Strain identifier

BacDive ID: 16666

Type strain: Yes

Species: Desulfomonile tiedjei

Strain Designation: DCB-1

Strain history: <- ATCC <- J.M. Tiedje, DCB-1

NCBI tax ID(s): 706587 (strain), 2358 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
2358species
706587strain

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

@refoxygen toleranceconfidence
2827anaerobe
69480anaerobe97.931

spore formation

@refspore formationconfidence
69481no99
69480no98.396

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Desulfomonile tiedjei DSM 6799GCA_000266945completencbi706587
66792Desulfomonile tiedjei DSM 6799706587.9plasmidpatric706587
66792Desulfomonile tiedjei DSM 6799706587.4completepatric706587
66792Desulfomonile tiedjei DCB-1, DSM 67992509601019completeimg706587

GC content

  • @ref: 2827
  • GC-content: 49.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno80.668no
flagellatedno98.106no
gram-positiveno98.497no
anaerobicyes96.745yes
aerobicno96.85yes
halophileno94.694no
spore-formingno85.379no
thermophileno79.401yes
glucose-utilyes54.153no
glucose-fermentno89.557no

External links

@ref: 2827

culture collection no.: DSM 6799, ATCC 49306

straininfo link

  • @ref: 85687
  • straininfo: 42414

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism1406492Microbial reductive dehalogenation.Mohn WW, Tiedje JMMicrobiol Rev10.1128/mr.56.3.482-507.19921992Bacteria/*metabolism, *Biodegradation, Environmental, *Environmental Microbiology, Environmental Pollutants/*metabolism, Oxidation-Reduction
Metabolism1539988Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O.Griffith GD, Cole JR, Quensen JF 3rd, Tiedje JMAppl Environ Microbiol10.1128/aem.58.1.409-411.19921992Bacteria, Anaerobic/*metabolism, Chlorobenzoates/*metabolism, Deuterium/*metabolism, Gas Chromatography-Mass Spectrometry
Metabolism1599254Reductive dehalogenation of chlorophenols by Desulfomonile tiedjei DCB-1.Mohn WW, Kennedy KJAppl Environ Microbiol10.1128/aem.58.4.1367-1370.19921992Bacteria, Anaerobic/*metabolism, Biodegradation, Environmental, Chlorine/metabolism, Chlorophenols/*metabolism, Oxidation-Reduction
Enzymology7665493Purification and characterization of a novel 3-chlorobenzoate-reductive dehalogenase from the cytoplasmic membrane of Desulfomonile tiedjei DCB-1.Ni S, Fredrickson JK, Xun LJ Bacteriol10.1128/jb.177.17.5135-5139.19951995Benzoates/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/metabolismMetabolism
Enzymology7772942Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced in Desulfomonile tiedjei DCB-1.Cole JR, Fathepure BZ, Tiedje JMBiodegradation10.1007/BF006953471995Bacteria, Anaerobic/enzymology/*metabolism, Biodegradation, Environmental, Chlorobenzoates/*metabolism, Culture Media, Electron Transport, Environmental Pollution, Enzyme Induction/physiology, Kinetics, Tetrachloroethylene/*metabolismMetabolism
Biotechnology7854251Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications.Fetzner S, Lingens FMicrobiol Rev10.1128/mr.58.4.641-685.19941994Bacteria/*enzymology, Biodegradation, Environmental, *Biotechnology, Hydrocarbons, Halogenated/*metabolism, Hydrolases/genetics/*physiologyGenetics
Enzymology9385144Purification, 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 WWArch Microbiol10.1007/s0020300505301997Amino 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, DNATranscriptome
Metabolism9864310Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1.Louie TM, Mohn WWJ Bacteriol10.1128/JB.181.1.40-46.19991999Cell 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/*metabolismEnzymology
Metabolism11222615snr-1 gene is required for nitrate reduction in Pseudomonas aeruginosa PAO1.Kerschen EJ, Irani VR, Hassett DJ, Rowe JJJ Bacteriol10.1128/JB.183.6.2125-2131.20012001Amino 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, GeneticGenetics
Phylogeny11321081Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments.Sun B, Cole JR, Tiedje JMInt J Syst Evol Microbiol10.1099/00207713-51-2-3652001Chlorobenzoates/*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 MicrobiologyMetabolism
16348447Influence of substituents on reductive dehalogenation of 3-chlorobenzoate analogs.Dolfing J, Tiedje JMAppl Environ Microbiol10.1128/aem.57.3.820-824.19911991
Metabolism33391191Long-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 AJFront Microbiol10.3389/fmicb.2020.5396042020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2827Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6799)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6799
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
85687Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42414.1StrainInfo: A central database for resolving microbial strain identifiers