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Bacterial strain

Achromobacter denitrificans (DSM 30026, ATCC 15173, NCTC 8582)

BacDive ID 318
Type strain
Strain Designation 12, 55B
Culture col. no. DSM 30026 ATCC 15173 NCTC 8582 CCUG 407 LMG 1231 CIP 77.15 JCM 5490 LMG 3510 CECT 449 12 55B BCRC 12838 BCRC 14342 CCM 3427 CGMCC 1.1800 IAM 12370 IFO 15125 JCM 9657 NBRC 15125 NCIMB 11961 VTT E-991293 NCIB 11961 17 more
NCBI tax ID(s) 1255278 32002
Special Collections DSMZ CCUG JCM CIP
Links

Morphology

Cell morphology

@refGram stainCell shapeMotility
124003negativerod-shaped
125438negative
125439negative

Colony morphology

Culture and growth conditions

Culture medium

@refNameGrowthMedium linkComposition
9090NUTRIENT AGAR (DSMZ Medium 1)Medium recipe at MediaDive MediaDiveName: 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 medium
124003CIP Medium 3Medium recipe at CIP

Culture temp

@refGrowthTypeTemperature (°C)Range
9090positivegrowth30mesophilic
67770positivegrowth24psychrophilic
124003positivegrowth15-41
124003negativegrowth5
124003negativegrowth45

Physiology and metabolism

Halophily

@refSaltGrowthTested relationConcentration
124003NaClpositivegrowth0-6 %
124003NaClgrowth8 %
124003NaClgrowth10 %

Spore formation

@refSpore formationConfidence
12543992.6

Enzymes

@refValueActivityEc
68382acid phosphatase+3.1.3.2
124003alcohol dehydrogenase-1.1.1.1
68382alkaline phosphatase+3.1.3.1
68382alpha-chymotrypsin-3.4.21.1
68382alpha-fucosidase-3.2.1.51
68382alpha-galactosidase-3.2.1.22
68374alpha-galactosidase-3.2.1.22
68382alpha-glucosidase-3.2.1.20
68374alpha-glucosidase-3.2.1.20
68374alpha-maltosidase-
68382alpha-mannosidase-3.2.1.24
124003amylase-
68374arginine dihydrolase-3.5.3.6
68382beta-galactosidase-3.2.1.23
124003beta-galactosidase-3.2.1.23
68368beta-galactosidase+3.2.1.23
68374beta-galactosidase-3.2.1.23
68382beta-glucosidase-3.2.1.21
68374beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68374beta-glucuronidase-3.2.1.31
124003caseinase-3.4.21.50
124003catalase+1.11.1.6
68382cystine arylamidase-3.4.11.3
68368cytochrome oxidase+1.9.3.1
124003DNase-
68382esterase (C 4)+
68382esterase lipase (C 8)+
124003gamma-glutamyltransferase-2.3.2.2
124003gelatinase-
68368gelatinase-
68374L-aspartate arylamidase+3.4.11.21
124003lecithinase-
68382leucine arylamidase+3.4.11.1
124003lipase-
68374lipase-
68382lipase (C 14)-
124003lysine decarboxylase-4.1.1.18
68374lysine decarboxylase-4.1.1.18
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68382naphthol-AS-BI-phosphohydrolase+
124003ornithine decarboxylase-4.1.1.17
68374ornithine decarboxylase-4.1.1.17
124003oxidase+
124003phenylalanine ammonia-lyase-4.3.1.24
124003protease-
68382trypsin-3.4.21.4
124003tryptophan deaminase-
68368tryptophan deaminase-4.1.99.1
124003tween esterase-
124003urease-3.5.1.5
68374urease-3.5.1.5
68382valine arylamidase-

Antibiotic resistance

@refMetaboliteIs antibioticIs sensitiveIs resistant
1240030129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@refChebi-IDMetaboliteProduction
6836815688 ChEBIacetoin
6836816136 ChEBIhydrogen sulfide
6837435581 ChEBIindole
12400335581 ChEBIindole
6836835581 ChEBIindole
6836816301 ChEBInitrite

Metabolite tests

@refChebi-IDMetaboliteVoges-proskauer-test
12400315688 ChEBIacetoin-
6836815688 ChEBIacetoin+
12400317234 ChEBIglucose
6837435581 ChEBIindole
6836835581 ChEBIindole

Metabolite utilization

@refChebi-IDMetaboliteUtilization activityKind of utilization tested
6836827613 ChEBIamygdalin-fermentation
6837429016 ChEBIarginine-hydrolysis
6837417057 ChEBIcellobiose-builds acid from
12400316947 ChEBIcitrate+carbon source
6836816947 ChEBIcitrate+assimilation
6837418333 ChEBID-arabitol-builds acid from
6837418024 ChEBID-galacturonic acid-builds acid from
6837417634 ChEBID-glucose-builds acid from
6836817634 ChEBID-glucose-fermentation
6837416899 ChEBID-mannitol-builds acid from
6836816899 ChEBID-mannitol-fermentation
1240034853 ChEBIesculin-hydrolysis
683685291 ChEBIgelatin-hydrolysis
124003606565 ChEBIhippurate+hydrolysis
6837430849 ChEBIL-arabinose-builds acid from
6836830849 ChEBIL-arabinose-fermentation
6837418403 ChEBIL-arabitol-builds acid from
6837462345 ChEBIL-rhamnose-builds acid from
6836862345 ChEBIL-rhamnose-fermentation
6837425094 ChEBIlysine-degradation
12400315792 ChEBImalonate+assimilation
6837415792 ChEBImalonate-assimilation
6837417306 ChEBImaltose-builds acid from
6836828053 ChEBImelibiose-fermentation
6837417268 ChEBImyo-inositol-builds acid from
6836817268 ChEBImyo-inositol-fermentation
12400317632 ChEBInitrate+builds gas from
12400317632 ChEBInitrate+reduction
12400317632 ChEBInitrate+respiration
6836817632 ChEBInitrate+reduction
12400316301 ChEBInitrite+builds gas from
12400316301 ChEBInitrite+reduction
6837418257 ChEBIornithine-degradation
6837418394 ChEBIpalatinose-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837415963 ChEBIribitol-builds acid from
6837430911 ChEBIsorbitol-builds acid from
6836830911 ChEBIsorbitol-fermentation
6837417992 ChEBIsucrose-builds acid from
6836817992 ChEBIsucrose-fermentation
6837427082 ChEBItrehalose-builds acid from
6837427897 ChEBItryptophan-energy source
6836827897 ChEBItryptophan-energy source
6837416199 ChEBIurea-hydrolysis

Oxygen tolerance

@refOxygen tolerance
124003obligate aerobe
125439aerobe

API biotype100

@ref ControlQ D-glucose as carbon sourceGLU D-fructose as carbon sourceFRU D-galactose as carbon sourceGAL D-trehalose as carbon sourceTRE D-mannose as carbon sourceMNE L-sorbose as carbon sourceSBE D-melibiose as carbon sourceMEL sucrose as carbon sourceSAC D-raffinose as carbon sourceRAF maltotriose as carbon sourceMTE maltose as carbon sourceMAL lactose as carbon sourceLAC lactulose as carbon sourceLTE 1-O-methyl-beta-galactopyranoside as carbon sourceMbGa 1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa D-cellobiose as carbon sourceCEL gentiobiose as carbon sourceGEN 1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu esculin as carbon sourceESC D-ribose as carbon sourceRIB L-arabinose as carbon sourceARA D-xylose as carbon sourceXYL palatinose as carbon sourcePLE L-rhamnose as carbon sourceRHA L-fucose as carbon sourceFUC D-melezitose as carbon sourceMLZ D-arabitol as carbon sourceDARL L-arabitol as carbon sourceLARL xylitol as carbon sourceXLT dulcitol as carbon sourceDUL D-tagatose as carbon sourceTAG glycerol as carbon sourceGLY myo-inositol as carbon sourceINO D-mannitol as carbon sourceMAN maltitol as carbon sourceMTL D-turanose as carbon sourceTUR D-sorbitol as carbon sourceSOR adonitol as carbon sourceADO hydroxyquinoline-beta-glucuronide as carbon sourceHBG D-lyxose as carbon sourceLYX i-erythritol as carbon sourceERY 1-O-methyl-alpha-D-glucoside as carbon sourceMDG 3-O-methyl-D-glucose as carbon source3MDG D-saccharate as carbon sourceSAT mucate as carbon sourceMUC L-tartrate as carbon sourceLTAT D-tartrate as carbon sourceDTAT meso-tartrate as carbon sourceMTAT D-malate as carbon sourceDMLT L-malate as carbon sourceLMLT cis-aconitate as carbon sourceCATE trans-aconitate as carbon sourceTATE tricarballylate as carbon sourceTTE citrate as carbon sourceCIT D-glucuronate as carbon sourceGRT D-galacturonate as carbon sourceGAT 2-ketogluconate as carbon source2KG 5-ketogluconate as carbon source5KG tryptophan as carbon sourceTRY N-acetyl-D-glucosamine as carbon sourceNAG D-gluconate as carbon sourceGNT phenylacetate as carbon sourcePAC protocatechuate as carbon sourcePAT 4-hydroxybenzoate as carbon sourcepOBE quinate as carbon sourceQAT gentisate as carbon sourceGTE 3-hydroxybenzoate as carbon sourcemOBE benzoate as carbon sourceBAT 3-phenylpropionate as carbon sourcePPAT m-coumarate as carbon sourceCMT trigonelline as carbon sourceTGE betaine as carbon sourceBET putrescine as carbon sourcePCE 4-aminobutyrate as carbon sourceABT histamine as carbon sourceHIN DL-lactate as carbon sourceLAT caprate as carbon sourceCAP caprylate as carbon sourceCYT L-histidine as carbon sourceHIS succinate as carbon sourceSUC fumarate as carbon sourceFUM glutarate as carbon sourceGRE DL-glycerate as carbon sourceGYT 5-aminovalerate as carbon sourceAVT ethanolamine as carbon sourceETN tryptamine as carbon sourceTTN D-glucosamine as carbon sourceGLN itaconate as carbon sourceITA 3-hydroxybutyrate as carbon source3OBU L-aspartate as carbon sourceAPT L-glutamate as carbon sourceGTT L-proline as carbon sourcePRO D-alanine as carbon sourceDALA L-alanine as carbon sourceLALA L-serine as carbon sourceSER malonate as carbon sourceMNT propionate as carbon sourcePROP L-tyrosine as carbon sourceTYR 2-ketoglutarate as carbon source2KT
124003 not determinedn.d. - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - + + + - + + + + - + + - - - - + - - + - - - + + + - - - - - + - + + - + + + + + - - + - + + + + + + + + - + + +

Isolation, sampling and environmental information

Isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil

Isolation

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

Safety information

Risk assessment

@refBiosafety levelBiosafety level comment
90902Risk group (German classification)
According to TRBA 466
1240031Risk group (French classification)
According to TRBA 466

Sequence information

GC content

@refGC-content (mol%)Method
6777068.8-69.4thermal denaturation, midpoint method (Tm)

16S sequences

@refDescriptionAccessionLengthDatabaseNCBI tax ID
20218A.xylosoxidans 16S ribosomal RNA, complete cdsM225091466


85698  
20218Achromobacter denitrificans strain CCUG 407 16S ribosomal RNA gene, partial sequenceJQ7464221309


32002  
20218Achromobacter xylosoxidans subsp. denitrificans partial 16S rRNA gene, strain DSM 30026 (T)AJ2784511523


32002  
20218Alcaligenes denitrificans 16S rRNA geneY149071489


32002  
20218Achromobacter denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 15125AB6807721456


32002  
124043Achromobacter denitrificans partial 16S rRNA gene, type strain CCM3427TFM9997341381

32002  

Genome sequences

@refDescriptionAccessionAssembly levelDatabaseNCBI tax ID
66792Achromobacter denitrificans NCTC8582GCA_900444675contig

32002  
66792Achromobacter denitrificans NBRC 151251255278.4wgs
PATRIC
1255278  
66792Achromobacter denitrificans strain FDAARGOS_78632002.39complete
PATRIC
32002  
66792Achromobacter denitrificans strain LMG 123132002.36wgs
PATRIC
32002  
66792Achromobacter denitrificans strain NCTC858232002.30wgs
PATRIC
32002  
66792Achromobacter denitrificans NBRC 151252731957627draft
JGI IMG/M
1255278  
66792Achromobacter denitrificans NCTC 85822811995195draft
JGI IMG/M
32002  
67770Achromobacter denitrificans NBRC 15125GCA_001571365contig

1255278  
67770Achromobacter denitrificans LMG 1231GCA_902859715contig

32002  

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Achromobacter denitrificans NCTC8582
 NCBI: GCA_900444675
@ref Trait Model Prediction Confidence in % In training data
125439 oxygen_tolerance BacteriaNetⓘ aerobe 91.90 no
125439 gram_stain BacteriaNetⓘ negative 94.60 no
125439 motility BacteriaNetⓘ yes 76.80 no
125439 spore_formation BacteriaNetⓘ no 92.60 no
Predictions from Diaspora project based on:
Achromobacter denitrificans strain FDAARGOS_786 strain Not applicable
 PATRIC: 32002.39
@ref Trait Model Prediction Confidence in % In training data
125438 gram-positive gram-positiveⓘ no 96.68 no
125438 anaerobic anaerobicⓘ no 96.85 yes
125438 spore-forming spore-formingⓘ no 87.37 no
125438 aerobic aerobicⓘ yes 87.62 yes
125438 thermophilic thermophileⓘ no 98.49 no
125438 flagellated motile2+ⓘ yes 85.32 no

External links

Literature

TopicTitleAuthorsJournalDOIYear
MetabolismA 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/s41467-021-27357-72021
PhylogenyEmendation 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.x1998
Structure 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
EnzymologyEvidence 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/bi00032a0111995
EnzymologyStructure 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.a1246611994
PhylogenyAchromobacter 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.0.0037862020
PhylogenyAchromobacter 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.0.062265-02014
PhylogenyPusillimonas 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.0.018358-02009
@refStraininfoCulture collections
69999389403LMG 1231, ATCC 15173, CCUG 407, CECT 449, DSM 30026, JCM 5490, LMG 3510, NCIB 11961, NCTC 8582, CIP 7715, IFO 15125, DSM 4612, JCM 9657, NCIMB 11961, IAM12370, CCM 3427, CCRC 12838, CCRC 14342, AS 1.1800, NBRC 15125, BCRC 12838, BCRC 14342, KCTC 12447, CGMCC 1.1800, VTT E-991293, DSM 60, CIP 77.15

References

#9090 Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 30026
#20215 Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218 Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#44188 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 407
#66792 Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368 Automatically annotated from API 20E .
#68374 Automatically annotated from API ID32E .
#68382 Automatically annotated from API zym .
#69999 Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID389403.1 )
#124003 Collection of Institut Pasteur ; Curators of the CIP; CIP 77.15
#124043 Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438 Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439 Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

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