Microbial drivers of nitrogen metabolism: Searching Tara Oceans metagenomes

Marine nitrogen cycle plays a central role in ocean primary productivity, as well as the global climate. As microbes are the main drivers of nitrogen fixation and denitrification, a mechanistic understanding of nitrogen cycling relies on our knowledge of distribution and diversity of these organisms. Microbial nitrogen metabolism is traditionally studied in the “free-living” fraction (0.2-0.8µm), yet the contributions of microbes in the larger size fractions (>0.8µm), including particle-associated bacteria, may be underestimated. The Tara Oceans metagenomic dataset offers the opportunity to investigate hypotheses related to global nitrogen metabolism among these larger size fractions. Six genes of interest within the nitrogen cycle were selected as targets: nifH (nitrogenase), nirS (nitrite reductase), nosZ (nitrous oxide reductase), amoA (ammonium monooxygenase subunit alpha), ureC (urease), and narG (nitrate reductase). Reference sequence alignments were generated from manually curated reference sequence databases for each gene and predicted proteins from the assembled metagenomes were searched against these alignments. Evaluated hits were used to estimate gene abundance across ocean regions, serving as a proxy for metabolic potential. Nitrate reductase (narG) was abundant in the mesopelagic realm, with 77.2% of narG sequences in reads per kilobase million (RPKM) occurring at this water layer. Samples with high narG abundance were also typically oxygen depleted. In contrast, nitrogenase (nifH) was found abundant in surface waters, with 69.2% of nifH sequences in RPKM found in sunlit waters. By mapping the confirmed protein sequences against metagenome assembled genomes (MAGs), we identified 471 high quality MAGs containing one or more of the six proteins of interest. Investigation of these MAGs will shed light on the potential contributions of different taxonomic groups to observed patterns in nitrogen cycling.