Rhodocyclus gracilis (DSM 110, Pfennig 3760, 3760)

Name: Rhodocyclus gracilis (DSM 110, Pfennig 3760, 3760)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13927

Type strain

Strain Designation 3760

Culture col. no. DSM 110 Pfennig 3760 3760 JCM 35354

NCBI tax ID(s) 2929842

Special Collections DSMZ JCM

History <- N. Pfennig, 3760 (deposited as a strain of Rhodocyclus tenuis)

Links

Rhodocyclus gracilis 3760 is an anaerobe, mesophilic prokaryote that was isolated from dystrophic pond.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 47061

JCM 35354,DSM 110

@ref 20215

Last LPSN update 2026-02-09 11:21:16

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Rhodocyclales

Family Rhodocyclaceae

Genus Rhodocyclus

Species Rhodocyclus gracilis

Full scientific name Rhodocyclus gracilis Kyndt et al. 2022

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.6
125438	negative	98.994

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2082	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)	Range
2082	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

2082

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.3

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
2082	dystrophic pond	Black Forest, Nonnenmattweiher	Germany	DEU	Europe	47.7944	7.7993 47.7944/7.7993

Taxonmaps

69479

Global distribution of 16S sequence D16209 (>99% sequence identity) for Rhodocyclus from Microbeatlas

Aquatic Samples	465
Soil Samples	71
Animal Samples	14
Plant Samples	23
Total Samples	573

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2082	1	Risk group (German 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	ASM961757v1 assembly for Rhodocyclus gracilis DSM 110	contig	GCA_009617575	1066.14	8063021511	2929842	70.74

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2082	Rhodocyclus tenuis gene for 16S ribosomal RNA, partial sequence, strain: DSM110	D16209	1460		1066
124043	Rhodocyclus sp. strain DSM 110 16S ribosomal RNA gene, partial sequence.	OM179767	1541		2929842

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodocyclus gracilis DSM 110
NCBI: GCA_009617575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.30	no
125439	motility	BacteriaNetⓘ	yes	85.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	80.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodocyclus tenuis strain DSM 110
PATRIC: 1066.14

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.99	no
125438	anaerobic	anaerobicⓘ	yes	61.76	yes
125438	spore-forming	spore-formingⓘ	no	88.99	no
125438	aerobic	aerobicⓘ	no	67.94	no
125438	thermophilic	thermophileⓘ	no	94.84	no
125438	flagellated	motile2+ⓘ	yes	80.55	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dentiradicibacter hellwigii gen. nov., sp. nov., isolated from a secondary infected root canal in the human oral cavity.	Bartsch S, Wittmer A, Weber AK, Neumann-Schaal M, Wolf J, Gronow S, Turnbull JD, Tennert C, Hacker G, Cieplik F, Al-Ahmad A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006690	2025
Phylogeny	Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species.	Kyndt JA, Aviles FA, Imhoff JF, Kunzel S, Neulinger SC, Meyer TE	Microorganisms	10.3390/microorganisms10030649	2022

References

#2082	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 110
#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 )
#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) .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Rhodocyclus gracilis (DSM 110, Pfennig 3760, 3760)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_009617575

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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