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We used a 16S\/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with <jats:italic>Methylococcales<\/jats:italic> (putative methanotrophs) but had lower abundances of <jats:italic>Rhodospirillales<\/jats:italic>, <jats:italic>Nitrospirales<\/jats:italic> and SAR202 in the more active MVs. Within microeukaryotic communities, members of the <jats:italic>Lobosa<\/jats:italic> (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between <jats:italic>Methylococcales<\/jats:italic> populations and lobose amoeba in active MVs. 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