Strain identifier

BacDive ID: 6017

Type strain: Yes

Species: Halomonas pacifica

Strain Designation: 62

Strain history: CIP <- 1988, NCIB <- 1974, ATCC <- P. Baumann, Hawaii Univ., USA: strain 62, Alcaligenes pacificus

NCBI tax ID(s): 77098 (species)

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General

@ref: 1748

BacDive-ID: 6017

DSM-Number: 4742

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Halomonas pacifica 62 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 77098
  • Matching level: species

strain history

@refhistory
1748<- ATCC <- P. Baumann, 62
67770IAM 12553 <-- ATCC 27122 <-- P. Baumann 62.
121498CIP <- 1988, NCIB <- 1974, ATCC <- P. Baumann, Hawaii Univ., USA: strain 62, Alcaligenes pacificus

doi: 10.13145/bacdive6017.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas pacifica
  • full scientific name: Halomonas pacifica (Baumann et al. 1972) Dobson and Franzmann 1996

  • synonyms

    @refsynonym
    20215Bisbaumannia pacifica
    20215Alcaligenes pacificus
    20215Alcaligenes pacifus
    20215Deleya pacifica

@ref: 1748

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas pacifica

full scientific name: Halomonas pacifica (Baumann et al. 1972) Dobson and Franzmann 1996

strain designation: 62

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.448
6948099.995negative
121498yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1748BACTO 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
1748MARINE AGAR (DSMZ Medium 123)yeshttps://mediadive.dsmz.de/medium/123Name: MARINE AGAR (DSMZ Medium 123) Composition: NaCl 24.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 11.0 g/l Bacto peptone 5.0 g/l Na2SO4 4.0 g/l CaCl2 x 6 H2O 2.0 g/l Yeast extract 1.0 g/l KCl 0.7 g/l KBr 0.1 g/l SrCl2 x 6 H2O 0.04 g/l H3BO3 0.03 g/l NaSiO3 x 9 H2O 0.005 g/l NaF 0.003 g/l NH4NO3 0.002 g/l Fe(III)PO4 x 4 H2O 0.001 g/l Distilled water
36493Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121498CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1748positivegrowth26mesophilic
36493positivegrowth25mesophilic
67770positivegrowth25mesophilic
121498positivegrowth15-41
121498nogrowth5psychrophilic
121498nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121498
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
121498NaClpositivegrowth2-10 %
121498NaClnogrowth0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12149816947citrate+carbon source
1214984853esculin-hydrolysis
121498606565hippurate-hydrolysis
12149817632nitrate-reduction
12149816301nitrite-reduction
12149815792malonate-assimilation
12149817632nitrate-respiration

antibiotic resistance

  • @ref: 121498
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121498
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121498oxidase+
121498beta-galactosidase-3.2.1.23
121498alcohol dehydrogenase-1.1.1.1
121498gelatinase-
121498amylase-
121498DNase-
121498caseinase-3.4.21.50
121498catalase+1.11.1.6
121498tween esterase-
121498gamma-glutamyltransferase+2.3.2.2
121498lecithinase-
121498lipase-
121498lysine decarboxylase-4.1.1.18
121498ornithine decarboxylase-4.1.1.17
121498phenylalanine ammonia-lyase-4.3.1.24
121498protease-
121498tryptophan deaminase-
121498urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121498-++--+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121498++-+---+--+--------+-----------+---+-------------++--+-----+++++---++--+++++--++++-+----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1748seawater
121498Environment, SeawaterHawaiiUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_13132.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_8110;98_9945;99_13132&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: L42616
  • Sequence Identity:
  • Total samples: 8744
  • soil counts: 920
  • aquatic counts: 2819
  • animal counts: 4761
  • plant counts: 244

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17481Risk group (German classification)
1214981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas pacifica 16S ribosomal RNA gene, partial sequenceEU3730881449ena77098
20218Deleya pacifica 16S ribosomal RNA (16S rRNA) geneL426161480ena77098
20218Halomonas pacifica genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 790AB367218790ena77098
20218Halomonas pacifica genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1255AB3672191255ena77098
20218Halomonas pacifica gene for 16S rRNA, partial sequence, strain: NBRC 102220AB6817341463ena77098

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas pacifica NBRC 102220GCA_007989625contigncbi77098
66792Halomonas pacifica strain NBRC 10222077098.3wgspatric77098

GC content

  • @ref: 67770
  • GC-content: 66
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.6no
flagellatedyes68.121no
gram-positiveno98.675no
anaerobicno98.974no
halophileyes96.369no
spore-formingno97.608no
glucose-utilyes85.022no
aerobicyes94.08no
thermophileno97.08no
glucose-fermentno73.657no

External links

@ref: 1748

culture collection no.: DSM 4742, ATCC 27122, JCM 20633, ACAM 345, CIP 103200, CIP 74.05, IAM 12553, LMG 3446, NBRC 102220, NCIMB 1977, CCUG 16079

straininfo link

  • @ref: 75503
  • straininfo: 92226

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity17453727Combinatorial materials research applied to the development of new surface coatings III. Utilisation of a high-throughput multiwell plate screening method to rapidly assess bacterial biofilm retention on antifouling surfaces.Stafslien S, Daniels J, Chisholm B, Christianson DBiofouling10.1080/089270106011273112007Bacteria/drug effects/*isolation & purification, Bacterial Adhesion, Biofilms/drug effects/*growth & development, Coated Materials, Biocompatible, Disinfectants/pharmacology, Marine Biology, Materials Testing/methods, Polymethyl Methacrylate, Ships, Water MicrobiologyEnzymology
Phylogeny35802152Halomonas salinarum sp. nov., a moderately halophilic bacterium isolated from saline soil in Yingkou, China.Yin YL, Li FL, Wang LArch Microbiol10.1007/s00203-022-03032-32022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Halomonas, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SoilTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1748Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4742)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4742
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36493Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14971
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75503Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92226.1StrainInfo: A central database for resolving microbial strain identifiers
121498Curators of the CIPCollection of Institut Pasteur (CIP 103200)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103200