Strain identifier

BacDive ID: 5789

Type strain: Yes

Species: Geopsychrobacter electrodiphilus

Strain Designation: A1

Strain history: D. Holmes A1.

NCBI tax ID(s): 1121918 (strain), 225196 (species)

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General

@ref: 6430

BacDive-ID: 5789

DSM-Number: 16401

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, psychrophilic, Gram-negative

description: Geopsychrobacter electrodiphilus A1 is an anaerobe, psychrophilic, Gram-negative bacterium that was isolated from electrode and Fe oxide.

NCBI tax id

NCBI tax idMatching level
225196species
1121918strain

strain history

@refhistory
6430<- D. E. Holmes, University of Massachusetts, Department of Microbiology, USA; A1 <- D. E. Holmes {2003}
67770D. Holmes A1.

doi: 10.13145/bacdive5789.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfuromonadales
  • family: Geobacteraceae
  • genus: Geopsychrobacter
  • species: Geopsychrobacter electrodiphilus
  • full scientific name: Geopsychrobacter electrodiphilus Holmes et al. 2005

@ref: 6430

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Geobacteraceae

genus: Geopsychrobacter

species: Geopsychrobacter electrodiphilus

full scientific name: Geopsychrobacter electrodiphilus Holmes et al. 2005

strain designation: A1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.999

Culture and growth conditions

culture medium

  • @ref: 6430
  • name: GEOANAEROBACTER MEDIUM (DSMZ Medium 838)
  • growth: yes
  • link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium838.pdf

culture temp

@refgrowthtypetemperaturerange
6430positivegrowth22psychrophilic
67770positivegrowth22psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6430anaerobe
69480anaerobe96.942

spore formation

@refspore formationconfidence
69481no100
69480no99.986

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6430electrode and Fe oxideBoston HarborUSAUSANorth America
67770Marine sediment fuel cell constructed with sedimentsBoston Harbor, MAUSAUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Industrial
  • Cat3: #Industrial production

taxonmaps

  • @ref: 69479
  • File name: preview.99_7142.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_50;96_3349;97_4107;98_5254;99_7142&stattab=map
  • Last taxonomy: Geopsychrobacter electrodiphilus subclade
  • 16S sequence: AY187303
  • Sequence Identity:
  • Total samples: 873
  • soil counts: 111
  • aquatic counts: 725
  • animal counts: 30
  • plant counts: 7

Safety information

risk assessment

  • @ref: 6430
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6430
  • description: Geopsychrobacter electrodiphilus strain A1 16S ribosomal RNA gene, partial sequence
  • accession: AY187303
  • length: 1493
  • database: ena
  • NCBI tax ID: 225196

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geopsychrobacter electrodiphilus DSM 164011121918.7wgspatric1121918
66792Geopsychrobacter electrodiphilus DSM 164012522572047draftimg1121918
67770Geopsychrobacter electrodiphilus DSM 16401GCA_000384395contigncbi1121918

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno70.886no
flagellatedno86.518no
gram-positiveno99.06no
anaerobicyes92.825yes
halophileno73.268no
spore-formingno91.525no
thermophileno98.607yes
glucose-utilyes57.203no
aerobicno94.942yes
glucose-fermentno87.284no

External links

@ref: 6430

culture collection no.: DSM 16401, ATCC BAA 880, JCM 12469

straininfo link

  • @ref: 75268
  • straininfo: 138005

literature

  • topic: Phylogeny
  • Pubmed-ID: 15466546
  • title: Potential role of a novel psychrotolerant member of the family Geobacteraceae, Geopsychrobacter electrodiphilus gen. nov., sp. nov., in electricity production by a marine sediment fuel cell.
  • authors: Holmes DE, Nicoll JS, Bond DR, Lovley DR
  • journal: Appl Environ Microbiol
  • DOI: 10.1128/AEM.70.10.6023-6030.2004
  • year: 2004
  • mesh: *Bioelectric Energy Sources, Cytochromes/metabolism, Deltaproteobacteria/classification/genetics/growth & development/*physiology, Electron Transport, Genes, Bacterial, Geologic Sediments/*microbiology, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
6430Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16401)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16401
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
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/
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
75268Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138005.1StrainInfo: A central database for resolving microbial strain identifiers