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Enrichment of abundant sulfate reducers from tidal sediments


Probandt,  David
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Probandt, D. (2013). Enrichment of abundant sulfate reducers from tidal sediments. Master Thesis, University of Bremen, Bremen / Germany.

Cite as: https://hdl.handle.net/21.11116/0000-0001-C703-B
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 group