Paracoccus denitrificans | Type strain | CCUG 30144, LMG 4049, LMG 4219, IFO 13301, DSM 413, ATCC 17741, ATCC 19367, CCM 982, LMD 22.21, NCIB 8944

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

Section

Name and taxonomic classification
Morphology and physiology
Culture and growth conditions
Isolation, sampling and environmental information
Application and interaction
Molecular biology
Strain availability

External links

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

[Ref.: #186]	Domain	Bacteria
[Ref.: #186]	Phylum	Proteobacteria
[Ref.: #186]	Class	Alphaproteobacteria
[Ref.: #186]	Order	Rhodobacterales
[Ref.: #186]	Family	Rhodobacteraceae
[Ref.: #186]	Genus	Paracoccus
[Ref.: #186]	Species	Paracoccus denitrificans
[Ref.: #186]	Full Scientific Name	Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 emend. Rainey et al. 1999
[Ref.: #186]	Type strain

		Prokaryotic Nomenclature Up-to-date (PNU)	Taxonomical status	Literature reference
	Last PNU update	19-11-2019 (DD-MM-YYYY)
[Ref.: #20215]	Domain	Bacteria
[Ref.: #20215]	Phylum	Proteobacteria
[Ref.: #20215]	Class	Alphaproteobacteria		Int. J. Syst. Evol. Microbiol. 56:1
[Ref.: #20215]	Family	Rhodobacteraceae		Int. J. Syst. Evol. Microbiol. 56:1
[Ref.: #20215]	Genus	Paracoccus	genus (AL)	Int. J. Syst. Bacteriol. 30:225
[Ref.: #20215]	Species	Paracoccus denitrificans	comb. nov. (VP)	Int. J. Syst. Bacteriol. 49:645*
[Ref.: #20215]	Full Scientific Name	Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 emend. Rainey et al. 1999

Information on morphological and physiological propertiesMorphology and physiology

Fatty acid profile

Type of FA analysis

whole cell analysis

Incubation medium

Agar/liquid

Incubation temperature (°C)

Incubation time (d)

Incubation pH

Incubation oxygen condition

Treatment/condition

Software version

Library/peak naming table

System

Instrument

Method/protocol

CCUG

Cutoff value

Reference

[Ref.: #49937]

Fatty acid	Percentage	ECL
16:0	13.2	16
17:0	0.9	17
18:0	4.5	18
10:0 3OH	2.7	11.423
14:0 3OH/16:1 ISO I	1.2	15.485
18:1 ω7c /12t/9t	72.3	17.824
19:0 CYCLO ω8c	1.9	18.9
Unidentified	1.6	16.297
unknown 11.798	2.5	11.798

[Ref.: #20216]

Observation

Degradation of creatine

[Ref.: #49937]

Oxygen tolerance

aerobe

Information on culture and growth conditionsCulture 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), 30°C

[Ref.: #186]

Culture medium growth

[Ref.: #186]

Culture medium link

medium recipe provided by DSMZ

[Ref.: #186]

Culture medium

MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81), 30°C

[Ref.: #186]

Culture medium growth

[Ref.: #186]

Culture medium link

medium recipe provided by DSMZ

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

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

Information on isolation source, the sampling and environmental conditionsIsolation, sampling and environmental information

[Ref.: #49937]

Sample type/isolated from

Soil,garden

Isolation sources categories

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

What are isolation sources categories?

* marker position based on {}

Information on possible application of the strain and its possible interaction with e.g. potential hostsApplication and interaction

[Ref.: #186]

Biosafety level

Risk group (German classification)

Information on genomic background e.g. entries in nucleic sequence databassMolecular biology

Sequence information:

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

	Sequence database	Sequence accession description	Sequence accession number	Sequence type	Sequence length (bp)	Associated NCBI tax ID
[Ref.: #20218]	INSDC Sequence	P.denitrificans bc1 operon genes encoding three subunits (FeS, b and c1) of the cytochrome bc1 complex, complete cds	M17522		3840	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans succinate dehydrogenase b-type cytochrome subunit (sdhC), succinate dehydrogenase hydrophobic membrane anchor (sdhD), succinate dehydrogenase flavoprotein subunit (sdhA), and succinate dehydrogenase iron-sulfur protein subunit (sdhB) genes, complete cds	U31902		6380	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans strain ATCC 17741 putative nitrite reductase (nirK) gene, partial cds	HM060299		516	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans strain ATCC 17741 clone ControlA04 16S ribosomal RNA gene, partial sequence	JF508186	16S	661	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans strain ATCC 17741 clone ControlB11 16S ribosomal RNA gene, partial sequence	JF508203	16S	673	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans 16S rRNA gene, strain ATCC 17741T	Y16927	16S	1395	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans NirI and NirX genes, and flanking regions	AJ001308		3158	318586	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans (ORF1) gene, partial cds, and LysR-type transcriptional activator (mauR), (mauF), and methylamine dehydrogenase large subunit (mauB) genes, complete cds	U12464		3007	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans Fnr-like transcriptional activator (nnr) gene, complete cds	U17435		993	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans recA gene, complete cds	U59631		1071	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans 16S rRNA gene, strain DSM 413	Y16929	16S	1395	266	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus plasmid pHG16-a RepB (repB) gene, partial cds; and RepC (repC) gene, complete cds	AF397210		2112	82367	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus pantotrophus partial nosZ gene for nitrous oxide reductase	AJ440508		353	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus insertion sequence ISPpa4 putative transposase gene, complete cds	AY177682		1053	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus strain DSM65 putative ABC transporter periplasmic binding protein (tauA) gene, partial cds; putative ABC transporter ATP binding protein (tauB), putative ABC transporter permease component (tauC), putative taurine dehydrogenase small subunit (tauX), putative taurine dehydrogenase large subunit (tauY), sulfoacetaldehyde acetyltransferase (xsc), and hypothetical membrane protein (tauZ) genes, complete cds; and phosphate acetyltransferase (pta) gene, partial cds	AY498614		8004	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus strain DSM 65 insertion sequence ISPpa7, complete sequence	EU909901		2731	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus strain DSM 65 insertion sequence ISPpa8, complete sequence	EU909902		1050	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus pantotrophus strain DSM 65 insertion sequence ISPpa9, complete sequence	EU909903		812	82367	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus pantotrophus 16S rRNA gene, strain DSM 65	Y16935	16S	1395	82367	*
[Ref.: #20218]	Marker Gene (DDBJ Direct submission)	Paracoccus denitrificans 16S rRNA	D13480	16S	1286	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans strain IAM12479 16S rRNA gene	Y17512	16S	1424	266	*
[Ref.: #20218]	Marker Gene (DDBJ Direct submission)	Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: JCM 6892	AB598745	16S	1385	82367	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans strain JCM6892 16S rRNA gene	Y17511	16S	1418	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	P.denitrificans 16S rRNA	X69159	16S	1458	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	P.denitrificans 23S rRNA gene	X87287		2847	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus pantotrophus 16S rRNA gene, strain LMG 4218	Y16936	16S	1395	82367	*
[Ref.: #20218]	Marker Gene (DDBJ Direct submission)	Paracoccus denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102528	AB681862	16S	1388	266	*
[Ref.: #20218]	Marker Gene (DDBJ Direct submission)	Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 16712	AB681113	16S	1388	82367	*
[Ref.: #20218]	Marker Gene (GenBank Direct submission)	Paracoccus denitrificans F1-ATPase gamma-subunit (atpC) and F1-ATPase beta-subunit (atpB) genes, partial cds	AF017097		903	266	*
[Ref.: #20218]	INSDC Sequence	P.denitrificans cytochrome c550 gene, complete cds, and iso-cytochrome oxidase subunit I (iso-COI) gene, 5' end	M27304		1045	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	P. denitrificans AMI gene coding for amicyanin	X55665		659	266	*
[Ref.: #20218]	Marker Gene (EMBL Direct submission)	Paracoccus denitrificans 16S rRNA gene, strain ATCC 19367	Y16930	16S	1395	266	*

Availability in culture collectionsStrain availability

[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

[Ref.: #186]

Strain history

<- IMG 1627 (Micrococcus denitrificans) <- J.G. Morris <- J. Lascelles <- W. Verhoeven

[Ref.: #20218]

Associated Passport(s) in StrainInfo

16103, 16114, 16100, 16101, 235066, 16110

References

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

#20215

Leibniz Institute DSMZ D.Gleim, M.Kracht, N.Weiss et. al.: Prokaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since .

#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
* These References are textmined

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