Strain identifier
BacDive ID: 13927
Type strain: 
Species: Rhodocyclus gracilis
Strain Designation: 3760
Strain history: <- N. Pfennig, 3760 (deposited as a strain of Rhodocyclus tenuis)
NCBI tax ID(s): 1066 (species)
version 8.1 (current version)
General
@ref: 2082
BacDive-ID: 13927
DSM-Number: 110
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Rhodocyclus gracilis 3760 is an anaerobe, mesophilic bacterium that was isolated from dystrophic pond.
NCBI tax id
- NCBI tax id: 1066
- Matching level: species
strain history
- @ref: 2082
- history: <- N. Pfennig, 3760 (deposited as a strain of Rhodocyclus tenuis)
doi: 10.13145/bacdive13927.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Rhodocyclales
- family: Rhodocyclaceae
- genus: Rhodocyclus
- species: Rhodocyclus gracilis
- full scientific name: Rhodocyclus gracilis Kyndt et al. 2022
@ref: 2082
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Rhodocyclales
family: Rhodocyclaceae
genus: Rhodocyclus
species: Rhodocyclus gracilis
full scientific name: Rhodocyclus gracilis Kyndt et al.
strain designation: 3760
type strain: no
Culture and growth conditions
culture medium
- @ref: 2082
- name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
- growth: yes
- link: https://mediadive.dsmz.de/medium/27
- composition: 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: 2082
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 2082
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 2082
- sample type: dystrophic pond
- geographic location: Black Forest, Nonnenmattweiher
- country: Germany
- origin.country: DEU
- continent: Europe
- latitude: 47.7944
- longitude: 7.7993
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Pond (small)
taxonmaps
- @ref: 69479
- File name: preview.99_167130.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_12982;97_15762;98_109716;99_167130&stattab=map
- Last taxonomy: Rhodocyclus
- 16S sequence: D16209
- Sequence Identity:
- Total samples: 573
- soil counts: 71
- aquatic counts: 465
- animal counts: 14
- plant counts: 23
Safety information
risk assessment
- @ref: 2082
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 2082
- description: Rhodocyclus tenuis gene for 16S ribosomal RNA, partial sequence, strain: DSM110
- accession: D16209
- length: 1460
- database: ena
- NCBI tax ID: 1066
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhodocyclus gracilis DSM 110 | GCA_009617575 | contig | ncbi | 2929842 |
| 66792 | Rhodocyclus tenuis strain DSM 110 | 1066.14 | wgs | patric | 1066 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 95.894 | no |
| flagellated | yes | 88.25 | no |
| gram-positive | no | 99.189 | no |
| anaerobic | yes | 93.379 | yes |
| aerobic | no | 95.826 | no |
| halophile | no | 98.127 | no |
| spore-forming | no | 92.289 | no |
| thermophile | no | 92.555 | yes |
| glucose-util | no | 70.234 | no |
| glucose-ferment | no | 86.448 | no |
External links
@ref: 2082
culture collection no.: DSM 110, Pfennig 3760, JCM 35354
straininfo link
- @ref: 83101
- straininfo: 47061
literature
- topic: Phylogeny
- Pubmed-ID: 35336224
- title: 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.
- authors: Kyndt JA, Aviles FA, Imhoff JF, Kunzel S, Neulinger SC, Meyer TE
- journal: Microorganisms
- DOI: 10.3390/microorganisms10030649
- year: 2022
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 2082 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-110 | |
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 83101 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47061.1 | StrainInfo: A central database for resolving microbial strain identifiers |