AUTHOR=Fuchsman Clara A. , Devol Allan H. , Saunders Jaclyn K. , McKay Cedar , Rocap Gabrielle TITLE=Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone JOURNAL=Frontiers in Microbiology VOLUME=8 YEAR=2017 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.02384 DOI=10.3389/fmicb.2017.02384 ISSN=1664-302X ABSTRACT=

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N₂O and N₂. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N₂O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N₂O in the ODZ was a form of qnorB related to the previously postulated “nitric oxide dismutase,” hypothesized to produce N₂ directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N₂O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N₂O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N₂O production rates from ammonia oxidation were insufficient to support the observed oxycline N₂O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N₂O and N₂. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.