Name: Paracoccus denitrificans DSM 104981
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 139766

Type strain:

Species: Paracoccus denitrificans

Culture col. no.: DSM 104981, PD 1222

Strain history: <- S. Hahnke; Leibniz-Institut DSMZ GmbH, Braunschweig, DEUTSCHLAND; PD1222<-de Vries D. E., Harms N., Hoogendijk J., Stouthamer A. H.<-van Spanning R.<-M. W. Beijerinck M. W., D. C. J. Minkman;

NCBI tax ID(s): 82367 (species)

SI-ID 406074

DSM 104981

Other strains from Paracoccus denitrificans

P. denitrificans CCUG 30144, LMG 4049, LMG 4219, ... (type strain)
P. denitrificans CCUG 30145, LMG 4218

Section

Paracoccus denitrificans DSM 104981 is a mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
mesophilic
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus denitrificans**
	Full Scientific Name (LPSN)	Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 (Approved Lists 1980)

Synonym

"Micrococcus denitrificans"

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.995

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42376]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #42376]

Culture medium growth

[Ref.: #42376]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42376]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #42376]			growth	28 °C

[Ref.: #42376]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.985

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

[Ref.: #42376]	Sample type/isolated from	soil
[Ref.: #42376]	Geographic location (country and/or sea, region)	Delft
[Ref.: #42376]	Country	Netherlands
[Ref.: #42376]	Country ISO 3 Code	NLD
[Ref.: #42376]	Continent	Europe
* marker position based on {}

Isolation sources categories

#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.: #42376]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus denitrificans PD1222	GCA_000203895	complete	GenBank	318586 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans DSM 104981	GCA_014199715	scaffold	GenBank	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans strain DSM 104981	266.64	wgs	PATRIC	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans DSM 104981	2828653696	draft	JGI IMG/M	266 tax ID	*
[Ref.: #66792]	Paracoccus denitrificans PD1222	639633048	complete	JGI IMG/M	318586 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paracoccus denitrificans PD1222 PD1222 NCBI: GCA_000203895.1
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus denitrificans PD1222 PD1222 NCBI: GCA_000203895.1
[Ref.: #69480]	motile	no	56.951	no
[Ref.: #69480]	flagellated	no	87.456	no
[Ref.: #69480]	gram-positive	no	98.544	no
[Ref.: #69480]	anaerobic	no	97.242	no
[Ref.: #69480]	aerobic	yes	84.384	no
[Ref.: #69480]	halophile	no	84.557	no
[Ref.: #69480]	spore-forming	no	95.693	no
[Ref.: #69480]	glucose-util	yes	88.338	no
[Ref.: #69480]	thermophile	no	98.153	yes
[Ref.: #69480]	glucose-ferment	no	86.894	no

Availability in culture collections External links

[Ref.: #42376]

Culture collection no.

DSM 104981, PD 1222

[Ref.: #96211]

SI-ID 406074

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222.	Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivian C, Richardson DJ, Roldan MD	Sci Rep	10.1038/s41598-021-96559-2	2021	*
Metabolism	Identification and Validation of Four Novel Promoters for Gene Engineering with Broad Suitability across Species.	Wang CY, Liu LC, Wu YC, Zhang YX	J Microbiol Biotechnol	10.4014/jmb.2103.03049	2021	*
Genetics	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	*
Proteome	Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222.	Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivian C, Richardson DJ, Roldan MD	Front Microbiol	10.3389/fmicb.2018.01137	2018	*
Metabolism	Environmental Adaptability and Quorum Sensing: Iron Uptake Regulation during Biofilm Formation by Paracoccus denitrificans.	Zhang Y, Gao J, Wang L, Liu S, Bai Z, Zhuang X, Zhuang G	Appl Environ Microbiol	10.1128/AEM.00865-18	2018	*
Metabolism	Poly(3-hydroxybutyrate) hyperproduction by a global nitrogen regulator NtrB mutant strain of Paracoccus denitrificans PD1222.	Olaya-Abril A, Luque-Almagro VM, Manso I, Gates AJ, Moreno-Vivian C, Richardson DJ, Roldan MD	FEMS Microbiol Lett	10.1093/femsle/fnx251	2018	*
Metabolism	Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans.	Luque-Almagro VM, Manso I, Sullivan MJ, Rowley G, Ferguson SJ, Moreno-Vivian C, Richardson DJ, Gates AJ, Roldan MD	Biochem J	10.1042/BCJ20170115	2017	*
Metabolism	The metabolic impact of extracellular nitrite on aerobic metabolism of Paracoccus denitrificans.	Hartop KR, Sullivan MJ, Giannopoulos G, Gates AJ, Bond PL, Yuan Z, Clarke TA, Rowley G, Richardson DJ	Water Res	10.1016/j.watres.2017.02.011	2017	*
Enzymology	Conversion of cysteine to 3-mercaptopyruvic acid by bacterial aminotransferases.	Andreessen C, Gerlt V, Steinbuchel A	Enzyme Microb Technol	10.1016/j.enzmictec.2017.01.004	2017	*
Metabolism	Paracoccus denitrificans PD1222 utilizes hypotaurine via transamination followed by spontaneous desulfination to yield acetaldehyde and, finally, acetate for growth.	Felux AK, Denger K, Weiss M, Cook AM, Schleheck D	J Bacteriol	10.1128/JB.00307-13	2013	*
Enzymology	Redox dependent changes at the heme propionates in cytochrome c oxidase from Paracoccus denitrificans: direct evidence from FTIR difference spectroscopy in combination with heme propionate 13C labeling.	Behr J, Hellwig P, Mantele W, Michel H	Biochemistry	10.1021/bi9731697	1998	*
Metabolism	Respiratory inhibitors activate an Fnr-like regulatory protein in Paracoccus denitrificans: implications for the regulation of the denitrification pathway.	Kucera I, Matchova I, Spiro S	Biochem Mol Biol Int		1994	*

References

#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 )

#42376

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104981

#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) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96211

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406074.1 )

* These data were automatically processed and therefore are not curated

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Paracoccus denitrificans PD1222 PD1222

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