Strain identifier
BacDive ID: 16666
Type strain:
Species: Desulfomonile tiedjei
Strain Designation: DCB-1
Strain history: <- ATCC <- J.M. Tiedje, DCB-1
NCBI tax ID(s): 706587 (strain), 2358 (species)
General
@ref: 2827
BacDive-ID: 16666
DSM-Number: 6799
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Desulfomonile tiedjei DCB-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sewage sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
2358 | species |
706587 | strain |
strain history
- @ref: 2827
- history: <- ATCC <- J.M. Tiedje, DCB-1
doi: 10.13145/bacdive16666.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Deltaproteobacteria
- order: Syntrophobacterales
- family: Syntrophaceae
- genus: Desulfomonile
- species: Desulfomonile tiedjei
- full scientific name: Desulfomonile tiedjei De Weerd et al. 1991
@ref: 2827
domain: Bacteria
phylum: Proteobacteria
class: Deltaproteobacteria
order: Syntrophobacterales
family: Syntrophaceae
genus: Desulfomonile
species: Desulfomonile tiedjei
full scientific name: Desulfomonile tiedjei De Weerd et al. 1991
strain designation: DCB-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.14
colony morphology
- @ref: 2827
- incubation period: 3-7 days
multimedia
- @ref: 66793
- multimedia content: EM_DSM_6799_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 2827
- name: DESULFOMONILE MEDIUM (DSMZ Medium 521)
- growth: yes
- link: https://mediadive.dsmz.de/medium/521
- composition: Name: DESULFOMONILE MEDIUM (DSMZ Medium 521) Composition: Na-pyruvate 2.5 g/l Na2SO4 2.0 g/l Yeast extract 1.0 g/l NaHCO3 1.0 g/l NH4Cl 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l MgSO4 x 7 H2O 1.0 g/l KH2PO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na2S x 9 H2O 0.1 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l Nicotinamide 0.0005 g/l NaOH 0.0005 g/l 1,4-Naphthoquinone 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Haemin 5e-05 g/l Vitamin B12 5e-05 g/l Pyridoxine hydrochloride 5e-05 g/l Folic acid 5e-05 g/l Biotin 5e-05 g/l Thioctic acid 5e-05 g/l p-Aminobenzoate 5e-05 g/l Calcium pantothenate 5e-05 g/l Riboflavin 5e-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
culture temp
- @ref: 2827
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
2827 | anaerobe | |
69480 | anaerobe | 97.931 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 98.396 |
Isolation, sampling and environmental information
isolation
- @ref: 2827
- sample type: sewage sludge
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Sewage sludge
taxonmaps
- @ref: 69479
- File name: preview.99_8122.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_692;96_3747;97_4607;98_5915;99_8122&stattab=map
- Last taxonomy: Desulfomonile tiedjei subclade
- 16S sequence: AM086646
- Sequence Identity:
- Total samples: 5274
- soil counts: 1582
- aquatic counts: 3190
- animal counts: 211
- plant counts: 291
Safety information
risk assessment
- @ref: 2827
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Desulfomonile tiedjei partial 16S rRNA gene, strain DSM 6799
- accession: AM086646
- length: 1345
- database: ena
- NCBI tax ID: 706587
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Desulfomonile tiedjei DSM 6799 | GCA_000266945 | complete | ncbi | 706587 |
66792 | Desulfomonile tiedjei DSM 6799 | 706587.9 | plasmid | patric | 706587 |
66792 | Desulfomonile tiedjei DSM 6799 | 706587.4 | complete | patric | 706587 |
66792 | Desulfomonile tiedjei DCB-1, DSM 6799 | 2509601019 | complete | img | 706587 |
GC content
- @ref: 2827
- GC-content: 49.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 80.668 | no |
flagellated | no | 98.106 | no |
gram-positive | no | 98.497 | no |
anaerobic | yes | 96.745 | yes |
aerobic | no | 96.85 | yes |
halophile | no | 94.694 | no |
spore-forming | no | 85.379 | no |
thermophile | no | 79.401 | yes |
glucose-util | yes | 54.153 | no |
glucose-ferment | no | 89.557 | no |
External links
@ref: 2827
culture collection no.: DSM 6799, ATCC 49306
straininfo link
- @ref: 85687
- straininfo: 42414
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 1406492 | Microbial reductive dehalogenation. | Mohn WW, Tiedje JM | Microbiol Rev | 10.1128/mr.56.3.482-507.1992 | 1992 | Bacteria/*metabolism, *Biodegradation, Environmental, *Environmental Microbiology, Environmental Pollutants/*metabolism, Oxidation-Reduction | |
Metabolism | 1539988 | Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O. | Griffith GD, Cole JR, Quensen JF 3rd, Tiedje JM | Appl Environ Microbiol | 10.1128/aem.58.1.409-411.1992 | 1992 | Bacteria, Anaerobic/*metabolism, Chlorobenzoates/*metabolism, Deuterium/*metabolism, Gas Chromatography-Mass Spectrometry | |
Metabolism | 1599254 | Reductive dehalogenation of chlorophenols by Desulfomonile tiedjei DCB-1. | Mohn WW, Kennedy KJ | Appl Environ Microbiol | 10.1128/aem.58.4.1367-1370.1992 | 1992 | Bacteria, Anaerobic/*metabolism, Biodegradation, Environmental, Chlorine/metabolism, Chlorophenols/*metabolism, Oxidation-Reduction | |
Enzymology | 7665493 | Purification and characterization of a novel 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of Desulfomonile tiedjei DCB-1. | Ni S, Fredrickson JK, Xun L | J Bacteriol | 10.1128/jb.177.17.5135-5139.1995 | 1995 | Benzoates/metabolism, Benzoic Acid, Biodegradation, Environmental, Cell Fractionation, Cell Membrane/*enzymology, Chlorobenzoates/metabolism, Gram-Negative Anaerobic Bacteria/*enzymology, Hydrolases/chemistry/*isolation & purification, Oxidation-Reduction, Spectrophotometry, Subcellular Fractions/metabolism | Metabolism |
Enzymology | 7772942 | Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1. | Cole JR, Fathepure BZ, Tiedje JM | Biodegradation | 10.1007/BF00695347 | 1995 | Bacteria, Anaerobic/enzymology/*metabolism, Biodegradation, Environmental, Chlorobenzoates/*metabolism, Culture Media, Electron Transport, Environmental Pollution, Enzyme Induction/physiology, Kinetics, Tetrachloroethylene/*metabolism | Metabolism |
Biotechnology | 7854251 | Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. | Fetzner S, Lingens F | Microbiol Rev | 10.1128/mr.58.4.641-685.1994 | 1994 | Bacteria/*enzymology, Biodegradation, Environmental, *Biotechnology, Hydrocarbons, Halogenated/*metabolism, Hydrolases/genetics/*physiology | Genetics |
Enzymology | 9385144 | Purification, characterization and gene sequence analysis of a novel cytochrome c co-induced with reductive dechlorination activity in Desulfomonile tiedjei DCB-1. | Louie TM, Ni S, Xun L, Mohn WW | Arch Microbiol | 10.1007/s002030050530 | 1997 | Amino Acid Sequence, Bacterial Outer Membrane Proteins/genetics/isolation & purification, Biodegradation, Environmental, Cloning, Molecular, Cytochrome c Group/biosynthesis/chemistry/*genetics/*isolation & purification, Enzyme Induction, *Genes, Bacterial, Gram-Negative Anaerobic Bacteria/*enzymology/metabolism, Molecular Sequence Data, Oxidation-Reduction, Sequence Analysis, DNA | Transcriptome |
Metabolism | 9864310 | Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1. | Louie TM, Mohn WW | J Bacteriol | 10.1128/JB.181.1.40-46.1999 | 1999 | Cell Membrane/metabolism, Cytoplasm/metabolism, Electron Transport, Environmental Pollutants/metabolism, Formate Dehydrogenases/metabolism, Hydrocarbons, Halogenated/metabolism, Hydrogenase/metabolism, *Models, Biological, Oxidation-Reduction, *Proton-Motive Force, Quinones/metabolism, Sulfates/metabolism, Sulfur-Reducing Bacteria/growth & development/*metabolism | Enzymology |
Metabolism | 11222615 | snr-1 gene is required for nitrate reduction in Pseudomonas aeruginosa PAO1. | Kerschen EJ, Irani VR, Hassett DJ, Rowe JJ | J Bacteriol | 10.1128/JB.183.6.2125-2131.2001 | 2001 | Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/*metabolism, Cytochrome c Group/chemistry/*genetics/metabolism, Gene Expression Regulation, Bacterial, Genetic Complementation Test, Molecular Sequence Data, Nitrates/*metabolism, Oxidation-Reduction, Plasmids/genetics, Pseudomonas aeruginosa/*enzymology/*genetics/growth & development, Sequence Homology, Amino Acid, Transcription, Genetic | Genetics |
Phylogeny | 11321081 | Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments. | Sun B, Cole JR, Tiedje JM | Int J Syst Evol Microbiol | 10.1099/00207713-51-2-365 | 2001 | Chlorobenzoates/*metabolism, Deltaproteobacteria/*classification/isolation & purification/metabolism, Geologic Sediments/microbiology, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/isolation & purification/metabolism, Marine Biology, Molecular Sequence Data, Phylogeny, Seawater, Terminology as Topic, *Water Microbiology | Metabolism |
16348447 | Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs. | Dolfing J, Tiedje JM | Appl Environ Microbiol | 10.1128/aem.57.3.820-824.1991 | 1991 | |||
Metabolism | 33391191 | Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of "Candidatus Desulfomonile Palmitatoxidans". | Alves JI, Salvador AF, Castro AR, Zheng Y, Nijsse B, Atashgahi S, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ | Front Microbiol | 10.3389/fmicb.2020.539604 | 2020 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2827 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6799) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6799 | |||
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 | |||
85687 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID42414.1 | StrainInfo: A central database for resolving microbial strain identifiers |