Strain identifier

BacDive ID: 6039

Type strain: Yes

Species: Halomonas sulfidaeris

Strain Designation: Esulfide1, NZp

Strain history: CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Esulfide1, N2p <- J. Kaye, Washington Univ., Washington, USA

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6080

BacDive-ID: 6039

DSM-Number: 15722

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

description: Halomonas sulfidaeris Esulfide1 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from sulfide rock, Main Endearour field.

NCBI tax id

NCBI tax idMatching level
891402strain
115553species

strain history

@refhistory
6080<- M. C. Marquez; NZp <- J. Z. Kaye
123380CIP <- 2003, C. Marquez, Sevilla Univ., Sevilla, Spain: strain Esulfide1, N2p <- J. Kaye, Washington Univ., Washington, USA

doi: 10.13145/bacdive6039.20230509.8.1

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 sulfidaeris
  • full scientific name: Halomonas sulfidaeris Kaye et al. 2004
  • synonyms

    • @ref: 20215
    • synonym: Vreelandella sulfidaeris

@ref: 6080

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas sulfidaeris

full scientific name: Halomonas sulfidaeris Kaye et al. 2004

strain designation: Esulfide1, NZp

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29992negative2.5 µm1 µmrod-shapedyes
123380negativerod-shapedyes

pigmentation

  • @ref: 29992
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6080BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 60.0 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
33874Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123380CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6080positivegrowth28mesophilic
29992positiveoptimum27.5mesophilic
33874positivegrowth30mesophilic
123380positivegrowth5-37
123380nogrowth41thermophilic
123380nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
29992positivegrowth05-10alkaliphile
29992positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29992
  • oxygen tolerance: facultative aerobe

spore formation

  • @ref: 29992
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29992NaClpositivegrowth0.5-24 %
29992NaClpositiveoptimum2.5 %
123380NaClpositivegrowth4-10 %
123380NaClnogrowth0 %
123380NaClnogrowth2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2999222599arabinose+carbon source
2999229016arginine+carbon source
2999222653asparagine+carbon source
2999216236ethanol+carbon source
2999228757fructose+carbon source
2999225115malate+carbon source
2999215792malonate+carbon source
2999229864mannitol+carbon source
2999217992sucrose+carbon source
2999227082trehalose+carbon source
2999218222xylose+carbon source
2999217632nitrate+reduction
12338016947citrate-carbon source
1233804853esculin-hydrolysis
123380606565hippurate-hydrolysis
12338017632nitrate+reduction
12338016301nitrite-reduction
12338015792malonate-assimilation

metabolite production

  • @ref: 123380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29992catalase+1.11.1.6
29992cytochrome oxidase+1.9.3.1
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
123380oxidase+
123380beta-galactosidase+3.2.1.23
123380alcohol dehydrogenase-1.1.1.1
123380gelatinase-
123380amylase-
123380caseinase-3.4.21.50
123380catalase+1.11.1.6
123380tween esterase-
123380gamma-glutamyltransferase+2.3.2.2
123380lecithinase-
123380lipase-
123380lysine decarboxylase-4.1.1.18
123380ornithine decarboxylase-4.1.1.17
123380phenylalanine ammonia-lyase+4.3.1.24
123380protease-
123380tryptophan deaminase-
123380urease-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
123380-+++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6080sulfide rock, Main Endearour fieldNE Pacific OceanCanadaCANNorth America
123380Sulfide rockPacific OceanCanadaCANNorth America1995

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Condition#Sulfuric

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60801Risk group (German classification)
1233801Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas sulfidaeris genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 874AB367237874ena891402
20218Halomonas sulfidaeris genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1224AB3672381224ena891402
6080Halomonas sulfidaeris strain Esulfide1 16S ribosomal RNA gene, complete sequenceAF2122041430ena891402

GC content

  • @ref: 29992
  • GC-content: 56

External links

@ref: 6080

culture collection no.: DSM 15722, CIP 108041, ATCC BAA 803, CECT 5817

straininfo link

  • @ref: 75526
  • straininfo: 131421

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023967Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments.Kaye JZ, Marquez MC, Ventosa A, Baross JAInt J Syst Evol Microbiol10.1099/ijs.0.02799-02004DNA, Bacterial/genetics, Environment, Halomonas/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, TemperatureGenetics
Phylogeny26431725Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil.Lee JC, Kim YS, Yun BS, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0006502015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Genetics31171615Complete Genome Sequence of Halomonas sulfidaeris Strain Esulfide1 Isolated from a Metal Sulfide Rock at a Depth of 2,200 Meters, Obtained Using Nanopore Sequencing.Saito M, Nishigata A, Galipon J, Arakawa KMicrobiol Resour Announc10.1128/MRA.00327-192019Phylogeny
Phylogeny32816656Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau.Gao P, Lu H, Xing P, Wu QLInt J Syst Evol Microbiol10.1099/ijsem.0.0043952020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Halomonas/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6080Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15722)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15722
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
29992Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126358
33874Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5620
68382Automatically annotated from API zym
75526Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131421.1StrainInfo: A central database for resolving microbial strain identifiers
123380Curators of the CIPCollection of Institut Pasteur (CIP 108041)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108041