Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment–water interface in lakes Plußsee and Schöhsee, and a near-shore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying bacteria, little information is available for stratified freshwater lakes and brackish water. The aim of the present study was to fill this gap and to demonstrate specific distribution patterns of denitrifying bacteria in specific aquatic habitats using two functional markers for the nitrite reductase (<i>nirK</i> and <i>nirS</i> genes) as a proxy for the communities. The leading question to be answered was whether communities containing the genes <i>nirK</i> and <i>nirS</i> have similar, identical, or different distribution patterns, and occupy the same or different ecological niches. The genes <i>nirK</i> and <i>nirS</i> were analyzed by PCR amplification with specific primers followed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequence analysis. Overall, <i>nirS</i>-denitrifiers were more diverse than <i>nirK</i>-denitrifiers. Denitrifying communities in sediments were clearly different from those in the water column in all aquatic systems, regardless of the gene analyzed. A differential distribution of denitrifying assemblages was observed for each particular site. In the Baltic Sea and Lake Plußsee, <i>nirK</i>-denitrifiers were more diverse throughout the water column, while <i>nirS</i>-denitrifiers were more diverse in the sediment. In Lake Schöhsee, <i>nirS</i>-denitrifiers showed high diversity across the whole water body. Habitat-specific clusters of <i>nirS</i> sequences were observed for the freshwater lakes, while <i>nirK</i> sequences from both freshwater lakes and the Baltic Sea were found in common phylogenetic clusters. These results demonstrated differences in the distribution of bacteria containing <i>nirS</i> and those containing <i>nirK</i> indicating that both types of denitrifiers apparently occupy different ecological niches.