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Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil

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Abstract

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.

Introduction

The first step in the aerobic nitrification process is the oxidation of ammonia to nitrite, mediated mainly by AOB or AOA in soil environments. The most numerous AOB isolated or detected by non-cultural methods in aerobic agricultural surface soils are consistently members of the Nitrosospira genus [1]. Nitrosospira briensis C-128 [2] is a chemolithoautotrophic ammonia-oxidizing betaproteobacterium (order Nitrosomonadales , family Nitrosomonadaceae , genus Nitrosospira [39]) isolated from a fertilized soil under cultivation for blueberry in Falmouth, Massachusetts, USA in 1971. The genome of Nitrosospira briensis C-128 is the third genome sequence from the genus Nitrosospira [810] to be published [1113] and thus provides an important comparison among Nitrosospira . This report includes a summary of the genome sequence and selected features for Nitrosospira briensis C-128 and results are publically available in GenBank accession CP012371.

Organism information

Classification and features

Nitrosospira briensis was described by Winogradsky and & Winogradsky in 1933 [8] as an ammonia-oxidizing bacterium isolated from soil. The genus name, Nitrosospira , is derived from two Latin roots: nitrosus, meaning nitrous, and spira, indicating spiral. The species name briensis, refers to the original isolation location near Brie, France. The culture described by Winogradsky & Winogradsky [8] was not maintained and reisolation of a replacement strain was reported by Watson in 1971 [14]. At approximately the same time, N. briensis strain C-128 was isolated by enrichment culturing [15] from a surface soil sample (pH 6.2) collected from a fertilized blueberry patch in East Falmouth, Massachusetts in 1971 (Frederica Valois). In 1993, the genus Nitrosospira was emended to include the former genera of Nitrosovibrio and Nitrosolobus [9] based on the high identities of the 16S rRNA gene sequences. Nitrosospira briensis was designated the type species for the genus with strain C-76 as the type strain (also known as strain Nsp10 [16]Footnote 1). The full-length 16S rRNA gene sequence of N. briensis C-128 is 99 % identical to the N. briensis strain C-76/Nsp10 sequence (Fig. 1). The culture of N. briensis strain C-128 was received in the Norton laboratory from F. Valois (Woods Hole Oceanographic Institution) in 1995. Nitrosospira briensis C-128 is presently maintained in a culture collection at WHOI and may be obtained upon request from J.M. Norton. Classification and general features of Nitrosospira briensis C-128 are provided as Minimum Information about the Genome Sequence (MIGS) in Table 1. Electron micrographs of the pure culture organism are shown in Fig. 2 revealing the tight spirals visible with TEM negative staining and the convoluted surface of this Nitrosospira as revealed by SEM.

Fig. 1
figure1

The phylogenetic tree highlighting the position of Nitrosospira briensis C-128 relative to other Nitrosomonadaceae [48] and Spirillum volutans (outgroup). The tree was inferred from 1417 aligned characters of the 16S rRNA gene sequence by the neighbour-joining method [49] using the sotware MEGA [50]. Support values (%) at branch points are from 1000 NJ bootstrap replicates and shown only for values exceeding 60 %. GenBank references are for genomes (full-length 16S rRNA gene extracted) or are the near full-length 16S rRNA sequences [51]. Bold denotes a genome sequence available (NCBI or GOLD), whereas bold blue denotes the published genomes: Nitrosomonas europaea [52], “Nitrosomonas eutropha” [53], “Nitrosomonas communis” [54], Nitrosomonas sp. AL212 [55], “Nitrosomonas ureae” [56], Nitrosomonas sp. Is79A3 [57], Nitrosospira briensis C-128 (this study), Nitrosospira lacus APG3 [11] and Nitrosospira multiformis [12]

Table 1 Classification and general features of Nitrosospira briensis C-128 [42, 43]
Fig. 2
figure2

Electron micrographs of N. briensis. A) TEM prepared by negative staining as previously described [14, 15]. Scale is 1000 nm. B) SEM of Nitrosospira briensis C-128. Glass coverslips were placed in a growing culture for approximately one month, removed and then fixed with 2 % glutaraldehyde in 0.1 % HEPES buffer overnight. The samples were subjected to alcohol series dehydration (50-100 % ethanol) and then chemically dried using hexamethyldisilazane. The image shows presumptive invaginations of the membranes of the cell. Scale is 500 nm

Genome sequencing information

Genome project history

Nitrosospira briensis C-128 was chosen for sequencing through the Community Science Program (2010) of the DOE Joint Genome Institute as an important representative of the AOB to improve the scope and quality of intra- and inter-generic comparisons in the Nitrosomonadales . The chemolithotrophic metabolism of the AOB, the pathways for production of nitrous oxide and urea metabolism were additional motivating interests in sequencing this genome. Sequencing, finishing, and annotation were accomplished by JGI. The genome sequence has been deposited in the Genome OnLine Database [17] and is part of the NCBI Reference Sequence Collection [18]. A summary of the project information is found in Table 2.

Table 2 Genome sequencing project information

Growth conditions and genomic DNA preparation

Nitrosospira briensis C-128 was grown in a 25 mM ammonium medium pH 7 containing mineral salts and phenol red at 28 °C in 100 ml of media in 500 ml flasks as described previously [19]. The pH was adjusted to neutral using 0.5 M KHCO3 as needed during growth. Early stationary phase cultures were checked at harvest for heterotrophic contamination by plating 0.1 mL on ¼ strength nutrient agar plates and incubating for two weeks. Cells were harvested from four 100 mL cultures by centrifugation (13,000 RCF for 30 min). Bacterial genomic DNA (gDNA) was isolated using the CTAB protocol recommended by JGI [20]. Size and quality of the gDNA was assessed via gel electrophoresis and amplification of the V4 region of the 16S rRNA gene using universal primers [21] followed by sequencing at the Center for Integrative Biosystems, USU on the ABI PRISM™ 3730 DNA Analyzer using BigDye terminator chemistry. The gDNA was of the expected size (greater than 23 kbp) and no contaminating organisms were detected by partial 16S rRNA gene sequencing of 10 replicate reactions or by plating. Approximately 20 μg of DNA was submitted to JGI for sequencing.

Genome sequencing and assembly

The genomic DNA of Nitrosospira briensis C-128 was sequenced at the DOE JGI using the Pacific Biosciences (PacBio) sequencing technology [22]. All general aspects of sample handling, library construction and sequencing followed JGI isolate sequencing protocols. A PacBio SMRTbell™ library was constructed and sequenced on the PacBio RS platform, which generated 148,206 reads totaling 519.8Mbp. Raw reads were assembled using HGAP v. 2.2.0.p1 [23]. The final draft assembly contained one contig in one scaffold, totaling 3.2 Mbp in size. The input read coverage was 176.1×. An earlier version of the genome was sequenced using the Illumina Hi-Seq 2000 platform. However, this earlier sequence assembly JHVX00000000.1 remained in 31 scaffolds (sequences JHVX01000001.1-JHVX01000031.1) with the nearly identical repeats of several key catabolic gene clusters remaining unresolved. Previously, genome closure for Nitrosospira [12] was achieved only after extensive directed finishing to correctly assemble long nearly identical repeats of gene clusters encoding key catabolic modules including ammonia monooxygenase (amo) for the activation of substrate and hydroxylamine dehydrogense (haoA) and heme-cytochrome c proteins (cycAB) for the extraction of electrons and their delivery to the quinone pool in the membrane [24]. The long read capability of the PacBio platform and our depth of coverage enabled sufficient discrimination of repeats to assemble across multiple nearly identical regions into a single contig representing the chromosome of the bacterium. For predicted genes outside of gaps and repeat regions the PacBio and the Illumina predicted genes were 100 % identical. Therefore, we did not combine the Illumina Hi-Seq data with the PacBio data for the complete genome sequence CP012371 reported here.

Genome annotation

Genes were identified using Prodigal [25], as part of the JGI’s Microbial annotation pipeline followed by a round of manual curation using GenePRIMP [26]. The predicted CDSs were translated and used to search the NCBI nonredundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. Transfer RNA genes were identified using the tRNAScanSE tool [27]. Ribosomal RNA genes were found by searches against models of the ribososmal RNA genes built from SILVA [28]. Other non-coding RNAs were found using INFERNAL [29]. Further gene prediction and manual curation was performed within the Integrated Microbial Genomes (IMG) platform [30] developed at JGI.

Genome properties

The genome of Nitrosospira briensis C-128 contains 3,210,113-bp in one chromosome with a GC content of 53.25 % and no plasmids (Fig. 3). The genome contains one complete ribosomal RNA operon similar to other AOB [3]. Coding bases (2,758,471) comprised 85.93 % of the total. We identified 3018 protein encoding genes, 55 RNA genes and 130 pseudogenes. For the identified genes, 74.23 % had a function prediction associated with them. The two-way average nucleotide identity [31] between the chromosomes of Nitrosospira multiformis ATCC 25196 [9, 32, 33] and Nitrosospira briensis C-128 was found to be 77.2 % confirming species delineation [34]. The genome statistics are summarized in Table 3 and genes associated with COG functional categories are summarized in Table 4.

Fig. 3
figure3

a Graphical map of the genome. From the outside to the center: genes on forward stand and Genes on reverse strand (color by COG categories see legend), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. b Legend for COG category colors

Table 3 Genome statistics
Table 4 Number of genes associated with general COG functional categories

Insights from the genome sequence

Selected functional inventory in the complete genome sequence

Nitrosospira briensis C-128 contains complete “amo” and “hao” gene clusters in three nearly identical copies on the chromosome. The full-length amoCABEDcopCD gene cluster is repeated twice (F822_1680-1686, & 2228–2234) while the third cluster contains only the three structural “amo” genes, amoCAB (F822_0880-0878). As in most other betaproteobacterial AOB genomes, the N. briensis C-128 genome contains three additional amoC singleton genes (F822_0485, 1530, & 2742). The “hydroxylamine-ubiquinone redox module” (HURM) [24] is encoded by the haoAB-cycAB gene cluster, which occurs three times (F822_0640-0643, 0873–0876, 1808–1811) in the genome sequence. The N. briensis C-128 genome also encodes nitrosocyanin (ncyA; F822_2886), a protein unique to ammonia-oxidizing bacteria, which possibly functions in the regulation of electron transfer [35]. A urease operon containing α, β, & γ subunit-encoding genes as well as genes encoding accessory proteins E, F, G, & H (F822_0450-0456) is preceded by a urea transporter gene (utp; F822_0449). Genes encoding alternative catabolic inventory such as hydrogenase were not identified. The N. briensis C-128 genome contains a single gene cluster encoding the Calvin-Benson-Bassham cycle for carbon assimilation including the carboxylation reaction, which is encoded by a single-copy cbb operon in the Form 1C (red-like) subgroup (F822_1009-1012) with > 90 % identity with homologous genes in Nitrosospira multiformis [36] and Nitrosospira sp. 40KI [37].

Genes encoding inventory implicated in nitrogen oxide metabolism and /or nitrosative stress [38] include those for copper nitrite reductase (nirK, singleton F822_2604) and a possible quinol nitric oxide reductase (qNOR) encoding gene (F822_0115). Similar to arrangements in many AOB genomes, a gene cluster (norSY-senC-orf1) (F822_ 1803–1806) encoding nitric oxide reductase heme-copper oxidase (sNOR) was found upstream of a nitrite transporter gene (F822_1807) and one of the three haoAB-cycAB clusters. However, the norCBQD cluster encoding cytochrome C nitric oxide reductase (cNOR) was not found. The genes encoding precursors of cytochromes c’-beta (cytS) and P-460 (cytL) were not detected in the C-128 genome sequence. The gene of NO-responsive regulator (nnrS) was present albeit truncated.

CRISPR/Cas System Nitrosospira briensis C-128 contains a CRISPR/Cas system located at F822_1846-1851 suggestive of phage interactions [39]. The CRISPR-associated (CAS) proteins belong to the subtype 1-F ( Yersinia pestis type) [40]. The CRISPR contains 11 spacers each with 32 bp. No matches between these spacers and protospacers in viral genomes were detected in the NCBI non-redundant database. The direct repeat sequence in the CRISPR is 28 bp: TTTCTGAGCTGCCTATGCGGCAGTGAAC. As soil viral metagenomes become better characterized, associations between viral protospacers and the spacers found in N. briensis CRISPR may help to identify possible phage types of N. briensis .

Conclusions

Nitrosospira briensis C-128 has a suite of genes enabling it to survive in soil environments as a chemolithoautotroph. The completion of several genomes in the Nitrosospira genus will facilitate a comprehensive analysis of the genetic toolkit that enables these AOB to co-inhabit the terrestrial niche. Further experiments elucidating gene function, especially those involved in the metabolism of nitrogen oxides and related to nitrosative stress [41], will increase the relevance of the completed genome of Nitrosospira briensis C-128. The evolutionary relationships in the genera of the Nitrosomonadaceae are currently under reconsideration.

Notes

  1. 1.

    Editor’s note – Readers are advised that the published record regarding the type strain and a proposed neotype strain of Nitrosospira briensis is problematic. Although the Approved Lists of Bacterial Names (Int J Syst Bacteriol 1980; 30:225) list the type as “no culture available”, Koops and Harms subsequently published on strain Nsp 10 as the equivalent to ATCC 25971 (Arch Microbiol 1985; 141:214–218)

Abbreviations

AOA:

Ammonia-oxidizing archaea

AOB:

Ammonia-oxidizing bacteria

WHOI:

Woods Hole Oceanographic Institution

References

  1. 1.

    Norton JM. Nitrification in Agricultural Soils. In: Schepers JS, Raun WR, editors. Nitrogen in Agricultural Systems. Madison: American Society of Agronomy, Inc.; Crop Science Society of America, Inc.; Soil Science Society of America, Inc; 2008. p. 173–99.

  2. 2.

    Exemplar Abstract for Nitrosospira briensis C-128. NamesforLife, LLC. Retrieved May 4, 2016. http://doi.org/10.1601/ex.18586

  3. 3.

    Prosser JI, Head IM, Stein L. The family Nitrosomonadaceae. In: Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F, editors. The prokaryotes. Heidelberg: Springer; 2014. p. 901–18.

  4. 4.

    Garrity G, Bell J, Lilburn T, Family I. Nitrosomonadaceae fam. nov. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s manual of systematic bacteriology volume 2 part C. New York: Springer; 2005. p. 864.

  5. 5.

    Garrity G, Bell J, Lilburn T, Order V. Nitrosomonadales ord. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s manual of systematic bacteriology volume 2 part C. New York: Springer; 2005. p. 863.

  6. 6.

    Skerman V, McGowan V, Sneath P, Moore W, Moore LV. Approved lists of bacterial names. Int J Syst Bacteriol. 1980;30:225–420.

  7. 7.

    Garrity G, Bell J, Lilburn T, Class II. Betaproteobacteria class. nov. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s manual of systematic bacteriology. Volume 2 part C. New York: Springer; 2005. p. 575.

  8. 8.

    Winogradsky S, Winogradsky H. Etudes sur la microbiologie du sol. VII. Nouvelles recherches sur les organismes de la nitrification. Ann Inst Pasteur (Paris). 1933;50:350–432.

  9. 9.

    Head IM, Hiorns WD, Embley TM, McCarthy AJ, Saunders JR. The phylogeny of autotrophic ammonia -oxidizing bacteria as determined by analysis of 16S ribosomal -RNA sequences. J Gen Microbiol. 1993;139:1147–53.

  10. 10.

    Name Abstract for Nitrosospira. NamesforLife, LLC. Retrieved May 5, 2016. http://doi.org/10.1601/nm.2005.

  11. 11.

    Garcia JC, Urakawa H, Le VQ, Stein LY, Klotz MG, Nielsen JL. Draft genome sequence of Nitrosospira sp. strain APG3, a psychrotolerant ammonia-oxidizing bacterium isolated from sandy lake sediment. Genome Announc. 2013;1(6):e00930–13.

  12. 12.

    Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PSG, Hauser LJ, Land ML, Larimer FW, Shin MW, et al. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol. 2008;74(11):3559–72.

  13. 13.

    Urakawa H, Garcia JC, Nielsen JL, Le VQ, Kozlowski JA, Stein LY, Lim CK, Pommerening-Röser A, Martens-Habbena W, Stahl DA, et al. Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment. Int J Syst Evol Microbiol. 2015;65:242–50.

  14. 14.

    Watson SW. Reisolation of Nitrosospira briensis S. Winogradsky and H. Winogradsky 1933. Arch Mikrobiol. 1971;75:179–88.

  15. 15.

    Watson S, Valois F, Waterbury J. The family Nitrobacteraceae. In: Starr MP, Stolp H, Schlegel HG, editors. Prokaryotes: a handbooks on habits, isolation, and identification of bacteria, vol. 1. New York: Springer; 1981. p. 1005–22.

  16. 16.

    Watson SW. Taxonomic considerations of the family Nitrobacteraceae Buchanan. Int J Syst Bacteriol. 1971;21(1):254–70.

  17. 17.

    Reddy TB, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta)genome project classification. Nucleic Acids Res. 2015;43(Database issue):D1099–106.

  18. 18.

    Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42(Database issue):D553–9.

  19. 19.

    Norton JM, Alzerreca JJ, Suwa Y, Klotz MG. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol. 2002;177(2):139–49.

  20. 20.

    Feil WS, Feil H, Copeland A. Bacterial DNA Isolation, CTAB Protocol. DOE Joint Genome Institute [http://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2014/02/JGI-Bacterial-DNA-isolation-CTAB-Protocol-2012.pdf]. Accessed 19 Apr 2016.

  21. 21.

    He ZL, Xu MY, Deng Y, Kang SH, Kellogg L, Wu LY, Van Nostrand JD, Hobbie SE, Reich PB, Zhou JZ. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol Lett. 2010;13(5):564–75.

  22. 22.

    Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323(5910):133–8.

  23. 23.

    Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10(6):563–9.

  24. 24.

    Simon J, Klotz MG. Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations. Biochim Biophys Acta (BBA)-Bioenergetics. 2013;1827(2):114–35.

  25. 25.

    Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):119.

  26. 26.

    Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010;7(6):455–7.

  27. 27.

    Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.

  28. 28.

    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35(21):7188–96.

  29. 29.

    Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29(22):2933–5.

  30. 30.

    Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2013; gkt963

  31. 31.

    Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57(1):81–91.

  32. 32.

    List_Editor. Validation List no. 54. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1995;45:619–620.

  33. 33.

    Watson SW, Graham LB, Remsen CC, Valois FW. A lobular, ammonia-oxidizing bacterium, Nitrosolobus multiformis nov. gen. nov. sp. Arch Mikrobiol. 1971;76:183–203.

  34. 34.

    Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Phil Trans R Soc B. 2006;361(1475):1929–40.

  35. 35.

    Stein LY, Campbell MA, Klotz MG. Energy-mediated vs. ammonium-regulated gene expression in the obligate ammonia-oxidizing bacterium, Nitrosococcus oceani. Front Microbiol. 2013;4:00277.

  36. 36.

    Name Abstract for Nitrosospira multiformis. NamesforLife, LLC. Retrieved May 4, 2016. http://doi.org/10.1601/nm.2007.

  37. 37.

    Utaker JB, Andersen K, Aakra A, Moen B, Nes IF. Phylogeny and functional expression of ribulose 1,5-bisphosphate carboxylase/oxygenase from the autotrophic ammonia-oxidizing bacterium Nitrosospira sp. isolate 40KI. J Bacteriol. 2002;184(2):468–78.

  38. 38.

    Stein LY. Surveying N2O-producing pathways in bacteria. In: Klotz MG, editor. Methods in enzymology: research on nitrification and related processes, Vol 486, Part A. San Diego: Academic; 2011. p. 131–52.

  39. 39.

    Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol. 2010;64(1):475–93.

  40. 40.

    Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJM, Wolf YI, Yakunin AF, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011;9(6):467–77.

  41. 41.

    Kozlowski JA, Price J, Stein LY. Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718. Appl Environ Microbiol. 2014;80(16):4930–5.

  42. 42.

    Chain PSG, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, et al. Genome project standards in a new era of sequencing. Science. 2009;326(5950):236–7.

  43. 43.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26(5):541–7.

  44. 44.

    Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87(12):4576–9.

  45. 45.

    Garrity G, Bell J, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s manual of systematic bacteriology. Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.

  46. 46.

    List_Editor. Validation list No.107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2006;56(1):1–6.

  47. 47.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9.

  48. 48.

    Name Abstract for Nitrosomonadaceae. NamesforLife, LLC. Retrieved May 5, 2016. http://doi.org/10.1601/nm.1991

  49. 49.

    Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–25.

  50. 50.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.

  51. 51.

    Koops HP, Bottcher B, Moller UC, Pommerening-Roser A, Stehr G. Classification of eight new species of ammonia-oxidizing bacteria: Nitrosomonas communis sp nov., Nitrosomonas ureae sp nov., Nitrosomonas aestuarii sp nov., Nitrosomonas marina sp nov., Nitrosomonas nitrosa sp nov., Nitrosomonas oligotropha sp nov., Nitrosomonas halophila sp nov. J Gen Microbiol. 1991;137:1689–99.

  52. 52.

    Chain PSG, Lamerdin J, Larimer F, Regala W, Lao V, Land M, Hauser L, Hooper A, Klotz M, Norton J, et al. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J Bacteriol. 2003;185(9):2759–73.

  53. 53.

    Stein LY, Arp DJ, Berube PM, Chain PSG, Hauser L, Jetten MSM, Klotz MG, Larimer FW, Norton JM, Op den Camp HJ, et al. Whole-genome analysis of the ammonia-oxidzing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol. 2007;9(12):2993–3007.

  54. 54.

    Kozlowski JA, Kits KD, Stein LY. Genome sequence of Nitrosomonas communis strain Nm2, a mesophilic ammonia-oxidizing bacterium isolated from mediterranean soil. Genome Announc. 2016;4(1):e01541–15.

  55. 55.

    Suwa Y, Norton JM, Bollmann A, Klotz MG, Stein LY, Laanbroek HJ, Arp DJ, Goodwin LA, Chertkov O, Held B, et al. Genome sequence of Nitrosomonas sp. Strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia. J Bacteriol. 2011;193(18):5047–8.

  56. 56.

    Kozlowski JA, Kits KD, Stein LY. Complete genome sequence of Nitrosomonas ureae strain Nm10, an Oligotrophic Group 6a Nitrosomonad. Genome Announc. 2016;4(2):e00094–16.

  57. 57.

    Bollmann A, Sedlacek CJ, Norton JM, Laanbroek HJ, Suwa Y, Stein LY, Klotz MG, Arp DJ, Sayavedra-Soto L, Goodwin LA, et al. Complete genome sequence of Nitrosomonas sp. Is79 - an ammonia oxidizing bacterium adapted to low ammonium concentrations. Stand Genomic Sci. 2013;7:469–82.

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Acknowledgements

We thank Frederica Valois for years of maintenance and documentation of the Stanley Watson and John Waterbury collection of AOB at WHOI and for sending us this organism. Original TEM micrographs were obtained from the WHOI Archives by F. Valois. We would like to thank Fen-Ann Shen (USU) for her help in obtaining the SEM. We thank JGI for re-sequencing this genome using improved sequencing technologies. The work was supported by the U.S. Department of Energy, Office of Science JGI under Contract No. DE-AC02-05CH11231 for CSP 2010 project 1012224; USDA NIFA Award 2011-67019-30178, and the Utah Agricultural Experiment Station, Utah State University project UTA00371 and approved as journal paper 8806.

Authors’ contributions

MCR isolated the DNA, worked on directed sequencing, obtained the SEM and wrote the first draft of the article; FV maintains AOB culture collection at WHOI and provided the strain and original TEM, JMN was the PI of the original CSP and lab director; sequencing, assembly and annotation at JGI, project manager at JGI was NS. JMN drafted the manuscript, which was subsequently discussed, revised and improved by all co-authors. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Author information

Correspondence to Jeanette M. Norton.

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Keywords

  • Nitrosospira
  • Ammonia-oxidizing bacteria
  • Nitrification
  • Agricultural soil
  • Ammonia monooxygenase
  • Nitrous oxide
  • Chemolithotroph