Strain identifier

BacDive ID: 130339

Type strain: Yes

Species: Geoalkalibacter subterraneus

Strain Designation: Red1

Strain history: T. Itoh; RIKEN BRC-JCM, Japan <-- J. Badalamenti; Univ. of Minnesota, USA <-- DSMZ <-- JCM <-- A. Greene; Griffith Univ., Australia; Red1.

NCBI tax ID(s): 483547 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22043

BacDive-ID: 130339

DSM-Number: 29995

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

description: Geoalkalibacter subterraneus Red1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from oilfield production water.

NCBI tax id

  • NCBI tax id: 483547
  • Matching level: species

strain history

@refhistory
22043<- J. Badalamenti, Univ. Minnesota; Red1 <- Leibniz-Institut DSMZ; DSM 23483 <- T. Itoh, JCM; JCM 15104 <- A. C. Greene, Griffith Univ., Brisbane, Australia; Red1
67770T. Itoh; RIKEN BRC-JCM, Japan <-- J. Badalamenti; Univ. of Minnesota, USA <-- DSMZ <-- JCM <-- A. Greene; Griffith Univ., Australia; Red1.

doi: 10.13145/bacdive130339.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfuromonadales
  • family: Desulfuromonadaceae
  • genus: Geoalkalibacter
  • species: Geoalkalibacter subterraneus
  • full scientific name: Geoalkalibacter subterraneus Greene et al. 2009

@ref: 22043

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Desulfuromonadaceae

genus: Geoalkalibacter

species: Geoalkalibacter subterraneus

full scientific name: Geoalkalibacter subterraneus Greene et al. 2009

strain designation: Red1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28919negative3 µm0.55 µmrod-shapedyes
69480yes95.035
69480negative99.999

pigmentation

  • @ref: 28919
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 22043
  • name: GEOALKALIBACTER SUBTERRANEUS MEDIUM (DSMZ Medium 1249)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1249
  • composition: Name: GEOALKALIBACTER SUBTERRANEUS MEDIUM (DSMZ Medium 1249) Composition: NaCl 16.9661 g/l MgCl2 x 6 H2O 4.49102 g/l Yeast extract 2.99401 g/l NaNO3 2.54491 g/l Na2CO3 1.49701 g/l Na-acetate 0.998004 g/l NH4Cl 0.998004 g/l CaCl2 x 2 H2O 0.349301 g/l KH2PO4 0.0798403 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l NaOH 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l H3BO3 5.98802e-06 g/l Na2WO4 x 2 H2O 3.99202e-06 g/l Na2SeO3 x 5 H2O 2.99401e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22043positivegrowth37mesophilic
28919positivegrowth30-50
28919positiveoptimum40thermophilic
67770positivegrowth40thermophilic

culture pH

@refabilitytypepHPH range
28919positivegrowth06-09alkaliphile
28919positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22043anaerobe
28919anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
28919no
69481no100
69480no99.876

halophily

@refsaltgrowthtested relationconcentration
28919NaClpositivegrowth<10 %
28919NaClpositiveoptimum2 %

observation

  • @ref: 28919
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2891930089acetate+carbon source
2891916947citrate+carbon source
2891916236ethanol+carbon source
2891917754glycerol+carbon source
2891924996lactate+carbon source
2891915792malonate+carbon source
2891917272propionate+carbon source
2891915361pyruvate+carbon source
2891930031succinate+carbon source
2891931011valerate+carbon source
2891917632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22043oilfield production waterUtah, RedwashUSAUSANorth America
67770Produced water from the Redwash petroleum reservoirUTUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3116.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_50;96_1625;97_1944;98_2391;99_3116&stattab=map
  • Last taxonomy: Geoalkalibacter subterraneus subclade
  • 16S sequence: EU182247
  • Sequence Identity:
  • Total samples: 1233
  • soil counts: 307
  • aquatic counts: 881
  • animal counts: 34
  • plant counts: 11

Safety information

risk assessment

  • @ref: 22043
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22043
  • description: Geoalkalibacter subterraneus strain Red1 16S ribosomal RNA gene, partial sequence
  • accession: EU182247
  • length: 1555
  • database: ena
  • NCBI tax ID: 483547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geoalkalibacter subterraneus Red1GCA_000827125completencbi483547
66792Geoalkalibacter subterraneus Red1483547.12completepatric483547
66792Geoalkalibacter subterraneus Red12593339207completeimg483547

GC content

  • @ref: 22043
  • GC-content: 52.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.221no
flagellatedno66.81no
gram-positiveno98.503yes
anaerobicyes99.571yes
aerobicno98.546yes
halophileyes62.878yes
spore-formingno92.483yes
glucose-utilno51.545no
thermophileno92.782no
glucose-fermentno79.394no

External links

@ref: 22043

culture collection no.: DSM 29995, DSM 23483, JCM 15104, JCM 30610, DSM 28483, KCTC 5626

straininfo link

  • @ref: 88871
  • straininfo: 403444

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329606Geoalkalibacter subterraneus sp. nov., an anaerobic Fe(III)- and Mn(IV)-reducing bacterium from a petroleum reservoir, and emended descriptions of the family Desulfuromonadaceae and the genus Geoalkalibacter.Greene AC, Patel BK, Yacob SInt J Syst Evol Microbiol10.1099/ijs.0.001537-02009Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deltaproteobacteria/*classification/genetics/*isolation & purification/physiology, *Environmental Microbiology, Molecular Sequence Data, *Petroleum, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, United StatesGenetics
25767222Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria.Badalamenti JP, Krajmalnik-Brown R, Torres CI, Bond DRGenome Announc10.1128/genomeA.00039-152015

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22043Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29995Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29995)
28919Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172535828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88871Reimer, 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 identifiers10.60712/SI-ID403444.1