformation ; *Nuclear Magnetic Resonance, Biomolecular/methods ; Magnetic Resonance Spectroscopy/methods ; Protein Folding ; Models, Molecular ; },
abstract = {Accurate dynamic protein structures are essential for drug design. NMR experiments can detect protein structures and potential dynamics, but the spectrum assignment and structure determination requires expertise and is time-consuming, while deep-learning-based structure predictions may be inconsistent with experimental observations. A symbiosis between experiments and AI methods is therefore essential for solving such problems. Here, we developed a Restraint Assisted Structure Predictor (RASP) model and an iterative Folding Assisted peak ASsignmenT (FAAST) pipeline directly leveraging experimental information to improve the AI-assisted structure prediction and facilitate experimental data analysis in an integrative way. The RASP model improves structure prediction, especially for multi-domain and few-MSA proteins. The FAAST pipeline for NMR NOESY analysis reduces the time consumption to hours and yields high quality structure ensemble. Both methods show high consistency between predicted structures and restraints, provided or iteratively assigned. This strategy can be expanded to other types of sparse experimental information in structure prediction.},
}

*Proteins/chemistry
Protein Conformation
*Nuclear Magnetic Resonance, Biomolecular/methods
Magnetic Resonance Spectroscopy/methods
Protein Folding
Models, Molecular

@article {pmid40681031,
year = {2025},
author = {Lu, J and Zhang, S and Wu, S and Gao, C},
title = {l-malic acid: A multifunctional metabolite at the crossroads of redox signaling, microbial symbiosis, and therapeutic innovation.},
journal = {Archives of biochemistry and biophysics},
volume = {772},
number = {},
pages = {110554},
doi = {10.1016/j.abb.2025.110554},
pmid = {40681031},
issn = {1096-0384},
abstract = {l-Malic acid, a crucial tricarboxylic acid (TCA) cycle intermediate and gut metabolite, has transcended its traditional role as a mere metabolic substrate. It is now recognized as a multifunctional signaling molecule intricately involved in energy metabolism, redox balance, cellular signaling, and host-microbiota crosstalk. l-Malic acid act both as nutrients and as messenger molecules and can signal to distant organs in the body to shape host pathophysiology. Accumulating evidence demonstrates that dysregulation in the physiological concentration of l-Malic acid within the host is closely associated with various diseases. Consequently, supplementation of l-Malic acid within an appropriate range holds significant potential for the prevention and treatment of certain diseases. This review discusses recent groundbreaking advances elucidating the dual roles of l-malic acid as both a metabolic modulator and a therapeutic carrier. We critically evaluate its emerging potential in precision medicine, particularly for cardiovascular diseases, intestinal disorders, and skeletal muscle pathologies, highlighting the mechanistic links and translational opportunities. We argue that targeting l-malate pathways represents a promising, yet underexplored, therapeutic frontier.},
}

@article {pmid40638828,
year = {2025},
author = {Webster, AL and Polak, M},
title = {Priming for protection: inducible attachment-resistance to ectoparasitic mites in Drosophila.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0031182025100437},
pmid = {40638828},
issn = {1469-8161},
abstract = {Ectoparasites are ubiquitous and are often harmful to host fitness. Whereas protective responses to ectoparasitism in vertebrate hosts are well documented, our understanding of such defences in invertebrates remains limited. Here, we examined attachment-resistance in adult Drosophila to their naturally co-occurring ectoparasitic mites, Gamasodes pachysetis (Parasitidae). Significant differences in mite attachment duration were documented among 6 species of Drosophila, providing evidence for interspecific differentiation in attachment-resistance. Experiments with D. malerkotliana, a species exhibiting a relatively high rate of mite detachment, revealed that pre-infesting flies significantly reduced mite attachment duration compared to naïve controls, indicating a priming effect. In contrast, a reduction in attachment duration was not observed in D. malerkotliana after experimentally wounding the abdominal cuticle. These results suggest that the priming effect is not simply a response to cuticle damage, and that its activation may depend on mite-specific factors. Eight genes were individually tested for their effects on the rate of mite detachment from adult flies by deploying the GAL4-UAS gene knockdown system in D. melanogaster. Knockdown of heat shock protein 70Ba (Hsp70Ba) and prophenoloxidase 2 (PPO2), which underlie general stress and melanization responses, respectively, significantly prolonged mite attachment duration, implicating their involvement in host attachment-resistance to mites. Together the results support the existence of inducible protective mechanisms mediating parasitism by mites in a naturally occurring invertebrate host-ectoparasite symbiosis.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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