Distribution and relative quantification of key genes involved in fixed nitrogen loss from the Arabian Sea oxygen minimum zone

Abstract

The Arabian Sea (AS) oxygen minimum zone (OMZ) is one of the largest pelagic low-oxygen environments in the open ocean. It is responsible for the removal of up to 60 Tg of nitrogen annually, roughly an eighth of the global fixed nitrogen sink. Although denitrification has long been believed to be the major process responsible for fixed nitrogen loss from the oceans, recent studies show that anaerobic ammonium oxidation (anammox) is potentially a more important process involved. We have investigated the phylogeny of both anammox and denitrifying microbes in the AS, and here we report on their diversity in terms of their characteristic genes. Denitrifiers were targeted using nirS and nirK genes and anammox bacteria with the 16S rRNA gene. The nirK gene was amplified from all the samples, but nirS gene could only be detected when nitrite was present. The distribution of phylotypes was related to the concentration of nitrite and the apparent stage of denitrification. Most nirK or nirS genes from the AS had low identities with other published sequences. The closest identities were to sequences from other water column denitrifying environments rather than sedimentary or terrestrial environments. Phylogenetic analysis of the nirS and nirK genes revealed overall lower diversity than the very high diversities reported from estuarine and sedimentary environments. 16S rRNA partial gene sequences revealed very limited diversity among anammox sequences. All the anammox sequences were >98% identical to each other and were similar to sequences from other marine and water column environments, which are distantly related to Scalindua sp. Quantification using quantitative polymerase chain reaction assays showed that both nirS genes and anammox 16S rRNA genes were more abundant at depths with higher nitrite concentrations. The presence and abundance of genes indicative of both processes suggest that both canonical denitrification and anammox likely occur in the OMZ of the AS. However, the abundance of the nirS gene, one of the genes responsible for canonical denitrification, was an order of magnitude higher than the abundance of the anammox 16S gene, indicating that denitrifiers are numerically dominant in this environment. The greater diversity of nirS and nirK genes relative to anammox genes both among and within stations also suggests that the denitrifier assemblages are more dynamic in response to environmental conditions.