Genome-resolved metagenomics of nitrogen cycling processes in Saanich Inlet

Abstract

In the oxygen-starved water of the Saanich Inlet, genes encoding nitrogen loss processes e.g. denitrification were more abundant than those encoding nitrification or nitrogen fixation pathways. The most abundant denitrification genes recovered along the Saanich Inlet oxygen gradient spanning 100 and 200 meter depth intervals were the nitrate reductase subunits, napA and narG . Minor levels of nitrification genes such as nxrA and nxrB were identified by PROKKA, while the denitrification genes such as napA, narG and nirS were more abundant, implying denitrification pathways were favoured. Similarly, the increased denitrification gene abundances correlates with the accumulation of products typical in the denitrification pathway. For example, nitrate (NO₃^-), a reactant in the denitrification pathway, is completely consumed at 200 meters, whereas hydrogen sulfide (H₂S) concentration sharply increases. Taxonomic grouping of these denitrification genes, identified by Gtdb-Tk, indicate that they are primarily encoded by the Gammaproteobacteria class. Together, these results support a global trend of community metabolism shifting from utilizing oxygen to nitrogen as a terminal electron acceptor in response to oxygen minimum zones, in addition to identifying the key community members involved. This shift towards the denitrification pathways may potentially aggravate climate change in the coastal marine environments through the formation of potent greenhouse gases, mainly nitrous oxide (N₂O), in oxygen minimum zones.