Strain identifier
BacDive ID: 11283
Type strain:
Species: Neptunomonas antarctica
Strain Designation: S3-22
Strain history: <- Y.-Z. Zhang, State Key Lab. Microbial Technol., Marine Biotechnol. Res. Center, Shandong Univ., Jinan, China; S3-22 <- Y. Yong
NCBI tax ID(s): 619304 (species)
General
@ref: 16268
BacDive-ID: 11283
DSM-Number: 22306
keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Neptunomonas antarctica S3-22 is a facultative aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediments at a water depth of 20 m.
NCBI tax id
- NCBI tax id: 619304
- Matching level: species
strain history
- @ref: 16268
- history: <- Y.-Z. Zhang, State Key Lab. Microbial Technol., Marine Biotechnol. Res. Center, Shandong Univ., Jinan, China; S3-22 <- Y. Yong
doi: 10.13145/bacdive11283.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Oceanospirillaceae
- genus: Neptunomonas
- species: Neptunomonas antarctica
- full scientific name: Neptunomonas antarctica Zhang et al. 2010
@ref: 16268
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Oceanospirillaceae
genus: Neptunomonas
species: Neptunomonas antarctica
full scientific name: Neptunomonas antarctica Zhang et al. 2010
strain designation: S3-22
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29645 | negative | 1.6-1.8 µm | 0.6-1 µm | rod-shaped | yes | |
69480 | yes | 98.453 | ||||
69480 | negative | 99.999 |
pigmentation
- @ref: 29645
- production: yes
Culture and growth conditions
culture medium
- @ref: 16268
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16268 | positive | growth | 20 | psychrophilic |
29645 | positive | growth | 04-25 | |
29645 | positive | optimum | 15 | psychrophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29645 | positive | growth | 06-08 |
29645 | positive | optimum | 6.5-7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29645
- oxygen tolerance: facultative aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.969 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29645 | NaCl | positive | growth | 0.5-5 % |
29645 | NaCl | positive | optimum | 02-03 % |
observation
- @ref: 29645
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29645 | 28757 | fructose | + | carbon source |
29645 | 29864 | mannitol | + | carbon source |
29645 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29645 | catalase | + | 1.11.1.6 |
29645 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16268
- sample type: marine sediments at a water depth of 20 m
- geographic location: Nella Fjord, 69° 22' 06'' S 76° 22' 45'' E
- continent: Australia and Oceania
- latitude: -69.3683
- longitude: 76.3792
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_6418.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_1716;97_3735;98_4739;99_6418&stattab=map
- Last taxonomy: Neptunomonas antarctica subclade
- 16S sequence: FJ713802
- Sequence Identity:
- Total samples: 2130
- soil counts: 166
- aquatic counts: 1657
- animal counts: 240
- plant counts: 67
Safety information
risk assessment
- @ref: 16268
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16268
- description: Neptunomonas antarctica strain S3-22 16S ribosomal RNA gene, partial sequence
- accession: FJ713802
- length: 1508
- database: ena
- NCBI tax ID: 619304
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Neptunomonas antarctica DSM 22306 | GCA_900156635 | scaffold | ncbi | 619304 |
66792 | Neptunomonas antarctica S3-22 | GCA_001305295 | contig | ncbi | 619304 |
66792 | Neptunomonas antarctica strain DSM 22306 | 619304.5 | wgs | patric | 619304 |
66792 | Neptunomonas antarctica DSM 22306 | 2681813508 | draft | img | 619304 |
66792 | Neptunomonas antarctica S3-22 | 2645727840 | draft | img | 619304 |
GC content
@ref | GC-content | method |
---|---|---|
16268 | 45.6 | high performance liquid chromatography (HPLC) |
29645 | 45.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.895 | yes |
flagellated | yes | 91.987 | no |
gram-positive | no | 99.021 | yes |
anaerobic | no | 98.48 | yes |
aerobic | yes | 56.39 | yes |
halophile | yes | 75.99 | no |
spore-forming | no | 94.84 | no |
thermophile | no | 99.557 | no |
glucose-util | yes | 72.046 | no |
glucose-ferment | no | 84.44 | no |
External links
@ref: 16268
culture collection no.: DSM 22306, CCTCC AB 209086, KACC 14056
straininfo link
- @ref: 80516
- straininfo: 408190
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19801396 | Neptunomonas antarctica sp. nov., isolated from marine sediment. | Zhang XY, Zhang YJ, Yu Y, Li HJ, Gao ZM, Chen XL, Chen B, Zhang YZ | Int J Syst Evol Microbiol | 10.1099/ijs.0.017756-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Oceanospirillaceae/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics | Metabolism |
Genetics | 26585344 | Insight into the genome sequence of a sediment-adapted marine bacterium Neptunomonas antarctica S3-22(T) from Antarctica. | Rong JC, Liu M, Li Y, Sun TY, Xie BB, Shi M, Chen XL, Qin QL | Mar Genomics | 10.1016/j.margen.2015.11.006 | 2015 | Adaptation, Physiological/*genetics, Bacterial Proteins/genetics/metabolism, Gene Expression Regulation, Bacterial/physiology, *Genome, Bacterial, Geologic Sediments, Oceanospirillaceae/*genetics | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16268 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22306) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22306 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
29645 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26034 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
80516 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408190.1 | StrainInfo: A central database for resolving microbial strain identifiers |