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However, anthropogenic activities and climate change are causing seagrass decline worldwide, broadly impacting ecosystem functioning. Although macrofaunal communities in seagrass habitats are relatively well studied, benthic microbial assemblages (including microeukaryote groups such as protists and microbial metazoa) remain underexplored. In this study, we used environmental DNA (eDNA) metabarcoding to characterize assemblages of bacteria\/archaea (16S rRNA gene), microeukaryotes (18S rRNA amplified from raw sediment), and meiofauna (18S rRNA amplified from sieved and Ludoxed sediment fractions) in seagrass fields and bare sediment habitats at three sites along an estuarine gradient in Bodega Harbor, California. We found that microbial and microeukaryote communities were primarily structured by location, with sediment properties (sand vs silt\/clay proportions) being the main driver of community assemblages. Habitat type was a secondary factor influencing benthic fauna, with bare sediments typically displaying higher biodiversity than seagrass beds, except at Westside Park mudflats, where bare sediments showed significantly reduced diversity compared to all other sampling locations. The differential recovery of nematode bioindicator taxa, including\n                      <jats:italic toggle=\"yes\">Terschellingia<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Daptonema<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Viscosia<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Microlaimus<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">Spilophorella<\/jats:italic>\n                      , suggested that abiotic factors, such as physical disturbance, pollution, or oxygen dynamics, may influence the success of specific taxa at each site. Finally, nematode-bacterial co-occurrence networks confirmed known symbiotic associations and suggest additional taxonomic relationships to explore in future studies. Our findings underscore the importance of environmental gradients and microhabitat features in shaping benthic biodiversity in temperate seagrass ecosystems.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>Seagrass meadows, which sustain a wide variety of plant and animal life, are vital coastal habitats. These submerged ecosystems support biodiversity, coastal protection, biogeochemical cycling, and carbon storage. However, seagrass habitats worldwide are declining due to pressures from climate change and human activity. This study characterizes the microbial and microeukaryote communities (including microbial animals with a body size &lt;1 mm) that inhabit and surround temperate seagrass meadows in Bodega Harbor, California. Our findings demonstrate that location is a primary factor that determines microbial communities inhabiting sediments at each site, with habitat type (bare sediment vs seagrass beds) exerting a secondary influence on the biodiversity and distribution of microbial species. By using nematode bioindicator taxa and nematode-bacterial co-occurrence patterns, our results also suggest specific environmental factors that shape sediment biodiversity, including tidal cycles, oxygen, sulfur, and decaying organic matter. A comprehensive understanding of the variation within benthic communities associated with seagrass habitats can significantly enhance conservation and restoration efforts for seagrass meadows.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msphere.00431-26","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T13:01:13Z","timestamp":1786539673000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Location and habitat specificity structure benthic microbial assemblages in a temperate seagrass ecosystem"],"prefix":"10.1128","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-5457-461X","authenticated-orcid":false,"given":"Gabriel A.","family":"Serrano","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02bjhwk41","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Marine Sciences, 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