Strain identifier
BacDive ID: 11310
Type strain:
Species: Collimonas arenae
Strain history: de Boer W, Centre for Terrestrial Ecology
NCBI tax ID(s): 279058 (species)
General
@ref: 15676
BacDive-ID: 11310
DSM-Number: 21398
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Collimonas arenae DSM 21398 is a mesophilic bacterium that was isolated from Acidic dune grassland soil.
NCBI tax id
- NCBI tax id: 279058
- Matching level: species
strain history
@ref | history |
---|---|
15676 | <- W. de Boer, Centre for Terrestrial Ecology, Heteren |
67772 | de Boer W, Centre for Terrestrial Ecology |
doi: 10.13145/bacdive11310.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Oxalobacteraceae
- genus: Collimonas
- species: Collimonas arenae
- full scientific name: Collimonas arenae Höppener-Ogawa et al. 2008
@ref: 15676
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Oxalobacteraceae
genus: Collimonas
species: Collimonas arenae
full scientific name: Collimonas arenae Höppener-Ogawa et al. 2008
type strain: yes
Morphology
pigmentation
- @ref: 32359
- production: yes
Culture and growth conditions
culture medium
- @ref: 15676
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15676 | positive | growth | 28 | mesophilic |
32359 | positive | growth | 20 | psychrophilic |
67772 | positive | optimum | 28 | mesophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32359 | 22599 | arabinose | + | carbon source |
32359 | 18403 | L-arabitol | + | carbon source |
32359 | 35391 | aspartate | + | carbon source |
32359 | 15740 | formate | + | carbon source |
32359 | 33984 | fucose | + | carbon source |
32359 | 24175 | galacturonate | + | carbon source |
32359 | 24265 | gluconate | + | carbon source |
32359 | 17754 | glycerol | + | carbon source |
32359 | 17596 | inosine | + | carbon source |
32359 | 37684 | mannose | + | carbon source |
32359 | 17268 | myo-inositol | + | carbon source |
32359 | 17272 | propionate | + | carbon source |
32359 | 30031 | succinate | + | carbon source |
32359 | 16704 | uridine | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32359 | catalase | + | 1.11.1.6 |
32359 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
15676 | Acidic dune grassland soil | Terschelling | Netherlands | NLD | Europe | |
60295 | (Semi-)natural grasslands | Netherlands | NLD | Europe | ||
67772 | (Semi-)Natural grassland | Netherlands | NLD | Europe | 1994 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Grassland |
#Environmental | #Terrestrial | #Soil |
#Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_2204.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_1012;98_1195;99_2204&stattab=map
- Last taxonomy: Collimonas arenae
- 16S sequence: AY281146
- Sequence Identity:
- Total samples: 420
- soil counts: 190
- aquatic counts: 142
- animal counts: 65
- plant counts: 23
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15676 | 1 | Risk group (German classification) |
67772 | 1 |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Collimonas arenae strain NCCB 100031 16S ribosomal RNA gene, partial sequence | AF530049 | 481 | ena | 279058 |
15676 | Collimonas arenae strain NCCB 100031 16S ribosomal RNA gene, partial sequence | AY281146 | 1453 | ena | 279058 |
Genome sequences
- @ref: 67772
- description: Collimonas arenae Ter10
- accession: GCA_001584165
- assembly level: complete
- database: ncbi
- NCBI tax ID: 279058
GC content
- @ref: 32359
- GC-content: 59
External links
@ref: 15676
culture collection no.: DSM 21398, CCUG 54727, LMG 23964, NCCB 100031, TER Ter10, TER 10, UCCCB19
straininfo link
- @ref: 80543
- straininfo: 111266
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18218941 | Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils. | Hoppener-Ogawa S, de Boer W, Leveau JH, van Veen JA, de Brandt E, Vanlaere E, Sutton H, Dare DJ, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijs.0.65375-0 | 2008 | Bacterial Typing Techniques, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification/physiology, Poaceae/*growth & development, Polymerase Chain Reaction/methods, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Genetics |
Phylogeny | 20935085 | Glaciimonas immobilis gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from alpine glacier cryoconite. | Zhang DC, Redzic M, Schinner F, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.028001-0 | 2010 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature | Genetics |
Phylogeny | 29906259 | Collimonas antrihumi sp. nov., isolated from a natural cave and emended description of the genus Collimonas. | Lee SD | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002855 | 2018 | Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
15676 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21398) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21398 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
32359 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 28588 | ||
60295 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54727) | https://www.ccug.se/strain?id=54727 | ||||
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 | ||||
80543 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID111266.1 | StrainInfo: A central database for resolving microbial strain identifiers |