Strain identifier
BacDive ID: 130339
Type strain:
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)
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
@ref | history |
---|---|
22043 | <- J. Badalamenti, Univ. Minnesota; Red1 <- Leibniz-Institut DSMZ; DSM 23483 <- T. Itoh, JCM; JCM 15104 <- A. C. Greene, Griffith Univ., Brisbane, Australia; Red1 |
67770 | T. 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
28919 | negative | 3 µm | 0.55 µm | rod-shaped | yes | |
69480 | yes | 95.035 | ||||
69480 | negative | 99.999 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
22043 | positive | growth | 37 | mesophilic |
28919 | positive | growth | 30-50 | |
28919 | positive | optimum | 40 | thermophilic |
67770 | positive | growth | 40 | thermophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
28919 | positive | growth | 06-09 | alkaliphile |
28919 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
22043 | anaerobe | |
28919 | anaerobe | |
69480 | anaerobe | 100 |
spore formation
@ref | spore formation | confidence |
---|---|---|
28919 | no | |
69481 | no | 100 |
69480 | no | 99.876 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
28919 | NaCl | positive | growth | <10 % |
28919 | NaCl | positive | optimum | 2 % |
observation
- @ref: 28919
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
28919 | 30089 | acetate | + | carbon source |
28919 | 16947 | citrate | + | carbon source |
28919 | 16236 | ethanol | + | carbon source |
28919 | 17754 | glycerol | + | carbon source |
28919 | 24996 | lactate | + | carbon source |
28919 | 15792 | malonate | + | carbon source |
28919 | 17272 | propionate | + | carbon source |
28919 | 15361 | pyruvate | + | carbon source |
28919 | 30031 | succinate | + | carbon source |
28919 | 31011 | valerate | + | carbon source |
28919 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
22043 | oilfield production water | Utah, Redwash | USA | USA | North America |
67770 | Produced water from the Redwash petroleum reservoir | UT | USA | USA | North America |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Geoalkalibacter subterraneus Red1 | GCA_000827125 | complete | ncbi | 483547 |
66792 | Geoalkalibacter subterraneus Red1 | 483547.12 | complete | patric | 483547 |
66792 | Geoalkalibacter subterraneus Red1 | 2593339207 | complete | img | 483547 |
GC content
- @ref: 22043
- GC-content: 52.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 84.221 | no |
flagellated | no | 66.81 | no |
gram-positive | no | 98.503 | yes |
anaerobic | yes | 99.571 | yes |
aerobic | no | 98.546 | yes |
halophile | yes | 62.878 | yes |
spore-forming | no | 92.483 | yes |
glucose-util | no | 51.545 | no |
thermophile | no | 92.782 | no |
glucose-ferment | no | 79.394 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19329606 | Geoalkalibacter 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 S | Int J Syst Evol Microbiol | 10.1099/ijs.0.001537-0 | 2009 | Anaerobiosis, 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 States | Genetics |
25767222 | Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria. | Badalamenti JP, Krajmalnik-Brown R, Torres CI, Bond DR | Genome Announc | 10.1128/genomeA.00039-15 | 2015 |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | ||||
22043 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29995 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29995) | ||||
28919 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 25358 | 28776041 | ||
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) | https://diaspora-project.de/progress.html#genomes | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
69479 | João 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 beta | https://microbeatlas.org/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | ||||
88871 | 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 | 10.60712/SI-ID403444.1 |