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.
Subscribe to Journal
Get full journal access for 1 year
only $53.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Arrigo KR. Marine microorganisms and global nutrient cycles. Nature. 2005;437:343–8.
Tyrrell T. The relative influences of nitrogen and phosohorus on oceanic primary production. Nature. 1999;400:525–31.
Lipschultz F, Wofsy SC, Ward BB, Codispoti LA, Friedrich G, Elkins JW. Bacterial transformations of inorganic nitrogen in the oxygen-deficient waters of the Eastern Tropical South Pacific Ocean. Deep Sea Res Part A, Oceanogr Res Pap. 1990;37:1513–41.
Füssel J, Lam P, Lavik G, Jensen MM, Holtappels M, Gunter M, et al. Nitrite oxidation in the Namibian oxygen minimum zone. ISME J. 2012;6:1200–9.
Sun X, Ji Q, Jayakumar A, Ward BB. Dependence of nitrite oxidation on nitrite and oxygen in low oxygen seawater. Geophys Res Lett. 2017;44:7883–91.
Beman JM, Shih JL, Popp BN. Nitrite oxidation in the upper water column and oxygen minimum zone of the eastern tropical North Pacific Ocean. ISME J. 2013;7:2192–205.
Casciotti KL, Buchwald C, McIlvin M. Implications of nitrate and nitrite isotopic measurements for the mechanisms of nitrogen cycling in the Peru oxygen deficient zone. Deep Res Part I Oceanogr Res Pap. 2013;80:78–93.
Peters BD, Babbin AR, Lettmann KA, Mordy CW, Ulloa O, Ward BB, et al. Vertical modeling of the nitrogen cycle in the eastern tropical South Pacific oxygen deficient zone using high-resolution concentration and isotope measurements. Global Biogeochem Cycles. 2016;30:1661–81.
Thamdrup B, Dalsgaard T, Revsbech NP. Widespread functional anoxia in the oxygen minimum zone of the Eastern South Pacific. Deep Res Part I Oceanogr Res Pap. 2012;65:36–45.
Garcia-Robledo E, Padilla CC, Aldunate M, Stewart FJ, Ulloa O, Paulmier A, et al. Cryptic oxygen cycling in anoxic marine zones. Proc Natl Acad Sci. 2017;114:201619844.
Bristow LA, Dalsgaard T, Tiano L, Mills DB, Bertagnolli AD, Wright JJ, et al. Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters. Proc Natl Acad Sci. 2016;113:10601–6.
Ganesh S, Bristow LA, Larsen M, Sarode N, Thamdrup B, Stewart FJ. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME J. 2015;9:2682–96.
Levipan HA, Molina V, Fernandez C. Nitrospina-like bacteria are the main drivers of nitrite oxidation in the seasonal upwelling area of the Eastern South Pacific (Central Chile ∼36°S). Environ Microbiol Rep. 2014;6:565–73.
Lücker S, Nowka B, Rattei T, Spieck E, Daims H. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol. 2013;4:1–19.
Spieck E, Keuter S, Wenzel T, Bock E, Ludwig W. Characterization of a new marine nitrite oxidizing bacterium, Nitrospina watsonii sp. nov., a member of the newly proposed phylum “Nitrospinae.”. Systermatic Appl Microbiol. 2014;37:170–6.
Watson SW, Waterbury JB. Characteristics of two marine nitrite oxidizing bacteria, Nitrospina gracilis nov. gen. nov. sp. and Nitrococcus mobilis nov. gen. nov. sp. Microscopy. 1971;77:203–30.
Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, DeLong EF. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol. 2007;9:1162–75.
Rani S, Koh HW, Rhee SK, Fujitani H, Park SJ. Detection and diversity of the nitrite oxidoreductase alpha subunit (nxrA) gene of nitrospina in marine sediments. Microb Ecol. 2017;73:111–22.
Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, et al. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science. 2017;358:1046–51.
Revsbech NP, Larsen LH, Gundersen J, Dalsgaard T, Ulloa O, Thamdrup B. Determination of ultra-low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnol Oceanogr Methods. 2009;7:371–81.
Sun X, Jayakumar A, Ward BB. Community composition of nitrous oxide consuming bacteria in the oxygen minimum zone of the Eastern Tropical South Pacific. Front Microbiol. 2017;8:1–11.
Babbin AR, Peters BD, Mordy CW, Widner B, Casciotti KL, Ward BB. Multiple metabolisms constrain the anaerobic nitrite budget in the Eastern Tropical South Pacific. Global Biogeochem Cycles. 2017;31:258–71.
Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, et al. The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Res. 2016;44:D590–4.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ. 2017;5:e3035.
Lu YY, Chen T, Fuhrman JA, Sun F, Sahinalp C. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. Bioinformatics. 2017;33:791–8.
Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144–6.
Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, et al. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature. 2016;536:179–83.
Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, et al. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Front Microbiol. 2015;6:1–13.
Stewart FJ, Ulloa O, DeLong EF. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol. 2012;14:23–40.
Hyatt D, Chen G, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:1–11.
Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes. ISME J. 2017;11:2864–8.
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol. 2018;56:281–5.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–13.
Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016;66:1100–3.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol. 2012;804:281–95.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016:44:W242–5.
Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM. Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ. 2016;4:1–28.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–60.
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13.
Ngugi DK, Blom J, Stepanauskas R, Stingl U. Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. ISME J. 2016;10:1383–99.
Thrash JC, Baker BJ, Seitz KW, Temperton B, Campbell LG, Rabalais NN, et al. Metagenomic assembly and prokaryotic metagenome-assembled genome sequences from the Northern Gulf of Mexico “Dead Zone”. Microbiol Res Announc. 2018;7:e01033–18.
Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol. 2007;10:504–9.
Daims H, Lücker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol. 2016;24:699–712.
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Comm. 2016;7:1–11.
Pitcher A, Villanueva L, Hopmans EC, Schouten S, Reichart G, Damste JSS. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone. ISME J.. 2011;5:1896–904.
Füssel J, Lücker S, Yilmaz P, Nowka B, Van Kessel MAHJ, Bourceau P, et al. Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus. Sci Adv. 2017;3:2–11.
Han H, Hemp J, Pace LA, Ganesan K, Roh JH, Daldal F, et al. Adaptation of aerobic respiration to low O2 environments. Proc Natl Acad Sci. 2012;109:7947–7947.
Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie. B, et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci. 2010;107:13479–84.
Farrenkopf AM, Luther GW. Iodine chemistry reflects productivity and denitrification in the Arabian Sea: Evidence for flux of dissolved species from sediments of western India into the OMZ. Deep Res Part II Top Stud Oceanogr. 2002;49:2303–18.
Griffin BM, Schott J, Schink B. Nitrite, an electron donor for anoxygenic photosynthesis. Science. 2007;316:1870.
van de Leemput IA, Veraart AJ, Dakos V, De Klein JJM, Strous M, Scheffer M. Predicting microbial nitrogen pathways from basic principles. Environ Microbiol. 2011;13:1477–87.
Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, et al. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci. 2015;112:11371–6.
Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, von Bergen M, et al. Cyanate as an energy source for nitrifiers. Nature. 2015;524:105–8.
Youngblut MD, Wang O, Barnum TP, Coates JD. Per)chlorate in biology on earth and beyond. Annu Rev Microbiol. 2016;70:435–57.
Sandy M, Butler A. Microbial iron acquisition: marine and terrestrial siderophores. Chem Rev. 2009;109:4580–95.
Chain P, Lamerdin J, Larimer F, Regala W, Lao V, Land M, et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol. 2003;185:2759–73.
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.
Conflict of interest
The authors declare that they have no conflict of interest.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
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
Nitrospina-Like Bacteria Are Potential Mercury Methylators in the Mesopelagic Zone in the East China Sea
Frontiers in Microbiology (2020)
Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira
The ISME Journal (2020)
Chemical Reviews (2020)
Frontiers in Marine Science (2020)
Scientific Reports (2019)