Ammonia released during organic matter mineralization is converted during nitrification to nitrate. We followed spatiotemporal dynamics of the nitrifying microbial community in deep oligotrophic Lake Constance. Depth-dependent decrease of total ammonium (0.01-0.84 μM) indicated the hypolimnion as the major place of nitrification with 15 N-isotope dilution measurements indicating a threefold daily turnover of hypolimnetic total ammonium. This was mirrored by a strong increase of ammonia-oxidizing Thaumarchaeota towards the hypolimnion (13%-21% of bacterioplankton) throughout spring to autumn as revealed by amplicon sequencing and quantitative polymerase chain reaction. Ammonia-oxidizing bacteria were typically two orders of magnitude less abundant and completely ammonia-oxidizing (comammox) bacteria were not detected. Both, 16S rRNA gene and amoA (encoding ammonia monooxygenase subunit B) analyses identified only one major species-level operational taxonomic unit (OTU) of Thaumarchaeota (99% of all ammonia oxidizers in the hypolimnion), which was affiliated to Nitrosopumilus spp. The relative abundance distribution of the single Thaumarchaeon strongly correlated to an equally abundant Chloroflexi clade CL500-11 OTU and a Nitrospira OTU that was one order of magnitude less abundant. The latter dominated among recognized nitrite oxidizers. This extremely low diversity of nitrifiers shows how vulnerable the ecosystem process of nitrification may be in Lake Constance as Central Europe's third largest lake.

The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.