Name: Rhodocyclus gracilis 3760
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13927

Type strain:

Species: Rhodocyclus gracilis

Strain Designation: 3760

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

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

NCBI tax ID(s): 1066 (species)

SI-ID 47061

DSM 110

Section

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

anaerobe
mesophilic
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	*Betaproteobacteria*
	Order	*Rhodocyclales*
	Family	*Rhodocyclaceae*
	Genus	*Rhodocyclus*
	Species	**Rhodocyclus gracilis**
	Full Scientific Name (LPSN)	Rhodocyclus gracilis Kyndt et al. 2022

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2082]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #2082]

Culture medium growth

[Ref.: #2082]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2082]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2082]			growth	25 °C

[Ref.: #2082]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2082]

Oxygen tolerance

anaerobe

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

[Ref.: #2082]	Sample type/isolated from	dystrophic pond
[Ref.: #2082]	Geographic location (country and/or sea, region)	Black Forest, Nonnenmattweiher
[Ref.: #2082]	Country	Germany
[Ref.: #2082]	Country ISO 3 Code	DEU
[Ref.: #2082]	Continent	Europe
[Ref.: #2082]	Geographic location	47.7944°/7.7993°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Pond (small)

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #2082]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #2082]	Rhodocyclus tenuis gene for 16S ribosomal RNA, partial sequence, strain: DSM110	D16209	1460	ENA	1066 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodocyclus gracilis DSM 110	GCA_009617575	contig	GenBank	2929842 tax ID	*
[Ref.: #66792]	Rhodocyclus tenuis strain DSM 110	1066.14	wgs	PATRIC	1066 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodocyclus tenuis strain DSM 110 PATRIC: 1066.14
[Ref.: #69480]	motile	yes	95.894	no
[Ref.: #69480]	flagellated	yes	88.25	no
[Ref.: #69480]	gram-positive	no	99.189	no
[Ref.: #69480]	anaerobic	yes	93.379	yes
[Ref.: #69480]	aerobic	no	95.826	no
[Ref.: #69480]	halophile	no	98.127	no
[Ref.: #69480]	spore-forming	no	92.289	no
[Ref.: #69480]	thermophile	no	92.555	yes
[Ref.: #69480]	glucose-util	no	70.234	no
[Ref.: #69480]	glucose-ferment	no	86.448	no

Availability in culture collections External links

[Ref.: #2082]

Culture collection no.

DSM 110, Pfennig 3760, JCM 35354

[Ref.: #83101]

SI-ID 47061

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#83101

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-ID47061.1 )

* These data were automatically processed and therefore are not curated

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Rhodocyclus tenuis strain DSM 110

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