Hydrogenophaga palleronii (DSM 63, ATCC 17724, Stanier 362)

Name: Hydrogenophaga palleronii (DSM 63, ATCC 17724, Stanier 362)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2965

Type strain

Strain Designation 362

Culture col. no. DSM 63 ATCC 17724 Stanier 362 362 VKM B-1328 11 more

NCBI tax ID(s) 1349791 65655

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- IMG <- R.Y. Stanier, 362 <- N.J. Palleroni IAM 14930 <-- DSM 63 <-- IMG <-- R. Y. Stanier 362 <-- N. J. Palleroni. CIP <- 1989, DSM <- R.Y. Stanier: strain 362, Pseudomonas palleronii <- D. Davis: strain 1-6-1

Links

Hydrogenophaga palleronii 362 is an aerobe, chemoorganotroph, Gram-negative bacterium that has a nondiffusible yellow pigmentation and was isolated from water enriched for hydrogen bacteria.

Gram-negative motile rod-shaped pigmented aerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 92268

LMG 2366,ATCC 17724,CCUG 1780,CCUG 20334,CIP 103304,CCM 4454,VKM B-1328,CECT 4107,CCRC 13886,CFBP 2445,BCRC 13886,IAM 14930,ICMP 13636,KCTC 12152,NBRC 102513,JCM 21412,VTT E-991279,DSM 63

@ref 20215

Last LPSN update 2026-02-09 11:18:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Hydrogenophaga

Species Hydrogenophaga palleronii

Full scientific name Hydrogenophaga palleronii (Davis 1970) Willems et al. 1989

Synonyms (1)

Pseudomonas palleronii

BacDive ID	Other strains from **Hydrogenophaga palleronii** (3)	Type strain
2964	H. palleronii 16-0-1, 366, DSM 650, ATCC 17728
143586	H. palleronii CCUG 20338, LMG 6348
154120	H. palleronii CCUG 52433

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
23086	negative	0.6-5.5 µm	0.3-0.6 µm	rod-shaped	monotrichous
125438	negative					99
125439	negative					99.7
125439						90.6

Pigmentation

@ref	Production	Color
23086		nondiffusible yellow

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2046	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
2046	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
35525	MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas genera		Distilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
121511	CIP Medium 18	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2046	positive	growth	30
35525	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23086	aerobe
125439	obligate aerobe	98.8

Nutrition type

@ref	Type
23086	chemoorganotroph
23086	chemolithoautotroph

Spore formation

@ref	Spore formation	Confidence
125438		92.184
125439		99.1

Compound production

2046

Compoundpolyhydroxyalkanoic acids

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23086	30916 ChEBI	2-oxoglutarate	-	carbon source
23086	87997 ChEBI	3-aminobutyrate	-	growth
23086	15887 ChEBI	5-aminovaleric acid	-	growth
23086	30089 ChEBI	acetate	-	carbon source
23086	22210 ChEBI	aconitate	-	carbon source
23086	78208 ChEBI	azelaate	+	growth
23086	43799 ChEBI	butan-1-amine	-	growth
23086	17057 ChEBI	cellobiose	-	growth
23086	16947 ChEBI	citrate	-	carbon source
23086	15570 ChEBI	D-alanine	+	carbon source
23086	18333 ChEBI	D-arabitol	-	growth
23086	15824 ChEBI	D-fructose	-	growth
23086	12936 ChEBI	D-galactose	-	growth
23086	16024 ChEBI	D-mannose	-	growth
23086	65327 ChEBI	D-xylose	-	growth
23086	16000 ChEBI	ethanolamine	-	growth
23086	29805 ChEBI	glycolate	+	growth
23086	48942 ChEBI	isovalerate	+	carbon source
23086	17240 ChEBI	itaconate	+	carbon source
23086	16977 ChEBI	L-alanine	+	carbon source
23086	30849 ChEBI	L-arabinose	-	growth
23086	18287 ChEBI	L-fucose	-	growth
23086	15971 ChEBI	L-histidine	-	growth
23086	17191 ChEBI	L-isoleucine	+	carbon source
23086	15603 ChEBI	L-leucine	+	carbon source
23086	18347 ChEBI	L-norleucine	+	carbon source
23086	17295 ChEBI	L-phenylalanine	+	carbon source
23086	30924 ChEBI	L-tartrate	-	carbon source
23086	17716 ChEBI	lactose	-	growth
23086	17306 ChEBI	maltose	-	growth
23086	29864 ChEBI	mannitol	-	growth
23086	17632 ChEBI	nitrate	-	reduction
23086	16301 ChEBI	nitrite	-	reduction
23086	36405 ChEBI	norleucine	+	carbon source
23086	17774 ChEBI	pimelate	+	carbon source
23086	41865 ChEBI	sebacic acid	+	carbon source
23086	30911 ChEBI	sorbitol	-	growth
23086	17992 ChEBI	sucrose	-	growth
23086	30043 ChEBI	terephthalate	+	carbon source
23086	32528 ChEBI	turanose	-	growth
23086	31011 ChEBI	valerate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
23086	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type
23086	water enriched for hydrogen bacteria
2046	water
67770	Atmosphere of 6% O₂
121511	Environment, Water enriched for isolation of hydrogen bacteria

Taxonmaps

69479

Global distribution of 16S sequence AF078769 (>99% sequence identity) for Hydrogenophaga from Microbeatlas

Aquatic Samples	1
Soil Samples
Animal Samples
Plant Samples
Total Samples	1

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2046	1	Risk group (German classification) According to TRBA 466
121511	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
67770	ASM157122v1 assembly for Hydrogenophaga palleronii NBRC 102513	contig	GCA_001571225	1349791.3	2681813002	1349791	57.56

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Hydrogenophaga palleronii 16S ribosomal RNA gene, partial sequence	AF078769	1510	65655
20218	Hydrogenophaga palleronii 16S ribosomal RNA gene, complete sequence	AF019073	1481	65655
20218	Hydrogenophaga palleronii gene for 16S rRNA, partial sequence, strain: NBRC 102513	AB681847	1454	65655

GC content

@ref	GC-content (mol%)	Method
23086	67.0	thermal denaturation, midpoint method (Tm)
2046	66.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hydrogenophaga palleronii NBRC 102513
NCBI: GCA_001571225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	90.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hydrogenophaga palleronii NBRC 102513
PATRIC: 1349791.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	94.31	no
125438	spore-forming	spore-formingⓘ	no	92.18	no
125438	aerobic	aerobicⓘ	yes	85.52	yes
125438	thermophilic	thermophileⓘ	no	98.94	yes
125438	flagellated	motile2+ⓘ	yes	82.63	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Isolation of a bacterial strain with the ability to utilize the sulfonated azo compound 4-carboxy-4'-sulfoazobenzene as the sole source of carbon and energy.	Blumel S, Contzen M, Lutz M, Stolz A, Knackmuss HJ.	Appl Environ Microbiol	10.1128/aem.64.6.2315-2317.1998	1998
Phylogeny	Diversity and abundance of bacteria in an underground oil-storage cavity.	Watanabe K, Kodama Y, Kaku N.	BMC Microbiol	10.1186/1471-2180-2-23	2002
Phylogeny	Bacterial diversity and function of aerobic granules engineered in a sequencing batch reactor for phenol degradation.	Jiang HL, Tay JH, Maszenan AM, Tay ST.	Appl Environ Microbiol	10.1128/aem.70.11.6767-6775.2004	2004
	Differentiation of gram-negative, nonfermentative bacteria isolated from biofilters on the basis of Fatty Acid composition, quinone system, and physiological reaction profiles.	Lipski A, Klatte S, Bendinger B, Altendorf K.	Appl Environ Microbiol	10.1128/aem.58.6.2053-2065.1992	1992
Enzymology	Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient.	Feris K, Ramsey P, Frazar C, Moore JN, Gannon JE, Holben WE.	Appl Environ Microbiol	10.1128/aem.69.9.5563-5573.2003	2003
Metabolism	Biodegradation of methyl tert-butyl ether by a pure bacterial culture.	Hatzinger PB, McClay K, Vainberg S, Tugusheva M, Condee CW, Steffan RJ.	Appl Environ Microbiol	10.1128/aem.67.12.5601-5607.2001	2001
Metabolism	Production of poly-3-hydroxybutyrate (P3HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) P(3HB-co-3HV) from synthetic wastewater using Hydrogenophaga palleronii.	Venkateswar Reddy M, Mawatari Y, Yajima Y, Satoh K, Venkata Mohan S, Chang YC.	Bioresour Technol	10.1016/j.biortech.2016.03.025	2016
Phylogeny	The Impacts of Different Biological Treatments on the Transformation of Explosives Waste Contaminated Sludge.	Aburto-Medina A, Shahsavari E, Taha M, Bates A, Van Ieperen L, Ball AS.	Molecules	10.3390/molecules26164814	2021
	A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery.	Satari L, Torrent D, Ortega-Legarreta A, Latorre-Perez A, Pascual J, Porcar M, Iglesias A.	Sci Rep	10.1038/s41598-023-49017-0	2023
	Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP.	Crampon M, Soulier C, Sidoli P, Hellal J, Joulian C, Charron M, Guillemoto Q, Picot-Colbeaux G, Pettenati M.	Front Microbiol	10.3389/fmicb.2021.742000	2021
Metabolism	Syntrophic interactions during degradation of 4-aminobenzenesulfonic acid by a two species bacterial culture.	Feigel BJ, Knackmuss HJ.	Arch Microbiol	10.1007/bf00250271	1993
Metabolism	Dual labeling of Pseudomonas putida with fluorescent proteins for in situ monitoring of conjugal transfer of the TOL plasmid.	Nancharaiah YV, Wattiau P, Wuertz S, Bathe S, Mohan SV, Wilderer PA, Hausner M.	Appl Environ Microbiol	10.1128/aem.69.8.4846-4852.2003	2003
Enzymology	Comparison of bacterial community structures in the rhizoplane of tomato plants grown in soils suppressive and conducive towards bacterial wilt.	Shiomi Y, Nishiyama M, Onizuka T, Marumoto T.	Appl Environ Microbiol	10.1128/aem.65.9.3996-4001.1999	1999
Metabolism	Aerobic degradation of dinitrotoluenes and pathway for bacterial degradation of 2,6-dinitrotoluene.	Nishino SF, Paoli GC, Spain JC.	Appl Environ Microbiol	10.1128/aem.66.5.2139-2147.2000	2000
	Characterization and performance of a toluene-degrading biofilm developed on pumice stones.	Di Lorenzo A, Varcamonti M, Parascandola P, Vignola R, Bernardi A, Sacceddu P, Sisto R, de Alteriis E.	Microb Cell Fact	10.1186/1475-2859-4-4	2005
Metabolism	Enantiomeric degradation of 2-(4-Sulfophenyl)Butyrate via 4-sulfocatechol in Delftia acidovorans SPB1.	Schulz S, Dong W, Groth U, Cook AM.	Appl Environ Microbiol	10.1128/aem.66.5.1905-1910.2000	2000
Enzymology	Representative freshwater bacterioplankton isolated from Crater Lake, Oregon.	Page KA, Connon SA, Giovannoni SJ.	Appl Environ Microbiol	10.1128/aem.70.11.6542-6550.2004	2004
Enzymology	Seasonal dynamics of bacterioplankton community structure in a eutrophic lake as determined by 5S rRNA analysis.	Hofle MG, Haas H, Dominik K.	Appl Environ Microbiol	10.1128/aem.65.7.3164-3174.1999	1999
Enzymology	Diversity and seasonal variability of beta-Proteobacteria in biofilms of polluted rivers: analysis by temperature gradient gel electrophoresis and cloning.	Brummer IH, Felske A, Wagner-Dobler I.	Appl Environ Microbiol	10.1128/aem.69.8.4463-4473.2003	2003
	Two complete genome sequences of antimonite-oxidizing bacteria, Mesorhizobium sp. strain ANAO-SY3R2 and Hydrogenophaga sp. strain ANAO-22, isolated from mine tailing soil.	Yamashita Y, Hamamura N.	Microbiol Resour Announc	10.1128/mra.01073-24	2025
	Identification of active gaseous-alkane degraders at natural gas seeps.	Farhan Ul Haque M, Hernandez M, Crombie AT, Murrell JC.	ISME J	10.1038/s41396-022-01211-0	2022
Phylogeny	Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge.	Kampfer P, Schulze R, Jackel U, Malik KA, Amann R, Spring S.	Int J Syst Evol Microbiol	10.1099/ijs.0.03041-0	2005
Phylogeny	Hydrogenophaga intermedia sp. nov., a 4-aminobenzenesulfonate degrading organism.	Contzen M, Moore ER, Blumel S, Stolz A, Kampfer P.	Syst Appl Microbiol	10.1016/s0723-2020(00)80022-3	2000
Phylogeny	Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene.	Banerjee S, Tancsics A, Toth E, Revesz F, Boka K, Kriszt B	Int J Syst Evol Microbiol	10.1099/ijsem.0.004743	2021
Phylogeny	Hydrogenophaga borbori sp. nov., isolated from activated sludge.	Choi GM, Lee SY, Kim SY, Wee JH, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.003787	2020
Phylogeny	Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea.	Kim YJ, Kim MK, Weon HY, Kim HB, Yang DC	J Gen Appl Microbiol	10.2323/jgam.56.419	2010

References

#2046	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 63
#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 )
#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 )
#23086	A. Willems,J. Busse,M. Goor,B. Pot,E. Falsen,E. Jantzen,B. Hoste,M. Gillis,K. Kersters,G. Auling,J. De Ley: Hydrogenophaga, a New Genus of Hydrogen-Oxidizing Bacteria That Includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonas pseudoflava and 'Pseudomonas carboxydoflava'), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis). IJSEM 39: 319 - 333 1989 ( DOI 10.1099/00207713-39-3-319 )
#35525	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#121511	Collection of Institut Pasteur ; Curators of the CIP; CIP 103304
#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 )

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Hydrogenophaga palleronii (DSM 63, ATCC 17724, Stanier 362)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Compound production

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001571225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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