Strain identifier

BacDive ID: 13895

Type strain: Yes

Species: Dechloromonas denitrificans

Strain Designation: ED1

Strain history: CIP <- 2007, DSMZ <- A. Schramm, Bayreuth Univ., Bayreuth, Germany: strain ED1 <- M. Horn <- J. Ihssen

NCBI tax ID(s): 281362 (species)

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General

@ref: 6142

BacDive-ID: 13895

DSM-Number: 15892

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Dechloromonas denitrificans ED1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from earthworm gut.

NCBI tax id

  • NCBI tax id: 281362
  • Matching level: species

strain history

@refhistory
6142<- A. Schramm; ED1 <- M. Horn <- J. Ihssen
118895CIP <- 2007, DSMZ <- A. Schramm, Bayreuth Univ., Bayreuth, Germany: strain ED1 <- M. Horn <- J. Ihssen

doi: 10.13145/bacdive13895.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Azonexaceae
  • genus: Dechloromonas
  • species: Dechloromonas denitrificans
  • full scientific name: Dechloromonas denitrificans Horn et al. 2005

@ref: 6142

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhizobiales

family: Azonexaceae

genus: Dechloromonas

species: Dechloromonas denitrificans

full scientific name: Dechloromonas denitrificans Horn et al. 2005

strain designation: ED1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31407negative1.7 µm0.5 µmrod-shapedyes
118895negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6142R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
34986MEDIUM 372 - for AquabacteriumyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Tween 80 (1.000 ml);Casamino acids (0.500 g);Proteose Peptone N°3 (0.500 g);Di Potassium mon
118895CIP Medium 372yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=372
118895CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
6142positivegrowth30mesophilic
31407positivegrowth5.0-36
31407positiveoptimum30mesophilic
34986positivegrowth30mesophilic

culture pH

@refabilitytypepH
31407positivegrowth6.1-8.3
31407positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31407
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3140730089acetate+carbon source
3140729987glutamate+carbon source
3140724996lactate+carbon source
3140725115malate+carbon source
3140717272propionate+carbon source
3140715361pyruvate+carbon source
3140730031succinate+carbon source
3140717632nitrate+reduction
11889517632nitrate+reduction
11889516301nitrite-reduction

metabolite production

  • @ref: 118895
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118895oxidase-
118895catalase-1.11.1.6
118895urease+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
118895--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6142earthworm (Aporrectodea caliginosa) gutAporrectodea caliginosaBavaria, BayreuthGermanyDEUEurope
118895Animal, Gut of earthworm, Aporrectodea caliginosaGermanyDEUEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Annelida

taxonmaps

  • @ref: 69479
  • File name: preview.99_5563.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_2421;97_2948;98_4151;99_5563&stattab=map
  • Last taxonomy: Dechloromonas
  • 16S sequence: AJ318917
  • Sequence Identity:
  • Total samples: 760
  • soil counts: 97
  • aquatic counts: 580
  • animal counts: 44
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61421Risk group (German classification)
1188951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6142
  • description: Dechloromonas denitrificans 16S rRNA gene, type strain ED1T
  • accession: AJ318917
  • length: 1487
  • database: ena
  • NCBI tax ID: 281362

GC content

  • @ref: 6142
  • GC-content: 61.2

External links

@ref: 6142

culture collection no.: DSM 15892, ATCC BAA 841, CIP 109443

straininfo link

  • @ref: 83070
  • straininfo: 138976

literature

  • topic: Phylogeny
  • Pubmed-ID: 15879265
  • title: Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa.
  • authors: Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63484-0
  • year: 2005
  • mesh: Aerobiosis, Anaerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/cytology/isolation & purification/physiology, Cytochromes c/isolation & purification, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Digestive System/microbiology, Endospore-Forming Bacteria/*classification/cytology/isolation & purification/physiology, Flavobacterium/*classification/cytology/isolation & purification/physiology, Genes, rRNA, Gentian Violet, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nitrates/metabolism, Nitrogen/metabolism, Nitrous Oxide/*metabolism, Oligochaeta/*microbiology, Oxidation-Reduction, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6142Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15892)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15892
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
31407Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2771628776041
34986Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7187
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
83070Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138976.1StrainInfo: A central database for resolving microbial strain identifiers
118895Curators of the CIPCollection of Institut Pasteur (CIP 109443)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109443