Paracoccus denitrificans (DSM 104981, PD 1222)

Name: Paracoccus denitrificans (DSM 104981, PD 1222)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 139766

Type strain

Culture col. no. DSM 104981 PD 1222

NCBI tax ID(s) 266

Special Collections DSMZ

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;

Links

Paracoccus denitrificans DSM 104981 is a bacterium that was isolated from soil.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 406074

DSM 104981

@ref 20215

Last LPSN update 2026-02-09 11:33:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species Paracoccus denitrificans

Full scientific name Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 (Approved Lists 1980)

Synonyms (1)

"Micrococcus denitrificans"

BacDive ID	Other strains from **Paracoccus denitrificans** (2)	Type strain
13693	P. denitrificans CCUG 30144, LMG 4049, LMG 4219, IFO 13301, ... (type strain)
146009	P. denitrificans CCUG 30145, LMG 4218

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.9
125439	negative	99.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
42376	LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)		Medium recipe at MediaDive	Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42376	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.5

Spore formation

@ref	Spore formation	Confidence
125438		91.678
125439		99.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
42376	soil	Delft	Netherlands	NLD	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42376	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM20389v1 assembly for Paracoccus denitrificans PD1222	complete	GCA_000203895	318586.5	639633048	318586	98.62
66792	ASM1419971v1 assembly for Paracoccus denitrificans DSM 104981	scaffold	GCA_014199715	266.64	2828653696	266	58.83

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paracoccus denitrificans PD1222
IMG: 639633048

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	78.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus denitrificans PD1222 PD1222
NCBI: GCA_000203895.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.90	no
125438	anaerobic	anaerobicⓘ	no	93.17	no
125438	aerobic	aerobicⓘ	yes	77.23	no
125438	spore-forming	spore-formingⓘ	no	91.68	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	no	51.04	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.	Li J, Gobel F, Hsu HY, Koch JN, Hager N, Flegler WA, Tanabe TS, Dahl C.	Commun Biol	10.1038/s42003-024-07270-7	2024
Metabolism	Diversity of Methylotrophy Pathways in the Genus Paracoccus (Alphaproteobacteria).	Czarnecki J, Bartosik D.	Curr Issues Mol Biol	10.21775/cimb.033.117	2019
Enzymology	Underestimation about the Contribution of Nitrate Reducers to Iron Cycling Indicated by Enterobacter Strain.	Li MJ, Wei MY, Fan XT, Zhou GW.	Molecules	10.3390/molecules27175581	2022
	Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation.	Jamieson J, Prommer H, Kaksonen AH, Sun J, Siade AJ, Yusov A, Bostick B.	Environ Sci Technol	10.1021/acs.est.8b01122	2018
Metabolism	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	2014
Metabolism	Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation.	Park S, Kim DH, Lee JH, Hur HG.	FEMS Microbiol Ecol	10.1111/1574-6941.12372	2014
	Evolution of respiratory complex I: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	Yip CY, Harbour ME, Jayawardena K, Fearnley IM, Sazanov LA.	J Biol Chem	10.1074/jbc.m110.194993	2011
Metabolism	Conserved small mRNA with an unique, extended Shine-Dalgarno sequence.	Hahn J, Thalmann S, Migur A, von Boeselager RF, Kubatova N, Kubareva E, Schwalbe H, Evguenieva-Hackenberg E.	RNA Biol	10.1080/15476286.2016.1256534	2017
Phylogeny	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
Enzymology	Identification of periplasmic nitrate reductase Mo(V) EPR signals in intact cells of Paracoccus denitrificans.	Sears HJ, Bennett B, Spiro S, Thomson AJ, Richardson DJ.	Biochem J	10.1042/bj3100311	1995
Metabolism	The transition between active and de-activated forms of NADH:ubiquinone oxidoreductase (Complex I) in the mitochondrial membrane of Neurospora crassa.	Grivennikova VG, Serebryanaya DV, Isakova EP, Belozerskaya TA, Vinogradov AD.	Biochem J	10.1042/bj20021165	2003
	Low oxygen eddies in the eastern tropical North Atlantic: Implications for N₂O cycling.	Grundle DS, Loscher CR, Krahmann G, Altabet MA, Bange HW, Karstensen J, Kortzinger A, Fiedler B.	Sci Rep	10.1038/s41598-017-04745-y	2017
Metabolism	Dynamics of denitrification activity of Paracoccus denitrificans in continuous culture during aerobic-anaerobic changes.	Baumann B, Snozzi M, Zehnder AJ, Van Der Meer JR.	J Bacteriol	10.1128/jb.178.15.4367-4374.1996	1996
	Deletion of the gene for subunit III leads to defective assembly of bacterial cytochrome oxidase.	Haltia T, Finel M, Harms N, Nakari T, Raitio M, Wikstrom M, Saraste M.	EMBO J	10.1002/j.1460-2075.1989.tb08529.x	1989
Metabolism	Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS.	Nordhoff M, Tominski C, Halama M, Byrne JM, Obst M, Kleindienst S, Behrens S, Kappler A.	Appl Environ Microbiol	10.1128/aem.00752-17	2017
Metabolism	Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase.	Muntyan MS, Cherepanov DA, Malinen AM, Bloch DA, Sorokin DY, Severina II, Ivashina TV, Lahti R, Muyzer G, Skulachev VP.	Proc Natl Acad Sci U S A	10.1073/pnas.1417071112	2015
	Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer.	Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M.	Front Microbiol	10.3389/fmicb.2015.00879	2015
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) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Paracoccus denitrificans (DSM 104981, PD 1222)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000203895

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media