Strain identifier

BacDive ID: 10585

Type strain: Yes

Species: Gordonia alkanivorans

Strain Designation: 2102-488

Strain history: CIP <- 1999, C. Kummer, Hans Knöll Inst., Jena, Germany: strain HKI 0136

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

@ref: 11710

BacDive-ID: 10585

DSM-Number: 44369

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive

description: Gordonia alkanivorans 2102-488 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from tar and phenol contaminated soil.

NCBI tax id

NCBI tax idMatching level
1027371strain
84096species

strain history

@refhistory
11710<- C. Kummer, Hans-Knöll Inst., Jena, HKI 0136
67770DSM 44369 <-- C. Kummer HKI 0136.
116254CIP <- 1999, C. Kummer, Hans Knöll Inst., Jena, Germany: strain HKI 0136

doi: 10.13145/bacdive10585.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia alkanivorans
  • full scientific name: Gordonia alkanivorans Kummer et al. 1999
  • synonyms

    • @ref: 20215
    • synonym: Gordonia nitida

@ref: 11710

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia alkanivorans

full scientific name: Gordonia alkanivorans Kummer et al. 1999

strain designation: 2102-488

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116254positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19655Pure orange10-14 daysISP 2
19655Pure orange10-14 daysISP 3
19655Pure orange10-14 daysISP 4
19655Pure orange10-14 daysISP 5
19655Pure orange10-14 daysISP 6
19655Pure orange10-14 daysISP 7
116254

multicellular morphology

@refforms multicellular complexmedium name
19655noISP 2
19655noISP 3
19655noISP 4
19655noISP 5
19655noISP 6
19655noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11710TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
19655ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19655ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19655ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19655ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19655ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19655ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40303MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
116254CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
19655positiveoptimum28mesophilic
11710positivegrowth28mesophilic
40303positivegrowth30mesophilic
67770positivegrowth28mesophilic
116254positivegrowth25-41
116254nogrowth10psychrophilic
116254nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116254
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.891

halophily

@refsaltgrowthtested relationconcentration
19655NaClpositivemaximum5 %
116254NaClpositivegrowth0-6 %
116254NaClnogrowth8 %
116254NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1965517234glucose+
1965522599arabinose-
1965517992sucrose+
1965518222xylose-
1965517268myo-inositol-
1965529864mannitol+
1965528757fructose+
1965526546rhamnose-
1965516634raffinose-
1965562968cellulose+
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
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11625416947citrate-carbon source
1162544853esculin-hydrolysis
116254606565hippurate-hydrolysis
11625417632nitrate+reduction
11625416301nitrite-reduction
11625417632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 116254
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11625435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11625415688acetoin-
11625417234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
116254oxidase-
116254beta-galactosidase-3.2.1.23
116254alcohol dehydrogenase-1.1.1.1
116254gelatinase-
116254amylase-
116254DNase+
116254caseinase-3.4.21.50
116254catalase+1.11.1.6
116254tween esterase+
116254gamma-glutamyltransferase-2.3.2.2
116254lecithinase-
116254lipase-
116254lysine decarboxylase-4.1.1.18
116254ornithine decarboxylase-4.1.1.17
116254phenylalanine ammonia-lyase-4.3.1.24
116254protease-
116254tryptophan deaminase-
116254urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19655---+--+--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19655+-+-++++-++---++---
116254+++-+++--++-+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19655-++++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116254----------++------------+-----++-------+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116254++-+---+---------------------------+-------------+---+------++-----++----------++---+---+-+-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11710tar and phenol contaminated soilThuringia, Rosnitz, area of the former tar factoryGermanyDEUEurope
67770Tar- and phenol-contaminated soil of the former tar factoryRositzGermanyDEUEurope
116254Environment, Tar and phenol contaminated soilThuringiaGermanyDEUEurope1996

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Industrial#Engineered product
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_952.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_952&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: Y18054
  • Sequence Identity:
  • Total samples: 706
  • soil counts: 155
  • aquatic counts: 238
  • animal counts: 301
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117101Risk group (German classification)
196551Risk group (German classification)
1162541Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia alkanivorans strain CIP 106363 16S ribosomal RNA gene, partial sequenceDQ020577464ena1027371
20218Gordonia alkalivorans 16S rRNA geneY180541490ena84096

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia alkanivorans NBRC 164331027371.3wgspatric1027371
66792Gordonia alkanivorans NBRC 164332512047058draftimg1027371
67770Gordonia alkanivorans NBRC 16433GCA_000225505contigncbi1027371

GC content

@refGC-contentmethod
1171068
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.283no
flagellatedno98.519no
gram-positiveyes85.162no
anaerobicno99.596no
aerobicyes90.059no
halophileno85.71no
spore-formingno86.593no
thermophileno98.73yes
glucose-utilyes89.306yes
glucose-fermentno90.1no

External links

@ref: 11710

culture collection no.: DSM 44369, IFO 16433, JCM 10677, NBRC 16433, HKI 0136, CIP 106363, IFM 10352, KCTC 9951, NCIMB 13615

straininfo link

  • @ref: 79860
  • straininfo: 50595

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555331Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil.Kummer C, Schumann P, Stackebrandt EInt J Syst Bacteriol10.1099/00207713-49-4-15131999Actinomycetales/*classification/genetics/isolation & purification/physiology, Alkanes/metabolism, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, Coal Tar/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/*metabolismMetabolism
Phylogeny11155977Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-50-6-20312000Actinomycetales/chemistry/*classification/genetics/isolation & purification, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Sulfur/*metabolism, Thiophenes/*metabolismGenetics
Phylogeny12148617Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete.Linos A, Berekaa MM, Steinbuchel A, Kim KK, Sproer C, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-52-4-11332002Actinomycetales/classification, *Automobiles, Bacterial Typing Techniques, Biodegradation, Environmental, Butadienes/metabolism, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gordonia Bacterium/chemistry/*classification/genetics/physiology, *Hemiterpenes, Molecular Sequence Data, Nucleic Acid Hybridization, *Pentanes, Phylogeny, RNA, Ribosomal, 16S/genetics, Rubber/*metabolism, Sequence Analysis, DNAMetabolism
Phylogeny15774645Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999.Arenskotter M, Linos A, Schumann P, Kroppenstedt RM, Steinbuchel AInt J Syst Evol Microbiol10.1099/ijs.0.63400-02005DNA, Bacterial/analysis/*genetics, Deoxyribonucleases, Type II Site-Specific, Gordonia Bacterium/*classification/*genetics, Nucleic Acid Hybridization, Phylogeny, Ribotyping, Species Specificity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11710Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44369)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44369
19655Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44369.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40303Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18485
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
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
79860Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50595.1StrainInfo: A central database for resolving microbial strain identifiers
116254Curators of the CIPCollection of Institut Pasteur (CIP 106363)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106363