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The vast majority of deep-sea ecosystems are sustained by exported organic material from the productive, sunlit surface ocean. Bacteria dominate benthic communities both in biomass and abundance, and have been recognized as the key players in the remineralization of organic material. Since most sediment bacteria remain however uncultivated and represent unknown taxa, we have very limited knowledge of their metabolic capabilities and enzymatic machinery. Here we studied deep-sea surface sediments along a seafloor depth gradient from 1200 m to 5500 m at the Arctic long-term ecological research station HAUSGARTEN. We applied Illumina 16S rRNA gene surveys based on DNA and cDNA, as well as metagenomic and -transcriptomic sequencing to elucidate total and active bacterial community composition and gain insight into the carbohydrate processing and uptake capabilities of deep-sea benthic bacteria. We identified specific taxa of interest and quantified their cellular abundance using CAtalyzed Reporter Deposition–Fluorescence In Situ Hybridization. Results from the different molecular approaches were in good agreement and suggested similar community structures with the same dominant members. Interestingly, typically predominant sediment taxa, i.e. the JTB255 marine group, the Sh765B.TzT29 group or the OM1 clade, were underrepresented in the active part of the community, while other usually low-abundant taxa, i.e. Flavobacteriia and the SAR202 clade, were overrepresented. At low taxonomic resolution, communities along the slope were similar, yet showed high turnover at species level. Although, the repertoire of carbohydrate-active enzymes (e.g. polysaccharide hydrolases) appeared unchanging along the depth gradient, the relative contribution of distinct enzyme-coding genes varied. Specific glycoside hydrolases involved in polysaccharide degradation of algae material (e.g. for laminarin; xylan) had higher counts at shallow depth, while others responsible for the breakdown of bacterial cell walls (e.g. for components of peptidoglycan) were more strongly represented at deep stations. Our findings indicate an adaptation of the communities to differences in organic matter quality.

Gammaproteobacterial Reinekea spp. were detected during North Sea spring algae blooms in the years 2009-2012, with relative abundances of up to 16% in the bacterioplankton. Here, we explore the ecophysiology of ‘R. forsetii' strain Hel1_31_D35 that was isolated during the 2010 spring bloom using (i) its manually annotated, high-quality closed genome, (ii) re-analysis of in situ data from the 2009–2012 blooms and (iii) physiological tests. High resolution analysis of 16S rRNA gene sequences suggested that ‘R. forsetii' dominated Reinekea populations during these blooms. This was corroborated by retrieval of almost complete Hel1_31_D35 genomes from 2009 and 2010 bacterioplankton metagenomes. Strain Hel1_31_D35 can use numerous low-molecular weight substrates including diverse sugar monomers, and few but relevant algal polysaccharides such as mannan, α-glucans, and likely bacterial peptidoglycan. It oxidizes thiosulfate to sulfate, and ferments under anoxic conditions. The strain can attach to algae and thrives at low phosphate concentrations as they occur during blooms. Its genome encodes RTX toxin and secretion proteins, and in cultivation experiments Hel1_31_D35 crude cell extracts inhibited growth of a North Sea Polaribacter strain. Our data suggest that the combination of these traits make strain Hel1_31_D35 a versatile opportunist that is particularly competitive during spring phytoplankton blooms.

Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N‐loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N2O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N2O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N2O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N2O emissions., Environmental Microbiology, 20 (12), ISSN:1462-2912, ISSN:1462-2920