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Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments

Abstract

Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3–5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.

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Acknowledgements

We thank all participants and crew in the Aurora SKA cruise, 2014, and Britta Poulsen, Jeanette Johansen, Karina Bomholt Oest and Susanne Nielsen for excellent technical assistance in the lab. The work was supported by the Danish National Research Foundation (grant no DNRF104); the ERC Advanced Grant MICROENERGY [grant no 294200], and the VILLUM Experiment project “FISHing for the ancestors of the eukaryotic cell”. The sampling cruise was supported by the Danish Center for Marine Research.

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Conflict of interest

The authors declare that they have no conflict of interest.

Correspondence to Ian P. G. Marshall.

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