Strain identifier

BacDive ID: 13920

Type strain: Yes

Species: Thauera chlorobenzoica

Strain Designation: 3CB-1

Strain history: CIP <- 2002, ATCC <- M.M. Haggblom

NCBI tax ID(s): 96773 (species)

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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

@refhistory
7331<- CIP <- ATCC <- M. M. Häggblom; 3CB-1
118239CIP <- 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

@refnamegrowthlinkcomposition
7331REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: 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
7331THAUERA AROMATICA MEDIUM (DSMZ Medium 586)yeshttps://mediadive.dsmz.de/medium/586Name: 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
39922MEDIUM 450 - for Thauera chlorobenzoicayesDistilled 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
118239CIP Medium 450yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=450

culture temp

@refgrowthtypetemperaturerange
7331positivegrowth30mesophilic
39922positivegrowth30mesophilic
118239positivegrowth25-37mesophilic
118239nogrowth5psychrophilic
118239nogrowth15psychrophilic
118239nogrowth41thermophilic
118239nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7331aerobe
7331anaerobe

halophily

@refsaltgrowthtested relationconcentration
118239NaClnogrowth0 %
118239NaClnogrowth2 %
118239NaClnogrowth4 %
118239NaClnogrowth6 %
118239NaClnogrowth8 %
118239NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1182394853esculin-hydrolysis
118239606565hippurate+hydrolysis
11823917632nitrate+builds gas from
11823917632nitrate+reduction
11823916301nitrite+builds gas from
11823916301nitrite+reduction
11823915792malonate-assimilation
11823917234glucose-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

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11823915688acetoin-
11823917234glucose-

enzymes

@refvalueactivityec
118239oxidase+
118239alcohol dehydrogenase-1.1.1.1
118239gelatinase-
118239amylase-
118239DNase-
118239caseinase-3.4.21.50
118239catalase+1.11.1.6
118239tween esterase-
118239gamma-glutamyltransferase-2.3.2.2
118239lecithinase-
118239lipase-
118239lysine decarboxylase-4.1.1.18
118239ornithine decarboxylase-4.1.1.17
118239phenylalanine ammonia-lyase-4.3.1.24
118239protease-
118239tryptophan deaminase-
118239urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118239--++-+----++++------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118239-------------------------------------------------------------+---++--------+---+-+------+-+-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7331river sedimentHudson RiverUSAUSANorth America
118239Environment, Sediment, Hudson RiverAlbany, New YorkUnited States of AmericaUSANorth America1993

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
73311Risk group (German classification)
1182391Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thauera chlorobenzoica 3CB-1GCA_900108255scaffoldncbi96773
66792Thauera chlorobenzoica strain 3CB196773.10completepatric96773
66792Thauera chlorobenzoica 3CB-12651870126draftimg96773

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.999no
flagellatedyes77.335no
gram-positiveno99.128no
anaerobicno88.316no
halophileno88.6no
spore-formingno95.669no
thermophileno95.86yes
glucose-utilno82.884no
aerobicno78.533no
glucose-fermentno90.021no

External links

@ref: 7331

culture collection no.: DSM 18012, ATCC 700723, CIP 107679, KCTC 12933

straininfo link

  • @ref: 83094
  • straininfo: 44104

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321105Characterization of halobenzoate-degrading, denitrifying Azoarcus and Thauera isolates and description of Thauera chlorobenzoica sp. nov.Song B, Palleroni NJ, Kerkhof LJ, Haggblom MMInt J Syst Evol Microbiol10.1099/00207713-51-2-5892001Azoarcus/*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/metabolismMetabolism
Phylogeny29236233Thauera sinica sp. nov., a phenol derivative-degrading bacterium isolated from activated sludge.Qiao N, Xi L, Zhang J, Liu D, Ge B, Liu JAntonie Van Leeuwenhoek10.1007/s10482-017-0993-52017Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Thauera/*genetics/isolation & purificationEnzymology
Metabolism29575501Liquid 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 IRapid Commun Mass Spectrom10.1002/rcm.81132018Benzoates/*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
Metabolism30884168Occurrence 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 SEnviron Microbiol Rep10.1111/1758-2229.127522019Anaerobiosis, 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/metabolismPhylogeny
Metabolism32220846An Aerobic Hybrid Phthalate Degradation Pathway via Phthaloyl-Coenzyme A in Denitrifying Bacteria.Ebenau-Jehle C, Soon CISL, Fuchs J, Geiger R, Boll MAppl Environ Microbiol10.1128/AEM.00498-202020Aerobiosis, Bacteria/metabolism, Bacterial Proteins/*metabolism, *Denitrification, Phthalic Acids/*metabolism, Rhodocyclaceae/enzymology/*metabolism, Thauera/enzymology/metabolismEnzymology
34302506Genome analysis of Thauera chlorobenzoica strain 3CB-1(T), a halobenzoate-degrading bacterium isolated from aquatic sediment.Louie TS, Pavlik EJ, Haggblom MMArch Microbiol10.1007/s00203-021-02497-y2021Anaerobiosis, Bacteria, *Nitrates, Substrate Specificity, *Thauera/genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7331Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18012)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18012
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
39922Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5141
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)
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
68382Automatically annotated from API zym
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
83094Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44104.1StrainInfo: A central database for resolving microbial strain identifiers
118239Curators of the CIPCollection of Institut Pasteur (CIP 107679)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107679