Strain identifier

BacDive ID: 13125

Type strain: Yes

Species: Halopseudomonas pachastrellae

Strain history: CIP <- 2005, CCUG <- 2002, KMM

NCBI tax ID(s): 254161 (species)

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General

@ref: 7064

BacDive-ID: 13125

DSM-Number: 17577

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Halopseudomonas pachastrellae KMM 330 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea sponge Pachastrella sp..

NCBI tax id

  • NCBI tax id: 254161
  • Matching level: species

strain history

@refhistory
7064<- M. Uchino, Tokyo Univ. of Agriculture <- L. A. Romanenko
67770M. Uchino <-- L. A. Romanenko KMM 330.
121496CIP <- 2005, CCUG <- 2002, KMM

doi: 10.13145/bacdive13125.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Halopseudomonas
  • species: Halopseudomonas pachastrellae
  • full scientific name: Halopseudomonas pachastrellae (Romanenko et al. 2005) Rudra and Gupta 2021

  • synonyms

    @refsynonym
    20215Neopseudomonas pachastrellae
    20215Pseudomonas pachastrellae

@ref: 7064

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas pachastrellae

full scientific name: Pseudomonas pachastrellae Romanenko et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31271negative1.5 µm0.45 µmrod-shapedyes
69480yes98.013
69480negative99.992
121496negativerod-shapedyes

pigmentation

  • @ref: 31271
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7064MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
7064TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
33264MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121496CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7064positivegrowth28mesophilic
31271positivegrowth07-41
31271positiveoptimum24psychrophilic
33264positivegrowth30mesophilic
57255positivegrowth30mesophilic
67770positivegrowth30mesophilic
121496positivegrowth10-37
121496nogrowth5psychrophilic
121496nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7064aerobe
31271aerobe
57255aerobe
121496obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31271NaClpositivegrowth0-10 %
31271NaClpositiveoptimum5 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3127116947citrate+carbon source
3127124996lactate+carbon source
3127153423tween 40+carbon source
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12149617632nitrate-reduction
12149616301nitrite-reduction
12149617632nitrate-respiration

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31271catalase+1.11.1.6
31271cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121496oxidase+
121496alcohol dehydrogenase-1.1.1.1
121496catalase+1.11.1.6
121496lysine decarboxylase-4.1.1.18
121496ornithine decarboxylase-4.1.1.17
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
121496-+++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7064---------------+-++-+
7064---------------+-++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationsampling datecountryorigin.countrycontinentisolation date
7064deep-sea sponge Pachastrella sp.Pachastrella spPhilippine Sea
57255Sponge (Pachastrella sp),a depth of 350 meterThe Philippine Sea1991-04-01
67770Sponge (Pachastrella sp.)Pachastrella sp.
121496SpongePhilippinesPHLAsia1991

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7672.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_1501;97_4381;98_5610;99_7672&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB125366
  • Sequence Identity:
  • Total samples: 2691
  • soil counts: 83
  • aquatic counts: 2395
  • animal counts: 169
  • plant counts: 44

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70641Risk group (German classification)
1214961Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7064
  • description: Pseudomonas pachastrellae gene for 16S rRNA, partial sequence, strain:KMM 330
  • accession: AB125366
  • length: 1479
  • database: ena
  • NCBI tax ID: 254161

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas pachastrellae strain CCUG 46540254161.4wgspatric254161
66792Pseudomonas pachastrellae strain JCM 12285254161.7wgspatric254161
67770Halopseudomonas pachastrellae JCM 12285GCA_900114765scaffoldncbi254161
67770Halopseudomonas pachastrellae CCUG 46540GCA_001989375contigncbi254161

GC content

@refGC-contentmethod
706461
3127161.1
6777061.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.328yes
gram-positiveno98.355no
anaerobicno97.854yes
aerobicyes93.67yes
halophileyes66.496no
spore-formingno96.311no
glucose-utilno78.207yes
flagellatedyes93.179no
thermophileno99.839no
glucose-fermentno90.02no

External links

@ref: 7064

culture collection no.: KMM 330, CIP 108699, DSM 17577, CCUG 46540, JCM 12285, NRIC 0583, CGMCC 1.7687

straininfo link

  • @ref: 82333
  • straininfo: 130830

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7064Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17577)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17577
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
31271Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2759128776041
33264Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6357
57255Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46540)https://www.ccug.se/strain?id=46540
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
82333Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID130830.1StrainInfo: A central database for resolving microbial strain identifiers
121496Curators of the CIPCollection of Institut Pasteur (CIP 108699)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108699