Strain identifier
BacDive ID: 13688
Type strain:
Species: Pseudooceanicola nanhaiensis
Strain Designation: SS011B1-20
Strain history: CIP <- 2007, X.L. Wu, Tsinghua Univ., Beijing, China: strain SS011B1-20
NCBI tax ID(s): 1122614 (strain), 375761 (species)
General
@ref: 7358
BacDive-ID: 13688
DSM-Number: 18065
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Pseudooceanicola nanhaiensis SS011B1-20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediments at a depth of around 1500 m.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1122614 | strain |
375761 | species |
strain history
@ref | history |
---|---|
7358 | <- X.-L. Wu, Tsinghua University, Beijing; SS011B1-20 <- B. Guo |
121232 | CIP <- 2007, X.L. Wu, Tsinghua Univ., Beijing, China: strain SS011B1-20 |
doi: 10.13145/bacdive13688.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Pseudooceanicola
- species: Pseudooceanicola nanhaiensis
- full scientific name: Pseudooceanicola nanhaiensis (Gu et al. 2007) Lai et al. 2015
synonyms
- @ref: 20215
- synonym: Oceanicola nanhaiensis
@ref: 7358
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pseudooceanicola
species: Pseudooceanicola nanhaiensis
full scientific name: Pseudooceanicola nanhaiensis (Gu et al. 2007) Lai et al. 2015
strain designation: SS011B1-20
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31853 | negative | 0.8 µm | 0.5 µm | rod-shaped | no | |
69480 | negative | 99.989 | ||||
121232 | negative | rod-shaped | no |
pigmentation
- @ref: 31853
- production: yes
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_18065_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_18065_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_18065_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_18065_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_18065_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7358 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
41993 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
121232 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7358 | positive | growth | 30 | mesophilic |
31853 | positive | growth | 10-37 | |
31853 | positive | optimum | 28 | mesophilic |
41993 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31853 | positive | growth | 6-9.5 | alkaliphile |
31853 | positive | optimum | 7.5-8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31853 | aerobe |
121232 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31853 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31853 | NaCl | positive | growth | 0-10 % |
31853 | NaCl | positive | optimum | 02-03 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31853 | 30089 | acetate | + | carbon source |
31853 | 17057 | cellobiose | + | carbon source |
31853 | 16947 | citrate | + | carbon source |
31853 | 23652 | dextrin | + | carbon source |
31853 | 16236 | ethanol | + | carbon source |
31853 | 28757 | fructose | + | carbon source |
31853 | 28260 | galactose | + | carbon source |
31853 | 24265 | gluconate | + | carbon source |
31853 | 17234 | glucose | + | carbon source |
31853 | 17716 | lactose | + | carbon source |
31853 | 15792 | malonate | + | carbon source |
31853 | 29864 | mannitol | + | carbon source |
31853 | 15361 | pyruvate | + | carbon source |
31853 | 33942 | ribose | + | carbon source |
31853 | 30911 | sorbitol | + | carbon source |
31853 | 30031 | succinate | + | carbon source |
31853 | 17992 | sucrose | + | carbon source |
31853 | 17632 | nitrate | + | reduction |
121232 | 17632 | nitrate | - | reduction |
121232 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121232
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31853 | catalase | + | 1.11.1.6 |
31853 | cytochrome oxidase | + | 1.9.3.1 |
121232 | oxidase | + | |
121232 | catalase | + | 1.11.1.6 |
121232 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121232 | - | + | + | + | - | + | + | + | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7358 | sediments at a depth of around 1500 m | South China Sea | China | CHN | Asia | |
121232 | Environment, Sea, sediment | China Sea | China | CHN | Asia | 2004 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Core sample |
#Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_3804.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1952;97_2348;98_2897;99_3804&stattab=map
- Last taxonomy: Pseudooceanicola nanhaiensis subclade
- 16S sequence: DQ414420
- Sequence Identity:
- Total samples: 2062
- soil counts: 111
- aquatic counts: 1754
- animal counts: 189
- plant counts: 8
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7358 | 1 | Risk group (German classification) |
121232 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7358
- description: Oceanicola nanhaiensis strain SS011B1-20 16S ribosomal RNA gene, partial sequence
- accession: DQ414420
- length: 1427
- database: ena
- NCBI tax ID: 375761
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudooceanicola nanhaiensis DSM 18065 | GCA_000688295 | contig | ncbi | 1122614 |
66792 | Pseudooceanicola nanhaiensis CGMCC 1.6293 | GCA_014645095 | scaffold | ncbi | 375761 |
66792 | Oceanicola nanhaiensis DSM 18065 | 1122614.3 | wgs | patric | 1122614 |
66792 | Pseudooceanicola nanhaiensis strain CGMCC 1.6293 | 375761.4 | wgs | patric | 375761 |
66792 | Pseudooceanicola nanhaiensis DSM 18065 | 2558309102 | draft | img | 1122614 |
GC content
- @ref: 7358
- GC-content: 64.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 84.428 | no |
flagellated | no | 93.988 | yes |
gram-positive | no | 97.87 | yes |
anaerobic | no | 97.844 | yes |
aerobic | yes | 87.945 | no |
halophile | yes | 67.156 | no |
spore-forming | no | 96.431 | yes |
glucose-util | yes | 88.539 | yes |
thermophile | no | 98.761 | yes |
glucose-ferment | no | 90.786 | no |
External links
@ref: 7358
culture collection no.: DSM 18065, CGMCC 1.6293, LMG 23508, CIP 109530
straininfo link
- @ref: 82871
- straininfo: 290411
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17220459 | Oceanicola nanhaiensis sp. nov., isolated from sediments of the South China Sea. | Gu J, Guo B, Wang YN, Yu SL, Inamori R, Qu R, Ye YG, Wu XL | Int J Syst Evol Microbiol | 10.1099/ijs.0.64532-0 | 2007 | Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
Phylogeny | 17625206 | Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan. | Lin KY, Sheu SY, Chang PS, Cho JC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.65020-0 | 2007 | Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Taiwan | Genetics |
Phylogeny | 19406811 | Oceanicola pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium. | Yuan J, Lai Q, Wang B, Sun F, Liu X, Du Y, Li G, Gu L, Zheng T, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.003400-0 | 2009 | Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Pacific Ocean, Phenotype, Phylogeny, Pyrenes/*metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 19717582 | Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea. | Zheng Q, Chen C, Wang YN, Jiao N | Int J Syst Evol Microbiol | 10.1099/ijs.0.016311-0 | 2009 | Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
Phylogeny | 25663028 | Pseudooceanicola atlanticus gen. nov. sp. nov., isolated from surface seawater of the Atlantic Ocean and reclassification of Oceanicola batsensis, Oceanicola marinus, Oceanicola nitratireducens, Oceanicola nanhaiensis, Oceanicola antarcticus and Oceanicola flagellatus, as Pseudooceanicola batsensis comb. nov., Pseudooceanicola marinus comb. nov., Pseudooceanicola nitratireducens comb. nov., Pseudooceanicola nanhaiensis comb. nov., Pseudooceanicola antarcticus comb. nov., and Pseudooceanicola flagellatus comb. nov. | Lai Q, Li G, Liu X, Du Y, Sun F, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0398-2 | 2015 | Atlantic Ocean, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
Phylogeny | 32579095 | Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean. | Lyu L, Lai Q, Li J, Shao Z, Yu Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004298 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7358 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18065) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18065 | ||||
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 | ||||
31853 | 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 | 28117 | 28776041 | ||
41993 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7284 | |||||
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 | ||
68382 | Automatically annotated from API zym | ||||||
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 | ||||
82871 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID290411.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
121232 | Curators of the CIP | Collection of Institut Pasteur (CIP 109530) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109530 |