Strain identifier

BacDive ID: 11864

Type strain: Yes

Species: Aquamicrobium defluvii

Strain Designation: NKK

Strain history: CIP <- 1998, J. Winter, Karlsruhe Univ., Karlsruhe, Germany: strain NKK

NCBI tax ID(s): 69279 (species)

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General

@ref: 4239

BacDive-ID: 11864

DSM-Number: 11603

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

description: Aquamicrobium defluvii NKK is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 69279
  • Matching level: species

strain history

@refhistory
4239<- J. Winter and A. Bambauer, NKK
402591998, J. Winter, Univ. Karlsruhe, Karlsruhe, Germany: strain NKK
118865CIP <- 1998, J. Winter, Karlsruhe Univ., Karlsruhe, Germany: strain NKK

doi: 10.13145/bacdive11864.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Aquamicrobium
  • species: Aquamicrobium defluvii
  • full scientific name: Aquamicrobium defluvii Bambauer et al. 1998

@ref: 4239

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Phyllobacteriaceae

genus: Aquamicrobium

species: Aquamicrobium defluvii

full scientific name: Aquamicrobium defluvii Bambauer et al. 1998

strain designation: NKK

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.972
118865negativerod-shapedyes

pigmentation

  • @ref: 118865
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4239RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water
40259MEDIUM 296 - for RhizobiumyesDistilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
118865CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
4239positivegrowth30mesophilic
40259positivegrowth30mesophilic
118865positivegrowth22-41
118865nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118865
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
118865NaClpositivegrowth0-4 %
118865NaClnogrowth6 %
118865NaClnogrowth8 %
118865NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11886516947citrate-carbon source
11886517632nitrate+reduction
11886516301nitrite-reduction
11886517632nitrate-respiration

antibiotic resistance

  • @ref: 118865
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118865
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118865oxidase+
118865beta-galactosidase-3.2.1.23
118865alcohol dehydrogenase-1.1.1.1
118865gelatinase-
118865amylase-
118865DNase-
118865caseinase-3.4.21.50
118865catalase+1.11.1.6
118865tween esterase-
118865gamma-glutamyltransferase+2.3.2.2
118865lecithinase-
118865lipase-
118865lysine decarboxylase-4.1.1.18
118865ornithine decarboxylase-4.1.1.17
118865protease-
118865tryptophan deaminase-
118865urease-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
118865-+++-++-+-++-----+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118865++--+--------------------------+-+--+----------------------++----------+-+----+--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4239activated sludgeRegensburgGermanyDEUEurope
118865Environment, Activated sewage sludgeGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_6910.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_3245;97_3983;98_5083;99_6910&stattab=map
  • Last taxonomy: Aquamicrobium defluvii subclade
  • 16S sequence: Y15403
  • Sequence Identity:
  • Total samples: 535
  • soil counts: 222
  • aquatic counts: 192
  • animal counts: 75
  • plant counts: 46

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42391Risk group (German classification)
1188651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Aquamicrobium defluvium 16S rRNA gene
  • accession: Y15403
  • length: 1423
  • database: ena
  • NCBI tax ID: 69279

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aquamicrobium defluvii DSM 11603GCA_004363725scaffoldncbi69279
66792Aquamicrobium defluvii strain DSM 1160369279.8wgspatric69279
66792Aquamicrobium defluvii DSM 116032770939570draftimg69279

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes73.288no
flagellatedno85.611no
gram-positiveno97.659no
anaerobicno97.611no
aerobicyes92.849no
halophileno86.892no
spore-formingno96.506no
glucose-utilyes84.094no
thermophileno95.966yes
glucose-fermentno92.851no

External links

@ref: 4239

culture collection no.: DSM 11603, CIP 105610

straininfo link

  • @ref: 81081
  • straininfo: 49145

literature

  • topic: Phylogeny
  • Pubmed-ID: 9531630
  • title: Characterization of Aquamicrobium defluvii gen. nov. sp. nov., a thiophene-2-carboxylate-metabolizing bacterium from activated sludge.
  • authors: Bambauer A, Rainey FA, Stackebrandt E, Winter J
  • journal: Arch Microbiol
  • DOI: 10.1007/s002030050575
  • year: 1998
  • mesh: Carboxylic Acids, Cell Division/drug effects, Coenzyme A Ligases/drug effects/metabolism, DNA, Ribosomal/analysis/genetics, Gram-Negative Bacteria/genetics/*isolation & purification/metabolism, Microbiological Techniques, Molybdenum/pharmacology, Palmitoyl-CoA Hydrolase/drug effects/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, *Soil Microbiology, Thiophenes/*metabolism/pharmacology, Tungsten Compounds/pharmacology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11603)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11603
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
40259Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17649
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
81081Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49145.1StrainInfo: A central database for resolving microbial strain identifiers
118865Curators of the CIPCollection of Institut Pasteur (CIP 105610)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105610