Strain identifier
BacDive ID: 17627
Type strain: 
Species: Desulfarculus baarsii
Strain Designation: Konstanz, 2st14
Strain history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; 2st14 <- F. Widdel {1981}
NCBI tax ID(s): 644282 (strain), 453230 (species)
version 8.1 (current version)
General
@ref: 711
BacDive-ID: 17627
DSM-Number: 2075
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile
description: Desulfarculus baarsii Konstanz is an anaerobe, mesophilic, motile bacterium that was isolated from ditch mud.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 644282 | strain |
| 453230 | species |
strain history
- @ref: 711
- history: <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; 2st14 <- F. Widdel {1981}
doi: 10.13145/bacdive17627.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfarculales
- family: Desulfarculaceae
- genus: Desulfarculus
- species: Desulfarculus baarsii
- full scientific name: Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006
synonyms
- @ref: 20215
- synonym: Desulfovibrio baarsii
@ref: 711
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfarculales
family: Desulfarculaceae
genus: Desulfarculus
species: Desulfarculus baarsii
full scientific name: Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006
strain designation: Konstanz, 2st14
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 96.006 | |
| 69480 | 99.998 | negative |
colony morphology
- @ref: 711
- incubation period: 3-7 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_2075_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 711
- name: DESULFOFABA MEDIUM (DSMZ Medium 193b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/193b
- composition: Name: DESULFOFABA MEDIUM (DSMZ Medium 193b; with strain-specific modifications) Composition: MgCl2 x 6 H2O 11.4656 g/l NaCl 6.97906 g/l Na2SO4 2.99102 g/l Na2CO3 1.49551 g/l CaCl2 x 2 H2O 1.49551 g/l Na-butyrate 0.697906 g/l KCl 0.498505 g/l Na2S x 9 H2O 0.398804 g/l Na-caproate 0.299103 g/l NH4Cl 0.299102 g/l KH2PO4 0.199402 g/l Sodium octanoate 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l Nicotinic acid 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
culture temp
- @ref: 711
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 711 | anaerobe | |
| 69480 | anaerobe | 99.999 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 93 |
| 69480 | no | 99.873 |
Isolation, sampling and environmental information
isolation
- @ref: 711
- sample type: ditch mud
- geographic location: Konstanz
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
taxonmaps
- @ref: 69479
- File name: preview.99_3704.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16157;96_1910;97_2298;98_2831;99_3704&stattab=map
- Last taxonomy: Desulfarculus baarsii subclade
- 16S sequence: AF418174
- Sequence Identity:
- Total samples: 723
- soil counts: 122
- aquatic counts: 531
- animal counts: 60
- plant counts: 10
Safety information
risk assessment
- @ref: 711
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | D.baarsi 16S ribosomal rRNA | M34403 | 1395 | ena | 644282 |
| 711 | Desulfoarculus baarsii DSM 2075 16S ribosomal RNA gene, partial sequence | AF418174 | 1522 | ena | 644282 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfarculus baarsii DSM 2075 | GCA_000143965 | complete | ncbi | 644282 |
| 66792 | Desulfarculus baarsii DSM 2075 | 644282.4 | complete | patric | 644282 |
| 66792 | Desulfarculus baarsii 2st14, DSM 2075 | 648028023 | complete | img | 644282 |
GC content
- @ref: 711
- GC-content: 66
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 93 | no |
| motile | yes | 88.057 | no |
| flagellated | no | 81.176 | no |
| gram-positive | no | 99.354 | no |
| anaerobic | yes | 99.223 | no |
| aerobic | no | 97.747 | yes |
| halophile | no | 70.946 | no |
| spore-forming | no | 87.124 | no |
| thermophile | no | 83.85 | yes |
| glucose-util | no | 63.158 | no |
| glucose-ferment | no | 84.741 | no |
External links
@ref: 711
culture collection no.: DSM 2075, ATCC 33931, VKM B-1802
straininfo link
- @ref: 86619
- straininfo: 2184
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 21304732 | Complete genome sequence of Desulfarculus baarsii type strain (2st14). | Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M | Stand Genomic Sci | 10.4056/sigs.1243258 | 2010 | ||
| Phylogeny | 24876241 | Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed. | An TT, Picardal FW | Int J Syst Evol Microbiol | 10.1099/ijs.0.064873-0 | 2014 | Bacterial Typing Techniques, Base Composition, Benzoates/*metabolism, Coal, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Indiana, Molecular Sequence Data, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur-Reducing Bacteria/*classification/genetics/isolation & purification, *Water Microbiology | Enzymology |
| Phylogeny | 26704417 | Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae. | Davidova IA, Wawrik B, Callaghan AV, Duncan K, Marks CR, Suflita JM | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000864 | 2015 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 711 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2075) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2075 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 86619 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID2184.1 | StrainInfo: A central database for resolving microbial strain identifiers |