Strain identifier
BacDive ID: 3965
Type strain:
Species: Desulforapulum autotrophicum
Strain Designation: HRM2
Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; HRM2 <- K. Brysch {1983}
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 93.769 | |
69480 | 99.999 | negative |
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
@ref | oxygen tolerance | confidence |
---|---|---|
1368 | anaerobe | |
69480 | anaerobe | 98.647 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.985 |
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfobacterium autotrophicum HRM2 | 177437.4 | complete | patric | 177437 |
66792 | Desulfobacterium autotrophicum HRM2 | 177437.21 | plasmid | patric | 177437 |
66792 | Desulfobacterium autotrophicum HRM2, DSM 3382 | 643692021 | complete | img | 177437 |
66792 | Desulforapulum autotrophicum HRM2 | GCA_000020365 | complete | ncbi | 177437 |
GC content
- @ref: 1368
- GC-content: 47.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 82.971 | no |
gram-positive | no | 98.748 | no |
anaerobic | yes | 97.715 | no |
aerobic | no | 95.808 | yes |
halophile | no | 60.693 | no |
spore-forming | no | 90.306 | no |
thermophile | no | 98.496 | no |
glucose-util | yes | 50.782 | no |
flagellated | no | 69.672 | no |
glucose-ferment | no | 85.123 | no |
External links
@ref: 1368
culture collection no.: DSM 3382, ATCC 43914
straininfo link
- @ref: 73473
- straininfo: 42121
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1368 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3382) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-3382 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
73473 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42121.1 | StrainInfo: A central database for resolving microbial strain identifiers |