Strain identifier

BacDive ID: 4043

Type strain: Yes

Species: Desulfohalobium retbaense

Strain Designation: HR100, HR100

Strain history: DSM 5692 <-- J.-L. Garcia HR100.

NCBI tax ID(s): 485915 (strain), 45663 (species)

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General

@ref: 2289

BacDive-ID: 4043

DSM-Number: 5692

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

description: Desulfohalobium retbaense HR100 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from saline sediment.

NCBI tax id

NCBI tax idMatching level
485915strain
45663species

strain history

@refhistory
2289<- J.-L. Garcia, Université de Provence, Marseille, France; HR100 <- B. Ollivier {1989}
67770DSM 5692 <-- J.-L. Garcia HR100.

doi: 10.13145/bacdive4043.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfovibrionales
  • family: Desulfohalobiaceae
  • genus: Desulfohalobium
  • species: Desulfohalobium retbaense
  • full scientific name: Desulfohalobium retbaense Ollivier et al. 1991

@ref: 2289

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfohalobiaceae

genus: Desulfohalobium

species: Desulfohalobium retbaense

full scientific name: Desulfohalobium retbaense Ollivier et al. 1991

strain designation: HR100, HR100

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43365negative1-3 µm0.7-0.9 µmrod-shapedyespolar
69480yes92.213
69480negative99.999

colony morphology

  • @ref: 43365
  • colony shape: circular
  • incubation period: 30 days

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_5692_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2289DESULFOHALOBIUM MEDIUM (DSMZ Medium 499)yeshttps://mediadive.dsmz.de/medium/499Name: DESULFOHALOBIUM MEDIUM (DSMZ Medium 499) Composition: NaCl 100.0 g/l MgCl2 x 6 H2O 20.0 g/l KCl 4.0 g/l Na2SO4 3.0 g/l CaCl2 x 2 H2O 2.7 g/l Na-(L)-lactate 2.5 g/l Na-acetate 1.0 g/l Trypticase peptone 1.0 g/l Yeast extract 1.0 g/l NH4Cl 1.0 g/l K2HPO4 0.3 g/l KH2PO4 0.3 g/l Na2S x 9 H2O 0.3 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NaOH 0.0005 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
43365yes50% water from the lake, sulfate, H2, 1 g of acetate per liter
43365yesper liter: 1.0g NH4Cl, 0.3g K2HPO4, 20g MgCl2*6H2O, 2g CaCl2, 4g KCL, 0.3g KH2PO4, 3g Na2SO4, 100g NaCl, 1g sodium acetate, 0.001g resazurin, 1mL trace element solution, 1mL sodium selenite solution

culture temp

@refgrowthtypetemperaturerange
2289positivegrowth35mesophilic
43365nogrowth45-52thermophilic
43365positiveoptimum37-40
67770positivegrowth35mesophilic

culture pH

@refabilitytypepH
43365positivegrowth5.5-8
43365positiveoptimum6.5-7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
2289anaerobe
43365obligate anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
43365no
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
43365NaClpositivegrowth5-24 %
43365NaClpositiveoptimum10 %

observation

  • @ref: 43365
  • observation: NaCl and MgCl2 are required for growth

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4336515354choline-assimilation
4336524996lactate+/-oxidation
4336525115malate-assimilation
4336533403elemental sulfur+electron acceptor
4336516236ethanol+/-oxidation
4336528757fructose-assimilation
4336529806fumarate-assimilation
4336517234glucose-assimilation
4336517754glycerol-assimilation
4336515361pyruvate+fermentation
4336515361pyruvate+/-oxidation
4336530031succinate-assimilation
4336516189sulfate+electron acceptor
4336517359sulfite+electron acceptor
4336516094thiosulfate+electron acceptor
43365yeast extract-assimilation

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
2289saline sedimentRetba LakeSenegalSENAfrica
43365sediments of Retba Lake, a pink hypersaline LakeSenegal, Retba LakeSenegalSENAfrica14-17
67770Sediments from a hypersaline lakeRatba Lake, near DakarSenegalSENAfrica

isolation source categories

Cat1Cat2Cat3
#Condition#Saline
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7823.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_671;96_3626;97_4455;98_5716;99_7823&stattab=map
  • Last taxonomy: Desulfohalobium retbaense subclade
  • 16S sequence: X99235
  • Sequence Identity:
  • Total samples: 615
  • soil counts: 46
  • aquatic counts: 494
  • animal counts: 65
  • plant counts: 10

Safety information

risk assessment

  • @ref: 2289
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Desulfohalobium retbaense 16S ribosomal RNA geneU482441548ena485915
20218D.retbaense 16S rRNA geneX992351506ena485915

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfohalobium retbaense DSM 5692GCA_000024325completencbi485915
66792Desulfohalobium retbaense DSM 5692485915.10plasmidpatric485915
66792Desulfohalobium retbaense DSM 5692485915.5completepatric485915
66792Desulfohalobium retbaense HR100, DSM 5692644736349completeimg485915

GC content

@refGC-contentmethod
228957.1
4336556.9-57.3high performance liquid chromatography (HPLC)
6777057.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno58no
motileyes88.029no
flagellatedyes53.857yes
gram-positiveno99.165yes
anaerobicyes99.269no
aerobicno98.043yes
halophileyes75.671no
spore-formingno96.354yes
thermophileno63.744no
glucose-utilno66.319yes
glucose-fermentno85.529no

External links

@ref: 2289

culture collection no.: DSM 5692, JCM 16813, ATCC 49708

straininfo link

  • @ref: 73548
  • straininfo: 47983

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957100Desulfohalobium utahense sp. nov., a moderately halophilic, sulfate-reducing bacterium isolated from Great Salt Lake.Jakobsen TF, Kjeldsen KU, Ingvorsen KInt J Syst Evol Microbiol10.1099/ijs.0.64323-02006Base Sequence, Deltaproteobacteria/genetics/*isolation & purification/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/genetics, Sodium Chloride/metabolism, Sulfates/*metabolism, Sulfur-Reducing Bacteria/isolation & purification/metabolism, Temperature, UtahMetabolism
Metabolism28168783A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.Wu R, Wilton R, Cuff ME, Endres M, Babnigg G, Edirisinghe JN, Henry CS, Joachimiak A, Schiffer M, Pokkuluri PRProtein Sci10.1002/pro.31342017Bacterial Proteins/*chemistry/genetics/metabolism, Deltaproteobacteria/*chemistry/genetics/metabolism, Protein Domains, *Signal Transduction

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2289Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5692)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5692
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
43365B. Olliver, C. E. Hatchikian, G. Prensier, J. Guezennec, J. L. Garcia10.1099/00207713-41-1-74Desulfohalobium retbaense gen. nov., sp. nov., a Halophilic Sulfate-Reducing Bacterium from Sediments of a Hypersaline Lake in SenegalIJSB 41: 74-81 1991
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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
73548Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47983.1StrainInfo: A central database for resolving microbial strain identifiers