Strain identifier
BacDive ID: 13920
Type strain:
Species: Thauera chlorobenzoica
Strain Designation: 3CB-1
Strain history: CIP <- 2002, ATCC <- M.M. Haggblom
NCBI tax ID(s): 96773 (species)
General
@ref: 7331
BacDive-ID: 13920
DSM-Number: 18012
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Thauera chlorobenzoica 3CB-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from river sediment.
NCBI tax id
- NCBI tax id: 96773
- Matching level: species
strain history
@ref | history |
---|---|
7331 | <- CIP <- ATCC <- M. M. Häggblom; 3CB-1 |
118239 | CIP <- 2002, ATCC <- M.M. Haggblom |
doi: 10.13145/bacdive13920.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Rhodocyclales
- family: Zoogloeaceae
- genus: Thauera
- species: Thauera chlorobenzoica
- full scientific name: Thauera chlorobenzoica Song et al. 2001
@ref: 7331
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhizobiales
family: Zoogloeaceae
genus: Thauera
species: Thauera chlorobenzoica
full scientific name: Thauera chlorobenzoica Song et al. 2001
strain designation: 3CB-1
type strain: yes
Morphology
cell morphology
- @ref: 118239
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7331 | REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) | yes | https://mediadive.dsmz.de/medium/830c | Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
7331 | THAUERA AROMATICA MEDIUM (DSMZ Medium 586) | yes | https://mediadive.dsmz.de/medium/586 | Name: THAUERA AROMATICA MEDIUM (DSMZ Medium 586) Composition: K2HPO4 5.83251 g/l KNO3 1.97044 g/l KH2PO4 0.803941 g/l Na-benzoate 0.70936 g/l NH4Cl 0.522168 g/l MgSO4 x 7 H2O 0.197044 g/l CaCl2 x 2 H2O 0.0246305 g/l HCl 0.0246305 g/l FeCl2 x 4 H2O 0.0147783 g/l CoCl2 x 6 H2O 0.00187192 g/l MnCl2 x 4 H2O 0.000985222 g/l ZnCl2 0.000689655 g/l Na2MoO4 x 2 H2O 0.00035468 g/l p-Aminobenzoic acid 0.000246305 g/l alpha-lipoic acid 0.000246305 g/l Riboflavin 0.000246305 g/l Pantothenic acid 0.000246305 g/l Vitamin B12 0.000246305 g/l Thiamine-HCl x 2 H2O 0.000246305 g/l NiCl2 x 6 H2O 0.000236453 g/l Nicotine amide 0.000123153 g/l Nicotinic acid 0.000123153 g/l Folic acid 9.85222e-05 g/l Biotin 9.85222e-05 g/l H3BO3 5.91133e-05 g/l Pyridoxamine hydrochloride 4.92611e-05 g/l CuCl2 x 2 H2O 1.97044e-05 g/l Distilled water |
39922 | MEDIUM 450 - for Thauera chlorobenzoica | yes | Distilled water make up to (1000.000 ml);Iron (II) sulphate heptahydrate (7.000 mg);ManganeseII chloride tetrahydrate (5.000 mg);Boric acid (0.500 mg);Magnesium chloride hexahydrate (20.000 mg);Calcium chloride dihydrate (15.000 mg);Sodium sulphate (5.000 | |
118239 | CIP Medium 450 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=450 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7331 | positive | growth | 30 | mesophilic |
39922 | positive | growth | 30 | mesophilic |
118239 | positive | growth | 25-37 | mesophilic |
118239 | no | growth | 5 | psychrophilic |
118239 | no | growth | 15 | psychrophilic |
118239 | no | growth | 41 | thermophilic |
118239 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7331 | aerobe |
7331 | anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118239 | NaCl | no | growth | 0 % |
118239 | NaCl | no | growth | 2 % |
118239 | NaCl | no | growth | 4 % |
118239 | NaCl | no | growth | 6 % |
118239 | NaCl | no | growth | 8 % |
118239 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118239 | 4853 | esculin | - | hydrolysis |
118239 | 606565 | hippurate | + | hydrolysis |
118239 | 17632 | nitrate | + | builds gas from |
118239 | 17632 | nitrate | + | reduction |
118239 | 16301 | nitrite | + | builds gas from |
118239 | 16301 | nitrite | + | reduction |
118239 | 15792 | malonate | - | assimilation |
118239 | 17234 | glucose | - | degradation |
antibiotic resistance
- @ref: 118239
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 118239
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
118239 | 15688 | acetoin | - | |
118239 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
118239 | oxidase | + | |
118239 | alcohol dehydrogenase | - | 1.1.1.1 |
118239 | gelatinase | - | |
118239 | amylase | - | |
118239 | DNase | - | |
118239 | caseinase | - | 3.4.21.50 |
118239 | catalase | + | 1.11.1.6 |
118239 | tween esterase | - | |
118239 | gamma-glutamyltransferase | - | 2.3.2.2 |
118239 | lecithinase | - | |
118239 | lipase | - | |
118239 | lysine decarboxylase | - | 4.1.1.18 |
118239 | ornithine decarboxylase | - | 4.1.1.17 |
118239 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
118239 | protease | - | |
118239 | tryptophan deaminase | - | |
118239 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118239 | - | - | + | + | - | + | - | - | - | - | + | + | + | + | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118239 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - | - | - | - | - | - | + | - | - | - | + | - | + | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7331 | river sediment | Hudson River | USA | USA | North America | |
118239 | Environment, Sediment, Hudson River | Albany, New York | United States of America | USA | North America | 1993 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #River (Creek) |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_1036.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_594;97_695;98_810;99_1036&stattab=map
- Last taxonomy: Thauera chlorobenzoica
- 16S sequence: AF123264
- Sequence Identity:
- Total samples: 89
- soil counts: 6
- aquatic counts: 74
- animal counts: 7
- plant counts: 2
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7331 | 1 | Risk group (German classification) |
118239 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 20218
- description: Thauera chlorobenzoica 16S ribosomal RNA gene, partial sequence
- accession: AF123264
- length: 1488
- database: ena
- NCBI tax ID: 96773
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Thauera chlorobenzoica 3CB-1 | GCA_900108255 | scaffold | ncbi | 96773 |
66792 | Thauera chlorobenzoica strain 3CB1 | 96773.10 | complete | patric | 96773 |
66792 | Thauera chlorobenzoica 3CB-1 | 2651870126 | draft | img | 96773 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.999 | no |
flagellated | yes | 77.335 | no |
gram-positive | no | 99.128 | no |
anaerobic | no | 88.316 | no |
halophile | no | 88.6 | no |
spore-forming | no | 95.669 | no |
thermophile | no | 95.86 | yes |
glucose-util | no | 82.884 | no |
aerobic | no | 78.533 | no |
glucose-ferment | no | 90.021 | no |
External links
@ref: 7331
culture collection no.: DSM 18012, ATCC 700723, CIP 107679, KCTC 12933
straininfo link
- @ref: 83094
- straininfo: 44104
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11321105 | Characterization of halobenzoate-degrading, denitrifying Azoarcus and Thauera isolates and description of Thauera chlorobenzoica sp. nov. | Song B, Palleroni NJ, Kerkhof LJ, Haggblom MM | Int J Syst Evol Microbiol | 10.1099/00207713-51-2-589 | 2001 | Azoarcus/*classification/cytology/metabolism, Bacterial Typing Techniques, Base Composition, Benzoates/*metabolism, Biodegradation, Environmental, DNA, Ribosomal/genetics, Fatty Acids, Halogens/*metabolism, Molecular Sequence Data, Nitrates/*metabolism, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminology as Topic, Thauera/*classification/cytology/metabolism | Metabolism |
Phylogeny | 29236233 | Thauera sinica sp. nov., a phenol derivative-degrading bacterium isolated from activated sludge. | Qiao N, Xi L, Zhang J, Liu D, Ge B, Liu J | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0993-5 | 2017 | Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Thauera/*genetics/isolation & purification | Enzymology |
Metabolism | 29575501 | Liquid chromatography/isotope ratio mass spectrometry analysis of halogenated benzoates for characterization of the underlying degradation reaction in Thauera chlorobenzoica CB-1(T). | Franke S, Kummel S, Nijenhuis I | Rapid Commun Mass Spectrom | 10.1002/rcm.8113 | 2018 | Benzoates/*analysis/chemistry, Biodegradation, Environmental, Carbon Isotopes, Chlorobenzoates/analysis/chemistry/metabolism, Chromatography, Liquid/*methods, Environmental Pollutants/analysis/chemistry/metabolism, Halogenation, Mass Spectrometry/*methods, Reproducibility of Results, Thauera/chemistry/*metabolism | |
Metabolism | 30884168 | Occurrence and diversity of the oxidative hydroxyhydroquinone pathway for the anaerobic degradation of aromatic compounds in nitrate-reducing bacteria. | Pacheco-Sanchez D, Rama-Garda R, Marin P, Martirani-Von Abercron SM, Marques S | Environ Microbiol Rep | 10.1111/1758-2229.12752 | 2019 | Anaerobiosis, Bacterial Proteins/genetics, Betaproteobacteria/classification/genetics/*isolation & purification/*metabolism, Environmental Microbiology, Genetic Variation, Genome, Bacterial/genetics, Hydroquinones/*metabolism, Hydroxybenzoates/metabolism, Metabolic Networks and Pathways/*genetics, Multigene Family, Nitrates/*metabolism, Oxidation-Reduction, Phylogeny, Resorcinols/metabolism | Phylogeny |
Metabolism | 32220846 | An Aerobic Hybrid Phthalate Degradation Pathway via Phthaloyl-Coenzyme A in Denitrifying Bacteria. | Ebenau-Jehle C, Soon CISL, Fuchs J, Geiger R, Boll M | Appl Environ Microbiol | 10.1128/AEM.00498-20 | 2020 | Aerobiosis, Bacteria/metabolism, Bacterial Proteins/*metabolism, *Denitrification, Phthalic Acids/*metabolism, Rhodocyclaceae/enzymology/*metabolism, Thauera/enzymology/metabolism | Enzymology |
34302506 | Genome analysis of Thauera chlorobenzoica strain 3CB-1(T), a halobenzoate-degrading bacterium isolated from aquatic sediment. | Louie TS, Pavlik EJ, Haggblom MM | Arch Microbiol | 10.1007/s00203-021-02497-y | 2021 | Anaerobiosis, Bacteria, *Nitrates, Substrate Specificity, *Thauera/genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7331 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18012) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18012 | |||
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 | |
39922 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5141 | ||||
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) | |||
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 | |
68382 | Automatically annotated from API zym | |||||
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 | |||
83094 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID44104.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118239 | Curators of the CIP | Collection of Institut Pasteur (CIP 107679) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107679 |