Strain identifier

BacDive ID: 14255

Type strain: Yes

Species: Sphingomonas haloaromaticamans

Strain Designation: A175

Strain history: CIP <- 2007, CCUG <- 2006, W.R. Abraham, Braunschweig, Germany: strain A175

NCBI tax ID(s): 653954 (species)

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General

@ref: 5055

BacDive-ID: 14255

DSM-Number: 13477

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

description: Sphingomonas haloaromaticamans A175 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from water and soil samples.

NCBI tax id

  • NCBI tax id: 653954
  • Matching level: species

strain history

@refhistory
5055<- M. Salkinoja-Salonen <- G. Schraa; A175 (Alcaligenes sp.)
119798CIP <- 2007, CCUG <- 2006, W.R. Abraham, Braunschweig, Germany: strain A175

doi: 10.13145/bacdive14255.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas haloaromaticamans
  • full scientific name: Sphingomonas haloaromaticamans Wittich et al. 2007

@ref: 5055

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas haloaromaticamans

full scientific name: Sphingomonas haloaromaticamans Wittich et al. 2007

strain designation: A175

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32029positive1.2 µm0.5 µmrod-shapedyes
119798negativeoval-shapedyes

colony morphology

  • @ref: 59908
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5055R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
5055CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
5055MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461)yeshttps://mediadive.dsmz.de/medium/461Name: MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 1.44135 g/l MgSO4 x 7 H2O 0.497018 g/l NH4Cl 0.298211 g/l KH2PO4 0.248509 g/l NaCl 0.0497018 g/l CaCl2 0.00994036 g/l MnSO4 0.00994036 g/l Yeast extract 0.0025 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l Riboflavin 0.000248509 g/l p-Aminobenzoic acid 0.000248509 g/l alpha-lipoic acid 0.000248509 g/l Thiamine-HCl x 2 H2O 0.000248509 g/l Vitamin B12 0.000248509 g/l Pantothenic acid 0.000248509 g/l CoCl2 x 6 H2O 0.000188867 g/l Nicotinic acid 0.000124254 g/l Nicotine amide 0.000124254 g/l MnCl2 x 4 H2O 9.94036e-05 g/l Folic acid 9.94036e-05 g/l Biotin 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l Pyridoxamine hydrochloride 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l H3BO3 5.96421e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Distilled water
39836MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
119798CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
5055positivegrowth30mesophilic
32029positivegrowth10-40
32029positiveoptimum33.5mesophilic
39836positivegrowth30mesophilic
59908positivegrowth30mesophilic

culture pH

  • @ref: 32029
  • ability: positive
  • type: optimum
  • pH: 6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32029aerobe
59908aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32029370543-hydroxybutyrate+carbon source
3202930089acetate+carbon source
3202916449alanine+carbon source
3202922599arabinose+carbon source
3202935391aspartate+carbon source
3202917057cellobiose+carbon source
3202928260galactose+carbon source
320295417glucosamine+carbon source
3202917234glucose+carbon source
3202927570histidine+carbon source
3202924996lactate+carbon source
3202925017leucine+carbon source
3202917306maltose+carbon source
3202928053melibiose+carbon source
32029506227N-acetylglucosamine+carbon source
3202926271proline+carbon source
3202917272propionate+carbon source
3202915361pyruvate+carbon source
3202916296D-tryptophan+carbon source
3202918222xylose+carbon source
320294853esculin+hydrolysis
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose+builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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
11979817632nitrate-reduction
11979816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11979835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119798oxidase+
119798catalase+1.11.1.6
119798urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119798-+++-++++-+++---+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5055-----+-+++--+-------+
5055-----+-+++--+-------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119798---++/-+---++-------------+-+--+--------+---+-----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5055water and soil samplesNetherlandsNLDEurope
59908Water and soilNetherlandsNLDEurope
119798Environment, Water, soilNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2962.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_798;97_1861;98_2286;99_2962&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: X94101
  • Sequence Identity:
  • Total samples: 389
  • soil counts: 167
  • aquatic counts: 116
  • animal counts: 33
  • plant counts: 73

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50551Risk group (German classification)
1197981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 32029
  • description: Sphingomonas haloaromaticamans partial 16S rRNA gene, type strain A175T
  • accession: X94101
  • length: 1443
  • database: nuccore
  • NCBI tax ID: 653954

GC content

  • @ref: 32029
  • GC-content: 66.1

External links

@ref: 5055

culture collection no.: CIP 109723, DSM 13477, CCUG 53463

straininfo link

  • @ref: 83414
  • straininfo: 49473

literature

  • topic: Phylogeny
  • Pubmed-ID: 17684248
  • title: Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas.
  • authors: Wittich RM, Busse HJ, Kampfer P, Macedo AJ, Tiirola M, Wieser M, Abraham WR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64835-0
  • year: 2007
  • mesh: Base Composition, Chlorophenols/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5055Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13477)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13477
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
32029Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2828028776041
39836Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7498
59908Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53463)https://www.ccug.se/strain?id=53463
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
83414Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49473.1StrainInfo: A central database for resolving microbial strain identifiers
119798Curators of the CIPCollection of Institut Pasteur (CIP 109723)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109723