ISME communicationsPub Date : 2026-08-17eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag224
{"title":"Correction to: Intracellular vesicle-mediated biomineralization of arsenic and barium by a sponge symbiotic bacterium.","authors":"","doi":"10.1093/ismeco/ycag224","DOIUrl":"https://doi.org/10.1093/ismeco/ycag224","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycag039.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag224"},"PeriodicalIF":6.4,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13479251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-13eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag230
Knut Rudi, Sanna Majaneva, Jessica Louise Ray, Maud Sundt, Julie Martin, Inga Leena Angell, Stian Nylund, Gro Harlaug Refseth, Nigel Keeley, Lars-Gustav Snipen
{"title":"Contrasting associations between microbiota respiratory strategies and seafloor macrofauna.","authors":"Knut Rudi, Sanna Majaneva, Jessica Louise Ray, Maud Sundt, Julie Martin, Inga Leena Angell, Stian Nylund, Gro Harlaug Refseth, Nigel Keeley, Lars-Gustav Snipen","doi":"10.1093/ismeco/ycag230","DOIUrl":"10.1093/ismeco/ycag230","url":null,"abstract":"<p><p>Microbe-macrofauna associations are central to coastal benthic ecosystems, yet the microbial functions that underpin these remain poorly understood. To address functional microbe-macrofauna associations, we analyzed 245 seafloor samples from Norwegian and Icelandic coastal zones, encompassing 1204 macrofaunal taxa, 121 543 zero-radius operational taxonomic units, and 302 high-quality metagenome-assembled genomes (MAGs). We first analyzed potential confounding factors and found that macrofauna showed the strongest association with a north-south geographic gradient, while overall there was a concordance for metadata associations. We found that macrofaunal assemblages were positively correlated with either a Bacteroidota-enriched cluster of MAGs (\"BA\"; <i>n</i> = 178 MAGs) or a cluster enriched in Actinomycetota and Pseudomonadota (\"AP\"; <i>n</i> = 124 MAGs). Functionally, the AP cluster was enriched in oxidases, cytochrome c-based respiratory processes, and fatty-acid β-oxidation. In contrast, the BA cluster showed enrichment in hydrolases, polysaccharide-degradation functions, and microaerobic/anaerobic respiration via cytochrome bd. Macrofaunal taxa associated with BA tended to have higher tolerance values for anthropogenic disturbance than those associated with AP, although this association was weak. Taken together, these results identify contrasting microbial respiratory strategies that co-vary with macrofaunal assemblages, while further experimental work is required to establish directionality and mechanism.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag230"},"PeriodicalIF":6.4,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13590888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-08eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag228
Carly E Karrick, Alex J Veglia, Sonora Meiling, Kerry Maxwell, Lindsay K Huebner, Daniel M Holstein, Laura Mydlarz, Marilyn Brandt, Amy Apprill, Erinn M Muller, Adrienne M S Correa
{"title":"Key coral symbiont lineages (family Symbiodiniaceae) are differentially associated with stony coral tissue loss disease.","authors":"Carly E Karrick, Alex J Veglia, Sonora Meiling, Kerry Maxwell, Lindsay K Huebner, Daniel M Holstein, Laura Mydlarz, Marilyn Brandt, Amy Apprill, Erinn M Muller, Adrienne M S Correa","doi":"10.1093/ismeco/ycag228","DOIUrl":"10.1093/ismeco/ycag228","url":null,"abstract":"<p><p>Stony coral tissue loss disease (SCTLD) has caused unprecedented coral mortality across the Caribbean, and its etiology remains unresolved. SCTLD affects >30 coral species that differ in their associations with dinoflagellate endosymbionts (family Symbiodiniaceae), and symbiont lineage-level dynamics may underlie variation in holobiont disease response. We analyzed 491 apparently healthy and SCTLD-affected corals in Florida (USA) and the United States Virgin Islands, representing 9 coral species sampled <i>in situ</i> or during an SCTLD transmission experiment. Based on the internal transcribed spacer-2 (ITS-2) region of rDNA, we identified 114 Symbiodiniaceae ITS-2 type profiles spanning 6 genera. Symbiodiniaceae composition varied significantly by coral species, disease susceptibility group, tissue health state, and region. In the corals <i>Orbicella annularis</i> and <i>Colpophyllia natans</i>, lesion-adjacent tissues had enriched relative abundance of a <i>Durusdinium</i> lineage, whereas <i>Symbiodinium</i> and <i>Cladocopium</i> lineages were relatively more abundant in apparently healthy tissues. Accounting for biogeography and host identity, our results suggest that in corals harboring multiple Symbiodiniaceae lineages, more susceptible lineages are lost first, leaving relatively resistant lineages in lesion-adjacent tissue until sloughing occurs. These findings indicate SCTLD acts as a selective filter on coral symbiont assemblages. Our results provide the first multi-species, multi-region evidence of fine-scale associations between Symbiodiniaceae lineages and SCTLD, establishing a framework for testing lineage-specific disease susceptibility in future experiments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag228"},"PeriodicalIF":6.4,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13590891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-08eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag219
Minjie Fu, Yeojoo Yoon, Haeun Cho, Piotr G Jablonski, Sang-Im Lee, Jae Chun Choe
{"title":"Significant impact of threshold adjustments on microbiome characterization following Nanopore sequencing.","authors":"Minjie Fu, Yeojoo Yoon, Haeun Cho, Piotr G Jablonski, Sang-Im Lee, Jae Chun Choe","doi":"10.1093/ismeco/ycag219","DOIUrl":"10.1093/ismeco/ycag219","url":null,"abstract":"<p><p>Sequencing the full-length 16S rRNA gene is essential for improving the taxonomic resolution of bacterial identification. Long-read Oxford Nanopore Technologies (ONT) sequencing, coupled with its real-time analysis platform EPI2ME, has become increasingly competitive in microbial community profiling studies. However, the impact of threshold settings in EPI2ME Agent on the alignment-based confidence (hereafter \"Alignment accuracy\") and the proportion of reads successfully assigned to a taxon (hereafter \"Classification success\") has not yet been systematically evaluated. In this study, we performed ONT-based full-length 16S rRNA gene sequencing on samples collected from eggshells of wild Oriental Tits (<i>Parus minor</i>). By adjusting different threshold settings in the EPI2ME Agent, we examined how filtering conditions affect Alignment accuracy, Classification success, and downstream microbiome diversity analysis. Our results revealed that filtering thresholds had substantial effects on these outputs. These findings highlight the importance of carefully selecting filtering parameters in the EPI2ME Agent to balance alignment accuracy and classification success, and to improve the interpretability and consistency of taxonomic profiles generated from ONT sequencing data.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag219"},"PeriodicalIF":6.4,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148876562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-06eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag227
Carina Peters, C-Elisa Schaum, Luisa Listmann
{"title":"Warming disrupts infection patterns and primarily accelerates <i>Ostreococcus</i>-virus infection dynamics in the Baltic Sea.","authors":"Carina Peters, C-Elisa Schaum, Luisa Listmann","doi":"10.1093/ismeco/ycag227","DOIUrl":"10.1093/ismeco/ycag227","url":null,"abstract":"<p><p>Warming affects phytoplankton host-virus dynamics, but only a few model systems in a handful of ecosystems have been experimentally explored. Viruses influence biogeochemical cycling, phytoplankton population dynamics, and drive coevolution and adaptation. Assessing how host-virus interactions are affected by changing environmental conditions is crucial for understanding and predicting shifts in phytoplankton community structure and function. We first characterized general infection network dynamics through a comprehensive cross-infection experiment involving 31 <i>Ostreococcus</i> strains and 83 viruses, predominantly from the Baltic Sea. We found a modular network structure, characterized by generalist and specialist infections, coevolutionary history and phylogeny. To assess the impact of warming on infection dynamics, we then performed cross-infections with a representative subset of 12 selected host strains and 17 virus lysates per host each at 20°C, 22°C, and 24°C, temperatures generally below the optimal growth temperature for most hosts. We measured spot-plaque growth rates by tracking the timing and growth dynamics of spot-plaque formation through daily photos. Increasing temperature significantly affected susceptibility, spot-plaque formation, and growth, generally increasing rates but with variable responses among host-virus pairs, especially among generalist viruses. Such differences, often decoupled from host growth, indicate that warming adds more complexity to infection dynamics and further increases unpredictability of infection patterns. These results suggest that a shift in infection dynamics could potentially alter the role of the viral shunt in future oceans, reshape infection networks, and therefore affect biogeochemical cycling and food webs.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag227"},"PeriodicalIF":6.4,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148835130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-05eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag226
Juliette Audemard, Nicolas Creusot, Julie Leloup, Charlotte Duval, Sébastien Halary, Lou Mary, Mélissa Eon, Thomas Forjonel, Mohamed Mouffok, Rémy Puppo, Elodie Belmonte, Veronique Gautier, Jeanne Got, Marie Lefebvre, Gabriel V Markov, Coralie Muller, Benjamin Marie, Binta Diémé, Clémence Frioux
{"title":"Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivated <i>Microcystis</i> phycospheres.","authors":"Juliette Audemard, Nicolas Creusot, Julie Leloup, Charlotte Duval, Sébastien Halary, Lou Mary, Mélissa Eon, Thomas Forjonel, Mohamed Mouffok, Rémy Puppo, Elodie Belmonte, Veronique Gautier, Jeanne Got, Marie Lefebvre, Gabriel V Markov, Coralie Muller, Benjamin Marie, Binta Diémé, Clémence Frioux","doi":"10.1093/ismeco/ycag226","DOIUrl":"10.1093/ismeco/ycag226","url":null,"abstract":"<p><p>Favored by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economic, and public health challenges. <i>Microcystis</i>, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialized interactions with its microbiome occur, that are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomics, metabolomics, and metabolic modeling, we characterized the culture-associated phycospheres of 12 <i>Microcystis</i> strains isolated from a French pond. The distribution of metabolic reactions within <i>Microcystis</i> was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny, indicating partial functional decoupling between cyanobacteria and their associated microbiomes. Bacteria associated with the simplified phycospheres substantially expanded the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, endometabolomic profiles were largely driven by cyanobacterial metabolic outputs, whereas exometabolomic analysis did not reveal metabolites involved in exchange processes. Metabolic modeling, together with the identification of toxic specialized metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of <i>Microcystis</i>' phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag226"},"PeriodicalIF":6.4,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148876459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-04eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag223
Sumudu Rajakaruna, Cristina Howard-Varona, Marion Urvoy, Roya AminiTabrizi, Christian Ayala-Ortiz, Marissa Gittrich, Natalie Solonenko, Marie Burris, Courtney Sanderson, Cara Noel, Jonathan Leopold, Lillyanna Quillin, Kush Doshi, Lawrence R Walker, Matthew B Sullivan, Malak M Tfaily
{"title":"Metabolome restructuring reveals distinct virocell infection strategies in bacteriophage-host interaction.","authors":"Sumudu Rajakaruna, Cristina Howard-Varona, Marion Urvoy, Roya AminiTabrizi, Christian Ayala-Ortiz, Marissa Gittrich, Natalie Solonenko, Marie Burris, Courtney Sanderson, Cara Noel, Jonathan Leopold, Lillyanna Quillin, Kush Doshi, Lawrence R Walker, Matthew B Sullivan, Malak M Tfaily","doi":"10.1093/ismeco/ycag223","DOIUrl":"10.1093/ismeco/ycag223","url":null,"abstract":"<p><p>Viral infection transforms microbial cells into metabolically reprogrammed \"virocells,\" yet the metabolic architecture underlying this transition remains poorly resolved. Here we investigate how bacteriophages reshape host metabolism in <i>Cellulophaga baltica</i> across time and phage types, uncovering coordinated metabolic reorganization during infection that includes pathway-level patterns consistent with membrane remodeling, amino-acid recycling, and redistribution of cellular resources. Temporal analyses further distinguished infection strategies: efficient phages produced structured, phased metabolic shifts indicative of controlled host reprogramming, whereas inefficient infection triggered abrupt metabolic collapse. These results suggest that the organization and timing of host metabolome restructuring represent defining features of the virocell state and may reflect underlying viral life-history strategies. These biological patterns were made accessible by an integrative annotation framework that combines previously validated computational tools, substantially expanding interpretable metabolite coverage beyond conventional approaches. This approach reveals coherent infection signatures that would otherwise remain hidden, demonstrating how expanded metabolite interpretability can uncover functional principles of virus-host interactions. The analytical strategy presented here is readily transferable to other virus-host systems and complex microbial communities, providing a path toward mechanistic interpretation of untargeted metabolomic data in microbial ecology.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag223"},"PeriodicalIF":6.4,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148889620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-08-04eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag225
Nicolas Romillac, Gianpaolo Zampicinini, Adriana Zingone, Diana Sarno
{"title":"Niche divergence suggests ecophysiological differences between cryptic phytoplankton species.","authors":"Nicolas Romillac, Gianpaolo Zampicinini, Adriana Zingone, Diana Sarno","doi":"10.1093/ismeco/ycag225","DOIUrl":"10.1093/ismeco/ycag225","url":null,"abstract":"<p><p>Species-based ecology is fundamental to understanding and predicting the role of phytoplankton diversity in the production and biogeochemical cycles of marine ecosystems. However, microscopy fails to distinguish genetically distinct but morphologically identical (cryptic) or near-identical (pseudocryptic) species, which are lumped into species complexes under the assumption that they have similar ecological characteristics. To test this hypothesis, we analysed a 12-year V4-18S rDNA metabarcoding dataset (168 dates) from the Long-Term Ecological Research Site MareChiara (Gulf of Naples, Mediterranean Sea). Using Kernel Density Estimations and Outlying Mean Index niche analysis, we investigated the seasonality and ecology of 33 cryptic and pseudocryptic species or genetic variants, identified as amplicon sequence variants (ASVs). These belonged to eight species complexes, selected based on their abundance and frequency, within the diatoms <i>Leptocylindrus</i>, <i>Pseudo-nitzschia</i>, and <i>Chaetoceros</i>, the dinoflagellates <i>Azadinium</i> and <i>Heterocapsa</i>, and the chlorophyte <i>Micromonas</i>. Within each complex, ASVs exhibited distinct, annually recurrent seasonal dynamics, with peaks of the most abundant variants matching morphotype peaks for >60% of the timeline. Crucially, 75% of the sister ASVs rarely co-occurred (<30% of the samples), while their seasonality and ecological niches overlapped <60% in 72% and 56% of the couples, respectively. Divergence between species pairs suggests underrated ecophysiological differences and high adaptive potential within species complexes, highlighting the importance of identifying cryptic and pseudo-cryptic species. These findings demonstrate the power of long-term metabarcoding time-series in refining species-based ecological theories, while pointing to the need to uncover the molecular mechanisms driving phytoplankton phenology.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag225"},"PeriodicalIF":6.4,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13590887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2026-07-31eCollection Date: 2026-01-01DOI: 10.1093/ismeco/ycag221
Qiqi Pan, Eleni Tsompanidou, Wenbing Hu, Muhammad Tanweer Khan, Jan Maarten van Dijl
{"title":"<i>Faecalibacterium harmsenii</i> sp. nov.<i>,</i> an abundant but previously overlooked <i>Faecalibacterium</i> in the human gut.","authors":"Qiqi Pan, Eleni Tsompanidou, Wenbing Hu, Muhammad Tanweer Khan, Jan Maarten van Dijl","doi":"10.1093/ismeco/ycag221","DOIUrl":"10.1093/ismeco/ycag221","url":null,"abstract":"<p><p><i>Faecalibacterium</i> is one of the most abundant anaerobes in the human colon. At the genus level, this bacterium shows a strong positive association with human health. Expanding collections of isolates and metagenome-assembled genomes have revealed its species diversity, yet species-level functions remain so far underexplored. Here, we describe a novel species, <i>Faecalibacterium harmsenii</i>. In addition, we reclassify another isolate as a member of the recently reported <i>Faecalibacterium langellae</i> species. Despite close genomic relatedness, these isolates exhibit distinct physiological and biochemical traits, including differences in carbohydrate utilization, stress tolerance, enzymatic activity, Gram-staining and fatty acid composition. Our present comparative genomics analyses further uncover extensive functional diversity and plasticity across type strains, with <i>F. harmsenii</i> being distinguished by an expanded carbohydrate gene repertoire and reduced defense systems, mobile genetic elements and antibiotic resistance genes. Extending to the species, we identify species-specific ecological niches across hosts and differential sensitivities to human diseases, highlighting certain species as reliable biomarkers of gut health. Together, these findings refine our understanding of <i>Faecalibacterium</i> diversity and provide a framework for its use in microbiome-based diagnostics and therapeutic development.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag221"},"PeriodicalIF":6.4,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148889398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Seagrass-derived carbon suppresses nitrification and N<sub>2</sub>O emissions by Comammox and canonical nitrifier communities.","authors":"Ruilin Su, Pui Ting Chan, Xiaodong Zhang, Jiawei Chen, Sangwook Lee, Xinlei Yang, Hoi Yau Chan, Yuxuan Lin, Jiying Li, Qingyun Yan, Hongbin Liu, Zhili He","doi":"10.1093/ismeco/ycag220","DOIUrl":"10.1093/ismeco/ycag220","url":null,"abstract":"<p><p>Seagrass meadows are critical regulators of coastal biogeochemical cycling, particularly through the exudation and accumulation of organic carbon that enriches their rhizosphere far beyond ambient marine levels. Microbially driven nitrification is a key process controlling nitrous oxide (N<sub>2</sub>O) emissions, yet the ecological roles of complete ammonia oxidizers (Comammox) and canonical nitrifiers in seagrass ecosystems are poorly understood. Here, seagrass sediments (SS) exhibited significantly (<i>P</i> < .05) lower nitrification and N<sub>2</sub>O production rates than non-seagrass sediments, where nitrification was the dominant N<sub>2</sub>O source. We characterized Comammox for the first time in a seagrass ecosystem, revealing that they displayed potential nitrification rates lower than ammonia-oxidizing bacteria or ammonia-oxidizing archaea. Notably, Comammox showed the lowest potential N<sub>2</sub>O production rates and negative CO<sub>2</sub> fluxes. Metagenomic profiles revealed lower relative abundances of genes associated with nitrification and N<sub>2</sub>O-producing pathways in SS, while metatranscriptomic analysis identified significant (<i>P</i> < .05) down-regulation of the core nitrification genes. In contrast, genes involved in sugar transport and metabolism generally showed positive transcriptional changes. This study identifies a key microbial mechanism through which seagrass-derived carbon may contribute to lower nitrification and N<sub>2</sub>O emissions, highlighting the potential of microbiome engineering in seagrass restoration and conservation for climate mitigation.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag220"},"PeriodicalIF":6.4,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148833994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}