Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones

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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References

  1. 1.

    Arrigo KR. Marine microorganisms and global nutrient cycles. Nature. 2005;437:343–8.

    Article  Google Scholar 

  2. 2.

    Tyrrell T. The relative influences of nitrogen and phosohorus on oceanic primary production. Nature. 1999;400:525–31.

    CAS  Article  Google Scholar 

  3. 3.

    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.

    CAS  Article  Google Scholar 

  4. 4.

    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.

    Article  Google Scholar 

  5. 5.

    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.

    CAS  Article  Google Scholar 

  6. 6.

    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.

    CAS  Article  Google Scholar 

  7. 7.

    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.

    CAS  Article  Google Scholar 

  8. 8.

    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.

    CAS  Article  Google Scholar 

  9. 9.

    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.

    CAS  Article  Google Scholar 

  10. 10.

    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.

    CAS  Article  Google Scholar 

  11. 11.

    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.

    CAS  Article  Google Scholar 

  12. 12.

    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.

    CAS  Article  Google Scholar 

  13. 13.

    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.

    CAS  Article  Google Scholar 

  14. 14.

    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.

    Article  Google Scholar 

  15. 15.

    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.

    CAS  Article  Google Scholar 

  16. 16.

    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.

    Google Scholar 

  17. 17.

    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.

    CAS  Article  Google Scholar 

  18. 18.

    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.

    CAS  Article  Google Scholar 

  19. 19.

    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.

    CAS  Article  Google Scholar 

  20. 20.

    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.

    CAS  Article  Google Scholar 

  21. 21.

    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.

    Google Scholar 

  22. 22.

    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.

    CAS  Google Scholar 

  23. 23.

    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.

    CAS  Article  Google Scholar 

  24. 24.

    Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.

    CAS  Article  Google Scholar 

  25. 25.

    Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

    CAS  Article  Google Scholar 

  26. 26.

    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.

    Article  Google Scholar 

  27. 27.

    Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ. 2017;5:e3035.

    Article  Google Scholar 

  28. 28.

    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.

    CAS  PubMed  Google Scholar 

  29. 29.

    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.

    CAS  Article  Google Scholar 

  30. 30.

    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.

    CAS  Article  Google Scholar 

  31. 31.

    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.

    Article  Google Scholar 

  32. 32.

    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.

    CAS  Article  Google Scholar 

  33. 33.

    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.

    CAS  Article  Google Scholar 

  34. 34.

    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.

    CAS  Article  Google Scholar 

  35. 35.

    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.

    Article  Google Scholar 

  36. 36.

    Stewart FJ, Ulloa O, DeLong EF. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol. 2012;14:23–40.

    CAS  Article  Google Scholar 

  37. 37.

    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.

    Article  Google Scholar 

  38. 38.

    Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS  Article  Google Scholar 

  39. 39.

    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.

  40. 40.

    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.

    Article  Google Scholar 

  41. 41.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–13.

    CAS  Article  Google Scholar 

  42. 42.

    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.

    CAS  Article  Google Scholar 

  43. 43.

    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.

    Article  Google Scholar 

  44. 44.

    van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol. 2012;804:281–95.

    Article  Google Scholar 

  45. 45.

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    CAS  Article  Google Scholar 

  46. 46.

    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    CAS  Article  Google Scholar 

  47. 47.

    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.

    CAS  Article  Google Scholar 

  48. 48.

    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.

    Google Scholar 

  49. 49.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–60.

    CAS  Article  Google Scholar 

  50. 50.

    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.

    CAS  Article  Google Scholar 

  51. 51.

    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.

    CAS  Article  Google Scholar 

  52. 52.

    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.

    Google Scholar 

  53. 53.

    Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol. 2007;10:504–9.

    CAS  Article  Google Scholar 

  54. 54.

    Daims H, Lücker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol. 2016;24:699–712.

    CAS  Article  Google Scholar 

  55. 55.

    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.

    Article  Google Scholar 

  56. 56.

    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.

    CAS  Article  Google Scholar 

  57. 57.

    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.

    Article  Google Scholar 

  58. 58.

    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.

    CAS  Article  Google Scholar 

  59. 59.

    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.

    Article  Google Scholar 

  60. 60.

    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.

    CAS  Article  Google Scholar 

  61. 61.

    Griffin BM, Schott J, Schink B. Nitrite, an electron donor for anoxygenic photosynthesis. Science. 2007;316:1870.

    CAS  Article  Google Scholar 

  62. 62.

    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.

    Article  Google Scholar 

  63. 63.

    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.

    CAS  Article  Google Scholar 

  64. 64.

    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.

    CAS  Article  Google Scholar 

  65. 65.

    Youngblut MD, Wang O, Barnum TP, Coates JD. Per)chlorate in biology on earth and beyond. Annu Rev Microbiol. 2016;70:435–57.

    CAS  Article  Google Scholar 

  66. 66.

    Sandy M, Butler A. Microbial iron acquisition: marine and terrestrial siderophores. Chem Rev. 2009;109:4580–95.

    CAS  Article  Google Scholar 

  67. 67.

    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.

    CAS  Article  Google Scholar 

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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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Correspondence to Xin Sun.

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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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