Archive BacDiveID:10.13145/bacdive11761.20230509.8.1

Strain identifier

BacDive ID: 11761

Type strain:

Species: Dehalobacter restrictus

Strain Designation: PER-K23

Strain history: <- W. Schumacher and C. Holliger; PER-K23

NCBI tax ID(s): 871738 (strain), 55583 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 3579

BacDive-ID: 11761

DSM-Number: 9455

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive

description: Dehalobacter restrictus PER-K23 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from PCE-dechlorinating packed-bed column.

NCBI tax id

NCBI tax id	Matching level
55583	species
871738	strain

strain history

@ref: 3579
history: <- W. Schumacher and C. Holliger; PER-K23

doi: 10.13145/bacdive11761.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Desulfitobacteriaceae
genus: Dehalobacter
species: Dehalobacter restrictus
full scientific name: Dehalobacter restrictus Holliger et al. 1998

@ref: 3579

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Peptococcaceae

genus: Dehalobacter

species: Dehalobacter restrictus

full scientific name: Dehalobacter restrictus Holliger et al. 1998

strain designation: PER-K23

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

colony morphology

@ref: 3579
incubation period: 3-7 days

Culture and growth conditions

culture medium

@ref: 3579
name: DEHALOBACTER RESTRICTUS MEDIUM (TCE) (DSMZ Medium 732)
growth: yes
link: https://mediadive.dsmz.de/medium/732
composition: Name: DEHALOBACTER RESTRICTUS MEDIUM (TCE) (DSMZ Medium 732) Composition: NaHCO3 3.7004 g/l K2HPO4 0.644841 g/l Na-acetate 0.45635 g/l Na2S x 9 H2O 0.297619 g/l (NH4)2CO3 0.267857 g/l NaH2PO4 x H2O 0.168651 g/l CaCl2 x 2 H2O 0.109127 g/l Peptone 0.0992068 g/l MgCl2 x 6 H2O 0.0992064 g/l FeCl2 x 4 H2O 0.00198413 g/l Na2-EDTA 0.000496032 g/l Sodium resazurin 0.000496032 g/l Pyridoxine hydrochloride 0.000297619 g/l Nicotinic acid 0.000198413 g/l Thiamine-HCl x 2 H2O 0.000198413 g/l CoCl2 x 6 H2O 0.000188492 g/l Vitamin B12 9.92064e-05 g/l Calcium pantothenate 9.92064e-05 g/l MnCl2 x 4 H2O 9.92064e-05 g/l p-Aminobenzoic acid 7.93651e-05 g/l ZnCl2 6.94444e-05 g/l Calcium D-(+)-pantothenate 4.96032e-05 g/l (DL)-alpha-Lipoic acid 4.96032e-05 g/l Thiamine HCl 4.96032e-05 g/l Riboflavin 4.96032e-05 g/l Na2MoO4 x 2 H2O 3.57143e-05 g/l NiCl2 x 6 H2O 2.38095e-05 g/l Folic acid 1.98413e-05 g/l D-(+)-biotin 1.98413e-05 g/l Biotin 1.98413e-05 g/l AlCl3 9.92063e-06 g/l H3BO3 5.95238e-06 g/l CuCl2 x 2 H2O 1.98413e-06 g/l Hexadecane Tetrachloroethene Distilled water

culture temp

@ref: 3579
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
3579	anaerobe
69480	anaerobe	99.389

spore formation

@ref: 69480
spore formation: yes
confidence: 99.448

Isolation, sampling and environmental information

isolation

@ref: 3579
sample type: PCE-dechlorinating packed-bed column
country: Netherlands
origin.country: NLD
continent: Europe

isolation source categories

Cat1: #Engineered
Cat2: #Industrial
Cat3: #Engineered product

taxonmaps

@ref: 69479
File name: preview.99_2332.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_311;96_1258;97_1493;98_1819;99_2332&stattab=map
Last taxonomy: Dehalobacter
16S sequence: U84497
Sequence Identity:
Total samples: 3543
soil counts: 1627
aquatic counts: 1164
animal counts: 530
plant counts: 222

Safety information

risk assessment

@ref: 3579
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Dehalobacter restrictus strain DSM 9455 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	DQ834682	608	ena	871738
3579	Dehalobacter restrictus 16S ribosomal RNA gene, partial sequence	U84497	1525	ena	871738

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Dehalobacter restrictus DSM 9455 PER-K23; DSM 9455	GCA_000512895	complete	ncbi	871738
66792	Dehalobacter restrictus DSM 9455	871738.5	complete	patric	871738
66792	Dehalobacter restrictus DSM 9455	2510065016	complete	img	871738

GC content

@ref: 3579
GC-content: 44.6
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	56	no
motile	yes	79.454	no
flagellated	no	86.813	no
gram-positive	no	67.842	no
anaerobic	yes	99.172	no
halophile	no	97.499	no
spore-forming	yes	88.671	no
thermophile	no	86.955	yes
glucose-util	yes	63.346	no
aerobic	no	97.328	yes
glucose-ferment	no	69.371	no

External links

@ref: 3579

culture collection no.: DSM 9455

straininfo link

@ref: 80979
straininfo: 48618

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	9531632	Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration.	Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJ	Arch Microbiol	10.1007/s002030050577	1998	Anaerobiosis, Bacteria, Anaerobic/genetics/metabolism/ultrastructure, Cell Division/physiology, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Tetrachloroethylene/metabolism, Trichloroethylene/*metabolism	Metabolism
Enzymology	14706755	Development of degenerate and specific PCR primers for the detection and isolation of known and putative chloroethene reductive dehalogenase genes.	Regeard C, Maillard J, Holliger C	J Microbiol Methods	10.1016/j.mimet.2003.09.019	2004	Amino Acid Sequence, Bacteria, Anaerobic/enzymology/genetics, Base Sequence, Cloning, Molecular, DNA Primers/chemistry/genetics, DNA, Bacterial/chemistry/genetics/isolation & purification, Genes, Bacterial, Molecular Sequence Data, Oxidoreductases/*genetics, Polymerase Chain Reaction/methods, Sequence Alignment, Sequence Analysis, DNA	Phylogeny
Metabolism	17626425	Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates.	Lee PK, Conrad ME, Alvarez-Cohen L	Environ Sci Technol	10.1021/es062763d	2007	Bacteria/isolation & purification/metabolism, Biodegradation, Environmental, Carbon Isotopes, Chemical Fractionation, Chloroflexi/isolation & purification/metabolism, Dichloroethylenes/chemistry/metabolism, Epsilonproteobacteria/isolation & purification/metabolism, Hydrocarbons, Chlorinated/chemistry/metabolism, Oxidation-Reduction, Peptococcaceae/isolation & purification/metabolism, Trichloroethylene/chemistry/metabolism, Vinyl Chloride/chemistry/metabolism, Water Pollutants, Chemical/*metabolism	Enzymology
Metabolism	18497133	Pathways for the anaerobic microbial debromination of polybrominated diphenyl ethers.	Robrock KR, Korytar P, Alvarez-Cohen L	Environ Sci Technol	10.1021/es0720917	2008	Bacteria/metabolism, Bromine/metabolism, Environmental Pollutants/metabolism, Flame Retardants/metabolism, Phenyl Ethers/metabolism, Polybrominated Biphenyls/*metabolism
Metabolism	23479754	The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics.	Rupakula A, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2012.0325	2013	Bacterial Proteins/analysis/genetics/metabolism, Cloning, Molecular, Corrinoids/biosynthesis/genetics, Electron Transport, Energy Metabolism, Escherichia coli/genetics/metabolism, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Genetic Variation, Genome, Bacterial, Genomics, Hydrogen/metabolism, Hydrogenase/genetics/metabolism, Hydrogenation, Multigene Family, Peptococcaceae/enzymology/genetics/growth & development/*metabolism, Proteome/analysis/genetics/metabolism, Species Specificity, Transcription, Genetic	Genetics
Genetics	24501624	Complete genome sequence of Dehalobacter restrictus PER-K23(T.).	Kruse T, Maillard J, Goodwin L, Woyke T, Teshima H, Bruce D, Detter C, Tapia R, Han C, Huntemann M, Wei CL, Han J, Chen A, Kyrpides N, Szeto E, Markowitz V, Ivanova N, Pagani I, Pati A, Pitluck S, Nolan M, Holliger C, Smidt H	Stand Genomic Sci	10.4056/sigs.3787426	2013
Genetics	25610435	Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23.	Rupakula A, Lu Y, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J	Front Microbiol	10.3389/fmicb.2014.00751	2015
	26903979	Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates.	Tang S, Wang PH, Higgins SA, Loffler FE, Edwards EA	Front Microbiol	10.3389/fmicb.2016.00100	2016
Metabolism	27898054	Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates.	Wang PH, Tang S, Nemr K, Flick R, Yan J, Mahadevan R, Yakunin AF, Loffler FE, Edwards EA	ISME J	10.1038/ismej.2016.158	2016	Autotrophic Processes, Biosynthetic Pathways, Biotin/biosynthesis, Chloroform/metabolism, Corrinoids/biosynthesis, Heme/biosynthesis, Peptococcaceae/classification/isolation & purification/metabolism, *Water Microbiology	Phylogeny
Phylogeny	28421054	Isolation and Characterization of Dehalobacter sp. Strain TeCB1 Including Identification of TcbA: A Novel Tetra- and Trichlorobenzene Reductive Dehalogenase.	Alfan-Guzman R, Ertan H, Manefield M, Lee M	Front Microbiol	10.3389/fmicb.2017.00558	2017
	29740408	The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC.	Buttet GF, Willemin MS, Hamelin R, Rupakula A, Maillard J	Front Microbiol	10.3389/fmicb.2018.00755	2018
Metabolism	30607026	An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community.	Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA	ISME J	10.1038/s41396-018-0333-4	2019	Malates/metabolism, Microbial Consortia, NADP/metabolism, Oxidation-Reduction, Peptococcaceae/metabolism, Pyruvic Acid/metabolism
	35283847	Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT.	Cimmino L, Schmid AW, Holliger C, Maillard J	Front Microbiol	10.3389/fmicb.2022.838026	2022

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
3579	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9455)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-9455
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)
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)
80979	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID48618.1	StrainInfo: A central database for resolving microbial strain identifiers