Environmental gradients and habitat specificity structure benthic microbial assemblages in a temperate seagrass ecosystem

Abstract Seagrass meadows are globally distributed coastal ecosystems that provide habitats for diverse species and facilitate ecosystem services, such as carbon storage and nutrient cycling. However, factors linked to human activities and climate change are causing seagrass decline worldwide, thus impacting benthic community structure and ecosystem functioning. Although macrofaunal communities in seagrass habitats are well studied, the structure and function of bacteria/archaea and microeukaryote assemblages remains underexplored. In this study, we used environmental DNA (eDNA) metabarcoding (16S and 18S rRNA genes) to analyze bacteria/archaea (16S), microeukaryotes (18S raw sediment), and meiofauna (18S Ludox) communities in seagrass and bare sediment habitats across three sites along an estuarine gradient in Bodega Harbor, California. We found that microbial and microeukaryote communities were primarily structured by site as a response to the environmental gradient (e.g., sediment properties), whereas meiofauna responded more strongly to the presence of seagrass. Beta diversity showed strong differentiation among estuarine sites, while alpha diversity varied within sites, with bare sediments often displaying higher diversity. Network analysis revealed significant co-occurrences between bacteria and nematodes, including chemosynthetic symbiont-bearing lineages in mudflats and stress-tolerant bioindicators. Our findings underscore the importance of environmental gradients and microhabitat features in shaping benthic biodiversity in temperate seagrass ecosystems. Furthermore, it highlights potential microbial-nematode associations, likely a response to environmental variation. By integrating multiple benthic components, our study advances understanding of biodiversity drivers in temperate estuarine seagrass habitats and provides new insights on microbial community structure in these ecosystems. Importance Seagrass meadows, which sustain a wide variety of plant and animal life, are vital coastal habitats. These submerged ecosystems support biodiversity, protection of coasts, nitrogen cycling, and carbon storage. However, they are declining due to pressures from climate change and human activity. This study characterizes the microbial and microeukaryote communities, including meiofauna, that inhabit and surround temperate seagrass meadows. By analyzing these communities across different areas of Bodega Harbor, California, we demonstrate how seagrass and environmental factors affect the resilience and overall health of the ecosystem. Our findings highlight the importance of seagrass in maintaining biodiversity and suggest that microscale interactions and habitat variation are important factors shaping these temperate coastal ecosystems. A comprehensive understanding of the variation within benthic communities associated with seagrass habitats can significantly enhance conservation and restoration efforts for seagrass meadows..