Rhodopseudomonas palustris (DSM 8283, ATCC 33872, DSM 5869)

Name: Rhodopseudomonas palustris (DSM 8283, ATCC 33872, DSM 5869)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1822

Type strain

Strain Designation R1

Culture col. no. DSM 8283 ATCC 33872 DSM 5869 R1 NBRC 16661 4 more

NCBI tax ID(s) 1076

Special Collections DSMZ JCM CIP

History <- ATCC <- T. Akiba, R1 T. Akiba R1. CIP <- 1993, ATCC <- T. Akiba, Japan: strain R1, Rhodopseudomonas rutila

Links

Rhodopseudomonas palustris R1 is an anaerobe bacterium that was isolated from soil, rice field.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 40737

ATCC 33872,CIP 103836,JCM 2524,DSM 8283,DSM 5869,AS 1.2180,IFO 16661,NBRC 16661,CGMCC 1.2180

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Nitrobacteraceae

Genus Rhodopseudomonas

Species Rhodopseudomonas palustris

Full scientific name Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 (Approved Lists 1980)

Synonyms (2)

Rhodopseudomonas rutila
"Rhodobacillus palustris"

BacDive ID	Other strains from **Rhodopseudomonas palustris** (6)	Type strain
168493	R. palustris Pa16, 2.1.6, ATH 2.1.6, ATCC 17001, BCRC ... (type strain)
1819	R. palustris 7850, DSM 127, Pfennig 7850
1821	R. palustris Klemme S1, S-1, DSM 131
100656	R. palustris SF000326(FSU),
100657	R. palustris SF000717(FSU),
169288	R. palustris 1850, DSM 126, Pfennig 1850

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.319
125439	negative	99.2

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3224	R 8 A H MEDIUM (DSMZ Medium 651)	Medium recipe at MediaDive	Name: R 8 A H MEDIUM (DSMZ Medium 651) Composition: Malic acid 2.5 g/l (NH4)2SO4 1.25 g/l Yeast extract 1.0 g/l K2HPO4 0.9 g/l KH2PO4 0.6 g/l MgSO4 x 7 H2O 0.2 g/l Na2-EDTA 0.02 g/l Fe(III) citrate 0.003 g/l Thiamine-HCl x 2 H2O 0.003 g/l Nicotinamide 0.0015 g/l Nicotinic acid 0.0015 g/l EDTA 0.0005 g/l CaCl2 x 2 H2O 0.0002 g/l Biotin 6e-05 g/l MnSO4 x H2O 2e-05 g/l (NH4)6Mo7O24 x 4 H2O 2e-05 g/l H3BO3 1e-05 g/l CuSO4 x 5 H2O 1e-05 g/l ZnSO4 1e-05 g/l Distilled water
38476	MEDIUM 69 - for Rhodopseudomonas palustris		Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (0.070 g);E.D.T.A (0.020 g);Yeast extract (1.000 g);Ammonium sulphate (1.250 g);Ferric citrate (0.010 g);Potassium di-hydrogen phosphate (0.600g)
121520	CIP Medium 69	Medium recipe at CIP
3224	RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)	Medium recipe at MediaDive	Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
3224	positive	growth	28
38476	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
3224	anaerobe
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		96.7

Observation

67770

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	quinate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	threonine metabolism	100	10 of 10
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	gallate degradation	100	5 of 5
66794	propionate fermentation	100	10 of 10
66794	cyanate degradation	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	gluconeogenesis	100	8 of 8
66794	adipate degradation	100	2 of 2
66794	photosynthesis	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	tyrosine metabolism	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	propanol degradation	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	alanine metabolism	82.76	24 of 29
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	methionine metabolism	76.92	20 of 26
66794	urea cycle	76.92	10 of 13
66794	tryptophan metabolism	76.32	29 of 38
66794	toluene degradation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	chlorophyll metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	lipid metabolism	70.97	22 of 31
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	oxidative phosphorylation	69.23	63 of 91
66794	histidine metabolism	68.97	20 of 29
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	sulfoquinovose degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	phenol degradation	65	13 of 20
66794	lysine metabolism	64.29	27 of 42
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	nitrate assimilation	55.56	5 of 9
66794	pyrimidine metabolism	55.56	25 of 45
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	pantothenate biosynthesis	50	3 of 6
66794	carnitine metabolism	50	4 of 8
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	degradation of sugar acids	48	12 of 25
66794	polyamine pathway	47.83	11 of 23
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	cholesterol biosynthesis	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	degradation of hexoses	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine betaine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	methanogenesis from CO2	25	3 of 12
66794	vitamin E metabolism	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
3224	soil, rice field	Japan	JPN	Asia
67770	Soil in rice field
121520	Environment, Soil, rice field	Japan	JPN	Asia	1980

Taxonmaps

69479

Global distribution of 16S sequence AB598740 (>99% sequence identity) for Rhodopseudomonas from Microbeatlas

Aquatic Samples	2339
Soil Samples	2712
Animal Samples	2268
Plant Samples	1509
Total Samples	8828

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3224	1	Risk group (German classification) According to TRBA 466
121520	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	ASM1341584v1 assembly for Rhodopseudomonas palustris CGMCC 1.2180	complete	GCA_013415845	1076.68		1076	99.06
66792	Rhodopseudomonas palustris R1, DSM 8283	complete			2516653015	1076	56.52
66792	ASM354714v1 assembly for Rhodopseudomonas palustris R1	scaffold	GCA_003547145	1076.32	2838991096	1076	54.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Rhodopseudomonas palustris gene for 16S rRNA, partial sequence, strain: JCM 2524	AB598740	1411		1076

GC content

@ref	GC-content (mol%)	Method
3224	67.6	thermal denaturation, midpoint method (Tm)
3224	65.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodopseudomonas palustris CGMCC 1.2180
NCBI: GCA_013415845

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	motility	BacteriaNetⓘ	yes	75.10	no
125439	spore_formation	BacteriaNetⓘ	no	96.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodopseudomonas palustris CGMCC 1.2180
NCBI: GCA_013415845.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.32	no
125438	anaerobic	anaerobicⓘ	no	64.99	no
125438	aerobic	aerobicⓘ	yes	69.40	no
125438	spore-forming	spore-formingⓘ	no	87.90	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	76.65	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A distinct pathway for tetrahymanol synthesis in bacteria.	Banta AB, Wei JH, Welander PV.	Proc Natl Acad Sci U S A	10.1073/pnas.1511482112	2015
	Non-Respiratory Extracellular Electron Transfer Competes with Nitrogenase for Electrons in Rhodopseudomonas Palustris.	Liu X, Qi P, Fan W, Liu W, Li X, Nie Y, Wu XL.	Adv Sci (Weinh)	10.1002/advs.202501376	2025
	Enhancement of photo-driven biomethanation under visible light by nano-engineering of Rhodopseudomonas palustris.	Chen MY, Fang Z, Xu LX, Zhou D, Yang XJ, Zhu HJ, Yong YC.	Bioresour Bioprocess	10.1186/s40643-021-00383-5	2021
	The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis.	Guardia AE, Wagner A, Busalmen JP, Di Capua C, Cortez N, Beligni MV.	BMC Microbiol	10.1186/s12866-022-02685-w	2022
	Syntrophic interspecies electron transfer drives carbon fixation and growth by Rhodopseudomonas palustris under dark, anoxic conditions.	Liu X, Huang L, Rensing C, Ye J, Nealson KH, Zhou S.	Sci Adv	10.1126/sciadv.abh1852	2021
	Light-independent anaerobic microbial oxidation of manganese driven by an electrosyntrophic coculture.	Huang L, Liu X, Rensing C, Yuan Y, Zhou S, Nealson KH.	ISME J	10.1038/s41396-022-01335-3	2023
	Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture.	Huang L, Liu X, Zhang Z, Ye J, Rensing C, Zhou S, Nealson KH.	ISME J	10.1038/s41396-021-01078-7	2022
	Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review.	Stephens S, Mahadevan R, Allen DG.	Front Bioeng Biotechnol	10.3389/fbioe.2020.610723	2020
Genetics	Complete genome sequence of polylactic acid degrading Rhodopseudomonas palustris strain R1 isolated from rice field soil.	Ito L, Masui M, Galipon J, Arakawa K.	Microbiol Resour Announc	10.1128/mra.00814-24	2024
	Comparative computational study to augment UbiA prenyltransferases inherent in purple photosynthetic bacteria cultured from mangrove microbial mats in Qatar for coenzyme Q₁₀ biosynthesis.	George DM, Ramadoss R, Mackey HR, Vincent AS.	Biotechnol Rep (Amst)	10.1016/j.btre.2022.e00775	2022
	An overview of anoxygenic phototrophic bacteria and their applications in environmental biotechnology for sustainable Resource recovery.	George DM, Vincent AS, Mackey HR.	Biotechnol Rep (Amst)	10.1016/j.btre.2020.e00563	2020
Metabolism	Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas.	McGrath JE, Harfoot CG	Appl Environ Microbiol	10.1128/aem.63.8.3333-3335.1997	1997

References

#3224	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 8283
#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 )
#38476	; Curators of the CIP;
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 .
#121520	Collection of Institut Pasteur ; Curators of the CIP; CIP 103836
#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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Rhodopseudomonas palustris (DSM 8283, ATCC 33872, DSM 5869)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013415845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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