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This study uses shotgun metagenomics to assess microbial diversity and functional potential in a seagrass-dominated Mexican Pacific coastal lagoon influenced by seasonal upwelling and minimal human impact. Despite strong physicochemical gradients, communities were diverse and taxonomically conserved, showing high site and season sharing for taxa, while nitrate and ferric iron best explained community structure and functional variation.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/taxonomic-and-functional-stability-of-sedimentary-microbial-communities-in-a-pristine-upwelling-influenced-coastal-lagoon/439246/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/taxonomic-and-functional-stability-of-sedimentary-microbial-communities-in-a-pristine-upwelling-influenced-coastal-lagoon/439246.png","ImageObject",300,407,{"name":92,"@type":93},"Damian","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-09-30","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":8},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What method was used to study microbial diversity and function in the coastal lagoon?","Question",{"text":112,"@type":113},"Shotgun metagenomics was used to investigate microbial diversity and functional potential in sediment samples.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What did the study find about taxonomic and functional stability across sites and seasons?",{"text":117,"@type":113},"A diverse but taxonomically conserved microbial community was observed, with most genera and a substantial fraction of species consistently shared across sites and the two upwelling seasons.",{"name":119,"@type":110,"acceptedAnswer":120},"Which environmental variables most influenced microbial community structure and functional repertoire?",{"text":121,"@type":113},"Among measured physicochemical variables, nitrate and ferric iron significantly influenced both community structure and functional repertoire.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},439246,1790752246,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":8,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},137451208677,"https://ap-avatar.wpscdn.com/davatar_155a257f0dc6eb9ab79c44ca47cae57d","ISME Communications, 2025, 5(1), ycaf241  \n[https://doi.org/10.1093/ismeco/ycaf241](https://doi.org/10.1093/ismeco/ycaf241)  \nAdvance access publication: 18 December 2025  \nOriginal Article  \nTaxonomic and functional stability of sedimentary microbial communities in a pristine  \nupwelling-influenced coastal lagoon  \nJorge Rojas-Vargas1 , 2 , 3 , Guillermo Samperio-Ramos4 , Víctor F. Camacho-Ibar4 , Silvia Pajares 1 , *  \n1Unidad Académica de Ecología y Biodiversidad Acuática, Institute of Marine Sciences and Limnology, National Autonomous University of Mexico (UNAM), Circuito exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico  \n2 Department of Biology, University of Western Ontario (UWO), 1151 Richmond St. N. , London, Ontario, N6A 5B7, Canada  \n3 Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario (UWO), 1151 Richmond St. N. , London, Ontario, N6A 5C1, Canada  \n4Nutrient Cycling in Marine Ecosystems Research Group, Institute of Oceanological Research, Autonomous University of Baja California (UABC), Carretera Ensenada-Tijuana No. 3917, Fracc. Playitas, Ensenada, 22860, Baja California, Mexico  \n*Corresponding author. Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, National Autonomous University of Mexico, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico. E-mail: [spajares@cmarl.unam.mx](spajares@cmarl.unam.mx)  \nAbstract  \nCoastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.  \nGraphical abstract  \nKeywords: coastal sediments; seasonal upwelling; pristine environment; microbial communities; microbial diversity; functional potential; shotgun metagenomics  \nReceived: 20 August 2025 . Revised: 23 November 2025 . Accepted: 15 December 2025  \n© The Author(s) 2025. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.  \nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License ([https://creativecommons.org/licenses/by/4.0/](https://creativecommons.org/licenses/by/4.0/)), which permits unrestricted reuse, distribu","cbCaisjV3xrrpBFJ","https://ap.wps.com/l/cbCaisjV3xrrpBFJ","pdf",2511571,14,"English","# Abstract\n# Introduction\n## Coastal lagoons as dynamic interfaces\n## Drivers of microbial diversity in sediments","[{\"question\":\"What method was used to study microbial diversity and function in the coastal lagoon?\",\"answer\":\"Shotgun metagenomics was used to investigate microbial diversity and functional potential in sediment samples.\"},{\"question\":\"What did the study find about taxonomic and functional stability across sites and seasons?\",\"answer\":\"A diverse but taxonomically conserved microbial community was observed, with most genera and a substantial fraction of species consistently shared across sites and the two upwelling seasons.\"},{\"question\":\"Which environmental variables most influenced microbial community structure and functional repertoire?\",\"answer\":\"Among measured physicochemical variables, nitrate and ferric iron significantly influenced both community structure and functional repertoire.\"}]","Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon | PDF",1790687943,35]