Rhodopseudomonas rhenobacensis (DSM 12706, R1, CIP 106682)

Name: Rhodopseudomonas rhenobacensis (DSM 12706, R1, CIP 106682)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1827

Type strain

Strain Designation R1, Rb

Culture col. no. DSM 12706 R1 CIP 106682 Rb

NCBI tax ID(s) 87461

Special Collections DSMZ CIP

History <- J.-H. Klemme; R1 2000, J.H. Klemme, IFMB, Univ. Bonn, Germany: strain Rb CIP <- 2000, J.H. Klemme, Bonn Univ., Bonn, Germany: strain Rb

Links

Rhodopseudomonas rhenobacensis R1 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from sediment of eutrophic pond.

Gram-negative motile rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49345

DSM 12706,CIP 106682

@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 rhenobacensis

Full scientific name Rhodopseudomonas rhenobacensis Hougardy et al. 2000

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122196	negative	rod-shaped
125439	negative		98.8
125438	negative		97.819

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4793	ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26)	Medium recipe at MediaDive	Name: ACID RHODOSPIRILLACEAE MEDIUM (DSMZ Medium 26) Composition: Disodium succinate 1.0 g/l Ammonium acetate 0.5 g/l KH2PO4 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.2 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
39553	MEDIUM 374 - for Rhodopseudomonas rhenobacensis		Distilled water make up to (944.500 ml);Agar (20.000 g);Yeast extract (1.000 ml);Solution A - M00720 (40.000 ml);Solution B - M00721 (10.000 ml);Solution C - M00722 (2.000 ml);Solution D - M00723 (1.000 ml);Solution E - M00724 (1.500 ml);Solution trace el
122196	CIP Medium 374	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4793	positive	growth	28	mesophilic
39553	positive	growth	30	mesophilic
122196	positive	growth	15-30
122196	negative	growth	5
122196	negative	growth	37
122196	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4793	anaerobe
122196	microaerophile
125439	obligate aerobe	99.6

Spore formation

@ref	Spore formation	Confidence
125439		97.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122196	NaCl	positive	growth	0-4 %
122196	NaCl		growth	6 %
122196	NaCl		growth	8 %
122196	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122196	16947 ChEBI	citrate	-	carbon source
122196	4853 ChEBI	esculin	-	hydrolysis
122196	17234 ChEBI	glucose	+/-	degradation
122196	17632 ChEBI	nitrate	+	reduction
122196	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122196	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122196	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122196	15688 ChEBI	acetoin	-
122196	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
122196	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122196	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122196	gamma-glutamyltransferase	+	2.3.2.2
122196	gelatinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122196	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
122196	ornithine decarboxylase	-	4.1.1.17
122196	oxidase	+
122196	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122196	tryptophan deaminase	-
122196	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

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
122196	-	-	+	+	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4793	sediment of eutrophic pond	Rheinbach	Germany	DEU	Europe
122196	Environment, Eutrophic freshwater pond	Bonn	Germany	DEU	Europe	1995

Taxonmaps

69479

Global distribution of 16S sequence AB087719 (>99% sequence identity) for Rhodopseudomonas from Microbeatlas

Aquatic Samples	158
Soil Samples	280
Animal Samples	55
Plant Samples	62
Total Samples	555

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4793	1	Risk group (German classification) According to TRBA 466
122196	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	ASM1420312v1 assembly for Rhodopseudomonas rhenobacensis DSM 12706	scaffold	GCA_014203125	87461.3	2861707373	87461	62.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4793	Rhodopseudomonas rhenobacensis gene for 16S rRNA, complete sequence	AB087719	1485		87461

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodopseudomonas rhenobacensis DSM 12706
NCBI: GCA_014203125

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	yes	66.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodopseudomonas rhenobacensis DSM 12706
NCBI: GCA_014203125.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.82	no
125438	anaerobic	anaerobicⓘ	no	75.35	no
125438	aerobic	aerobicⓘ	yes	63.43	no
125438	spore-forming	spore-formingⓘ	no	88.32	no
125438	thermophilic	thermophileⓘ	no	95.50	yes
125438	flagellated	motile2+ⓘ	yes	80.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
Phylogeny	Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris.	Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.026815-0	2011

References

#4793	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12706
#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 )
#39553	; 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) .
#68382	Automatically annotated from API zym .
#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 .
#122196	Collection of Institut Pasteur ; Curators of the CIP; CIP 106682
#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 rhenobacensis (DSM 12706, R1, CIP 106682)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014203125

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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