Strain identifier
BacDive ID: 24669
Type strain: 
Species: Arenimonas metalli
Strain Designation: CF5-1
Strain history: <- F Chen, Huzhong Agri. Univ., China
NCBI tax ID(s): 948077 (species)
version 8.1 (current version)
General
@ref: 20312
BacDive-ID: 24669
DSM-Number: 27855
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Arenimonas metalli CF5-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from From copper- iron mining powder, Hongshan iron mine.
NCBI tax id
- NCBI tax id: 948077
- Matching level: species
strain history
| @ref | history |
|---|---|
| 20312 | <- KCTC <- F. Chen et al., Huazhong Agricultural University, Wuhan, China |
| 67771 | <- F Chen, Huzhong Agri. Univ., China |
doi: 10.13145/bacdive24669.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Lysobacterales
- family: Lysobacteraceae
- genus: Arenimonas
- species: Arenimonas metalli
- full scientific name: Arenimonas metalli Chen et al. 2012
@ref: 20312
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Lysobacteraceae, not assigned to order
family: Lysobacteraceae
genus: Arenimonas
species: Arenimonas metalli
full scientific name: Arenimonas metalli Chen et al. 2012
strain designation: CF5-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 30350 | negative | 1.1 µm | 0.45 µm | rod-shaped | no |
| 67771 | negative |
pigmentation
- @ref: 30350
- production: yes
multimedia
- @ref: 20312
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27855.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 20312
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20312 | positive | growth | 28 | mesophilic |
| 30350 | positive | growth | 04-37 | |
| 30350 | positive | optimum | 28 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30350 | positive | growth | 06-10 | alkaliphile |
| 30350 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30350 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 30350
- spore formation: no
halophily
- @ref: 30350
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 67771
- observation: quinones: Q-8
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30350 | 21217 | L-alaninamide | + | carbon source |
| 30350 | 29987 | glutamate | + | carbon source |
| 30350 | 26271 | proline | + | carbon source |
| 30350 | 51850 | methyl pyruvate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30350 | acid phosphatase | + | 3.1.3.2 |
| 30350 | alkaline phosphatase | + | 3.1.3.1 |
| 30350 | catalase | + | 1.11.1.6 |
| 30350 | gelatinase | + | |
| 30350 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 67771 | From copper- iron mining powder, Hongshan iron mine | Daye city, Hubei province | China | CHN | Asia |
| 20312 | copper-iron mining powder | Hubei province, Daye city, Hongshan iron mine | China | CHN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
taxonmaps
- @ref: 69479
- File name: preview.99_4059.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_2057;97_2482;98_3073;99_4059&stattab=map
- Last taxonomy: Arenimonas metalli
- 16S sequence: HQ698842
- Sequence Identity:
- Total samples: 1698
- soil counts: 569
- aquatic counts: 849
- animal counts: 242
- plant counts: 38
Safety information
risk assessment
- @ref: 20312
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20312
- description: Arenimonas metalli CF5-1 16S ribosomal RNA gene, partial sequence
- accession: HQ698842
- length: 1506
- database: ena
- NCBI tax ID: 1384056
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Arenimonas metalli CF5-1 | GCA_000747155 | contig | ncbi | 1384056 |
| 66792 | Arenimonas metalli CF5-1 | 1384056.3 | wgs | patric | 1384056 |
| 66792 | Arenimonas metalli CF5-1 | 2645728050 | draft | img | 1384056 |
GC content
- @ref: 20312
- GC-content: 70.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 87.682 | yes |
| gram-positive | no | 98.479 | yes |
| anaerobic | no | 99.056 | yes |
| halophile | no | 91.999 | yes |
| spore-forming | no | 98.142 | yes |
| glucose-util | yes | 82.632 | no |
| thermophile | no | 98.631 | no |
| aerobic | yes | 88.163 | yes |
| flagellated | no | 95.024 | yes |
| glucose-ferment | no | 90.002 | no |
External links
@ref: 20312
culture collection no.: DSM 27855, CCTCC AB 2010449, CGMCC 1.10787, KCTC 23460, KCTC 23904
straininfo link
- @ref: 88508
- straininfo: 403240
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21930678 | Arenimonas metalli sp. nov., isolated from an iron mine. | Chen F, Shi Z, Wang G | Int J Syst Evol Microbiol | 10.1099/ijs.0.034132-0 | 2011 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Iron, Mining, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification | Genetics |
| Phylogeny | 22493175 | Arenimonas daechungensis sp. nov., isolated from the sediment of a eutrophic reservoir. | Huy H, Jin L, Lee YK, Lee KC, Lee JS, Yoon JH, Ahn CY, Oh HM | Int J Syst Evol Microbiol | 10.1099/ijs.0.035410-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 28456894 | Arenimonas alkanexedens sp. nov., isolated from a frozen soil sample. | Zhu J, Wang HM, Zhang Q, Dong WW, Kong DL, Wang YW, Song JL, Jiang X, Zhao SM, Zhang W, Ruan ZY | Antonie Van Leeuwenhoek | 10.1007/s10482-017-0876-9 | 2017 | Bacteria/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, *DNA, Bacterial, Fatty Acids, Phospholipids, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 | |||
| 20312 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27855 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27855) | |||
| 30350 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26691 | 28776041 | |
| 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) | https://diaspora-project.de/progress.html#genomes | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | https://microbeatlas.org/ | |||
| 88508 | 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 | 10.60712/SI-ID403240.1 |