Strain identifier

BacDive ID: 13688

Type strain: Yes

Species: Pseudooceanicola nanhaiensis

Strain Designation: SS011B1-20

Strain history: CIP <- 2007, X.L. Wu, Tsinghua Univ., Beijing, China: strain SS011B1-20

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1122614strain
375761species

strain history

@refhistory
7358<- X.-L. Wu, Tsinghua University, Beijing; SS011B1-20 <- B. Guo
121232CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31853negative0.8 µm0.5 µmrod-shapedno
69480negative99.989
121232negativerod-shapedno

pigmentation

  • @ref: 31853
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18065_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18065_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18065_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18065_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18065_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7358BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
41993Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121232CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7358positivegrowth30mesophilic
31853positivegrowth10-37
31853positiveoptimum28mesophilic
41993positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31853positivegrowth6-9.5alkaliphile
31853positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31853aerobe
121232obligate aerobe

spore formation

@refspore formationconfidence
31853no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31853NaClpositivegrowth0-10 %
31853NaClpositiveoptimum02-03 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3185330089acetate+carbon source
3185317057cellobiose+carbon source
3185316947citrate+carbon source
3185323652dextrin+carbon source
3185316236ethanol+carbon source
3185328757fructose+carbon source
3185328260galactose+carbon source
3185324265gluconate+carbon source
3185317234glucose+carbon source
3185317716lactose+carbon source
3185315792malonate+carbon source
3185329864mannitol+carbon source
3185315361pyruvate+carbon source
3185333942ribose+carbon source
3185330911sorbitol+carbon source
3185330031succinate+carbon source
3185317992sucrose+carbon source
3185317632nitrate+reduction
12123217632nitrate-reduction
12123216301nitrite-reduction

metabolite production

  • @ref: 121232
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31853catalase+1.11.1.6
31853cytochrome oxidase+1.9.3.1
121232oxidase+
121232catalase+1.11.1.6
121232urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121232-+++-+++--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7358sediments at a depth of around 1500 mSouth China SeaChinaCHNAsia
121232Environment, Sea, sedimentChina SeaChinaCHNAsia2004

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
73581Risk group (German classification)
1212321Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudooceanicola nanhaiensis DSM 18065GCA_000688295contigncbi1122614
66792Pseudooceanicola nanhaiensis CGMCC 1.6293GCA_014645095scaffoldncbi375761
66792Oceanicola nanhaiensis DSM 180651122614.3wgspatric1122614
66792Pseudooceanicola nanhaiensis strain CGMCC 1.6293375761.4wgspatric375761
66792Pseudooceanicola nanhaiensis DSM 180652558309102draftimg1122614

GC content

  • @ref: 7358
  • GC-content: 64.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno84.428no
flagellatedno93.988yes
gram-positiveno97.87yes
anaerobicno97.844yes
aerobicyes87.945no
halophileyes67.156no
spore-formingno96.431yes
glucose-utilyes88.539yes
thermophileno98.761yes
glucose-fermentno90.786no

External links

@ref: 7358

culture collection no.: DSM 18065, CGMCC 1.6293, LMG 23508, CIP 109530

straininfo link

  • @ref: 82871
  • straininfo: 290411

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220459Oceanicola 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 XLInt J Syst Evol Microbiol10.1099/ijs.0.64532-02007Alphaproteobacteria/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, DNAGenetics
Phylogeny17625206Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan.Lin KY, Sheu SY, Chang PS, Cho JC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65020-02007Bacterial 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, TaiwanGenetics
Phylogeny19406811Oceanicola 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 ZInt J Syst Evol Microbiol10.1099/ijs.0.003400-02009Bacterial 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 SpecificityGenetics
Phylogeny19717582Oceanicola nitratireducens sp. nov., a marine alphaproteobacterium isolated from the South China Sea.Zheng Q, Chen C, Wang YN, Jiao NInt J Syst Evol Microbiol10.1099/ijs.0.016311-02009Alphaproteobacteria/*classification/genetics/isolation & purification/physiology, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyGenetics
Phylogeny25663028Pseudooceanicola 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 ZAntonie Van Leeuwenhoek10.1007/s10482-015-0398-22015Atlantic 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, TemperatureGenetics
Phylogeny32579095Pseudooceanicola pacificus sp. nov., isolated from deep-sea sediment of the Pacific Ocean.Lyu L, Lai Q, Li J, Shao Z, Yu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0042982020Bacterial 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, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7358Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18065)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18065
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31853Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2811728776041
41993Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7284
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82871Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290411.1StrainInfo: A central database for resolving microbial strain identifiers
121232Curators of the CIPCollection of Institut Pasteur (CIP 109530)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109530