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Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a  Zostera marina  meadow. High-throughput sequencing of 16S rDNA showed that  Woesearchaeota ,  Bathyarchaeota , and  Thaumarchaeota  were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance,  Woesearchaeota  and  Bathyarchaeota  were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments ( P  < 0.05), while  Thaumarchaeota  was favored in unvegetated sites ( P  = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community,  Bathyarchaeota , and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments ( P  < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of  Woesearchaeota  and  Bathyarchaeota , in terms of both relative proportions and absolute quantities.

Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites