Abstract
Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.
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Acknowledgements
This study was funded by NSF grants to BBW and AJ. LFMK, JF, and SL were supported by the Netherlands Organization for Scientific Research (grants 863.14.019, 016.Vidi.189.050, and SIAM Gravitation Grant 024.002.002). We would like to acknowledge all scientists and the crew of the R/V Nathaniel B. Palmer for assistance in sample collection. We are grateful to Wei Wang for his help in the Princeton Genomics Core Facility. We also thank two anonymous reviewers for their very helpful insights.
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XS and BBW planned the study. XS and LFMK performed all metagenomic analyses. JF and MCYL set up pipelines for metagenomic analyses. AJ provided DNA samples. XS, LFMK, SL, and BBW analyzed data and wrote the paper. All authors approved the final paper.
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Sun, X., Kop, L.F.M., Lau, M.C.Y. et al. Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones. ISME J 13, 2391–2402 (2019). https://doi.org/10.1038/s41396-019-0443-7
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DOI: https://doi.org/10.1038/s41396-019-0443-7
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