Strain identifier
BacDive ID: 163789
Type strain: 
Species: Nitrosococcus oceani
Strain history: M. G. Klotz; Univ. of N. Carolina at Charlotte, USA; C-107.
NCBI tax ID(s): 323261 (strain), 1229 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 163789
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Nitrosococcus oceani JCM 30415 is a mesophilic, Gram-negative bacterium that was isolated from North Atlantic seawater.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1229 | species |
| 323261 | strain |
strain history
- @ref: 67770
- history: M. G. Klotz; Univ. of N. Carolina at Charlotte, USA; C-107.
doi: 10.13145/bacdive163789.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Nitrosococcus
- species: Nitrosococcus oceani
- full scientific name: Nitrosococcus oceani corrig. (Watson 1965) Watson 1971 (Approved Lists 1980)
synonyms
@ref synonym 20215 Nitrosococcus oceanus 20215 Nitrosocystis oceanus
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Nitrosococcus
species: Nitrosococcus oceani
full scientific name: Nitrosococcus oceani (Watson 1965) Watson 1971
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 99.355 |
| 125439 | negative | 93.6 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.798 |
| 125439 | no | 94.8 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: North Atlantic seawater
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 124043 | Nitrosococcus oceani 16S ribosomal RNA gene, partial sequence. | AF363287 | 1337 | nuccore | 323261 |
| 124043 | Nitrosococcus oceani strain C-107 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, 23S ribosomal RNA gene, and 23S-5S ribosomal RNA intergenic spacer, complete sequence; and 5S ribosomal RNA gene, partial sequence. | AY690336 | 4768 | nuccore | 323261 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Nitrosococcus oceani ATCC 19707 ATCC 19707; JCM30415 (Type strain) | GCA_000012805 | complete | ncbi | 323261 |
| 66792 | Nitrosococcus oceani ATCC 19707 | 323261.6 | complete | patric | 323261 |
| 66792 | Nitrosococcus oceani ATCC 19707 strain ATCC 19707; JCM30415 (Type strain) | 323261.19 | plasmid | patric | 323261 |
| 66792 | Nitrosococcus oceani strain NS58 | 1229.7 | wgs | patric | 1229 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative anaerobe | 74.9 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 93.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 53.7 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.8 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.355 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 89.717 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 58.932 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.798 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 89.509 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.834 | no |
External links
@ref: 67770
culture collection no.: JCM 30415, ATCC 19707
straininfo link
- @ref: 114137
- straininfo: 11823
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 10547440 | The amo operon in marine, ammonia-oxidizing gamma-proteobacteria. | Alzerreca JJ, Norton JM, Klotz MG | FEMS Microbiol Lett | 10.1111/j.1574-6968.1999.tb08773.x | 1999 | Amino Acid Sequence, Ammonia/metabolism, Base Sequence, Blotting, Southern, Bradyrhizobiaceae/*genetics/metabolism, DNA, Ribosomal/genetics, Genes, Bacterial, Molecular Sequence Data, Operon/*genetics, Oxidoreductases/*genetics, Polymerase Chain Reaction, RNA, Ribosomal, 16S/analysis, Seawater, *Water Microbiology | Genetics |
| Metabolism | 12710742 | Susceptibility of ammonia-oxidizing bacteria to nitrification inhibitors. | Matsuba D, Takazaki H, Sato Y, Takahashi R, Tokuyama T, Wakabayashi K | Z Naturforsch C J Biosci | 10.1515/znc-2003-3-424 | 2003 | Ammonia/*pharmacokinetics, Bradyrhizobiaceae/classification/*drug effects/*metabolism, DNA, Ribosomal/genetics, Environment, Nitric Oxide/*metabolism, Nitrites/*metabolism, Nitrobacter/drug effects/metabolism, Nitrosomonas/drug effects/metabolism, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Triazines/*pharmacology | Phylogeny |
| Metabolism | 16957257 | Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. | Klotz MG, Arp DJ, Chain PS, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB | Appl Environ Microbiol | 10.1128/AEM.00463-06 | 2006 | Adenosine Triphosphate/biosynthesis, Amino Acids/metabolism, Ammonia/*metabolism, Base Composition, Carbon/metabolism, Chromatiaceae/*genetics/*metabolism/ultrastructure, Chromosomes, Bacterial/genetics, DNA, Bacterial/chemistry/genetics, Electron Transport, Energy Metabolism, *Genome, Bacterial, Glucosyltransferases/genetics/metabolism, Microscopy, Electron, Models, Biological, Molecular Sequence Data, Multigene Family, Nitrogen/metabolism, Nucleotides/metabolism, Operon, Oxidation-Reduction, Phosphorus/metabolism, Plasmids/genetics, Repetitive Sequences, Nucleic Acid, Seawater/microbiology, Sulfur/metabolism | Genetics |
| 17993553 | Characterization of two new genes, amoR and amoD, in the amo operon of the marine ammonia oxidizer Nitrosococcus oceani ATCC 19707. | El Sheikh AF, Poret-Peterson AT, Klotz MG | Appl Environ Microbiol | 10.1128/AEM.01654-07 | 2007 | Bacterial Proteins/*genetics, Chromatiaceae/*genetics, Genes, Bacterial, Multigene Family, Operon | ||
| Metabolism | 18973622 | Ammonia-dependent differential regulation of the gene cluster that encodes ammonia monooxygenase in Nitrosococcus oceani ATCC 19707. | El Sheikh AF, Klotz MG | Environ Microbiol | 10.1111/j.1462-2920.2008.01766.x | 2008 | Ammonia/*metabolism, Bacterial Proteins/genetics, Base Sequence, Chromatiaceae/*genetics/*metabolism, Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Gene Order, Molecular Sequence Data, *Multigene Family, Oxidoreductases/*biosynthesis, Promoter Regions, Genetic, Transcription Initiation Site | Genetics |
| Phylogeny | 21204874 | Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. | Campbell MA, Chain PS, Dang H, El Sheikh AF, Norton JM, Ward NL, Ward BB, Klotz MG | FEMS Microbiol Ecol | 10.1111/j.1574-6941.2010.01027.x | 2011 | Ammonia/*metabolism, China, Chromatiaceae/classification/genetics/metabolism, Cloning, Molecular, DNA, Bacterial/genetics, Ecosystem, Nitrosomonas/*classification/genetics/metabolism, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Metabolism |
| Genetics | 31467109 | Draft Genome Sequence of Nitrosococcus oceani Strain NS58, a Marine Ammonia-Oxidizing Gammaproteobacterium Isolated from Tokyo Bay Sediment. | Dohra H, Arai K, Urakawa H, Fujiwara T | Microbiol Resour Announc | 10.1128/MRA.00923-19 | 2019 | Phylogeny | |
| Phylogeny | 32397339 | High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. | Wang L, Lim CK, Klotz MG | Microorganisms | 10.3390/microorganisms8050693 | 2020 |
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 114137 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID11823.1 |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |