Strain identifier

BacDive ID: 365

Type strain: Yes

Species: Pusillimonas harenae

Strain Designation: B201

Strain history: C. O. Jeon B201.

NCBI tax ID(s): 657015 (species)

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General

@ref: 18083

BacDive-ID: 365

DSM-Number: 25667

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

description: Pusillimonas harenae B201 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat.

NCBI tax id

  • NCBI tax id: 657015
  • Matching level: species

strain history

@refhistory
18083<- Ch.-O. Jeon, Chung-Ang Univ., Seoul, Republic of Korea; B201 <- Ch. B. Sil, Chung-Ang Univ., Seoul, Republic of Korea
67770C. O. Jeon B201.

doi: 10.13145/bacdive365.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Pusillimonas
  • species: Pusillimonas harenae
  • full scientific name: Pusillimonas harenae Park et al. 2011

  • synonyms

    • @ref: 20215
    • synonym: Pollutimonas harenae

@ref: 18083

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pusillimonas

species: Pusillimonas harenae

full scientific name: Pusillimonas harenae Park et al. 2011

strain designation: B201

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23279negative0.6-0.9 µm0.5-0.7 µmrod-shapedyesamphitrichous
69480yes92.821
69480negative99.994

colony morphology

@refincubation periodcolony colorcolony shapemedium used
180832-3 days
23279ivorycircularR2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18083TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23279Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
18083positivegrowth28mesophilic
23279positivegrowth15-45
23279positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
23279positivegrowth5.0-9.0alkaliphile
23279positiveoptimum6.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 23279
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
23279NaClpositivemaximum6 %
23279NaClpositiveoptimum0-3 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2327927689decanoate-assimilation
2327916947citrate-assimilation
2327917634D-glucose-assimilation
2327916899D-mannitol-assimilation
2327916024D-mannose-assimilation
2327924265gluconate-assimilation
2327930849L-arabinose-assimilation
2327917306maltose-assimilation
23279506227N-acetylglucosamine-assimilation
2327918401phenylacetate-assimilation
2327917234glucose-builds acid from
232794853esculin-hydrolysis
232795291gelatin-hydrolysis
2327917632nitrate-reduction
2327917128adipate+assimilation
2327925115malate+assimilation
2327916199urea+hydrolysis
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

metabolite production

@refChebi-IDmetaboliteproduction
2327935581indoleno
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
23279acid phosphatase+3.1.3.2
23279alkaline phosphatase+/-3.1.3.1
23279alpha-chymotrypsin+/-3.4.21.1
23279alpha-fucosidase-3.2.1.51
23279alpha-galactosidase-3.2.1.22
23279alpha-glucosidase-3.2.1.20
23279alpha-mannosidase-3.2.1.24
23279arginine dihydrolase-3.5.3.6
23279beta-galactosidase-3.2.1.23
23279beta-glucosidase-3.2.1.21
23279beta-glucuronidase-3.2.1.31
23279catalase+1.11.1.6
23279cystine arylamidase+3.4.11.3
23279cytochrome oxidase+1.9.3.1
23279esterase (C 4)+
23279esterase lipase (C 8)+
23279leucine arylamidase+3.4.11.1
23279lipase (C 14)-
23279N-acetyl-beta-glucosaminidase-3.2.1.52
23279naphthol-AS-BI-phosphohydrolase+/-
23279trypsin+/-3.4.21.4
23279valine arylamidase+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18083----------------++--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation procedure
18083tidal flatTaean coastRepublic of KoreaKORAsia
23279tidal flatTaean coast36.8347126.152
23279soil sample was serially diluted in 0.9 % (w/v) saline and spread on marine agar 2216 (MA; Difco) plates and incubated under aerobic conditions at 25 uC for 5 days
67770Beach sand from the Taean coastRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_4686.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_2229;97_2828;98_3512;99_4686&stattab=map
  • Last taxonomy: Pusillimonas
  • 16S sequence: GQ232740
  • Sequence Identity:
  • Total samples: 170
  • soil counts: 61
  • aquatic counts: 14
  • animal counts: 94
  • plant counts: 1

Safety information

risk assessment

  • @ref: 18083
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
18083Pusillimonas harenae strain B201 16S ribosomal RNA gene, partial sequenceGQ2327401400ena657015
67770Pusillimonas harenae JCM 16917 gene for 16S ribosomal RNA, partial sequenceLC5088061463ena657015

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pollutimonas harenae DSM 25667GCA_013416515contigncbi657015
66792Pusillimonas harenae strain DSM 25667657015.5wgspatric657015
66792Pusillimonas harenae strain JCM 16917657015.4wgspatric657015
66792Pusillimonas harenae JCM 169172891687248draftimg657015
67770Pollutimonas harenae JCM 16917GCA_004153685contigncbi657015

GC content

  • @ref: 23279
  • GC-content: 53.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.723no
anaerobicno99.15yes
halophileno77.661no
spore-formingno95.894no
glucose-utilno75.953no
thermophileno98.971yes
flagellatedyes59.265no
aerobicyes89.643yes
glucose-fermentno87.131no
motileyes87.548yes

External links

@ref: 18083

culture collection no.: DSM 25667, JCM 16917, KACC 14927

straininfo link

  • @ref: 70045
  • straininfo: 402067

literature

  • topic: Phylogeny
  • Pubmed-ID: 21257696
  • title: Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas.
  • authors: Park MS, Park YJ, Jung JY, Lee SH, Park W, Lee K, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.029892-0
  • year: 2011
  • mesh: Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18083Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25667)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25667
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
23279Moon Su Park, Youn-Je Park, Ji Young Jung, Seung Hyeon Lee, Woojun Park, Kangseok Lee, Che Ok Jeon10.1099/ijs.0.029892-0Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus PusillimonasIJSEM 61: 2901-2906 201121257696
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
70045Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402067.1StrainInfo: A central database for resolving microbial strain identifiers