Name: Rhodopseudomonas palustris R1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1822

Type strain:

Species: Rhodopseudomonas palustris

Strain Designation: R1

Culture col. no.: DSM 8283, ATCC 33872, DSM 5869, JCM 2524, CGMCC 1.2180, IFO 16661, NBRC 16661, CIP 103836

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

NCBI tax ID(s): 1076 (species)

SI-ID 40737

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

Special Collections

Other strains from Rhodopseudomonas palustris

Section

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

Gram-negative
anaerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Nitrobacteraceae*
	Genus	*Rhodopseudomonas*
	Species	**Rhodopseudomonas palustris**
	Full Scientific Name (LPSN)	Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 (Approved Lists 1980)

	Synonym	"Rhodobacillus* palustris"*
	Synonym	Rhodopseudomonas rutila

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.319

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3224]

Culture medium

R 8 A H MEDIUM (DSMZ Medium 651)

[Ref.: #3224]

Culture medium growth

[Ref.: #3224]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3224]

Culture medium composition

expand / minimize

[Ref.: #38476]

Culture medium

MEDIUM 69 - for Rhodopseudomonas palustris

[Ref.: #38476]

Culture medium growth

[Ref.: #38476]

Culture medium composition

expand / minimize

[Ref.: #121520]

Culture medium

CIP Medium 69

[Ref.: #121520]

Culture medium growth

[Ref.: #121520]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3224]	growth	28 °C
[Ref.: #38476]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3224]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-10

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #3224]	Sample type/isolated from	soil, rice field
[Ref.: #3224]	Country	Japan
[Ref.: #3224]	Country ISO 3 Code	JPN
[Ref.: #3224]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil in rice field

[Ref.: #121520]	Sample type/isolated from	Environment, Soil, rice field
[Ref.: #121520]	Country	Japan
[Ref.: #121520]	Country ISO 3 Code	JPN
[Ref.: #121520]	Continent	Asia
[Ref.: #121520]	Isolation date	1980
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3224]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121520]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodopseudomonas palustris gene for 16S rRNA, partial sequence, strain: JCM 2524	AB598740	1411	GenBank ENA	1076 tax ID

Genome sequence information:

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

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodopseudomonas palustris CGMCC 1.2180	GCA_013415845	complete	GenBank ENA	1076 tax ID	*
[Ref.: #66792]	Rhodopseudomonas palustris strain CGMCC 1.2180	1076.68	complete	PATRIC	1076 tax ID	*
[Ref.: #66792]	Rhodopseudomonas palustris strain R1	1076.32	wgs	PATRIC	1076 tax ID	*
[Ref.: #66792]	Rhodopseudomonas palustris R1	2838991096	draft	JGI IMG/M	1076 tax ID	*
[Ref.: #66792]	Rhodopseudomonas palustris R1, DSM 8283	2516653015	draft	JGI IMG/M	1076 tax ID	*
[Ref.: #66792]	Rhodopseudomonas palustris R1	GCA_003547145	scaffold	GenBank ENA	1076 tax ID	*

[Ref.: #3224]	GC-content	67.6 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #3224]	GC-content	65.3 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodopseudomonas palustris CGMCC 1.2180 NCBI: GCA_013415845.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodopseudomonas palustris CGMCC 1.2180 NCBI: GCA_013415845.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.319	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	64.987	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	69.403	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.895	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.999	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	76.648	no

Availability in culture collections External links

[Ref.: #3224]

Culture collection no.

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

[Ref.: #71467]

SI-ID 40737

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71467

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID40737.1 )

#121520 Collection of Institut Pasteur ; Curators of the CIP; CIP 103836
* These data were automatically processed and therefore are not curated

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Rhodopseudomonas palustris CGMCC 1.2180

Rhodopseudomonas palustris CGMCC 1.2180

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