Strain identifier
BacDive ID: 13733
Type strain: 
Species: Pseudophaeobacter arcticus
Strain Designation: 20188
Strain history: D.-C. Zhang et al. 20188.
NCBI tax ID(s): 999550 (strain), 385492 (species)
version 8.1 (current version)
General
@ref: 17288
BacDive-ID: 13733
DSM-Number: 23566
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped
description: Pseudophaeobacter arcticus 20188 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 999550 | strain |
| 385492 | species |
strain history
| @ref | history |
|---|---|
| 17288 | <- JCM <- D.-C. Zhang, Ocean Univ. China, Qingdao, P. R. China; strain 20188 |
| 67770 | D.-C. Zhang et al. 20188. |
doi: 10.13145/bacdive13733.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Pseudophaeobacter
- species: Pseudophaeobacter arcticus
- full scientific name: Pseudophaeobacter arcticus (Zhang et al. 2008) Breider et al. 2014
synonyms
- @ref: 20215
- synonym: Phaeobacter arcticus
@ref: 17288
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pseudophaeobacter
species: Pseudophaeobacter arcticus
full scientific name: Pseudophaeobacter arcticus (Zhang et al. 2008) Breider et al. 2014
strain designation: 20188
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32569 | negative | 1.8 µm | 0.4 µm | rod-shaped | yes | |
| 69480 | negative | 100 |
colony morphology
- @ref: 17288
- incubation period: 1-2 days
pigmentation
- @ref: 32569
- production: yes
multimedia
- @ref: 66793
- multimedia content: EM_DSM_23566_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 17288
- 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 |
|---|---|---|---|---|
| 17288 | positive | growth | 20 | psychrophilic |
| 32569 | positive | growth | 0-25 | |
| 32569 | positive | optimum | 19.5 | psychrophilic |
| 67770 | positive | growth | 20 | psychrophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32569 | positive | growth | 05-10 | alkaliphile |
| 32569 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32569
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.997 |
halophily
- @ref: 32569
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 02-09 %
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32569 | 22599 | arabinose | + | carbon source |
| 32569 | 28757 | fructose | + | carbon source |
| 32569 | 24265 | gluconate | + | carbon source |
| 32569 | 17234 | glucose | + | carbon source |
| 32569 | 17754 | glycerol | + | carbon source |
| 32569 | 25115 | malate | + | carbon source |
| 32569 | 17306 | maltose | + | carbon source |
| 32569 | 29864 | mannitol | + | carbon source |
| 32569 | 37684 | mannose | + | carbon source |
| 32569 | 506227 | N-acetylglucosamine | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 17288 | catalase | + | 1.11.1.6 |
| 17288 | cytochrome-c oxidase | + | 1.9.3.1 |
| 32569 | alkaline phosphatase | + | 3.1.3.1 |
| 32569 | catalase | + | 1.11.1.6 |
| 32569 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | latitude | longitude |
|---|---|---|---|---|
| 17288 | marine sediment | (75° 00' 24" N 169° 59' 37" W) at a depth of 167 m | 75.0067 | -169.994 |
| 67770 | Marine sediment of the Arctic Ocean (75° 00' 24" N 169° 59' 37" W) at a depth of 167 m | 75.0067 | -169.994 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_3375.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_97;97_104;98_113;99_3375&stattab=map
- Last taxonomy: Pseudophaeobacter arcticus
- 16S sequence: DQ514304
- Sequence Identity:
- Total samples: 559
- soil counts: 31
- aquatic counts: 483
- animal counts: 41
- plant counts: 4
Safety information
risk assessment
- @ref: 17288
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17288
- description: Phaeobacter arcticus strain 20188 16S ribosomal RNA gene, partial sequence
- accession: DQ514304
- length: 1425
- database: ena
- NCBI tax ID: 999550
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudophaeobacter arcticus DSM 23566 | GCA_000473205 | scaffold | ncbi | 999550 |
| 66792 | Phaeobacter arcticus DSM 23566 | 999550.5 | wgs | patric | 999550 |
| 66792 | Pseudophaeobacter arcticus DSM 23566 | 2521172622 | draft | img | 999550 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17288 | 59.6 | thermal denaturation, midpoint method (Tm) |
| 32569 | 59.6 | |
| 67770 | 59.27 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 75.434 | yes |
| flagellated | no | 76.379 | no |
| gram-positive | no | 98.185 | yes |
| anaerobic | no | 99.359 | yes |
| aerobic | yes | 90.181 | no |
| halophile | yes | 75.333 | no |
| spore-forming | no | 94.851 | no |
| thermophile | no | 98.183 | yes |
| glucose-util | yes | 70.363 | yes |
| glucose-ferment | no | 90.985 | no |
External links
@ref: 17288
culture collection no.: DSM 23566, CGMCC 1.6500, JCM 14644
straininfo link
- @ref: 82915
- straininfo: 408279
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18523182 | Phaeobacter arcticus sp. nov., a psychrophilic bacterium isolated from the Arctic. | Zhang DC, Li HR, Xin YH, Liu HC, Chi ZM, Zhou PJ, Yu Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65708-0 | 2008 | Arctic Regions, Bacterial Typing Techniques, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Species Specificity | Genetics |
| Genetics | 24501630 | Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.). | Freese HM, Dalingault H, Petersen J, Pradella S, Davenport K, Teshima H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Brinkhoff T, Goker M, Overmann J, Klenk HP | Stand Genomic Sci | 10.4056/sigs.383362 | 2013 | ||
| Phylogeny | 25355001 | Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus). | Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YD | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0318-x | 2014 | Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Intestines/microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Stichopus/*microbiology, Temperature | Genetics |
| Phylogeny | 35639600 | Pseudophaeobacter flagellatus sp. nov., isolated from coastal water. | Guan Y, Jiang Y, Kim YM, Yu SY, Choi SH, Choe H, Li Z, Lee MK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005399 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Water | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 17288 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23566) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23566 | ||||
| 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 | ||||
| 32569 | 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 | 28784 | 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) | ||||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 28604660 | 35: 676-683 2017 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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 | ||||
| 82915 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408279.1 | StrainInfo: A central database for resolving microbial strain identifiers |