Environmental Microbiome最新文献

{"title":"Salinity-adapted and core microbiota along the soil salinity gradients encircling the Tarim Basin.","authors":"Xiaojing Liu, Qiong Jia, Qiyong Tang, Yanpeng Ding, Zhidong Zhang, Meiying Gu, Wei Huang, Ning Wang, Lijuan Zhang, Jing Zhu","doi":"10.1186/s40793-026-00918-3","DOIUrl":"10.1186/s40793-026-00918-3","url":null,"abstract":"<p><strong>Background: </strong>Soil salinization affects nearly one-tenth of global drylands and imposes strong environmental filters on microbial communities. The Tarim Basin in Xinjiang, China, is one of the world's largest inland basins and an extreme saline-arid ecosystem, yet a basin-scale understanding of its microbiota remains lacking. In this study, we collected 132 soil samples along a salinity gradient spanning more than 3,000 km encircling the Tarim Basin. By combining amplicon sequencing with measurements of soil physicochemical properties, we aimed to unravel the salinity-adapted microbiota and core microbial taxa characteristic of this extreme environment.</p><p><strong>Results: </strong>Our results showed that bacterial communities, rather than fungal communities, were strongly shaped by soil salinity. Extremely saline soils exhibited reduced bacterial diversity and were enriched in halophilic and halotolerant taxa, including Natronomonas, Salinimicrobium, Stenotrophomonas, Salinibacter, Halorussus, and Halomicrobium. In contrast, taxa such as Arthrobacter, Rubrobacter, Rubellimicrobium, and Fusarium declined with increasing salinity. Soil cation concentrations (Na⁺, K⁺, Ca²⁺, Mg²⁺), major anions (Cl^-, SO₄^2-), and electrical conductivity all increased significantly along the salinity gradient. Despite this strong environmental filtering, we identified a set of potential core microbiota consistently present across all soils, dominated by Halomonas, Salinimicrobium, Natronomonas, Rubrobacter, and members of the Palleronia-Pseudomaribius group. Their persistent occurrence across the basin suggests that these taxa play key roles in sustaining ecosystem functions within the extreme saline-arid environments of the Tarim Basin.</p><p><strong>Conclusions: </strong>Our basin-scale analysis reveals that soil salinity significantly contributes to microbial community assembly in the Tarim Basin, selecting for specialized halophilic and halotolerant taxa while reducing overall bacterial diversity. The discovery of core microbiota with known salt-adaptation mechanisms highlights the presence of a stable microbial backbone across heterogeneous saline landscapes. These findings provide new ecological insights into how extreme salinity shapes microbiome structure and identify candidate microbial groups potentially contributing to ecosystem stability and plant stress resilience in arid saline environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomics identifies distinct functional and taxonomic profiles between freshwaters and associated sediments in alpine habitats.","authors":"Anita Gattei, Sara Vettorazzo, Massimo Pindo, Nico Salmaso, Paolo Manghi, Stefano Larsen, Claudio Donati","doi":"10.1186/s40793-026-00931-6","DOIUrl":"https://doi.org/10.1186/s40793-026-00931-6","url":null,"abstract":"<p><strong>Background: </strong>Alpine freshwater habitats are biodiversity hotspots, home to uniquely adapted microbial communities. However, our understanding of how taxonomic composition and metabolic potential of microbial communities varies across habitat type and physiography remains limited.</p><p><strong>Results: </strong>Using metagenomic sequencing, we examined microbial diversity and functions in sediment and water habitats across a physiographic gradient, including deep and shallow lakes, pasture ponds, ponds and peat bogs. Overall, sediments supported more diverse and even microbial communities. Conversely, waters displayed higher heterogeneity across the physiographic gradient in both taxonomic and functional composition. Notably, water communities from small water bodies, especially peat bogs and ponds, showed comparable diversity to their respective sediment communities, with higher taxonomic richness than aquatic communities from larger water bodies. Sediment microbial communities showed higher functional potential for nitrogen and methane metabolism, a pattern related to the likely anoxic conditions. By contrast, water bodies favored higher potential for carbohydrate metabolism, carbon oxidation and photosynthesis. Lastly, we recovered 496 bacterial and archaeal metagenome-assembled genomes and found that 73% could not be assigned at the species level.</p><p><strong>Conclusions: </strong>Our findings shed new light on the microbial diversity and metabolic potential of alpine freshwater ecosystems, highlighting the vast and unknown diversity harbored by these fragile alpine ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149225264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Different synthetic chemical dispersants elicit distinct bacterial community responses to crude oil.","authors":"Ciara Keating, Laura Duran Suja, Stephen Summers, Ian M Head, Umer Z Ijaz, Tony Gutierrez","doi":"10.1186/s40793-026-00932-5","DOIUrl":"https://doi.org/10.1186/s40793-026-00932-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Dispersants are commonly used worldwide as a primary response tool to treat oil spills at sea, yet their use is debated due to their toxicological effects and potential to affect oil biodegradation rates. We examined the effect of three globally stockpiled synthetic chemical dispersants (Superdispersant 25, Slickgone EW, Slickgone NS) on the microbial response to crude oil and its biodegradation in a subarctic marine environment in two experiments using seawater sampled from the subarctic Faroe-Shetland Channel (FSC) in 2015 and 2017 and analysed by 16 S rRNA gene amplicon sequencing.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Across both years, communities were dominated by known hydrocarbon-degrading bacteria, including Alcanivorax, Alteromonas, and Pseudoalteromonas. In the 2015 experiment, Superdispersant 25 enriched for Dokdonia, Thalassospira, and Roseobacter, genera with demonstrated alkane and PAH degradation pathways. In the 2017 experiment, Slickgone EW and NS selected Marinomonas, Colwellia, Psychromonas, and Alcanivorax. Samples without dispersant also contained hydrocarbon degraders, however, the community composition was altered. In 2017, we quantified hydrocarbon degradation using GC-FID/MS for aliphatic and aromatic hydrocarbons respectively. Hydrocarbon biomarker ratios showed n-alkane depletion (Pr/C17 and Ph/C18 ratios increased 3-12 fold) in dispersant treatments. Selective weathering was evident in all treatments. 9MP/1MP ratios indicated limited or variable effects on aromatic hydrocarbon biodegradation, particularly in the presence of dispersant. We integrated aromatic hydrocarbon concentrations with microbial community data using DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). Several taxa were negatively correlated to specific aromatic hydrocarbons - i.e. they increased when the hydrocarbon was reduced suggesting the hydrocarbons may have served as a carbon source or the taxa were responding to hydrocarbon depletion. Taxa included Aquibacter, Hyphomonas, Thalassospira, Alteromonas, Sphingorhabdus, and Paraperlucidibaca. Marine oil snow (MOS) formed in all oil-amended treatments and showed high microbial colonisation, whereas marine dispersant snow showed little colonisation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study provides evidence that different dispersants affect different microbial responses to crude oil contamination, including the enrichment of key oil-degrading bacterial taxa. However, this did not correlate with enhanced aromatic hydrocarbon degradation. MOS formation with high microbial colonisation suggests natural aggregation processes may provide an effective biodegradation pathway. These findings raise questions about the functional benefit of synthetic chemical dispersants and highlight that the marine environment naturally harbours hydrocarbon-degrading microbial communities with the potential to respond to oil spills.&lt;","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148550696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.","authors":"Alexandra K Stiffler, Natascha S Varona, Bailey A Wallace, Cynthia B Silveira","doi":"10.1186/s40793-026-00925-4","DOIUrl":"10.1186/s40793-026-00925-4","url":null,"abstract":"<p><strong>Background: </strong>Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.</p><p><strong>Results: </strong>Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.</p><p><strong>Conclusion: </strong>Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148473616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surfactin-like lipopeptides contribute to interference competition of Bacillus velezensis against the marine Flavobacteriaceae in phycosphere.","authors":"Runlin Cai, Hao Feng, Yang Liu, Shuyi Liang, Danhong Wen, Zhimu Xie, Yongliang Gan, Guanjing Cai, Hui Wang","doi":"10.1186/s40793-026-00937-0","DOIUrl":"10.1186/s40793-026-00937-0","url":null,"abstract":"<p><strong>Background: </strong>The phycosphere is a nutrient-rich microenvironment surrounding phytoplankton cells and serves as a hotspot for microbial interactions by releasing phytoplankton-derived organic molecules to dynamically attract and support the colonization of heterotrophic bacteria. Although the taxonomic composition, metabolic profiles, and host-microbe interactions of phycosphere bacterial communities have been extensively characterized, the underlying mechanisms driving competition among these co-existing bacterial taxa remain poorly understood.</p><p><strong>Results: </strong>In this study, we demonstrate that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species. Through an integrative approach combining genetics and metabolomics, we show that the antagonistic behavior of strain SPE2 is primarily mediated by the production of bioactive secondary metabolites. Activity-guided purification further leads to the identification of two antibacterial surfactin-like lipopeptides as key exometabolites responsible for these inhibitory effects. Mechanistically, these lipopeptides exert their antibacterial activity against Flavobacteriaceae species by disrupting the integrity of bacterial cell membranes.</p><p><strong>Conclusions: </strong>Our findings reveal surfactin-like lipopeptides as key molecular mediators of bacterial interference competition, conferring a competitive strategy for Bacillus species to secure persistence in the phycosphere. Moreover, this work underscores phycosphere as a largely untapped ecological niche for discovering novel bioactive compounds with potential applications in pharmaceutical and biotechnological fields.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing the understanding of environmental microbiomes through topic modeling: a quantitative and qualitative analysis.","authors":"Anna S Kujat, Christiane Hassenrück, Stefan Lüdtke, Matthias Labrenz, Theodor Sperlea","doi":"10.1186/s40793-026-00927-2","DOIUrl":"10.1186/s40793-026-00927-2","url":null,"abstract":"<p><strong>Background: </strong>Understanding ecosystem dynamics is essential for assessing ecosystem health, yet remains challenging due to complex biotic and abiotic interactions. Microbial communities are valuable indicators of environmental change, but the high dimensionality of microbiome data requires advanced analytical methods. This study explores the use of topic modeling (TM), an unsupervised machine learning approach initially designed for text analysis, to analyze microbiome data from the dynamic Warnow Estuary on the southern Baltic Sea coast.</p><p><strong>Results: </strong>We applied TM to estuarine microbiome data and compared its performance to traditional dimensionality reduction methods, Principal Component Analysis (PCA) and Principal Coordinate Analysis (PCoA). Quantitative results indicate that TM performs comparably to conventional approaches in preserving ecological and functional information, and in certain aspects even superior. In addition, we show qualitatively that Non-Negative Matrix Factorization (NNMF), a TM method, captures latent patterns in the data providing an interpretable perspective on the microbiome. In this exploratory framework, NNMF suggested five distinct sub-communities within the estuary that appear to follow a seasonal succession influenced by freshwater inflow. These sub-communities were associated with specific ranges of salinity and temperature and showed distinct taxonomic profiles, with shared characteristics across the estuarine system.</p><p><strong>Conclusions: </strong>Our findings suggest that TM is a useful tool for exploring complex environmental microbiome datasets, offering a complementary perspective that can provide additional ecological insights. TM's ability to highlight coherent microbial community patterns indicates its promise for supporting environmental monitoring and informing targeted ecosystem management in dynamic habitats, though further studies are needed to fully assess its applicability.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts.","authors":"Lu Gan, Zhiyong Yang, Yuan Zhang, Shiping Wang, Fandong Meng, Yongwen Liu, Tsechoe Dorji","doi":"10.1186/s40793-026-00928-1","DOIUrl":"10.1186/s40793-026-00928-1","url":null,"abstract":"<p><strong>Background: </strong>The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear.</p><p><strong>Results: </strong>A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway.</p><p><strong>Conclusions: </strong>Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148449975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the role of biotic and abiotic factors in hardwood tree development in the Central Hardwood Region (CHR).","authors":"Shaneka S Lawson, Juan P Frene, Niall D Lue Sue","doi":"10.1186/s40793-026-00935-2","DOIUrl":"10.1186/s40793-026-00935-2","url":null,"abstract":"<p><strong>Background: </strong>Hardwood tree growth and development are influenced by the interplay between soil microbiota and tree physiology. Though unclear mechanistically, microbial community composition is associated with tree growth. We investigated how soil chemistry and prokaryotic communities impacted Quercus rubra (red oak) and Juglans nigra (black walnut) growth across three plantations in Indiana and Michigan. Trees exhibiting above- (high-performing or healthy) or below-average (low-performing or poor) growth rates were compared. Correlations with soil properties and microbial composition (16 S rRNA sequencing) were assessed to identify factors associated with variations in mean dominant tree height and diameter at breast height (DBH).</p><p><strong>Results: </strong>Tree growth differed by site, species, and performance class. High-performing trees showed 25-40% higher AGR and 10-20% higher RGR across study sites. Larger trees occurred in Southern and Western Indiana than in Michigan. J. nigra outperformed Q. rubra in Indiana, and the reverse occurred in Michigan. DH and DBH were strongly correlated (R² = 0.8046, P < 0.001), and soil pH differed by species. Organic C, N, and CEC differed among species, but not among sites or performance class. Prokaryotic composition varied by species and site and explained 10.7%, 9.4%, and 7.6% of the variance. Microbial community structure was linked to DBH in J. nigra (r = 0.14, P = 0.002) and Q. rubra (r = 0.078, P = 0.028), and height only in J. nigra (r = 0.20, P = 0.001). Differential abundance analysis identified 88 and 122 growth-associated ASVs in J. nigra and Q. rubra, respectively. Random Forest models explained that soil texture (sand and silt) and microbial taxa (Bacillus, Arthrobacter, GP1, GP3) are key elements for growth.</p><p><strong>Conclusions: </strong>Hardwood growth is more strongly associated with soil texture and specific microbial taxa than with overall microbial diversity. These species-dependent relationships suggest that microbial indicators of growth performance differ among hardwood species. Overall, the results improve our understanding of plant, soil, and microbe interactions and support using microbial indicators to monitor and improve hardwood plantation performance. Identifying microbial indicators associated with superior growth could inform reforestation and silvicultural practices in temperate hardwood ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148449941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disentangling the importance of microbiological and physico-chemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestation.","authors":"Tamera Taylor, Getahun Benti, Marcio F A Leite, Luisa M Arias-Giraldo, Desalegn W Etalo, Sewunet Abera, Lorenzo Lombard, Jose G Maciá-Vicente, Stefan Sanow, Dominika Rybka, Thomas Mostert, Einar Martinez de la Parte, Daniel Legesse, Urgesa Tsega Tulu, Jiregna Daksa, Roy van Doorn, Raycenne Rosa Leite, Taye Tessema, Pedro W Crous, Dorota Kawa, Eiko E Kuramae, Jos M Raaijmakers, Siobhan M Brady","doi":"10.1186/s40793-026-00926-3","DOIUrl":"10.1186/s40793-026-00926-3","url":null,"abstract":"<p><strong>Background: </strong>Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yield in sub-Saharan Africa. Recent studies highlighted the soil microbiome's potential to suppress Striga through interference with specific stages in its life cycle.</p><p><strong>Results: </strong>Statistical analyses of data collected from 48 Ethiopian sorghum field soils sampled across a > 1000-km-transect revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga occurrence in the field. Striga infestation of sorghum and seedbank levels were negatively correlated with potassium and sulfur soil content and positively correlated with calcium and magnesium nutrient profile proportions. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial composition even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora, which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.</p><p><strong>Conclusions: </strong>This study highlights the complexity of soil-microbiome-Striga interactions and the potential for observational studies to reveal candidates for biological control of Striga.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13397753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148438505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting the seed microbiome using phylogeny-driven machine learning.","authors":"Julia Herbinger, Dinesh Kumar Ramakrishnan, Jannik Reißfelder, Majharulislam Babor, Marina Höhne, Ahmed Abdelfattah","doi":"10.1186/s40793-026-00936-1","DOIUrl":"10.1186/s40793-026-00936-1","url":null,"abstract":"<p><strong>Background: </strong>The composition of the seed-associated bacterial microbiome can reflect host evolutionary relationships, a pattern consistent with phylosymbiosis. While machine learning offers new opportunities to predict microbial community composition, existing models often require prior microbial profiles or environmental variables, limiting their application to unsampled hosts. Here, we tested whether plant nuclear internal transcribed spacer (ITS) sequences, used as a marker of host relatedness, can predict species-level seed-associated bacterial communities using 16S rRNA data from 61 plant species.</p><p><strong>Results: </strong>We introduced customized machine learning models that use sequence-based Hamming distances to capture plant host relatedness. Among the tested models, the Hamming Distance-based k-Nearest Neighbor model (HD-KNN) achieved the highest overall predictive accuracy, yielding an average Jensen-Shannon divergence (JSD) of 0.276 between observed and predicted microbiome profiles. HD-KNN performed particularly well within densely sampled host groups, including Brassicaceae and Poaceae, where closely related reference species were available. In contrast, Hamming Distance-based Gaussian Process Regression (HD-GPR) showed slightly better performance for phylogenetically isolated species, suggesting that model performance depends on host representation within the training dataset.</p><p><strong>Conclusions: </strong>Our framework demonstrates that plant nuclear ITS-derived host relatedness carries a partial predictive signal for seed-associated bacterial microbiome composition. These results provide a foundation for low-input predictive modelling of seed-associated bacteria and may help prioritise microbiome predictions for unsampled plant species when closely related reference species are available. However, our conclusions are strictly limited to seed-associated bacterial communities and should not be directly generalized to fungal communities or other plant compartments, such as the rhizosphere or phyllosphere, which may be shaped by different environmental filtering mechanisms.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13366936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148431078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}