Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments

Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, <i>Breviatea, Labyrinthulomycetes</i>, and <i>Apicomplexa</i> were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.