Strain identifier

BacDive ID: 318

Type strain: Yes

Species: Achromobacter denitrificans

Strain Designation: 12, 55B

Strain history: CIP <- 1977, F. Pichinoty, CNRS, Marseille, France <- ATCC <- R. Hugh: strain 12 <- L.R. Fredrich: strain 55B

NCBI tax ID(s): 1255278 (strain), 32002 (species)

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General

@ref: 9090

BacDive-ID: 318

DSM-Number: 30026

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

description: Achromobacter denitrificans 12 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1255278strain
32002species

strain history

@refhistory
9090<- ATCC <- R. Hugh, 12 <- L.R. Fredrich, 55B (Alcaligenes faecalis subsp. faecalis)
67770Y. Kosako 85022 <-- Nissui Pharm. Co., Ltd. <-- ATCC 15173 <-- R. Hugh 12 <-- L. R. Fredrich 55B.
124003CIP <- 1977, F. Pichinoty, CNRS, Marseille, France <- ATCC <- R. Hugh: strain 12 <- L.R. Fredrich: strain 55B

doi: 10.13145/bacdive318.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Achromobacter
  • species: Achromobacter denitrificans
  • full scientific name: Achromobacter denitrificans (Rüger and Tan 1983 ex Leifson and Hugh 1954) Coenye et al. 2003

  • synonyms

    @refsynonym
    20215Alcaligenes denitrificans
    20215Achromobacter xylosoxidans subsp. denitrificans
    20215Alcaligenes xylosoxidans subsp. denitrificans

@ref: 9090

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Achromobacter

species: Achromobacter denitrificans

full scientific name: Achromobacter denitrificans (Rüger and Tan 1983) Coenye et al. 2003

strain designation: 12, 55B

type strain: yes

Morphology

cell morphology

  • @ref: 124003
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 124003

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9090NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
68368MacConkey mediumyes
124003CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
9090positivegrowth30mesophilic
67770positivegrowth24psychrophilic
124003positivegrowth15-41
124003nogrowth5psychrophilic
124003nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 124003
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
124003NaClpositivegrowth0-6 %
124003NaClnogrowth8 %
124003NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816947citrate+assimilation
12400316947citrate+carbon source
1240034853esculin-hydrolysis
124003606565hippurate+hydrolysis
12400317632nitrate+builds gas from
12400317632nitrate+reduction
12400316301nitrite+builds gas from
12400316301nitrite+reduction
12400315792malonate+assimilation
12400317632nitrate+respiration
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol-builds acid from
6837417306maltose-builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose-builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837462345L-rhamnose-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol-builds acid from

antibiotic resistance

  • @ref: 124003
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12400335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836815688acetoin+
6836835581indole-
12400315688acetoin-
12400317234glucose-

enzymes

@refvalueactivityec
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
68374L-aspartate arylamidase+3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase-3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368beta-galactosidase+3.2.1.23
124003oxidase+
124003beta-galactosidase-3.2.1.23
124003alcohol dehydrogenase-1.1.1.1
124003gelatinase-
124003amylase-
124003DNase-
124003caseinase-3.4.21.50
124003catalase+1.11.1.6
124003tween esterase-
124003gamma-glutamyltransferase-2.3.2.2
124003lecithinase-
124003lipase-
124003lysine decarboxylase-4.1.1.18
124003ornithine decarboxylase-4.1.1.17
124003phenylalanine ammonia-lyase-4.3.1.24
124003protease-
124003tryptophan deaminase-
124003urease-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
124003-+++-+----++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2MAC
9090++/-+/-+/-+-+/---+----------+++

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
44188--------+----------------------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
124003------------------+------------------------+++-++++-++----+--+---+++-----+-++-+++++--+-++++++++-+++

Isolation, sampling and environmental information

isolation

@refsample type
9090soil
44188Soil
67770Soil
124003Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
90902Risk group (German classification)
1240031Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.xylosoxidans 16S ribosomal RNA, complete cdsM225091466ena85698
20218Achromobacter denitrificans strain CCUG 407 16S ribosomal RNA gene, partial sequenceJQ7464221309ena32002
20218Achromobacter xylosoxidans subsp. denitrificans partial 16S rRNA gene, strain DSM 30026 (T)AJ2784511523ena32002
20218Alcaligenes denitrificans 16S rRNA geneY149071489ena32002
20218Achromobacter denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 15125AB6807721456ena32002
67770Citrus unshiu DNA, scaffold00817, cultivar: Miyagawa wase, whole genome shotgun sequenceM2246775260ena55188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Achromobacter denitrificans NCTC8582GCA_900444675contigncbi32002
66792Achromobacter denitrificans NBRC 151251255278.4wgspatric1255278
66792Achromobacter denitrificans strain FDAARGOS_78632002.39completepatric32002
66792Achromobacter denitrificans strain LMG 123132002.36wgspatric32002
66792Achromobacter denitrificans strain NCTC858232002.30wgspatric32002
66792Achromobacter denitrificans NBRC 151252731957627draftimg1255278
66792Achromobacter denitrificans NCTC 85822811995195draftimg32002
67770Achromobacter denitrificans NBRC 15125GCA_001571365contigncbi1255278
67770Achromobacter denitrificans LMG 1231GCA_902859715contigncbi32002

GC content

  • @ref: 67770
  • GC-content: 68.8-69.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.445no
anaerobicno98.568no
halophileno86.902no
spore-formingno94.003no
glucose-utilno67.783no
motileyes88.719no
flagellatedno56.974no
aerobicyes84.323no
thermophileno99.644yes
glucose-fermentno89.417yes

External links

@ref: 9090

culture collection no.: DSM 30026, ATCC 15173, NCTC 8582, CCUG 407, LMG 1231, CIP 77.15, JCM 5490, LMG 3510, CECT 449, BCRC 12838, BCRC 14342, CCM 3427, CGMCC 1.1800, IAM 12370, IFO 15125, JCM 9657, NBRC 15125, NCIMB 11961, VTT E-991293, NCIB 11961

straininfo link

  • @ref: 69999
  • straininfo: 389403

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7640272Evidence for two distinct azurins in Alcaligenes xylosoxidans (NCIMB 11015): potential electron donors to nitrite reductase.Dodd FE, Hasnain SS, Hunter WN, Abraham ZH, Debenham M, Kanzler H, Eldridge M, Eady RR, Ambler RP, Smith BEBiochemistry10.1021/bi00032a0111995Alcaligenes/*chemistry/enzymology, Amino Acid Sequence, Azurin/*chemistry/isolation & purification, Crystallography, X-Ray, Electrons, Molecular Sequence Data, Nitrite Reductases/*chemistry, Sequence Homology, Amino AcidGenetics
Enzymology7706206Structure of azurin from Achromobacter xylosoxidans NCIB11015 at 2.5 A resolution.Inoue T, Shibata N, Nakanishi H, Koyama S, Ishii H, Kai Y, Harada S, Kasai N, Ohshiro Y, Suzuki S, et al.J Biochem10.1093/oxfordjournals.jbchem.a1246611994Alcaligenes/*chemistry, Amino Acid Sequence, Azurin/*chemistry/isolation & purification, Bacterial Proteins/*chemistry/isolation & purification, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein ConformationPhylogeny
Phylogeny9688077Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Ruger and Tan) comb. nov.Yabuuchi E, Kawamura Y, Kosako Y, Ezaki TMicrobiol Immunol10.1111/j.1348-0421.1998.tb02306.x1998Alcaligenes/*classification/genetics, Bacterial Typing Techniques, Bordetella/classification, DNA, Bacterial/analysis/chemistry, Humans, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicPathogenicity
15299774Structure of a new azurin from the denitrifying bacterium Alcaligenes xylosoxidans at high resolution.Dodd FE, Hasnain SS, Abraham ZH, Eady RR, Smith BEActa Crystallogr D Biol Crystallogr10.1107/S09074449950075541995
Phylogeny19749028Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field.Srinivasan S, Kim MK, Sathiyaraj G, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.018358-02009Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny24711589Achromobacter sediminum sp. nov., isolated from deep subseafloor sediment of South Pacific Gyre.Zhang Z, Fan X, Gao X, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.062265-02014Achromobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny31613739Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production.Dumolin C, Peeters C, Ehsani E, Tahon G, De Canck E, Cnockaert M, Boon N, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0037862020Achromobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Belgium, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Hydrogen, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Metabolism34876568A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR.Xiao D, Zhang W, Guo X, Liu Y, Hu C, Guo S, Kang Z, Xu X, Ma C, Gao C, Xu PNat Commun10.1038/s41467-021-27357-72021Achromobacter denitrificans/enzymology/genetics/metabolism, Alcohol Oxidoreductases/genetics/*metabolism, Bacteria/metabolism, *Biosensing Techniques, *Gene Expression Regulation, Glutarates/*chemistry/*metabolism, HEK293 Cells, Humans, Isocitrate Dehydrogenase, Metabolic Networks and Pathways, Mutation, Neoplasms, Transcription FactorsEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9090Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30026)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30026
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
44188Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 407)https://www.ccug.se/strain?id=407
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
68374Automatically annotated from API ID32E
68382Automatically annotated from API zym
69999Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389403.1StrainInfo: A central database for resolving microbial strain identifiers
124003Curators of the CIPCollection of Institut Pasteur (CIP 77.15)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2077.15