Community composition of bacteria involved in fixed nitrogen loss in the water column of two major oxygen minimum zones in the ocean

The community composition of bacteria involved in nitrogen (N) transformations in the oxygen minimum zones (OMZ) may be related to the rates of fixed N loss in these systems. The abundance of both denitrifying and anammox bacteria and the assemblage composition of denitrifiers were investigated in the Eastern Tropical South Pacific and the Arabian Sea using assays based on bacterial molecular markers. Quantitative PCR was used to investigate the abundance and distribution of genes encoding nitrite reductase (nirK and nirS) in denitrifying bacteria and hydrazine oxidase (hzo) and 16S rRNA genes in anammox bacteria. All of these genes had depth distributions with maxima associated with the secondary nitrite maximum in low-oxygen waters. NirS was much more abundant than nirK and much more abundant than the 16S rRNA gene from anammox bacteria. The ratio of hzo:16S rRNA was low and variable, implying greater unexplored diversity in the hzo gene. Assemblage composition of the abundant nirS-type denitrifiers was evaluated using a functional gene microarray. Of the nirS archetypes represented on the microarray, very few occurred specifically in one region or depth interval, but the assemblages varied significantly. Community composition of denitrifiers based on microarray analysis of the nirS gene was most different between geographical regions. Within each region, the surface layer and OMZ assemblages clustered distinctly. Thus, in addition to spatial and temporal variation in denitrification and anammox rates, microbial abundance and community composition also vary between OMZ regions and depths.