Identification and activity of bacteria consuming key intermediates of carbon and sulfur cycling in coastal sands

Abstract

Coastal and shelf sediments are hot spots for carbon remineralization and also for carbon fixation. Here, a large fraction of organic carbon is mineralized under anoxic conditions by microorganisms via fermentation or respiration of fermentation products such as molecular hydrogen (H2) and acetate. Reduced inorganic metabolites released during these anaerobic processes and inorganic carbon are used by light-independent chemolithoautotrophs for socalled secondary production. However, still little is known about the in situ relevant organisms and how they contribute to key processes like chemoautotrophy as well as H2 and acetate turnover. To understand how inorganic carbon at sediment surfaces is turned over we surveyed the diversity of candidate bacterial chemolithoautotrophs in 13 tidal and sublittoral sediments and identified ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfuroxidizing bacteria. In a novel methodological approach we quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short term incubated with 14C-bicarbonate. Here, we show that uncultured Gammaproteobacteria dominate dark carbon fixation in coastal sediments and three distinct gammaproteobacterial clades made up more than half of dark carbon fixation in a tidal sediment. Meta- and single cell genomics along with metatranscriptomics provided evidence for a largely sulfur-based carbon fixation. These chemolithoautotrophic gammaproteobacterial clades also accounted for a substantial fraction of the microbial community in 1,000 to 2,000 year old subsurface sediments, suggesting that burial of chemolithoautotrophic bacteria could possibly be a yet-unrecognized mechanism of carbon sequestration. Microbial scavenging of H2 is an essential process in anoxic carbon mineralization, because only low H2 levels make H2-forming fermentation thermodynamically feasible. In a sediment metagenome we identified a high diversity of genes encoding the NiFe uptake hydrogenases of numerous yet-uncultured, potentially H2-oxidizing bacteria. Metatranscriptomics together with incubation experiments suggested uncultured Desulfobacteraceae, in particular the sulfate-reducing Sva0081-clade, as important H2 oxidizers in anoxic sediments. On the contrary, Gammaproteobacteria and Flavobacteria encoding O2-tolerant hydrogenases are possibly involved in H2 oxidation in oxic sediments. In a third study, we quantified the relative contribution of single bacterial populations to total acetate assimilation. Here, we showed that acetate was assimilated by physiologically and phylogenetically distinct bacterial groups such as Gammaproteobacteria, sulfate-reducing Desulfobacteraceae and Desulfobulbaceae as well as likely lithoheterotrophic sulfur-oxidizing Roseobacter-clade bacteria. We identified uncultured Gammaproteobacteria as a major contributor to acetate assimilation under oxic and anoxic conditions accounting for 31-62% of the total acetate assimilation. In summary, this thesis contributes to our understanding how distinct bacterial populations turn over key metabolites of organic carbon degradation in marine sediments. The quantification of uptake of 14C-labeleld model compounds by defined populations is a major step forward in the identification of key organisms in element cycling in marine sediments.