Permeability shapes bacterial communities in sublittoral surface sediments

Abstract

The first interaction of water column-derived organic matter with benthic microbial communities takes place in surface sediments which are acting as biological filters catalyzing central steps of elemental cycling. Here we analyzed the bacterial diversity and community structure of sediment top layers at seven sites in the North Sea where sediment properties ranged from coarse-grained and highly permeable to fine-grained and impermeable. Bacterial communities in surface sediments were richer, more even and significantly different from communities in bottom waters as revealed by Illumina tag sequencing of 16S rRNA genes. Sediment permeability had a clear influence on community composition which was confirmed by CARD-FISH. Sulfate-reducing Desulfobacteraceae (2-5% of total cells), Flavobacteriaceae (3-5%) were more abundant in impermeable than in highly permeable sediments where acidobacterial Sva0725 dominated (11-15%). Myxobacterial Sandaracinaceae were most abundant in medium permeable sediments (3-7%). Woeseiaceae/JTB255 and Planctomycetes were major groups in all sediments (4-6%, 8-22%). Planctomycetes were highly diverse and branched throughout the phylum. We propose Planctomycetes as key bacteria for degradation of high molecular weight compounds and recalcitrant material entering surface sediments from the water column. Benthic Flavobacteriaceae likely have restricted capabilities for macromolecule degradation and might profit with Sandaracinaceae and Acidobacteria from low molecular weight compounds.

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

“…5a, Table S3). Cells of Woeseiales bacteria accounted for 1-9% of all cells detected by DAPI staining (5 ± 3%, Table S3), similar to proportions reported from tidal (3-6% [6]) and sublittoral coastal sandy sediments (1-6% [9]). For comparison, Gammaproteobacteria accounted for 1-25% of DAPIstained cells in the surveyed deep-sea sediments with the exception of a single sediment sample (site AO.5c in Fram Strait; 4-5 cm below the seafloor surface) where they accounted for up to 67% of DAPI-stained cells (Table S3 and Supplementary text 13).…”

“…In these studies, members of this group account for 1-22% of the sequences retrieved. Cell counts in coastal sediments have indicated that these bacteria account on average for 6% of the surveyed microbial communities [6,8,9], yet their cell densities in deep-sea sediments remained unknown. Notably, distinct lineages within JTB255-MBG were detected in coastal and deep-sea sediments, suggesting that certain taxa within this group occur in specific types of environments, i.e., in either deep-sea or coastal environments [8].…”

Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments

“…Such a heterotrophic oxidation of H 2 is widespread among SRM (Rabus et al ., ) and is in line with very low CO 2 assimilation rates measured in sulfidic sediment layers at site Janssand (Lenk et al ., ). The Sva0081‐MBG accounted not only for a major fraction of all SRM‐related 16S rRNA genes in our study, but also made up the dominant fraction of 16S rRNA gene amplicons of SRM in other coastal sediments (Wang et al ., ; Zheng et al ., ; Liu et al ., ; Probandt et al ., ).…”

Metabolic specialization of denitrifiers in permeable sediments controls N2O emissions

“…At the same time, between 5% and 8% of 16S amplicon sequences derived from the upper layers of the sediment in the Wadden Sea are assigned to Flavobacteriia of which the genus Eudoraea were the most abundant single group (Dyksma et al, 2016). Similarly in subtidal sandy sediments from the German Bight, Flavobacteriia were very abundant (Probandt et al, 2017). Furthermore, Muricauda sp.…”