Paracoccus denitrificans (CCUG 30144, LMG 4049, LMG 4219)

Name: Paracoccus denitrificans (CCUG 30144, LMG 4049, LMG 4219)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13693

Type strain

Culture col. no. CCUG 30144 LMG 4049 LMG 4219 IFO 13301 DSM 413 14 more

NCBI tax ID(s) 1302247 266

Special Collections DSMZ CCUG JCM CIP

History <- IMG 1627 (Micrococcus denitrificans) <- J.G. Morris <- J. Lascelles <- W. Verhoeven IAM 15021 <-- NCCB 22021 <-- LMD 22.21 <-- M. W. Beijerinck. CIP <- 1999, A. Hiraishi, Toyohashi Univ. of Technology, Japan <- JCM

Links

Paracoccus denitrificans CCUG 30144 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from Soil,garden.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 92366

LMG 4218,ATCC 17741,DSM 65,IAM 12479,IMET 10380,NCIB 11627,NRRL B-3784,ATCC 13543,CIP 106306,CCUG 30145,NCIMB 11627,JCM 6892,CIP 105417,CIP106400,CCM 2922,VKM B-1324,LMD 22.21,KCTC 2528,KCTC 2530,IFO 16712,NBRC 16712,LMG4128,NCCB 22021,IAM 15021,CDBB 912,JCM 21484,NBRC 102528,JCM 20620,DSM 413

@ref 20215

Last LPSN update 2025-12-16 09:50:09

Domain Pseudomonadati

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
139766	P. denitrificans DSM 104981, PD 1222
146009	P. denitrificans CCUG 30145, LMG 4218

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118902	negative	rod-shaped
125438	negative		95.9
125439	negative		98.4

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
35203	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
37731	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
186	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
186	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	Medium recipe at MediaDive	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
118902	CIP Medium 3	Medium recipe at CIP
186	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
186	positive	growth	30	mesophilic
35203	positive	growth	30	mesophilic
37731	positive	growth	30	mesophilic
49937	positive	growth	26	mesophilic
67770	positive	growth	25	mesophilic
118902	positive	growth	25-41
118902	negative	growth	5
118902	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
49937	aerobe
118902	obligate aerobe
125439	obligate aerobe	94.4

Spore formation

@ref	Spore formation	Confidence
125438		91.678
125439		97.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118902	NaCl	positive	growth	0-4 %
118902	NaCl		growth	6 %
118902	NaCl		growth	8 %
118902	NaCl		growth	10 %

Observation

20216

ObservationDegradation of creatine

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118902	16947 ChEBI	citrate	-	carbon source
118902	4853 ChEBI	esculin	-	hydrolysis
118902	606565 ChEBI	hippurate	+	hydrolysis
118902	17632 ChEBI	nitrate	+	reduction
118902	17632 ChEBI	nitrate	+	respiration
118902	16301 ChEBI	nitrite	+	reduction
118902	35020 ChEBI	tributyrin	+	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118902	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
118902	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118902	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118902	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118902	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118902	caseinase	-	3.4.21.50
118902	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118902	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118902	gamma-glutamyltransferase	+	2.3.2.2
118902	gelatinase	-
118902	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118902	lipase	-
68382	lipase (C 14)	-		from API zym
118902	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118902	ornithine decarboxylase	-	4.1.1.17
118902	oxidase	+
118902	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118902	tryptophan deaminase	-
118902	tween esterase	-
118902	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@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

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118902	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
118902	not determinedn.d.	+	+	-	+	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	+	+	+	-	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	+	-	-	+	+	-	-	-	-	-	-	+	+	-	+	+	+	+	+	+	-	-	-	-	-	-	+	-	+	-	+	-	-	+	+	+	-	+	+	+	-	+	-	+	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Garden
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
49937	Soil,garden
67770	Garden soil, Delft	Netherlands	NLD	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
186	1	Risk group (German classification) According to TRBA 466
118902	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM406373v1 assembly for Paracoccus denitrificans ATCC 19367	complete	GCA_004063735	266.34	2841597668	266	98.65
66792	IMG-taxon 2597490357 annotated assembly for Paracoccus denitrificans DSM 413	scaffold	GCA_900100045	266.10	2597490357	266	60.11
66792	ASM798948v1 assembly for Paracoccus denitrificans NBRC 102528	contig	GCA_007989485	266.43		266	47.09
66792	ASM2559848v1 assembly for Paracoccus denitrificans ATCC 19367	contig	GCA_025598485	266.73	8114139700	266	46.27
66792	ASM131314v1 assembly for Paracoccus denitrificans JCM 21484	contig	GCA_001313145	1302247.4	2734481933	1302247

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Paracoccus denitrificans 16S rRNA gene, strain ATCC 17741T	Y16927	1395	266
20218	Paracoccus denitrificans 16S rRNA gene, strain DSM 413	Y16929	1395	266
20218	Paracoccus pantotrophus 16S rRNA gene, strain DSM 65	Y16935	1395	82367
20218	Paracoccus denitrificans strain JCM6892 16S rRNA gene	Y17511	1418	266
20218	P.denitrificans 16S rRNA	X69159	1458	266
20218	Paracoccus pantotrophus 16S rRNA gene, strain LMG 4218	Y16936	1395	82367
20218	Paracoccus denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102528	AB681862	1388	266
20218	Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 16712	AB681113	1388	82367
20218	Paracoccus denitrificans 16S rRNA gene, strain ATCC 19367	Y16930	1395	266

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paracoccus denitrificans strain ATCC 19367
PATRIC: 266.34

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.70	no
125439	motility	BacteriaNetⓘ	yes	68.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus denitrificans ATCC 19367
NCBI: GCA_004063735.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.90	no
125438	anaerobic	anaerobicⓘ	no	93.17	yes
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
Metabolism	The more, the merrier: heterotroph richness stimulates methanotrophic activity.	Ho A, de Roy K, Thas O, De Neve J, Hoefman S, Vandamme P, Heylen K, Boon N.	ISME J	10.1038/ismej.2014.74	2014
Phylogeny	Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers.	Decleyre H, Heylen K, Van Colen C, Willems A.	Front Microbiol	10.3389/fmicb.2015.01124	2015
	NAD-dependent dehydrogenases enable efficient growth of Paracoccus denitrificans on the PET monomer ethylene glycol.	Ren M, Li D, Addison H, Noteborn WEM, Andeweg EH, Glatter T, de Winde JH, Rebelein JG, Lamers MH, Schada von Borzyskowski L.	Nat Commun	10.1038/s41467-025-61056-x	2025
Metabolism	Multiple levels of transcriptional regulation control glycolate metabolism in Paracoccus denitrificans.	Schada von Borzyskowski L, Hermann L, Kremer K, Barthel S, Pommerenke B, Glatter T, Paczia N, Bremer E, Erb TJ.	mBio	10.1128/mbio.01524-24	2024
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
	Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits.	Hollensteiner J, Schneider D, Poehlein A, Brinkhoff T, Daniel R.	PLoS One	10.1371/journal.pone.0287947	2023
Metabolism	Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes.	Hassan J, Qu Z, Bergaust LL, Bakken LR.	PLoS Comput Biol	10.1371/journal.pcbi.1004621	2016
	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	Cumate-inducible gene expression system for sphingomonads and other Alphaproteobacteria.	Kaczmarczyk A, Vorholt JA, Francez-Charlot A.	Appl Environ Microbiol	10.1128/aem.02296-13	2013
	Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions.	Hofmann M, Heine T, Malik L, Hofmann S, Joffroy K, Senges CHR, Bandow JE, Tischler D.	Microorganisms	10.3390/microorganisms9010111	2021
Enzymology	Crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 A resolution.	Haltia T, Brown K, Tegoni M, Cambillau C, Saraste M, Mattila K, Djinovic-Carugo K.	Biochem J	10.1042/bj20020782	2003
	Identification and distribution of insertion sequences of Paracoccus solventivorans.	Bartosik D, Szymanik M, Baj J.	Appl Environ Microbiol	10.1128/aem.69.12.7002-7008.2003	2003
Enzymology	Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus.	Heylen K, Keltjens J.	Front Microbiol	10.3389/fmicb.2012.00371	2012
	Mass Spectrometric Studies of the Effect of pH on the Accumulation of Intermediates in Denitrification by Paracoccus denitrificans.	Thomsen JK, Geest T, Cox RP.	Appl Environ Microbiol	10.1128/aem.60.2.536-541.1994	1994
Phylogeny	Distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases.	Vorholt JA, Chistoserdova L, Stolyar SM, Thauer RK, Lidstrom ME.	J Bacteriol	10.1128/jb.181.18.5750-5757.1999	1999
Enzymology	Physiological regulation of Paracoccus denitrificans methanol dehydrogenase synthesis and activity.	de Vries GE, Harms N, Maurer K, Papendrecht A, Stouthamer AH.	J Bacteriol	10.1128/jb.170.8.3731-3737.1988	1988
Metabolism	Isolation and characterization of Paracoccus denitrificans mutants with defects in the metabolism of one-carbon compounds.	Harms N, de Vries GE, Maurer K, Veltkamp E, Stouthamer AH.	J Bacteriol	10.1128/jb.164.3.1064-1070.1985	1985
Metabolism	Population analysis in a denitrifying sand filter: conventional and in situ identification of Paracoccus spp. in methanol-fed biofilms.	Neef A, Zaglauer A, Meier H, Amann R, Lemmer H, Schleifer KH.	Appl Environ Microbiol	10.1128/aem.62.12.4329-4339.1996	1996
Metabolism	Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	Baker SC, Ferguson SJ, Ludwig B, Page MD, Richter OM, van Spanning RJ.	Microbiol Mol Biol Rev	10.1128/mmbr.62.4.1046-1078.1998	1998
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
	A Critical Review on the Economically Feasible and Sustainable Poly(3-Hydroxybutyrate-co-3-hydroxyvalerate) Production from Alkyl Alcohols.	Wong HSJ, Bhubalan K, Amirul AA.	Polymers (Basel)	10.3390/polym14040670	2022
Metabolism	3-Hydroxybutyrate oligomer hydrolase and 3-hydroxybutyrate dehydrogenase participate in intracellular polyhydroxybutyrate and polyhydroxyvalerate degradation in Paracoccus denitrificans.	Lu J, Takahashi A, Ueda S.	Appl Environ Microbiol	10.1128/aem.03396-13	2014
Pathogenicity	Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells.	Ting SY, Martinez-Garcia E, Huang S, Bertolli SK, Kelly KA, Cutler KJ, Su ED, Zhi H, Tang Q, Radey MC, Raffatellu M, Peterson SB, de Lorenzo V, Mougous JD.	Cell Host Microbe	10.1016/j.chom.2020.05.006	2020
	Trace Metal Availability Affects Greenhouse Gas Emissions and Microbial Functional Group Abundance in Freshwater Wetland Sediments.	Giannopoulos G, Hartop KR, Brown BL, Song B, Elsgaard L, Franklin RB.	Front Microbiol	10.3389/fmicb.2020.560861	2020
	Fractionation of N2O isotopomers during production by denitrifier	Toyoda S, Mutobe H, Yamagishi H, Yoshida N, Tanji Y.	Soil Biol Biochem	10.1016/j.soilbio.2005.01.009	2005
Genetics	Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp.	Dong X, Kleiner M, Sharp CE, Thorson E, Li C, Liu D, Strous M.	Front Microbiol	10.3389/fmicb.2017.01461	2017
	The Rhodobacter sphaeroides 2.4.1 rho gene: expression and genetic analysis of structure and function.	Gomelsky M, Kaplan S.	J Bacteriol	10.1128/jb.178.7.1946-1954.1996	1996
	The Modification of Regulatory Circuits Involved in the Control of Polyhydroxyalkanoates Metabolism to Improve Their Production.	Velazquez-Sanchez C, Espin G, Pena C, Segura D.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00386	2020
Metabolism	Steady-state nitrogen isotope effects of N2 and N2O production in Paracoccus denitrificans.	Barford CC, Montoya JP, Altabet MA, Mitchell R.	Appl Environ Microbiol	10.1128/aem.65.3.989-994.1999	1999
Metabolism	Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development.	Moskvin OV, Gomelsky L, Gomelsky M.	J Bacteriol	10.1128/jb.187.6.2148-2156.2005	2005
Metabolism	Iron corrosion induced by nonhydrogenotrophic nitrate-reducing Prolixibacter sp. strain MIC1-1.	Iino T, Ito K, Wakai S, Tsurumaru H, Ohkuma M, Harayama S.	Appl Environ Microbiol	10.1128/aem.03741-14	2015
	Molecular analysis of the poly(3-hydroxyalkanoate) synthase gene from a methylotrophic bacterium, Paracoccus denitrificans.	Ueda S, Yabutani T, Maehara A, Yamane T.	J Bacteriol	10.1128/jb.178.3.774-779.1996	1996
	Growth-Associated Production of Poly(3-Hydroxyvalerate) from n-Pentanol by a Methylotrophic Bacterium, Paracoccus denitrificans.	Yamane T, Chen X, Ueda S.	Appl Environ Microbiol	10.1128/aem.62.2.380-384.1996	1996
Metabolism	Hierarchical regulation of photosynthesis gene expression by the oxygen-responsive PrrBA and AppA-PpsR systems of Rhodobacter sphaeroides.	Gomelsky L, Moskvin OV, Stenzel RA, Jones DF, Donohue TJ, Gomelsky M.	J Bacteriol	10.1128/jb.01094-08	2008
Pathogenicity	Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4.1.	O'Gara JP, Gomelsky M, Kaplan S.	Appl Environ Microbiol	10.1128/aem.63.12.4713-4720.1997	1997
Metabolism	Iron-dependent production of a heat-modifiable, 23,000-Mr outer membrane protein in Paracoccus denitrificans.	Wee S, Madiraju MV, Wilkinson BJ.	J Bacteriol	10.1128/jb.168.1.455-457.1986	1986
	Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.	Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.	Appl Environ Microbiol	10.1128/aem.02772-10	2011
Metabolism	Analyses of a polyhydroxyalkanoic acid granule-associated 16-kilodalton protein and its putative regulator in the pha locus of Paracoccus denitrificans.	Maehara A, Ueda S, Nakano H, Yamane T.	J Bacteriol	10.1128/jb.181.9.2914-2921.1999	1999
Metabolism	Increase in spermine content coordinated with siderophore production in Paracoccus denitrificans.	Bergeron RJ, Weimar WR.	J Bacteriol	10.1128/jb.173.7.2238-2243.1991	1991
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
	Autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination.	Smith RL, Ceazan ML, Brooks MH.	Appl Environ Microbiol	10.1128/aem.60.6.1949-1955.1994	1994
Pathogenicity	Biocompatibilities and biodegradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate)s produced by a model metabolic reaction-based system.	Napathorn SC.	BMC Microbiol	10.1186/s12866-014-0285-4	2014
	Synthesis of Poly(3-Hydroxybutyrate-Co-3-Hydroxyvalerate) from Methanol and n-Amyl Alcohol by the Methylotrophic Bacteria Paracoccus denitrificans and Methylobacterium extorquens.	Ueda S, Matsumoto S, Takagi A, Yamane T.	Appl Environ Microbiol	10.1128/aem.58.11.3574-3579.1992	1992
Metabolism	Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues.	Henderson SL, Dandie CE, Patten CL, Zebarth BJ, Burton DL, Trevors JT, Goyer C.	Appl Environ Microbiol	10.1128/aem.02993-09	2010
Metabolism	Kinetics of iron acquisition from ferric siderophores by Paracoccus denitrificans.	Bergeron RJ, Weimar WR.	J Bacteriol	10.1128/jb.172.5.2650-2657.1990	1990
Enzymology	Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil.	Dandie CE, Miller MN, Burton DL, Zebarth BJ, Trevors JT, Goyer C.	Appl Environ Microbiol	10.1128/aem.00081-07	2007
Enzymology	Pseudomonas stutzeri nitrite reductase gene abundance in environmental samples measured by real-time PCR.	Gruntzig V, Nold SC, Zhou J, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.67.2.760-768.2001	2001
Metabolism	A repressor protein, PhaR, regulates polyhydroxyalkanoate (PHA) synthesis via its direct interaction with PHA.	Maehara A, Taguchi S, Nishiyama T, Yamane T, Doi Y.	J Bacteriol	10.1128/jb.184.14.3992-4002.2002	2002
	Molecular genetic analysis suggesting interactions between AppA and PpsR in regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1.	Gomelsky M, Kaplan S.	J Bacteriol	10.1128/jb.179.1.128-134.1997	1997
	A quorum-sensing system in the free-living photosynthetic bacterium Rhodobacter sphaeroides.	Puskas A, Greenberg EP, Kaplan S, Schaefer AL.	J Bacteriol	10.1128/jb.179.23.7530-7537.1997	1997
Metabolism	Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria.	Hovanec TA, DeLong EF.	Appl Environ Microbiol	10.1128/aem.62.8.2888-2896.1996	1996
	Domain structure, oligomeric state, and mutational analysis of PpsR, the Rhodobacter sphaeroides repressor of photosystem gene expression.	Gomelsky M, Horne IM, Lee HJ, Pemberton JM, McEwan AG, Kaplan S.	J Bacteriol	10.1128/jb.182.8.2253-2261.2000	2000
Phylogeny	Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils.	Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD.	Appl Environ Microbiol	10.1128/aem.69.10.5974-5982.2003	2003
Biotechnology	Detection of Salmonella spp. in oysters by PCR.	Bej AK, Mahbubani MH, Boyce MJ, Atlas RM.	Appl Environ Microbiol	10.1128/aem.60.1.368-373.1994	1994
Enzymology	Bacteriocuprein superoxide dismutases in pseudomonads.	Steinman HM.	J Bacteriol	10.1128/jb.162.3.1255-1260.1985	1985
Metabolism	Purification and properties of a protein linked to the soluble hydrogenase of hydrogen-oxidizing bacteria.	Karst U, Suetin S, Friedrich CG.	J Bacteriol	10.1128/jb.169.5.2079-2085.1987	1987
	PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid.	Greisen K, Loeffelholz M, Purohit A, Leong D.	J Clin Microbiol	10.1128/jcm.32.2.335-351.1994	1994
	Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation.	Visser AN, Wankel SD, Frey C, Kappler A, Lehmann MF.	Front Microbiol	10.3389/fmicb.2022.927475	2022
Genetics	Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome.	Puri A, Bajaj A, Lal S, Singh Y, Lal R.	Indian J Microbiol	10.1007/s12088-021-00929-3	2021
Metabolism	Efficient simultaneous adsorption-biodegradation of high-concentrated N,N-dimethylformamide from water by Paracoccus denitrificans-graphene oxide microcomposites.	Zheng Y, Chen D, Li N, Xu Q, Li H, He J, Lu J.	Sci Rep	10.1038/srep20003	2016
Pathogenicity	Alteration of intracellular protein expressions as a key mechanism of the deterioration of bacterial denitrification caused by copper oxide nanoparticles.	Su Y, Zheng X, Chen Y, Li M, Liu K.	Sci Rep	10.1038/srep15824	2015
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
Pathogenicity	Carboxyl-modified single-walled carbon nanotubes negatively affect bacterial growth and denitrification activity.	Zheng X, Su Y, Chen Y, Wan R, Li M, Wei Y, Huang H.	Sci Rep	10.1038/srep05653	2014
Pathogenicity	Carbon nanotubes affect the toxicity of CuO nanoparticles to denitrification in marine sediments by altering cellular internalization of nanoparticle.	Zheng X, Su Y, Chen Y, Wan R, Li M, Huang H, Li X.	Sci Rep	10.1038/srep27748	2016
Metabolism	Ligand-enhanced abiotic iron oxidation and the effects of chemical versus biological iron cycling in anoxic environments.	Kopf SH, Henny C, Newman DK.	Environ Sci Technol	10.1021/es3049459	2013
Metabolism	Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512.	Fujiwara T, Fukumori Y.	J Bacteriol	10.1128/jb.178.7.1866-1871.1996	1996
Enzymology	Nitric oxide reductase (norB) genes from pure cultures and environmental samples.	Braker G, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.69.6.3476-3483.2003	2003
Enzymology	Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples.	Braker G, Fesefeldt A, Witzel KP.	Appl Environ Microbiol	10.1128/aem.64.10.3769-3775.1998	1998
Metabolism	PCR detection of genes encoding nitrite reductase in denitrifying bacteria.	Hallin S, Lindgren PE.	Appl Environ Microbiol	10.1128/aem.65.4.1652-1657.1999	1999
Metabolism	Assessing the impact of denitrifier-produced nitric oxide on other bacteria.	Choi PS, Naal Z, Moore C, Casado-Rivera E, Abruna HD, Helmann JD, Shapleigh JP.	Appl Environ Microbiol	10.1128/aem.72.3.2200-2205.2006	2006
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
	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	Comparison of methods for quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples.	Michotey V, Mejean V, Bonin P.	Appl Environ Microbiol	10.1128/aem.66.4.1564-1571.2000	2000
Metabolism	Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans.	Carlson CA, Ingraham JL.	Appl Environ Microbiol	10.1128/aem.45.4.1247-1253.1983	1983
Metabolism	Demonstration of ferric L-parabactin-binding activity in the outer membrane of Paracoccus denitrificans.	Bergeron RJ, Weimar WR, Dionis JB.	J Bacteriol	10.1128/jb.170.8.3711-3717.1988	1988
Metabolism	Growth of Pseudomonas aeruginosa on nitrous oxide.	Bazylinski DA, Soohoo CK, Hollocher TC.	Appl Environ Microbiol	10.1128/aem.51.6.1239-1246.1986	1986
Metabolism	Heterotrophic nitrification among denitrifiers.	Castignetti D, Hollocher TC.	Appl Environ Microbiol	10.1128/aem.47.4.620-623.1984	1984
Metabolism	Polyclonal antibodies recognizing the AmoB protein of ammonia oxidizers of the beta-subclass of the class Proteobacteria.	Pinck C, Coeur C, Potier P, Bock E.	Appl Environ Microbiol	10.1128/aem.67.1.118-124.2001	2001
Metabolism	Reduction of iron and synthesis of protoheme by Spirillum itersonii and other organisms.	Dailey HA, Lascelles J.	J Bacteriol	10.1128/jb.129.2.815-820.1977	1977
	Effect of Chloramphenicol on Denitrification in Flexibacter canadensis and "Pseudomonas denitrificans".	Wu Q, Knowles R.	Appl Environ Microbiol	10.1128/aem.61.2.434-437.1995	1995
Metabolism	Substrate binding site for nitrate reductase of Escherichia coli is on the inner aspect of the membrane.	Kristjansson JK, Hollocher TC.	J Bacteriol	10.1128/jb.137.3.1227-1233.1979	1979
Phylogeny	Immunological identification and distribution of dissimilatory heme cd1 and nonheme copper nitrite reductases in denitrifying bacteria.	Coyne MS, Arunakumari A, Averill BA, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.55.11.2924-2931.1989	1989
Enzymology	Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria.	Smith GB, Tiedje JM.	Appl Environ Microbiol	10.1128/aem.58.1.376-384.1992	1992
	Evaluations of the Effects of Extremely Low-Frequency Electromagnetic Fields on Growth and Antibiotic Susceptibility of Escherichia coli and Pseudomonas aeruginosa.	Segatore B, Setacci D, Bennato F, Cardigno R, Amicosante G, Iorio R.	Int J Microbiol	10.1155/2012/587293	2012
Metabolism	Control of respiration rate in non-growing cells of Paracoccus denitrificans.	Kucera I, Lampardova L, Dadak V.	Biochem J	10.1042/bj2460779	1987
Metabolism	Oscillations of nitric oxide concentration in the perturbed denitrification pathway of Paracoccus denitrificans.	Kucera I.	Biochem J	10.1042/bj2860111	1992
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
Enzymology	The prosthetic group of methanol dehydrogenase. Purification and some of its properties.	Duine JA, Frank J.	Biochem J	10.1042/bj1870221	1980
	Simultaneous Nitrification and Denitrification in Aerobic Chemostat Cultures of Thiosphaera pantotropha.	Robertson LA, van Niel EW, Torremans RA, Kuenen JG.	Appl Environ Microbiol	10.1128/aem.54.11.2812-2818.1988	1988
Metabolism	Cell biology and molecular basis of denitrification.	Zumft WG.	Microbiol Mol Biol Rev	10.1128/mmbr.61.4.533-616.1997	1997
Enzymology	The nitric oxide reductase of Paracoccus denitrificans.	Carr GJ, Ferguson SJ.	Biochem J	10.1042/bj2690423	1990
Metabolism	Alpha-tocopheryl succinate induces apoptosis by targeting ubiquinone-binding sites in mitochondrial respiratory complex II.	Dong LF, Low P, Dyason JC, Wang XF, Prochazka L, Witting PK, Freeman R, Swettenham E, Valis K, Liu J, Zobalova R, Turanek J, Spitz DR, Domann FE, Scheffler IE, Ralph SJ, Neuzil J.	Oncogene	10.1038/onc.2008.69	2008
Enzymology	Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive.	Wang Z, Vishwanathan N, Kowaliczko S, Ishii S.	Microbiol Spectr	10.1128/spectrum.04709-22	2023
Metabolism	In vitro human colonic microbiota utilises D-beta-hydroxybutyrate to increase butyrogenesis.	Sasaki K, Sasaki D, Hannya A, Tsubota J, Kondo A.	Sci Rep	10.1038/s41598-020-65561-5	2020
Metabolism	Potential of aerobic denitrification by Pseudomonas stutzeri TR2 to reduce nitrous oxide emissions from wastewater treatment plants.	Miyahara M, Kim SW, Fushinobu S, Takaki K, Yamada T, Watanabe A, Miyauchi K, Endo G, Wakagi T, Shoun H.	Appl Environ Microbiol	10.1128/aem.01983-09	2010
Metabolism	Distribution of Nitrosomonas europaea and Paracoccus denitrificans immobilized in tubular polymeric gel for nitrogen removal.	Uemoto H, Saiki H.	Appl Environ Microbiol	10.1128/aem.66.2.816-819.2000	2000
Metabolism	Nitrogen removal by tubular gel containing Nitrosomonas europaea and Paracoccus denitrificans.	Uemoto H, Saiki H.	Appl Environ Microbiol	10.1128/aem.62.11.4224-4228.1996	1996
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
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
Enzymology	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
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	2013
Enzymology	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
Enzymology	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
Biotechnology	Production of ubiquinone-10 using bacteria.	Yoshida H, Kotani Y, Ochiai K, Araki K	J Gen Appl Microbiol	10.2323/jgam.44.19	1998
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
Metabolism	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
Genetics	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
Enzymology	Cytochrome c' of Paracoccus denitrificans.	Gilmour R, Goodhew CF, Pettigrew GW	Biochim Biophys Acta	10.1016/s0005-2728(05)80208-7	1991
Enzymology	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
Metabolism	Enhancement of biological denitrification by the addition of novel sRNA Pda200 under antibiotic pressure.	Wang M, Liang Y, Li F, Shen S, Huang X, Sun Y	Bioresour Technol	10.1016/j.biortech.2022.128113	2022
	Paracoccus broussonetiae subsp. drimophilus subsp. nov., a Novel Subspecies Salt-Tolerant Endophytic Bacterium from Maize Root in Hunan.	Li X, Zhou C, Li M, Zhang Q, Su L, Li X.	Life (Basel)	10.3390/life15030354	2025
Phylogeny	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
Phylogeny	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

References

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Paracoccus denitrificans (CCUG 30144, LMG 4049, LMG 4219)

Name and taxonomic classification