Strain identifier

BacDive ID: 3965

Type strain: Yes

Species: Desulforapulum autotrophicum

Strain Designation: HRM2

Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; HRM2 <- K. Brysch {1983}

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General

@ref: 1368

BacDive-ID: 3965

DSM-Number: 3382

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

description: Desulforapulum autotrophicum HRM2 is an anaerobe, mesophilic, motile bacterium that was isolated from marine mud.

strain history

  • @ref: 1368
  • history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; HRM2 <- K. Brysch {1983}

doi: 10.13145/bacdive3965.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfobacterales
  • family: Desulfobacteraceae
  • genus: Desulforapulum
  • species: Desulforapulum autotrophicum
  • full scientific name: Desulforapulum autotrophicum (Brysch et al. 1988) Galushko and Kuever 2021
  • synonyms

    • @ref: 20215
    • synonym: Desulfobacterium autotrophicum

@ref: 1368

domain: Bacteria

phylum: Pseudomonadota

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulforapulum

species: Desulforapulum autotrophicum

full scientific name: Desulforapulum autotrophicum

strain designation: HRM2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.769
6948099.999negative

Culture and growth conditions

culture medium

  • @ref: 1368
  • name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/383b
  • composition: Name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b; with strain-specific modifications) Composition: NaCl 20.8747 g/l Na2SO4 2.9821 g/l MgCl2 x 6 H2O 2.9821 g/l Na2CO3 0.994036 g/l KCl 0.497018 g/l Na2S x 9 H2O 0.397614 g/l NH4Cl 0.29821 g/l KH2PO4 0.198807 g/l CaCl2 x 2 H2O 0.149105 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l NaOH 0.000497018 g/l Sodium resazurin 0.000497018 g/l CoCl2 x 6 H2O 0.000188867 g/l Pyridoxine hydrochloride 9.94036e-05 g/l MnCl2 x 4 H2O 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l p-Aminobenzoic acid 4.97018e-05 g/l (DL)-alpha-Lipoic acid 4.97018e-05 g/l Riboflavin 4.97018e-05 g/l Calcium D-(+)-pantothenate 4.97018e-05 g/l Thiamine HCl 4.97018e-05 g/l Nicotinic acid 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l Biotin 1.98807e-05 g/l Folic acid 1.98807e-05 g/l H3BO3 5.96421e-06 g/l Na2WO4 x 2 H2O 3.97614e-06 g/l Na2SeO3 x 5 H2O 2.98211e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Vitamin B12 9.94036e-07 g/l Distilled water

culture temp

  • @ref: 1368
  • growth: positive
  • type: growth
  • temperature: 25
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
1368anaerobe
69480anaerobe98.647

spore formation

@refspore formationconfidence
69481no100
69480no99.985

Isolation, sampling and environmental information

isolation

  • @ref: 1368
  • sample type: marine mud
  • geographic location: Venice
  • country: Italy
  • origin.country: ITA
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_5436.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_522;96_2638;97_3231;98_4059;99_5436&stattab=map
  • Last taxonomy: Desulfobacterium autotrophicum subclade
  • 16S sequence: AF418177
  • Sequence Identity:
  • Total samples: 1249
  • soil counts: 201
  • aquatic counts: 805
  • animal counts: 219
  • plant counts: 24

Safety information

risk assessment

  • @ref: 1368
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Desulfobacterium autotrophicum DSM 3382 16S ribosomal RNA gene, partial sequence
  • accession: AF418177
  • length: 1523
  • database: ena
  • NCBI tax ID: 2296

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfobacterium autotrophicum HRM2177437.4completepatric177437
66792Desulfobacterium autotrophicum HRM2177437.21plasmidpatric177437
66792Desulfobacterium autotrophicum HRM2, DSM 3382643692021completeimg177437
66792Desulforapulum autotrophicum HRM2GCA_000020365completencbi177437

GC content

  • @ref: 1368
  • GC-content: 47.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes82.971no
gram-positiveno98.748no
anaerobicyes97.715no
aerobicno95.808yes
halophileno60.693no
spore-formingno90.306no
thermophileno98.496no
glucose-utilyes50.782no
flagellatedno69.672no
glucose-fermentno85.123no

External links

@ref: 1368

culture collection no.: DSM 3382, ATCC 43914

straininfo link

  • @ref: 73473
  • straininfo: 42121

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1368Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3382)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3382
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
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)
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
73473Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42121.1StrainInfo: A central database for resolving microbial strain identifiers