Strain identifier

BacDive ID: 6010

Type strain: Yes

Species: Halomonas aquamarina

Strain Designation: 558

Strain history: CIP <- 1998, NCIMB <- C.E. Zobell: strain 558

NCBI tax ID(s): 77097 (species)

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General

@ref: 9171

BacDive-ID: 6010

DSM-Number: 30161

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, animal pathogen

description: Halomonas aquamarina 558 is an aerobe, Gram-negative animal pathogen that was isolated from Seawater.

NCBI tax id

  • NCBI tax id: 77097
  • Matching level: species

strain history

@refhistory
9171<- ATCC <- C.E. ZoBell, 558 (Achromobacter aquamarinus)
67771<- DSM <- ATCC <- CE ZoBell, 558, `Achromobacter aquamarinus`
116427CIP <- 1998, NCIMB <- C.E. Zobell: strain 558

doi: 10.13145/bacdive6010.20240916.9.1

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 aquamarina
  • full scientific name: Halomonas aquamarina (ZoBell and Upham 1944) Dobson and Franzmann 1996

  • synonyms

    @refsynonym
    20215Vreelandella aquamarina
    20215Alcaligenes aquamarinus
    20215Achromobacter aquamarinus
    20215Alcaligenes aestus
    20215Alcaligenes faecalis subsp. homari
    20215Deleya aesta
    20215Deleya aquamarina

@ref: 9171

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas aquamarina

full scientific name: Halomonas aquamarina (ZoBell and Upham 1944) Dobson and Franzmann 1996

strain designation: 558

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
67771negative
116427negativerod-shapedyes
69480negative99.5

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40144Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
9171BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yesName: 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 waterhttps://mediadive.dsmz.de/medium/514
116427CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
40144positivegrowth25
9171positivegrowth25
46452positivegrowth20
67771positivegrowth26
116427positivegrowth5-30
116427nogrowth37
116427nogrowth41
116427nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no90.471
69481no100

halophily

@refsaltgrowthtested relationconcentration
116427NaClpositivegrowth6-10 %
116427NaClnogrowth0 %
116427NaClnogrowth2 %
116427NaClnogrowth4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1164274853esculin-hydrolysis
116427606565hippurate-hydrolysis
11642717632nitrate-builds gas from
11642717632nitrate+reduction
11642716301nitrite-builds gas from
11642716301nitrite-reduction

metabolite production

  • @ref: 116427
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11642715688acetoin-
11642717234glucose-

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
116427oxidase+
116427beta-galactosidase-3.2.1.23
116427alcohol dehydrogenase-1.1.1.1
116427gelatinase+/-
116427amylase-
116427caseinase-3.4.21.50
116427catalase+1.11.1.6
116427tween esterase-
116427gamma-glutamyltransferase+2.3.2.2
116427lecithinase-
116427lipase-
116427lysine decarboxylase-4.1.1.18
116427ornithine decarboxylase-4.1.1.17
116427phenylalanine ammonia-lyase-4.3.1.24
116427tryptophan deaminase-
116427urease-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
116427-+++-++---++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116427---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
46452Seawater
116427Environment, Sea water

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_137.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_104;97_111;98_121;99_137&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AJ306888
  • Sequence Identity:
  • Total samples: 10165
  • soil counts: 435
  • aquatic counts: 5177
  • animal counts: 4415
  • plant counts: 138

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
9171yes1Risk group (German classification)
1164271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Deleya aquamarina (ATCC 14400) 16S ribosomal RNA (16S rRNA) geneM933521466nuccore77097
20218Halomonas aquamarina partial 16S rRNA gene, strain DSM 30161AJ3068881528nuccore77097
20218Halomonas aquamarina genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 920AB367209920nuccore77097
20218Halomonas aquamarina genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1204AB3672101204nuccore77097

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas aquamarina 558GCA_900110265scaffoldncbi77097
66792Halomonas aquamarina 5582639762508draftimg77097

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.952yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.391yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.471no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.25yes
69480flagellatedmotile2+Ability to perform flagellated movementyes80.981no

External links

@ref: 9171

culture collection no.: DSM 30161, ATCC 14400, KCTC 22193, NCMB 557, CCUG 16157, LMG 3416, LMG 2853, IAM 12550, ZoBell and Upham 558, BCRC 12878, CECT 5000, CGMCC 1.2324, CIP 105454, LMD 73.17, NCIB 557, NCIMB 557, Zobell 558, ZoBell and Upham 558T, Zobell & Upham 55

straininfo link

  • @ref: 75497
  • straininfo: 92115

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19656933Halomonas andesensis sp. nov., a moderate halophile isolated from the saline lake Laguna Colorada in Bolivia.Guzman D, Quillaguaman J, Munoz M, Hatti-Kaul RInt J Syst Evol Microbiol10.1099/ijs.0.014522-02009Bacterial Typing Techniques, Base Composition, Bolivia, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fresh Water/chemistry/*microbiology, Genes, rRNA, Halomonas/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species SpecificityGenetics
Phylogeny24510978Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils.Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang KInt J Syst Evol Microbiol10.1099/ijs.0.056499-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Halomonas/*classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Ubiquinone/chemistryGenetics
Metabolism30266955Sphaerocyclamide, a prenylated cyanobactin from the cyanobacterium Sphaerospermopsis sp. LEGE 00249.Martins J, Leikoski N, Wahlsten M, Azevedo J, Antunes J, Jokela J, Sivonen K, Vasconcelos V, Fewer DP, Leao PNSci Rep10.1038/s41598-018-32618-52018Amino Acid Sequence, Anti-Bacterial Agents/chemistry/metabolism/pharmacology, Bacterial Proteins/chemistry/genetics/metabolism, Biosynthetic Pathways, Cyanobacteria/chemistry/genetics/*metabolism, Halomonas/drug effects, Multigene Family, Peptides, Cyclic/chemistry/genetics/*metabolism/pharmacology, PrenylationPathogenicity
Phylogeny32129736Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench.Yan F, Fang J, Cao J, Wei Y, Liu R, Wang L, Xie ZInt J Syst Evol Microbiol10.1099/ijsem.0.0040692020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/isolation & purification, Nucleic Acid Hybridization, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9171Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30161)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30161
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
40144Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17475
46452Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16157)https://www.ccug.se/strain?id=16157
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75497Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92115.1StrainInfo: A central database for resolving microbial strain identifiers
116427Curators of the CIPCollection of Institut Pasteur (CIP 105454)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105454