Name: Paracoccus denitrificans CCUG 30144
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13693

Type strain:

Species: Paracoccus denitrificans

Culture col. no.: CCUG 30144, LMG 4049, LMG 4219, IFO 13301, DSM 413, ATCC 17741, ATCC 19367, CCM 982, LMD 22.21, NCIB 8944, JCM 21484, IAM 15021, NBRC 102528, NCCB 22021

Strain history: IAM 15021 <-- NCCB 22021 <-- LMD 22.21 <-- M. W. Beijerinck.

NCBI tax ID(s): 1302247 (strain), 266 (species)

Other strains from Paracoccus denitrificans

P. denitrificans CCUG 30145, LMG 4218

Section

Paracoccus denitrificans CCUG 30144 is an aerobe, mesophilic bacterium that was isolated from Soil,garden.

aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	25-08-2022 (DD-MM-YYYY)
	Domain	Bacteria
	Phylum	Pseudomonadota
	Class	Alphaproteobacteria
	Order	Rhodobacterales
	Family	Rhodobacteraceae
	Genus	Paracoccus
	Species	Paracoccus denitrificans
	Full Scientific Name (PNU)	Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 (Approved Lists 1980)

Synonym

Micrococcus denitrificans

Information on culture and growth conditions Culture and growth conditions

[Ref.: #35203]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #35203]

Culture medium growth

[Ref.: #35203]

Culture medium composition

expand / minimize

[Ref.: #37731]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #37731]

Culture medium growth

[Ref.: #37731]

Culture medium composition

expand / minimize

[Ref.: #186]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #186]

Culture medium growth

[Ref.: #186]

Culture medium link

Medium recipe at MediaDive

[Ref.: #186]

Culture medium composition

expand / minimize

[Ref.: #186]

Culture medium

MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)

[Ref.: #186]

Culture medium growth

[Ref.: #186]

Culture medium link

Medium recipe at MediaDive

[Ref.: #186]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #186]	growth	30 °C
[Ref.: #35203]	growth	30 °C
[Ref.: #37731]	growth	30 °C
[Ref.: #49937]	growth	26 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #186]	Temperature range	mesophilic
[Ref.: #35203]	Temperature range	mesophilic
[Ref.: #37731]	Temperature range	mesophilic
[Ref.: #49937]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #49937]

Oxygen tolerance

aerobe

[Ref.: #20216]

Observation

Degradation of creatine

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #49937]

Fatty acid	Percentage	ECL
C18:1 ω7c /12t/9t	72.3	17.824
C16:0	13.2	16
C18:0	4.5	18
C10:0 3OH	2.7	11.423
unknown 11.798	2.5	11.798
C19:0 CYCLO ω8c	1.9	18.9
Unidentified	1.6	16.297
C14:0 3OH/C16:1 ISO I	1.2	15.485
C17:0	0.9	17

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #49937]	Sample type/isolated from	Soil,garden

[Ref.: #67770]	Sample type/isolated from	Garden soil, Delft
[Ref.: #67770]	Country	Netherlands
[Ref.: #67770]	Country ISO 3 Code	NLD
[Ref.: #67770]	Continent	Europe

Isolation sources categories

#Engineered	#Agriculture	#Garden
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #186]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Paracoccus denitrificans strain ATCC 17741 clone ControlA04 16S ribosomal RNA gene, partial sequence	JF508186	661	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans strain ATCC 17741 clone ControlB11 16S ribosomal RNA gene, partial sequence	JF508203	673	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans 16S rRNA gene, strain ATCC 17741T	Y16927	1395	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans 16S rRNA gene, strain DSM 413	Y16929	1395	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus pantotrophus 16S rRNA gene, strain DSM 65	Y16935	1395	ENA	82367 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans strain JCM6892 16S rRNA gene	Y17511	1418	ENA	266 tax ID	*
[Ref.: #20218]	P.denitrificans 16S rRNA	X69159	1458	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus pantotrophus 16S rRNA gene, strain LMG 4218	Y16936	1395	ENA	82367 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102528	AB681862	1388	ENA	266 tax ID	*
[Ref.: #20218]	Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 16712	AB681113	1388	ENA	82367 tax ID	*
[Ref.: #20218]	Paracoccus denitrificans 16S rRNA gene, strain ATCC 19367	Y16930	1395	ENA	266 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus denitrificans ATCC 19367	GCA_004063735	complete	GenBank	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans DSM 413	GCA_900100045	scaffold	GenBank	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans NBRC 102528	GCA_007989485	contig	GenBank	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans JCM 21484 JCM 21484	GCA_001313145	contig	GenBank	1302247 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans JCM 21484	1302247.4	wgs	PATRIC	1302247 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans strain ATCC 19367	266.34	complete	PATRIC	266 tax ID	*

Availability in culture collections External links

[Ref.: #186]

Culture collection no.

CCUG 30144, LMG 4049, LMG 4219, IFO 13301, DSM 413, ATCC 17741, ATCC 19367, CCM 982, LMD 22.21, NCIB 8944, JCM 21484, IAM 15021, NBRC 102528, NCCB 22021

[Ref.: #20218]

Associated Passport(s) in StrainInfo

16103, 16114, 16100, 16101, 235066, 16110

Literature:

Only first 10 entries are displayed. Click here to see all.

Title	Authors	Journal	DOI	Year	Mesh	Topic	Topic2
Cytochrome c' of Paracoccus denitrificans.	Gilmour R, Goodhew CF, Pettigrew GW	Biochim Biophys Acta	10.1016/s0005-2728(05)80208-7	1991	Amino Acid Sequence, Amino Acids/analysis, Chromatium/enzymology, Chromatography, Gel, Cytochrome c Group/isolation & purification, Molecular Sequence Data, Paracoccus denitrificans/enzymology, Protein Conformation, Rhodobacter capsulatus/enzymology, Rhodospirillum rubrum/enzymology	Enzymology	Genetics	*
The regulation of hydrogenase formation as a differentiating character of strains of Paracoccus denitrificans.	Nokhal TH, Schlegel HG	Antonie Van Leeuwenhoek	10.1007/BF00444069	1980	Aerobiosis, Anaerobiosis, Cell Membrane/enzymology, Cell-Free System, Culture Media, Enzyme Induction, Hydrogenase, Oxidoreductases/biosynthesis/metabolism, Paracoccus denitrificans/classification/enzymology/growth & development	Enzymology	Cultivation	*
Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event.	Van Spanning RJ, Reijnders WN, Stouthamer AH	J Bacteriol	10.1128/jb.177.16.4772-4778.1995	1995	Base Sequence, Blotting, Southern, DNA Transposable Elements/genetics, DNA, Bacterial/genetics, Genetic Vectors, Genome, Bacterial, Gram-Negative Chemolithotrophic Bacteria/genetics, Molecular Sequence Data, Paracoccus denitrificans/classification/genetics, Recombination, Genetic, Restriction Mapping, Sequence Analysis, DNA, Thiobacillus/genetics	Genetics	Transcriptome	*
The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase.	Pettigrew GW, Gilmour R, Goodhew CF, Hunter DJ, Devreese B, Van Beeumen J, Costa C, Prazeres S, Krippahl L, Palma PN, Moura I, Moura JJ	Eur J Biochem	10.1046/j.1432-1327.1998.2580559.x	1998	Amino Acid Sequence, Bacterial Proteins/chemistry, Carbodiimides/metabolism, Computer Simulation, Cross-Linking Reagents/metabolism, Cytochrome c Group/chemistry, Cytochrome-c Peroxidase/metabolism, Dimerization, Electron Transport/physiology, Kinetics, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Osmolar Concentration, Oxidation-Reduction, Paracoccus denitrificans/*chemistry, Protein Binding, Sequence Analysis	Metabolism	Enzymology	*
A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.	Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A, Katayama Y, Wood AP	Int J Syst Bacteriol	10.1099/00207713-49-2-645	1999	Cytochrome c Group/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/classification/genetics/physiology, Paracoccus denitrificans/classification/genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Phylogeny	Genetics	*
Production of ubiquinone-10 using bacteria.	Yoshida H, Kotani Y, Ochiai K, Araki K	J Gen Appl Microbiol	10.2323/jgam.44.19	1998		Biotechnology		*
Paracoccus yeeii sp. nov. (formerly CDC group EO-2), a novel bacterial species associated with human infection.	Daneshvar MI, Hollis DG, Weyant RS, Steigerwalt AG, Whitney AM, Douglas MP, Macgregor JP, Jordan JG, Mayer LW, Rassouli SM, Barchet W, Munro C, Shuttleworth L, Bernard K	J Clin Microbiol	10.1128/JCM.41.3.1289-1294.2003	2003	DNA, Bacterial/analysis, Gram-Negative Bacterial Infections/microbiology, Humans, Molecular Sequence Data, Paracoccus/classification/genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics	Phylogeny	Pathogenicity	*
A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning.	Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu S	Appl Microbiol Biotechnol	10.1007/s00253-003-1238-2	2003	Amino Acid Sequence, Aspartic Acid/analogs & derivatives/metabolism, Base Sequence, Cloning, Molecular, Fructose-Bisphosphate Aldolase/genetics/isolation & purification/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Molecular Weight, Paracoccus denitrificans/enzymology, Substrate Specificity, Temperature	Enzymology	Metabolism	*
Growth and nitrite and nitrous oxide accumulation of Paracoccus denitrificans ATCC 19367 in the presence of selected pesticides.	Saez F, Pozo C, Gomez MA, Rodelas B, Gonzalez-Lopez J	Environ Toxicol Chem	10.1897/02-351	2003	Carbon Dioxide/analysis, Nitrates/pharmacokinetics, Nitrous Oxide/pharmacokinetics, Paracoccus denitrificans/growth & development/physiology, Pesticides/toxicity, Water Pollutants, Chemical/*toxicity	Enzymology		*
Potential role of nitrite for abiotic Fe(II) oxidation and cell encrustation during nitrate reduction by denitrifying bacteria.	Klueglein N, Zeitvogel F, Stierhof YD, Floetenmeyer M, Konhauser KO, Kappler A, Obst M	Appl Environ Microbiol	10.1128/AEM.03277-13	2013	Acetates/metabolism, Anaerobiosis, Betaproteobacteria/growth & development/metabolism/ultrastructure, Comamonadaceae/growth & development/metabolism/ultrastructure, Denitrification, Ferrous Compounds/metabolism, Microscopy, Electron, Minerals/metabolism, Nitrates/metabolism, Nitrites/metabolism, Oxidation-Reduction, Periplasm/metabolism	Metabolism		*
Molecular, Physiological and Phenotypic Characterization of Paracoccus denitrificans ATCC 19367 Mutant Strain P-87 Producing Improved Coenzyme Q10.	Tokdar P, Sanakal A, Ranadive P, Khora SS, George S, Deshmukh SK	Indian J Microbiol	10.1007/s12088-014-0506-4	2014		Enzymology		*
Paracoccus suum sp. nov., isolated from a pig farm dust collector.	Heo J, Cho HY, Kim JS, Hong SB, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003226	2019	Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dust, Farms, Fatty Acids/chemistry, Paracoccus/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Ubiquinone/chemistry	Phylogeny	Transcriptome	*
Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics.	Si YY, Xu KH, Yu XY, Wang MF, Chen XH	Can J Microbiol	10.1139/cjm-2019-0037	2019	Base Sequence, Denitrification, Genome, Bacterial, Paracoccus denitrificans/genetics/metabolism, *Whole Genome Sequencing	Genetics	Metabolism	*
Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study.	Zhou Y, Suenaga T, Qi C, Riya S, Hosomi M, Terada A	Biotechnol Bioeng	10.1002/bit.27654	2020	Nitrous Oxide/metabolism, Paracoccus denitrificans/metabolism, Pseudomonas stutzeri/metabolism, Rhodocyclaceae/metabolism, *Temperature	Metabolism		*

References

#186	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 413

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20216

Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) .

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#35203 ; Curators of the CIP;
#37731 ; Curators of the CIP;
#49937 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30144

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
* These data were automatically processed and therefore are not curated

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