Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
This is a preview of subscription content, access via your institution
Subscribe to this journal
Receive 51 print issues and online access
$199.00 per year
only $3.90 per issue
Rent or buy this article
Get just this article for as long as you need it
Prices may be subject to local taxes which are calculated during checkout
European Nucleotide Archive
All raw sequence data is available in the European Nucleotide Archive (ENA) under the project accession number PRJEB10139. The genome sequence of Ca. N. inopinata has been deposited at ENA under the project PRJEB10818, sequence accession LN885086. The draft genome of the betaproteobacterium from ENR4 and ENR6 is available in the JGI Integrated Microbial Genomes Database (https://img.jgi.doe.gov/cgi-bin/m/main.cgi) under the IMG Genome ID 2636415980.
Bock, E. & Wagner, M. in The Prokaryotes: A Handbook on the Biology of Bacteria (eds Dworkin, M. et al.) 457–495 (Springer, 2001)
Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005)
Winogradsky, S. Contributions a la morphologie des organismes de la nitrification. Arch. Sci. Biol. (St. Petersb.) 1, 87–137 (1892)
Arp, D. & Bottomley, P. J. Nitrifiers: more than 100 years from isolation to genome sequences. Microbe 1, 229–234 (2006)
Pfeiffer, T. & Bonhoeffer, S. Evolution of cross-feeding in microbial populations. Am. Nat. 163, E126–E135 (2004)
Heinrich, R. & Schuster, S. The regulation of cellular systems . (Chapman & Hall, 1996)
Costa, E., Pérez, J. & Kreft, J. U. Why is metabolic labour divided in nitrification? Trends Microbiol. 14, 213–219 (2006)
Pester, M. et al. NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira . Environ. Microbiol. 16, 3055–3071 (2014)
Hovanec, T. A., Taylor, L. T., Blakis, A. & Delong, E. F. Nitrospira-like bacteria associated with nitrite oxidation in freshwater aquaria. Appl. Environ. Microbiol. 64, 258–264 (1998)
Daims, H., Nielsen, J. L., Nielsen, P. H., Schleifer, K. H. & Wagner, M. In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl. Environ. Microbiol. 67, 5273–5284 (2001)
Watson, S. W., Bock, E., Valois, F. W., Waterbury, J. B. & Schlosser, U. Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite-oxidizing bacterium. Arch. Microbiol. 144, 1–7 (1986)
Taylor, M. W., Radax, R., Steger, D. & Wagner, M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71, 295–347 (2007)
Lebedeva, E. V. et al. Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol. Ecol. 75, 195–204 (2011)
Martiny, A. C., Albrechtsen, H. J., Arvin, E. & Molin, S. Identification of bacteria in biofilm and bulk water samples from a nonchlorinated model drinking water distribution system: detection of a large nitrite-oxidizing population associated with Nitrospira spp. Appl. Environ. Microbiol. 71, 8611–8617 (2005)
Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W. & Bock, E. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164, 16–23 (1995)
Schramm, A., De Beer, D., Wagner, M. & Amann, R. Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor. Appl. Environ. Microbiol. 64, 3480–3485 (1998)
Lücker, S. et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc. Natl Acad. Sci. USA 107, 13479–13484 (2010)
Gruber-Dorninger, C. et al. Functionally relevant diversity of closely related Nitrospira in activated sludge. ISME J. 9, 643–655 (2015)
Koch, H. et al. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira . Proc. Natl Acad. Sci. USA 112, 11371–11376 (2015)
Palatinszky, M. et al. Cyanate as an energy source for nitrifiers. Nature 524, 105–108 (2015)
Koch, H. et al. Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation. Science 345, 1052–1054 (2014)
Mobarry, B. K., Wagner, M., Urbain, V., Rittmann, B. E. & Stahl, D. A. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62, 2156–2162 (1996)
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnol. 31, 533–538 (2013)
Arp, D. J., Chain, P. S. G. & Klotz, M. G. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu. Rev. Microbiol. 61, 503–528 (2007)
Berube, P. M. & Stahl, D. A. The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea . J. Bacteriol. 194, 3448–3456 (2012)
Klotz, M. G. et al. Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ. Microbiol. 10, 3150–3163 (2008)
Bergmann, D. J., Hooper, A. B. & Klotz, M. G. Structure and sequence conservation of hao cluster genes of autotrophic ammonia-oxidizing bacteria: evidence for their evolutionary history. Appl. Environ. Microbiol. 71, 5371–5382 (2005)
Klotz, M. G. & Stein, L. Y. Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol. Lett. 278, 146–156 (2008)
Rittmann, B. E., Regan, J. M. & Stahl, D. A. Nitrification as a source of soluble organic substrate in biological treatment. Water Sci. Technol. 30, 1–8 (1994)
Nowka, B., Off, S., Daims, H. & Spieck, E. Improved isolation strategies allowed the phenotypic differentiation of two Nitrospira strains from widespread phylogenetic lineages. FEMS Microbiol. Ecol. 91, fiu031 (2015)
Ushiki, N., Fujitani, H., Aoi, Y. & Tsuneda, S. Isolation of Nitrospira belonging to sublineage II from a wastewater treatment plant. Microbes Environ. 28, 346–353 (2013)
van Kessel, M. A. H. J. et al. Complete nitrification by a single microorganism. Nature http://dx.doi.org/10.1038/nature16459 (2015)
Pester, M. et al. amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. nviron. Microbiol . 14, 525–539 (2012)
Purkhold, U. et al. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl. Environ. Microbiol. 66, 5368–5382 (2000)
Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012)
Stein, L. Y. et al. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ. Microbiol. 9, 2993–3007 (2007)
Chain, P. et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea . J. Bacteriol. 185, 2759–2773 (2003)
Suwa, Y. et al. Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia. J. Bacteriol. 193, 5047–5048 (2011)
Norton, J. M. et al. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl. Environ. Microbiol. 74, 3559–3572 (2008)
Klotz, M. G. et al. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl. Environ. Microbiol. 72, 6299–6315 (2006)
Radajewski, S. et al. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148, 2331–2342 (2002)
Stoecker, K. et al. Cohn’s Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc. Natl Acad. Sci. USA 103, 2363–2367 (2006)
Schramm, A., de Beer, D., van den Heuvel, J. C., Ottengraf, S. & Amann, R. Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol. 65, 3690–3696 (1999)
Altmann, D., Stief, P., Amann, R., De Beer, D. & Schramm, A. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ. Microbiol. 5, 798–803 (2003)
Foesel, B. U. et al. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm. FEMS Microbiol. Ecol. 63, 192–204 (2008)
Winkler, M. K. H., Bassin, J. P., Kleerebezem, R., Sorokin, D. Y. & van Loosdrecht, M. C. M. Unravelling the reasons for disproportion in the ratio of AOB and NOB in aerobic granular sludge. Appl. Microbiol. Biotechnol. 94, 1657–1666 (2012)
Maixner, F. et al. Nitrite concentration influences the population structure of Nitrospira-like bacteria. Environ. Microbiol. 8, 1487–1495 (2006)
Nowka, B., Daims, H. & Spieck, E. Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl. Environ. Microbiol. 81, 745–753 (2015)
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R. & Stahl, D. A. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria . Nature 461, 976–979 (2009)
Prosser, J. I. & Nicol, G. W. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 20, 523–531 (2012)
Lebedeva, E. V. et al. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” representing a clade globally distributed in thermal habitats. PLoS One 8, e80835 (2013)
Widdel, F. Anaerober Abbau von Fettsäuren und Benzoesäure durch neu isolierte Arten Sulfat-reduzierender Bakterien. PhD thesis, Univ. Göttingen (1980)
Kandeler, E. & Gerber, H. Short-term assay of soil urease activity using colorimetric determination of ammonium. Biol. Fertil. Soils 6, 68–72 (1988)
Hood-Nowotny, R., Hinko-Najera Umana, N., Inselbacher, E., Oswald-Lachouani, P. & Wanek, W. Alternative methods for measuring inorganic, organic, and total dissolved nitrogen in soil. Soil Sci. Soc. Am. J . 74, 1018–1027 (2010)
Griess-Romijn van Eck, E. Physiological and chemical tests for drinking water. NEN 1056 IV-2 Nederlands Normalisatie Instituut, Rijswijk, The Netherlands (1966)
Miranda, K. M., Espey, M. G. & Wink, D. A. A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide 5, 62–71 (2001)
Daims, H., Stoecker, K. & Wagner, M. in Molecular Microbial Ecology (eds Osborn, A. M. & Smith, C. J. ) 213–239 (Bios-Garland, 2005)
Daims, H., Brühl, A., Amann, R., Schleifer, K.-H. & Wagner, M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22, 434–444 (1999)
Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919–1925 (1990)
Daims, H. Use of fluorescence in situ hybridization and the daime image analysis program for the cultivation-independent quantification of microorganisms in environmental and medical samples. Cold Spring Harb. Protoc . 2009, t5253 (2009)
Daims, H., Lücker, S. & Wagner, M. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8, 200–213 (2006)
Sorokin, D. Y. et al. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi . ISME J. 6, 2245–2256 (2012)
Rotthauwe, J.-H., Witzel, K.-P. & Liesack, W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ. Microbiol. 63, 4704–4712 (1997)
Tourna, M., Freitag, T. E., Nicol, G. W. & Prosser, J. I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 10, 1357–1364 (2008)
Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L. & Schleper, C. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ. Microbiol. 5, 787–797 (2003)
Angel, R., Claus, P. & Conrad, R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J. 6, 847–862 (2012)
Angel, R. Total nucleic acid extraction from soil. Protoc. Exch . http://dx.doi.org/10.1038/protex.2012.046 (2012)
Watson, M. et al. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics 31, 114–115 (2015)
Hackl, T., Hedrich, R., Schultz, J. & Förster, F. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus. Bioinformatics 30, 3004–3011 (2014)
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010)
Dupont, C. L. et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6, 1186–1199 (2012)
Huson, D. H., Mitra, S., Ruscheweyh, H. J., Weber, N. & Schuster, S. C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21, 1552–1560 (2011)
Gregor, I., Dröge, J., Schirmer, M., Quince, C. & McHardy, A. C. PhyloPythiaS+: A self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. Preprint at http://arxiv.org/abs/1406.7123 (2014)
Dick, G. J. et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10, R85 (2009)
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012)
Boetzer, M. & Pirovano, W. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 15, 211 (2014)
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013)
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015)
Vallenet, D. et al. MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res. 41, D636–D647 (2013)
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014)
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014)
Benson, D. A. et al. GenBank. Nucleic Acids Res. 43, D30–D35 (2015)
Markowitz, V. M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560–D567 (2014)
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990)
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010)
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002)
Lartillot, N., Lepage, T. & Blanquart, S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288 (2009)
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004)
Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004)
Ronquist, F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542 (2012)
Richter, M. & Rosselló-Móra, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl Acad. Sci. USA 106, 19126–19131 (2009)
The R Project. R: A language and environment for statistical computing. https://www.r-project.org/ (R Foundation for Statistical Computing, 2013)
We thank T. K. Lee and M. Steinberger for help with PCR analyses, N. V. Grigor’eva and M. Pogoda for assistance with culture maintenance, N. A. Kostrikina for assistance with electron microscopy, K. Kitzinger for support with FISH analyses, M. Mooshammer for help with chemical analyses, R. Hatzenpichler for designing probe Nmir1009, K. Eismann for help with proteome sample preparation, B. Scheer for help with mass spectrometer maintenance, Purena GmbH (Wolfenbüttel, Germany) for cooperation, N. Chernyh and J. Rosenthal for taking samples, and H. Koch and E. Bock for discussion. The authors are grateful for using the analytical facilities of the Centre for Chemical Microscopy (ProVIS) (Helmholtz Centre for Environmental Research), which is headed by H. Richnow (Department of Isotope Biochemistry) and supported by European Regional Development Funds (EFRE–Europe funds Saxony) and the Helmholtz Association. P.P. and H.D. were supported by the Austrian Science Fund (FWF) projects P27319-B21 and P25231-B21 (to H.D.). M.P., J.V., P.H., and M.W. were supported by the European Research Council Advanced Grant project NITRICARE 294343 (to M.W.). M.A., R.H.K., and P.H.N. were supported by the Danish Council for Independent Research, DFF – 4005-00369 and Innovation Fund Denmark (EcoDesign).
The authors declare no competing financial interests.
Extended data figures and tables
Extended Data Figure 1 Photomicrographs and cell diagram of Ca. Nitrospira inopinata.
a, Transmission electron micrograph of a spiral-shaped cell with a flagellum. The size of Ca. N. inopinata cells is 0.18 to 0.3 μm in width and 0.7 to 1.6 μm in length. Scale bar represents 200 nm. b, Transmission electron micrograph of a thin section preparation. Microcolony showing the wide periplasmic space (PS), which is a characteristic feature of Nitrospira15. Scale bar represents 200 nm. c, Fluorescence image of cells from enrichment ENR4 after hybridization with oligonucleotide probes targeting Nitrospira (Ntspa662 and Ntspa712 both labelled with Cy3, red), the betaproteobacterium (Nmir1009 labelled with Cy5, blue), and Bacteria (EUB338 probe mix labelled with FLUOS, green). Ca. N. inopinata cells and microcolonies appear yellow and the betaproteobacterial cells appear cyan due to simultaneous hybridization to the respective specific probe and the EUB338 probe mix. Scale bar represents 2 μm. d, Cell metabolic cartoon constructed from the annotation of the Ca. N. inopinata genome. Enzyme complexes of the electron transport chain are labelled by Roman numerals.
Extended Data Figure 2 Sequence composition-independent binning of the metagenome scaffolds from the nitrifying enrichment cultures.
Circles represent scaffolds, scaled by the square root of their length. Only scaffolds ≥5 kbp are shown. Clusters of similarly coloured circles represent potential genome bins. These differential coverage plots were the starting points for further refinement and finishing of genome assemblies as described elsewhere23. a, binning of the scaffolds from enrichment culture ENR4 containing Ca. N. inopinata and three heterotrophic populations related to the Betaproteobacteria, Alphaproteobacteria, and Actinobacteria. b, binning of the scaffolds from enrichment culture ENR6 containing only Ca. N. inopinata and the betaproteobacterial accompanying heterotrophic organism. Enrichment ENR4, sample A, was used for comparison in differential coverage binning of culture ENR6.
Extended Data Figure 3 Circular representation of the Ca. N. inopinata chromosome.
Predicted coding sequences (CDS; rings 1+2), genes of enzymes involved in nitrification and other pathways of catabolic nitrogen metabolism (ring 3), RNA genes (ring 4), and local nucleotide composition measures (rings 5+6) are shown. Very short features were enlarged to enhance visibility. Clustered genes, such as several transfer RNA genes, may appear as one line owing to space limitations. The tick interval is 0.2 Mbp. Amo, ammonia monooxygenase; HAO, hydroxylamine dehydrogenase; CycA and CycB, tetraheme c-type cytochromes that form the hydroxylamine ubiquinone redox module together with HAO; NirK, Cu-dependent nitrite reductase; Nrf, cytochrome c nitrite reductase; Nxr, nitrite oxidoreductase; Orf, open reading frame.
Extended Data Figure 4 Phylogenetic affiliation of Ca. N. inopinata.
The maximum likelihood tree, which is based on 16S ribosomal RNA sequences of cultured and uncultured representative members of the genus Nitrospira, shows that the comammox organism Ca. N. inopinata (highlighted green) is a member of Nitrospira lineage II. Another 16S rRNA gene sequence was extracted from MBR metagenomic Nitrospira bin 1 (also highlighted green). This sequence bin also contained amo and hao genes (main text Fig. 1, Extended Data Figs 8 and 9). The cultured Nitrospira strains other than Ca. N. inopinata, which are not known to use ammonia as a source of energy and reductant, are highlighted blue. Nitrospira lineages are labelled red. Pie charts indicate statistical support of branches based on maximum likelihood (ML; 1,000 bootstrap iterations) and Bayesian inference (BI; posterior probability, 4 independent chains). In total, 95 taxa and 1,543 nucleotide sequence alignment positions were considered. Numbers in wedges indicate the numbers of taxa. The scale bar indicates 0.1 estimated substitutions per nucleotide.
Extended Data Figure 5 Phylogeny of NXR from Ca. N. inopinata and related proteins.
a, b, Maximum likelihood trees showing the alpha (a) and beta (b) subunits of selected enzymes from the DMSO reductase type II family. Names of validated enzymes are indicated (Clr, chlorate reductase; Ddh, dimethylsulfide dehydrogenase; NAR, nitrate reductase; NXR, nitrite oxidoreductase; Pcr, perchlorate reductase; Ser, selenate reductase). More distantly related molybdoenzymes were used as outgroup. Black dots on branches indicate high maximum likelihood bootstrap support (≥90%; 1,000 iterations). Known NXR forms are highlighted in red. The inset in a contains a subtree, which shows the phylogenetic affiliation of the NAR of the betaproteobacterium from enrichments ENR4 and ENR6 (highlighted in blue) with canonical nitrate reductases of Proteobacteria. In total, 1,279 (a) and 556 (b) amino acid sequence alignment positions, and 134 (a) and 99 (b) taxa (including outgroups), were considered. c, d, Maximum likelihood trees showing only Nitrospira NxrA (c) and nxrB (d) phylogenies. The tree in d was calculated using nucleotide sequences aligned according to their amino acid translations. Ca. N. inopinata is highlighted in red, sequences from metagenomic Nitrospira bins obtained in this study are highlighted in green. Asterisks mark metagenomic bins that also contain amo genes. Metagenomic bins are numbered as in Supplementary Table 8. Sublineages of the genus Nitrospira are indicated. As recognized earlier8, lineage II is paraphyletic with respect to lineage I in nxrB phylogenies, but differentiation of the lineages is stable. Pie charts indicate statistical support of branches based on maximum likelihood (ML; 1,000 bootstrap iterations) and Bayesian inference (BI; posterior probability, 3 independent chains). In total, 1,279 amino acid sequence alignment positions (c) and 1,290 nucleotide sequence alignment positions (d), and 30 (c) and 40 (d) taxa (including outgroups), were considered. All panels: numbers in or next to wedges indicate the numbers of taxa. The scale bars indicate 0.1 estimated substitutions per residue.
Extended Data Figure 6 Absence of nitrifying activity in the betaproteobacterium found in enrichments ENR4 and ENR6.
a, b, Incubation of a pure culture of the betaproteobacterium in mineral medium containing 1 mM ammonium (a) or 0.5 mM nitrite plus 0.1 mM ammonium as nitrogen source (b). No conversion of ammonium to nitrite or nitrate, or of nitrite to nitrate, was observed. Data points in a and b show means, error bars show 1 s.d. of n = 3 biological replicates. If not visible, error bars are smaller than symbols. The mean initial densities of the cultures, as determined by qPCR of the single-copy soxB gene, were 7.15 ± 0.01 (log(soxB copies) ml−1, 1 s.d., n = 3) for the 1 mM ammonium experiment (a) and 7.22 ± 0.02 (log(soxB copies) ml−1, 1 s.d., n = 3) for the 0.5 mM nitrite plus 0.1 mM ammonium experiment (b). After 48 h of incubation, the mean densities were 7.06 ± 0.10 and 7.15 ± 0.29, respectively. A slight decrease in the ammonium concentration was observed in these experiments and also in an abiotic control incubation containing only medium and 1 mM ammonium, but no cells (data points for this control show means of two technical replicates). It might be explained by adsorption of ammonium to the glass bottles or by outgassing of NH3. c, Photographs of incubation bottles after 53 h of incubation. The mean optical density at 600 nm (OD600) of the cultures at this time point was 0.006 ± 0.003 (1 s.d., n = 3) for the 1 mM ammonium experiment and 0.007 ± 0.008 (1 s.d., n = 3) for the 0.5 mM nitrite plus 0.1 mM ammonium experiment. Control incubations were carried out in medium containing 4 mM acetate and 0.1 mM ammonium as nitrogen source for assimilation (three biological replicates). The inoculum for these cultures was 2.5-fold diluted compared to the experiments with ammonium or nitrite. After incubation, the acetate-grown cultures were visibly turbid with a mean OD600 of 0.068 ± 0.011 (1 s.d., n = 3) and the mean density was 8.12 ± 0.03 (log(soxB copies) ml−1, 1 s.d., n = 3). Thus, the culture of the betaproteobacterium, which was used to inoculate all experiments, was physiologically active and grew on acetate. d, Fluorescence images showing the culture of the betaproteobacterium after FISH with the EUB338 probe mix (labelled with FLUOS, green), probe Nmir1009 that is specific for this organism (labelled with Cy3, red), and DAPI counterstaining (blue). The images show the same field of view after splitting the colour channels. According to FISH, all detected cells were the betaproteobacterium.
Extended Data Figure 7 Protein abundance levels of Ca. N. inopinata during growth on ammonia.
Displayed are the 450 most abundant proteins from Ca. N. inopinata in the metaproteome from culture ENR4 after incubation with 1 mM ammonium for 48 h. Red arrows and labels highlight key proteins for ammonia and nitrite oxidation. Columns show the mean normalized spectral abundance factor (NSAF), error bars show 1 s.d. of n = 4 biological replicates. In total 1,083 proteins in the metaproteome were unambiguously assigned to Ca. N. inopinata. Only one of the four putative NXR gamma subunits (NxrC) was among the top 450 expressed proteins. The other three NxrC candidates ranked at positions 561, 605 and 931. The AmoE1 protein was ranked at position 520, and HaoB at position 653.
Extended Data Figure 8 Phylogenetic affiliation of comammox amoA sequences to amoA sequences from different environments.
Bayesian inference tree showing the phylogenetic relationship of the amoA sequences from Ca. N. inopinata and metagenomic bins from this study (224 taxa, 939 nucleotide alignment positions). Ca. N. inopinata clusters confidently into comammox amoA clade A. Comammox amoA clade B (116 taxa) has been collapsed for clarity and the proportion of database sequences from soil (95 taxa), freshwater (13 taxa), and engineered environments (4 taxa) is represented as a proportion of the collapsed clade. AmoA from the metagenomic Nitrospira bins generated for this study (5 taxa in clade A, 4 taxa in clade B) are numbered as in Supplementary Table 8. Scale bar indicates estimated change per nucleotide. The outgroup consists of 27 betaproteobacterial amoA and 29 diverse pmoA sequences.
Extended Data Figure 9 Phylogenetic relationship of comammox amoB, amoC and hao sequences to corresponding gene family members.
Trees were calculated with PhyloBayes using nucleotide sequences aligned according to their amino acid translations. Support values indicate the consensus probability from 5 independent chains. Sequences outside the comammox clades are coloured as in main text Fig. 3. Metagenomic bins are numbered as in Supplementary Table 8. Scale bars indicate the estimated substitutions per nucleotide. a, Phylogenetic relationship of Ca. N. inopinata amoB to other amoB and pmoB genes (57 taxa, 1,518 alignment positions). b, Phylogenetic relationship of Ca. N. inopinata amoC to other amoC and pmoC genes (81 taxa, 993 alignment positions). c, Phylogenetic relationship of Ca. N. inopinata hydroxylamine dehydrogenase (hao) to other hao genes (37 taxa, 2,875 alignment positions).
Extended Data Figure 10 Genome-wide tetranucleotide analysis of Ca. N. inopinata and other Nitrospira.
Correlation of tetranucleotide patterns in a 5 kb sliding window (step size 1 kb) against genome-wide tetranucleotide signatures. The positions of key nitrification genes are indicated. Regions where the tetranucleotide patterns significantly deviate from the genome-wide signature, and nitrification genes located in such regions, are highlighted in green. Asterisks mark genes that are outside significantly deviating regions but may appear to be inside due to space limitations in the figure. a, Ca. N. inopinata (member of Nitrospira lineage II). The hao, cycA, and cycB genes are located in a region whose tetranucleotide pattern deviates slightly but not significantly from the genome-wide signature. The P value cutoff from the Benjamini–Hochberg procedure, indicating a significantly low correlation for a window’s tetranucleotide signature, was 0.00065 for this genome. b, N. moscoviensis (member of Nitrospira lineage II). The P value cutoff for this genome was 0.0013. c, N. defluvii (member of Nitrospira lineage I). The P value cutoff for this genome was 0.00072. In N. moscoviensis (b) and N. defluvii (c), all nxr genes are outside regions with significantly deviating tetranucleotide patterns.
This file contains Supplementary Tables 1-3 and Supplementary Table 8. (PDF 242 kb)
Supplementary Table 4
This file contains Supplementary Table 4, which lists marker genes and their copy numbers detected by CheckM in the closed Ca. N. inopinata genome. (XLSX 17 kb)
Supplementary Table 5
This file contains Supplementary Table 5, which lists marker genes and their copy numbers detected by CheckM in the genome of the betaproteobacterium found in enrichment cultures ENR4 and ENR6. (XLSX 26 kb)
Supplementary Table 6
This file contains Supplementary Table 6, which lists marker genes and their copy numbers detected by CheckM in the genome of the alphaproteobacterium found in enrichment culture ENR4. (XLSX 26 kb)
Supplementary Table 7
This file contains Supplementary Table 7, which lists marker genes and their copy numbers detected by CheckM in the genome of the actinobacterium found in enrichment culture ENR4. (XLSX 17 kb)
Rights and permissions
About this article
Cite this article
Daims, H., Lebedeva, E., Pjevac, P. et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504–509 (2015). https://doi.org/10.1038/nature16461
This article is cited by
Nitrification inhibitor 1-octyne inhibits growth of comammox Nitrospira but does not alter their community structure in an acidic soil
Journal of Soils and Sediments (2023)
Effect of biochar and DMPP application alone or in combination on nitrous oxide emissions differed by soil types
Biology and Fertility of Soils (2023)
Soil nitrogen functional transformation microbial genes response to biochar application in different irrigation paddy field in southern China
Environmental Science and Pollution Research (2023)
Plant Species–Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland
Microbial Ecology (2023)
Enhanced biological phosphorus and nitrogen removal by high-concentration powder carriers: extracellular polymeric substance, microbial communities, and metabolic pathways
Environmental Science and Pollution Research (2023)
By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.