Strain identifier

BacDive ID: 10607

Type strain: Yes

Species: Gordonia paraffinivorans

Strain Designation: AS4.1730, HD321

Strain history: CIP <- 2004, Y. Xue, Chinese Academy Sciences, Beijing, China: strain HD321

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

@ref: 11919

BacDive-ID: 10607

DSM-Number: 44604

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

description: Gordonia paraffinivorans AS4.1730 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from production wellhead water sample.

NCBI tax id

NCBI tax idMatching level
1223543strain
175628species

strain history

@refhistory
11919<- Y. Xue, Chinese Academy of Science, Beijing; AS4.1730
404882004, Y. Xue, Beijing, China: strain HD321
67770AS 4.1730 <-- Y. Xue HD321.
121554CIP <- 2004, Y. Xue, Chinese Academy Sciences, Beijing, China: strain HD321

doi: 10.13145/bacdive10607.20230509.8.1

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 paraffinivorans
  • full scientific name: Gordonia paraffinivorans Xue et al. 2003

@ref: 11919

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia paraffinivorans

full scientific name: Gordonia paraffinivorans Xue et al. 2003

strain designation: AS4.1730, HD321

type strain: yes

Morphology

cell morphology

  • @ref: 121554
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19682Red orange10-14 daysISP 2
19682Ivory10-14 daysISP 3
19682Ivory10-14 daysISP 4
19682Red orange10-14 daysISP 5
19682Ivory10-14 daysISP 6
19682Red orange10-14 daysISP 7
1215541

multicellular morphology

@refforms multicellular complexmedium name
19682noISP 2
19682noISP 3
19682noISP 4
19682noISP 5
19682noISP 6
19682noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11919TRYPTICASE 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
19682ISP 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
19682ISP 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:
19682ISP 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
19682ISP 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
19682ISP 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
19682ISP 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
40488MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121554CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
11919positivegrowth28mesophilic
19682positiveoptimum28mesophilic
40488positivegrowth30mesophilic
67770positivegrowth28mesophilic
121554positivegrowth25-45
121554nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121554
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 121554
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1968217234glucose+
1968222599arabinose-
1968217992sucrose+
1968218222xylose-
1968217268myo-inositol-
1968229864mannitol-
1968228757fructose-
1968226546rhamnose-
1968216634raffinose-
1968262968cellulose-
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
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
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
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12155416947citrate-carbon source
1215544853esculin+hydrolysis
121554606565hippurate-hydrolysis
12155417632nitrate-reduction
12155416301nitrite-reduction
12155417632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12155435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12155415688acetoin-
12155417234glucose-

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
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
121554beta-galactosidase-3.2.1.23
121554alcohol dehydrogenase+1.1.1.1
121554gelatinase-
121554amylase-
121554DNase-
121554caseinase-3.4.21.50
121554catalase+1.11.1.6
121554tween esterase+
121554gamma-glutamyltransferase+2.3.2.2
121554lecithinase-
121554lipase-
121554lysine decarboxylase-4.1.1.18
121554ornithine decarboxylase-4.1.1.17
121554protease-
121554tryptophan deaminase-
121554urease+3.5.1.5
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19682-++--+-++--

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19682+++-++++-++---++---
11919+/-+/-+/--++/-+/---++/----+-----
11919--+-++/----+----++/-----
121554+++-+++--++-+-++----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11919-----+--+/--+/--+/--+-+/-++/-+/-
11919----++-+++/-+/-+/--+/-+-+++/-+/-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121554------------------------+/----------------+/---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121554+--++--+----------------------------------------++----------+------------------++-------+-+-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11919production wellhead water sampleDaqing oilfieldChinaCHNAsia
67770Water sample from oil-producing well of Daqing oilfieldChinaCHNAsia
121554Environment, Water sample, producing well of Daqing oilfieldChinaCHNAsia1996

isolation source categories

Cat1Cat2
#Engineered#Industrial
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_4363.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2187;97_2646;98_3280;99_4363&stattab=map
  • Last taxonomy: Gordonia paraffinivorans subclade
  • 16S sequence: AF432348
  • Sequence Identity:
  • Total samples: 1603
  • soil counts: 124
  • aquatic counts: 450
  • animal counts: 1012
  • plant counts: 17

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119191Risk group (German classification)
196821Risk group (German classification)
1215541Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11919
  • description: Gordonia sp. HD321 16S ribosomal RNA gene, partial sequence
  • accession: AF432348
  • length: 1477
  • database: ena
  • NCBI tax ID: 175628

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia paraffinivorans NBRC 1082381223543.3wgspatric1223543
66792Gordonia paraffinivorans NBRC 1082382523231042draftimg1223543
67770Gordonia paraffinivorans NBRC 108238GCA_000344155contigncbi1223543

GC content

  • @ref: 67770
  • GC-content: 66
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.954no
gram-positiveyes87.059no
anaerobicno99.295no
aerobicyes89.435no
halophileno87.446no
spore-formingno85.57no
glucose-utilyes88.397yes
flagellatedno98.698no
thermophileno98.552yes
glucose-fermentno91.746yes

External links

@ref: 11919

culture collection no.: DSM 44604, JCM 12461, BCRC 16372, CGMCC 4.1730, CIP 108331, IFM 10631, NBRC 108238, NCIMB 14305, AS 4.1730

straininfo link

  • @ref: 79881
  • straininfo: 127993

literature

  • topic: Phylogeny
  • Pubmed-ID: 13130063
  • title: Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well.
  • authors: Xue Y, Sun X, Zhou P, Liu R, Liang F, Ma Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02605-0
  • year: 2003
  • mesh: Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fuel Oils, Gordonia Bacterium/classification/genetics/*isolation & purification/*metabolism, Hydrocarbons/*metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
11919Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44604)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44604
19682Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44604.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
40488Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5942
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/
68369Automatically annotated from API 20NE
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
79881Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127993.1StrainInfo: A central database for resolving microbial strain identifiers
121554Curators of the CIPCollection of Institut Pasteur (CIP 108331)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108331