Strain identifier
BacDive ID: 17872
Type strain: 
Species: Geminicoccus roseus
Strain Designation: D2-3
Strain history: Fösel, B. Deptartment of Ecological Microbiology, University Bayreuth
NCBI tax ID(s): 1089551 (strain), 404900 (species)
version 8.1 (current version)
General
@ref: 7776
BacDive-ID: 17872
DSM-Number: 18922
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Geminicoccus roseus D2-3 is a mesophilic, Gram-negative bacterium that was isolated from biofilter of a recirculating marine aquaculture system .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 404900 | species |
| 1089551 | strain |
strain history
| @ref | history |
|---|---|
| 7776 | <- B. Fösel, Dept. Ecological Microbiology, Univ. Bayreuth, Germany; D2-3 |
| 67772 | Fösel, B. Deptartment of Ecological Microbiology, University Bayreuth |
doi: 10.13145/bacdive17872.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Geminicoccaceae
- genus: Geminicoccus
- species: Geminicoccus roseus
- full scientific name: Geminicoccus roseus Foesel et al. 2008
@ref: 7776
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Geminicoccaceae
genus: Geminicoccus
species: Geminicoccus roseus
full scientific name: Geminicoccus roseus Foesel et al. 2008 emend. Proença et al. 2018
strain designation: D2-3
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.987
multimedia
- @ref: 66793
- multimedia content: EM_DSM_18922_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 7776
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 7776 | positive | growth | 30 | mesophilic |
| 67772 | positive | optimum | 30-35 | mesophilic |
| 67772 | positive | minimum | 15 | psychrophilic |
| 67772 | positive | maximum | 45 | thermophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 67772 | positive | maximum | 11.0 | alkaliphile |
| 67772 | positive | optimum | 8.0 | |
| 67772 | positive | minimum | 5.5 |
Physiology and metabolism
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.956
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 7776 | biofilter of a recirculating marine aquaculture system (digestion basin) | Rehovot | Israel | ISR | Asia | ||
| 67772 | Biofilter of a recirculating marine aquaculture system (digestion basin) | Central District, Rehovot | Israel | ISR | Asia | 31.898 | 34.8081 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Bioremediation | #Biofilter |
| #Engineered | #Industrial | #Machines and devices |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_5812.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16612;96_2786;97_3424;98_4324;99_5812&stattab=map
- Last taxonomy: Geminicoccus roseus subclade
- 16S sequence: AM403172
- Sequence Identity:
- Total samples: 9087
- soil counts: 4823
- aquatic counts: 1563
- animal counts: 1543
- plant counts: 1158
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 7776 | 1 | Risk group (German classification) |
| 67772 | 1 |
Sequence information
16S sequences
- @ref: 7776
- description: Geminicoccus roseus partial 16S rRNA gene, type strain D2-3T
- accession: AM403172
- length: 1352
- database: ena
- NCBI tax ID: 404900
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geminicoccus roseus DSM 18922 | 1089551.3 | wgs | patric | 1089551 |
| 66792 | Geminicoccus roseus DSM 18922 | 2517093010 | draft | img | 1089551 |
| 67772 | Geminicoccus roseus DSM 18922 | GCA_000427665 | scaffold | ncbi | 1089551 |
GC content
- @ref: 7776
- GC-content: 60.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 82 | no |
| motile | yes | 72.98 | no |
| flagellated | no | 78.919 | no |
| gram-positive | no | 98.346 | no |
| anaerobic | no | 97.773 | no |
| aerobic | yes | 86.72 | no |
| halophile | no | 82.376 | no |
| spore-forming | no | 92.178 | no |
| glucose-util | yes | 91.333 | no |
| thermophile | no | 98.969 | no |
| glucose-ferment | no | 89.461 | no |
External links
@ref: 7776
culture collection no.: DSM 18922, ATCC BAA 1445, UCCCB102
straininfo link
- @ref: 86861
- straininfo: 403064
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17643894 | Geminicoccus roseus gen. nov., sp. nov., an aerobic phototrophic Alphaproteobacterium isolated from a marine aquaculture biofilter. | Foesel BU, Gossner AS, Drake HL, Schramm A | Syst Appl Microbiol | 10.1016/j.syapm.2007.05.005 | 2007 | Aerobiosis, Alphaproteobacteria/chemistry/*classification/genetics/*isolation & purification, Aquaculture, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, Carotenoids/analysis, Cell Membrane/chemistry, Cytochromes b/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Organic Chemicals/metabolism, Phototrophic Processes, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, *Water Microbiology | Genetics |
| Phylogeny | 29325988 | Arboriscoccus pini gen. nov., sp. nov., an endophyte from a pine tree of the class Alphaproteobacteria, emended description of Geminicoccus roseus, and proposal of Geminicoccaceae fam. nov. | Proenca DN, Whitman WB, Varghese N, Shapiro N, Woyke T, Kyrpides NC, Morais PV | Syst Appl Microbiol | 10.1016/j.syapm.2017.11.006 | 2017 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pinus/*microbiology, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Enzymology |
| Phylogeny | 36386637 | Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts. | Jiang ZM, Deng Y, Han XF, Su J, Wang H, Yu LY, Zhang YQ | Front Microbiol | 10.3389/fmicb.2022.1034816 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7776 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18922) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18922 | |||
| 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) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 67772 | Curators of the UCCCB | https://ucccb.uc.pt/ | ||||
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 86861 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403064.1 | StrainInfo: A central database for resolving microbial strain identifiers |