Enrichment of abundant sulfate reducers from tidal sediments

Up to 50% of carbon remineralization in marine sediments is mediated by the sulfatereducing bacterial community. Bacteria from the Desulfosarcina-Desulfococcus group that are related to the DPB1 endosymbiont of Olavius spp. (Sva0081-SRB) occur worldwide at all depths and account for up to 10% of all cells in sulfidic conditions. However, the physiology of this ecologically important group remains unknown. The complexity of the microbial community in sediments challenges traditional isolation and metagenomics. No Sva0081-SRB bacteria have been cultivated, nor are there available genomes for close relatives, which makes metagenome assembly more difficult. We present an alternative approach that combines culture-dependent and independent methods to study Sva0081-SRB. We developed a low substrate concentration continuous culture that allowed us to maintain the Sva0081- SRB group for more than 69 days in the laboratory. This culturing method allows physiological experiments of metabolically active cells at defined conditions in the laboratory. We specifically sorted cells through fluorescence-activated cell sorting (FACS) of the CARDFISH hybridized Sva0081-SRB community. Subsequently, whole genome amplification through multiple displacement amplification (MDA) allowed access to population derived metagenomic DNA. The PCR based screening for the adenosin-5’-phosphosulfate reductase subunit A indicated successful amplification of CARD-FISH treated and FACS sorted cells. Future sequence-based studies can reveal a potential core-genome of the population. We can directly verify it by testing the hypothesis obtained through sequence analysis with culture based physiological experiments. This combination of the strong characteristics of both approaches allows further investigation of the ecological relevance of this highly abundant grou

Microbial life on a sand grain: from bulk sediment to single grains

Globally, marine surface sediments constitute a habitat for estimated 1.7 x 10(28) prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 10(4)-10(5) cells were present on grains from 202 to 635 mu m diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5 +/- 5.9 mu m) and protected areas more densely populated (0.5 +/- 0.7 mu m). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)(0.97). Only 4-8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for 450% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates

Permeability shapes bacterial communities in sublittoral surface sediments

Probandt D, Knittel K, Tegetmeyer H, Ahmerkamp S, Holtappels M, Amann R. Permeability shapes bacterial communities in sublittoral surface sediments. Environmental Microbiology. 2017;19(4):1584-1599.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

The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle

Polysaccharides are major components of macroalgal and phytoplankton biomass and constitute a large fraction of the organic matter produced and degraded in the ocean. Until recently, however, our knowledge of marine polysaccharides was limited due to their great structural complexity, the correspondingly complicated enzymatic machinery used by microbial communities to degrade them, and a lack of readily applied means to isolate and characterize polysaccharides in detail. Advances in carbohydrate chemistry, bioinformatics, molecular ecology, and microbiology have led to new insights into the structures of polysaccharides, the means by which they are degraded by bacteria, and the ecology of polysaccharide production and decomposition. Here, we survey current knowledge, discuss recent advances, and present a new conceptual model linking polysaccharide structural complexity and abundance to microbially driven mechanisms of polysaccharide processing. We conclude by highlighting specific future research foci that will shed light on this central but poorly characterized component of the marine carbon cycle