Strain identifier
BacDive ID: 4032
Type strain: 
Species: Desulfopila inferna
Strain Designation: JS_SRB250Lac
Strain history: <- A. Gittel and M. Könneke, ICMB, Univ. Oldenburg, Germany; JS_SRB250Lac <- A. Gittel {2006}
NCBI tax ID(s): 468528 (species)
version 8.1 (current version)
General
@ref: 8274
BacDive-ID: 4032
DSM-Number: 19738
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemolithoautotroph, mesophilic, Gram-negative, rod-shaped
description: Desulfopila inferna JS_SRB250Lac is an anaerobe, chemolithoautotroph, mesophilic bacterium that was isolated from marine subsurface sediment at a depth of 2.5 m from a tidal sand-flat.
NCBI tax id
- NCBI tax id: 468528
- Matching level: species
strain history
- @ref: 8274
- history: <- A. Gittel and M. Könneke, ICMB, Univ. Oldenburg, Germany; JS_SRB250Lac <- A. Gittel {2006}
doi: 10.13145/bacdive4032.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Desulfobacterales
- family: Desulfobulbaceae
- genus: Desulfopila
- species: Desulfopila inferna
- full scientific name: Desulfopila inferna Gittel et al. 2010
@ref: 8274
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobulbaceae
genus: Desulfopila
species: Desulfopila inferna
full scientific name: Desulfopila inferna Gittel et al. 2010
strain designation: JS_SRB250Lac
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 23208 | negative | 1.0-2.0 µm | 0.3-0.5 µm | rod-shaped | no | |
| 69480 | yes | 94.462 | ||||
| 69480 | negative | 99.999 |
Culture and growth conditions
culture medium
- @ref: 8274
- name: MARINE DESULFOVIBRIO COMPLEX MEDIUM (DSMZ Medium 1040)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1040
- composition: Name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040) Composition: Sea Salt 34.9301 g/l Na-DL-lactate 2.49501 g/l Yeast extract 0.998004 g/l Na2CO3 0.998004 g/l Na2S x 9 H2O 0.299401 g/l MgSO4 x 7 H2O 0.0299401 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l CoCl2 x 6 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l FeSO4 x 7 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8274 | positive | growth | 28 | mesophilic |
| 23208 | positive | growth | 10-35 | |
| 23208 | positive | optimum | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 8274 | anaerobe | |
| 69480 | anaerobe | 96.445 |
nutrition type
- @ref: 23208
- type: chemolithoautotroph
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.828 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 23208 | NaCl | positive | growth | 0.5-5.0 %(w/v) |
| 23208 | NaCl | positive | optimum | 2-3 %(w/v) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23208 | 17632 | nitrate | - | carbon source |
| 23208 | 16094 | thiosulfate | - | carbon source |
| 23208 | 30089 | acetate | - | electron acceptor |
| 23208 | 16449 | alanine | - | electron acceptor |
| 23208 | 16150 | benzoate | - | electron acceptor |
| 23208 | 17750 | betaine | - | electron acceptor |
| 23208 | 15354 | choline | - | electron acceptor |
| 23208 | 15428 | glycine | - | electron acceptor |
| 23208 | 25115 | malate | - | electron acceptor |
| 23208 | 29864 | mannitol | - | electron acceptor |
| 23208 | 17272 | propionate | - | electron acceptor |
| 23208 | 17822 | serine | - | electron acceptor |
| 23208 | 30911 | sorbitol | - | electron acceptor |
| 23208 | 24996 | lactate | - | fermentation |
| 23208 | 25115 | malate | - | fermentation |
| 23208 | 16189 | sulfate | + | electron acceptor |
| 23208 | 17359 | sulfite | + | electron acceptor |
| 23208 | 28885 | butanol | + | electron donor |
| 23208 | 17968 | butyrate | + | electron donor |
| 23208 | 27689 | decanoate | + | electron donor |
| 23208 | 16236 | ethanol | + | electron donor |
| 23208 | 15740 | formate | + | electron donor |
| 23208 | 29806 | fumarate | + | electron donor |
| 23208 | 17754 | glycerol | + | electron donor |
| 23208 | 24996 | lactate | + | electron donor |
| 23208 | 26271 | proline | + | electron donor |
| 23208 | 28831 | propanol | + | electron donor |
| 23208 | 15361 | pyruvate | + | electron donor |
| 23208 | 30031 | succinate | + | electron donor |
| 23208 | 31011 | valerate | + | electron donor |
Isolation, sampling and environmental information
isolation
- @ref: 8274
- sample type: marine subsurface sediment at a depth of 2.5 m from a tidal sand-flat
- geographic location: Wadden Sea, 'Janssand'
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 53.7363
- longitude: 7.6995
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Tidal flat |
Safety information
risk assessment
- @ref: 8274
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8274
- description: Desulfopila inferna partial 16S rRNA gene, isolate JS_SRB250Lac
- accession: AM774321
- length: 1512
- database: ena
- NCBI tax ID: 468528
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Desulfopila inferna DSM 19738 | GCA_016919005 | contig | ncbi | 468528 |
| 66792 | Desulfopila inferna strain DSM 19738 | 468528.3 | wgs | patric | 468528 |
GC content
- @ref: 8274
- GC-content: 50.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.369 | yes |
| anaerobic | yes | 89.482 | yes |
| halophile | no | 69.123 | no |
| spore-forming | no | 88.739 | no |
| glucose-util | no | 63.823 | no |
| aerobic | no | 93.701 | yes |
| flagellated | no | 56.886 | no |
| thermophile | no | 99.086 | yes |
| motile | yes | 83.211 | yes |
| glucose-ferment | no | 90.755 | no |
External links
@ref: 8274
culture collection no.: DSM 19738, NBRC 103921
straininfo link
- @ref: 73537
- straininfo: 402980
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19717583 | Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat. | Gittel A, Seidel M, Kuever J, Galushko AS, Cypionka H, Konneke M | Int J Syst Evol Microbiol | 10.1099/ijs.0.015644-0 | 2009 | Base Sequence, Deltaproteobacteria/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sulfates/metabolism | Genetics |
| Phylogeny | 25278560 | Desulfoprunum benzoelyticum gen. nov., sp. nov., a Gram-stain-negative, benzoate-degrading, sulfate-reducing bacterium isolated from a wastewater treatment plant. | Junghare M, Schink B | Int J Syst Evol Microbiol | 10.1099/ijs.0.066761-0 | 2014 | Base Composition, Benzoates/*metabolism, DNA, Bacterial/genetics, Deltaproteobacteria/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Germany, Molecular Sequence Data, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sulfates/*metabolism, Vitamin K 2/chemistry | Metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 8274 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19738) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19738 | |||
| 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 | |||
| 23208 | Antje Gittel, Michael Seidel, Jan Kuever, Alexander S. Galushko, Heribert Cypionka, Martin Könneke | 10.1099/ijs.0.015644-0 | Desulfopila inferna sp. nov., a sulfate-reducing bacterium isolated from the subsurface of a tidal sand-flat | IJSEM 60: 1626-1630 2010 | 19717583 | |
| 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) | |||
| 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 | |||
| 73537 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402980.1 | StrainInfo: A central database for resolving microbial strain identifiers |