Strain identifier

BacDive ID: 17672

Type strain: Yes

Species: Geothrix fermentans

Strain Designation: H-5

Strain history: <- J. D. Coates; H-5

NCBI tax ID(s): 1121920 (strain), 44676 (species)

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General

@ref: 5222

BacDive-ID: 17672

DSM-Number: 14018

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Geothrix fermentans H-5 is an anaerobe, mesophilic bacterium that was isolated from sediment from a petroleum-contaminated aquifer.

NCBI tax id

NCBI tax idMatching level
1121920strain
44676species

strain history

  • @ref: 5222
  • history: <- J. D. Coates; H-5

doi: 10.13145/bacdive17672.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Holophagae
  • order: Holophagales
  • family: Holophagaceae
  • genus: Geothrix
  • species: Geothrix fermentans
  • full scientific name: Geothrix fermentans Coates et al. 1999

@ref: 5222

domain: Bacteria

phylum: Acidobacteria

class: Holophagae

order: Holophagales

family: Holophagaceae

genus: Geothrix

species: Geothrix fermentans

full scientific name: Geothrix fermentans Coates et al. 1999

strain designation: H-5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.439
6948099.998negative

colony morphology

  • @ref: 5222
  • incubation period: 3-7 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_14018_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14018_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14018_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14018_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14018_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14018_6.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 5222
  • name: GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/826
  • composition: Name: GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826) Composition: Na2-fumarate 7.91296 g/l NaHCO3 2.4728 g/l NH4Cl 1.48368 g/l Na-acetate 0.811078 g/l Na2HPO4 0.593472 g/l KCl 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

  • @ref: 5222
  • growth: positive
  • type: growth
  • temperature: 35
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 5222
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
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
5222-++--+++/-+++/-+/---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
5222+-------------------

Isolation, sampling and environmental information

isolation

  • @ref: 5222
  • sample type: sediment from a petroleum-contaminated aquifer
  • geographic location: SC, Hanahan
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_2796.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_351;96_1484;97_1772;98_2167;99_2796&stattab=map
  • Last taxonomy: Geothrix fermentans subclade
  • 16S sequence: U41563
  • Sequence Identity:
  • Total samples: 4313
  • soil counts: 1360
  • aquatic counts: 2586
  • animal counts: 131
  • plant counts: 236

Safety information

risk assessment

  • @ref: 5222
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5222
  • description: Geothrix fermentans 16S rRNA gene, partial sequence
  • accession: U41563
  • length: 1448
  • database: ena
  • NCBI tax ID: 44676

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geothrix fermentans DSM 14018GCA_000428885scaffoldncbi1121920
66792Geothrix fermentans DSM 140181121920.7wgspatric1121920
66792Geothrix fermentans DSM 140182523231062draftimg1121920

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.74no
flagellatedno94.925no
gram-positiveno96.821no
anaerobicno74.284no
aerobicno59.087no
halophileno92.369no
spore-formingno91.354no
glucose-utilno50yes
thermophileno90.374yes
glucose-fermentno89.081no

External links

@ref: 5222

culture collection no.: DSM 14018, ATCC 700665

straininfo link

  • @ref: 86663
  • straininfo: 44065

literature

  • topic: Phylogeny
  • Pubmed-ID: 36357805
  • title: Two ferric-reducing bacteria Geothrix terrae sp. nov. and Geothrix alkalitolerans sp. nov., isolated from paddy soil.
  • authors: Han S, Tang R, Yang S, Xie CJ, Narsing Rao MP, Liu GH, Zhou SG
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-022-03293-y
  • year: 2022
  • mesh: RNA, Ribosomal, 16S/genetics, Phylogeny, *Soil Microbiology, *Soil, Bacterial Typing Techniques, DNA, Bacterial/genetics, Sequence Analysis, DNA, Fatty Acids/analysis, Bacteria/genetics, Iron
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5222Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14018)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14018
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
68369Automatically annotated from API 20NE
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
86663Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44065.1StrainInfo: A central database for resolving microbial strain identifiers