Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients

Abstract

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.

Organic matter accumulation and degradation in subsurface coastal sediments: a model-based comparison of rapid sedimentation and aquifer transport

“…Köster, personal communication, 2008). Microbial investigations by Köpke et al (2005) and Wilms et al (2006a) found significantly enhanced activity at the edges of the sulfate free, methanogenic zone. Though less pronounced, ongoing diagenesis is also visible at site NN2 in the sulfate profile.…”

Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes

“…As sulfate reducers and methanogens can be easily detected by specific important genes, which either encode for the dissimilatory sulfate reductase or the methyl-coenzyme M reductase, the recent studies focused on these groups (Wilms et al, 2007). It is well known that the terminal oxidizers make only a minor part of the community, whereas the fermentative microorganisms are more abundant (Schink, 2002;Kö pke et al, 2005;Wilms et al, 2006b). Thus, owing to a lack of a fermentation important gene, the largest part of the community remains unexplored.…”

Imprint of past and present environmental conditions on microbiology and biogeochemistry of coastal Quaternary sediments

“…Böttcher et al, 2000;Llobet-Brossa et al, 2002;Billerbeck et al, 2006;Al-Raei et al, 2009;Jansen et al, 2009) as well as on deeper sediment layers down to 5 m below the seafloor (mbsf) (e.g. Köpke et al, 2005;Wilms et al, 2006b;Beck et al, 2008b;Gittel et al, 2008;Røy et al, 2008). In addition, biogeochemical and microbial processes were studied in the water column and on suspended particulate matter (e.g.…”