Strain identifier

BacDive ID: 6044

Type strain: Yes

Species: Halomonas organivorans

Strain Designation: G-16.1

Strain history: CIP <- 2004, A. Ventosa, Sevilla, Spain: strain G-16.1

NCBI tax ID(s): 257772 (species)

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

@ref: 6341

BacDive-ID: 6044

DSM-Number: 16226

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

description: Halomonas organivorans G-16.1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from saline soils.

NCBI tax id

  • NCBI tax id: 257772
  • Matching level: species

strain history

@refhistory
6341<- A. Ventosa, Univ. Seville, Dept. Microbiol. Parasitol., Spain; G-16.1 <- M. T. García et al.
121433CIP <- 2004, A. Ventosa, Sevilla, Spain: strain G-16.1

doi: 10.13145/bacdive6044.20230509.8.1

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 organivorans
  • full scientific name: Halomonas organivorans García et al. 2004

@ref: 6341

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas organivorans

full scientific name: Halomonas organivorans García et al. 2004

strain designation: G-16.1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31242negative2.5 µm1.1 µmrod-shapedyes
69480yes97.929
69480negative99.961
121433negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6341BACTO 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
33934Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121433CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6341positivegrowth37mesophilic
31242positivegrowth15-45
31242positiveoptimum37mesophilic
33934positivegrowth30mesophilic
121433positivegrowth15-41
121433nogrowth5psychrophilic
121433nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31242positivegrowth06-10alkaliphile
31242positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31242aerobe
121433facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.899

halophily

@refsaltgrowthtested relationconcentration
31242NaClpositivegrowth1.5-30 %
31242NaClpositiveoptimum8.75 %
121433NaClpositivegrowth10 %
121433NaClnogrowth0 %
121433NaClnogrowth2 %
121433NaClnogrowth4 %
121433NaClnogrowth6 %
121433NaClnogrowth8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3124216000ethanolamine+carbon source
3124216449alanine+carbon source
3124218403L-arabitol+carbon source
3124222653asparagine+carbon source
3124235391aspartate+carbon source
3124228757fructose+carbon source
3124228260galactose+carbon source
3124217234glucose+carbon source
3124229987glutamate+carbon source
3124217754glycerol+carbon source
3124228087glycogen+carbon source
3124227570histidine+carbon source
3124217596inosine+carbon source
3124225017leucine+carbon source
3124229864mannitol+carbon source
3124237684mannose+carbon source
3124251850methyl pyruvate+carbon source
31242506227N-acetylglucosamine+carbon source
3124226271proline+carbon source
3124217148putrescine+carbon source
3124226546rhamnose+carbon source
3124217822serine+carbon source
3124230911sorbitol+carbon source
3124230031succinate+carbon source
3124217992sucrose+carbon source
3124226986threonine+carbon source
3124227082trehalose+carbon source
3124253423tween 40+carbon source
3124253426tween 80+carbon source
3124216704uridine+carbon source
3124227248urocanic acid+carbon source
312424853esculin+hydrolysis
12143316947citrate-carbon source
1214334853esculin-hydrolysis
121433606565hippurate+hydrolysis
12143317632nitrate+reduction
12143316301nitrite-reduction
12143315792malonate-assimilation
12143317632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
3124216136hydrogen sulfideyes
12143335581indoleno

enzymes

@refvalueactivityec
31242catalase+1.11.1.6
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
121433oxidase+
121433beta-galactosidase-3.2.1.23
121433alcohol dehydrogenase-1.1.1.1
121433gelatinase-
121433amylase-
121433caseinase-3.4.21.50
121433catalase+1.11.1.6
121433tween esterase+
121433gamma-glutamyltransferase+2.3.2.2
121433lecithinase-
121433lipase-
121433lysine decarboxylase-4.1.1.18
121433ornithine decarboxylase-4.1.1.17
121433phenylalanine ammonia-lyase-4.3.1.24
121433protease-
121433tryptophan deaminase-
121433urease+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
121433-++--+++--++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121433+++++--+-++-------+-+-++--+-----+--+-----+------++----+++--+--++-----+--+-++---++-------+++---+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6341saline soilsHuelva, Isla CristinaSpainESPEurope
121433Environment, Saline soil in Isla CristinaSpainESPEurope2003

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_56260.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_1361;97_3720;98_15343;99_56260&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AJ616910
  • Sequence Identity:
  • Total samples: 47
  • soil counts: 7
  • aquatic counts: 34
  • animal counts: 5
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63411Risk group (German classification)
1214331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6341
  • description: Halomonas organivorans partial 16S rRNA gene, type strain G-16.1T
  • accession: AJ616910
  • length: 1472
  • database: ena
  • NCBI tax ID: 257772

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas organivorans CECT 5995GCA_014192055scaffoldncbi257772
66792Halomonas organivorans strain CECT 5995257772.3wgspatric257772
66792Halomonas organivorans CECT 59952824377609draftimg257772

GC content

@refGC-content
634161.0
3124261.95

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes69.152no
gram-positiveno98.406yes
anaerobicno98.443yes
aerobicyes86.648no
halophileyes91.158yes
spore-formingno95.421no
glucose-utilyes95.314yes
thermophileno99.216yes
motileyes91.601yes
glucose-fermentno66.284no

External links

@ref: 6341

culture collection no.: DSM 16226, CCM 7142, CECT 5995, CIP 108269

straininfo link

  • @ref: 75531
  • straininfo: 134288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388735Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds.Garcia MT, Mellado E, Ostos JC, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.63114-02004Aminosalicylic Acid/metabolism, Bacterial Typing Techniques, Base Composition, Benzoic Acid/metabolism, Biodegradation, Environmental, Cinnamates/metabolism, Coumaric Acids/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Halomonas/*classification/genetics/isolation & purification/*metabolism, Hydrocarbons, Aromatic/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Parabens/metabolism, Phenol/metabolism, Phenylacetates/metabolism, Phylogeny, Propionates, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salicylic Acid/metabolism, Sequence Analysis, DNA, Soil Microbiology, SpainMetabolism
Metabolism21695219Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans.de Lourdes Moreno M, Sanchez-Porro C, Piubeli F, Frias L, Garcia MT, Mellado EPLoS One10.1371/journal.pone.00210492011Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/*metabolism, Benzoates/*metabolism, Catechol 1,2-Dioxygenase/metabolism, Cloning, Molecular, DNA, Intergenic/genetics, Halomonas/enzymology/*genetics/*metabolism, Industrial Waste, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salinity, Sequence AlignmentEnzymology
Phylogeny22328606Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium.Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan DInt J Syst Evol Microbiol10.1099/ijs.0.037036-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Polysaccharides, Bacterial/*biosynthesis, Ponds, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Turkey, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16226)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16226
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
31242Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2756628776041
33934Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5872
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)
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
75531Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134288.1StrainInfo: A central database for resolving microbial strain identifiers
121433Curators of the CIPCollection of Institut Pasteur (CIP 108269)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108269