Strain identifier
BacDive ID: 17444
Type strain:
Species: Arenimonas donghaensis
Strain Designation: HO3-R19
Strain history: <- B.-Y. Kim; HO3-R19
NCBI tax ID(s): 1121014 (strain), 375061 (species)
General
@ref: 7407
BacDive-ID: 17444
DSM-Number: 18148
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Arenimonas donghaensis HO3-R19 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seashore sand.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121014 | strain |
375061 | species |
strain history
- @ref: 7407
- history: <- B.-Y. Kim; HO3-R19
doi: 10.13145/bacdive17444.20230509.8.1
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 donghaensis
- full scientific name: Arenimonas donghaensis Kwon et al. 2007
@ref: 7407
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Xanthomonadales
family: Lysobacteraceae
genus: Arenimonas
species: Arenimonas donghaensis
full scientific name: Arenimonas donghaensis Kwon et al. 2007
strain designation: HO3-R19
type strain: yes
Morphology
cell morphology
- @ref: 31832
- gram stain: negative
- cell length: 2.25 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 31832
- production: no
Culture and growth conditions
culture medium
- @ref: 7407
- 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 |
---|---|---|---|---|
7407 | positive | growth | 28 | mesophilic |
31832 | positive | growth | 04-37 | |
31832 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31832 | positive | growth | 07-09 | alkaliphile |
31832 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 31832
- oxygen tolerance: aerobe
spore formation
- @ref: 31832
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31832 | NaCl | positive | growth | 0-3 % |
31832 | NaCl | positive | optimum | 1.5 % |
metabolite utilization
- @ref: 31832
- Chebi-ID: 5291
- metabolite: gelatin
- utilization activity: +
- kind of utilization tested: carbon source
enzymes
@ref | value | activity | ec |
---|---|---|---|
31832 | acid phosphatase | + | 3.1.3.2 |
31832 | alkaline phosphatase | + | 3.1.3.1 |
31832 | catalase | + | 1.11.1.6 |
31832 | gelatinase | + | |
31832 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7407
- sample type: seashore sand
- geographic location: Pohang
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Sandy |
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_67910.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_3434;97_36979;98_47846;99_67910&stattab=map
- Last taxonomy: Arenimonas donghaensis subclade
- 16S sequence: DQ411038
- Sequence Identity:
- Total samples: 1301
- soil counts: 497
- aquatic counts: 569
- animal counts: 143
- plant counts: 92
Safety information
risk assessment
- @ref: 7407
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7407
- description: Arenimonas donghaensis strain HO3-R19 16S ribosomal RNA gene, partial sequence
- accession: DQ411038
- length: 1499
- database: ena
- NCBI tax ID: 375061
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arenimonas donghaensis DSM 18148 = HO3-R19 | GCA_000743535 | contig | ncbi | 1121014 |
66792 | Arenimonas donghaensis DSM 18148 = HO3-R19 | 1121014.3 | wgs | patric | 1121014 |
66792 | Arenimonas donghaensis DSM 18148, HO3-R19 | 2597489983 | complete | img | 1121014 |
66792 | Arenimonas donghaensis DSM 18148, HO3-R19 | 2574179743 | draft | img | 1121014 |
GC content
- @ref: 31832
- GC-content: 65
External links
@ref: 7407
culture collection no.: DSM 18148, KACC 11381
straininfo link
- @ref: 86440
- straininfo: 396980
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17473240 | Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand. | Kwon SW, Kim BY, Weon HY, Baek YK, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64457-0 | 2007 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA/genetics, Korea, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Silicon Dioxide, *Soil Microbiology, Temperature | Genetics |
Phylogeny | 18048725 | Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oil-contaminated site. | Young CC, Kampfer P, Ho MJ, Busse HJ, Huber BE, Arun AB, Shen FT, Lai WA, Rekha PD | Int J Syst Evol Microbiol | 10.1099/ijs.0.64975-0 | 2007 | Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Petroleum/*microbiology, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Taiwan, Ubiquinone/analysis, Xanthomonadaceae/chemistry/*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 | 25731739 | Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China. | Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NM | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0409-3 | 2015 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Oryza/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolism | Metabolism |
26380644 | High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T). | Chen F, Wang H, Cao Y, Li X, Wang G | Stand Genomic Sci | 10.1186/s40793-015-0055-4 | 2015 | |||
Phylogeny | 26801058 | Arenimonas aestuarii sp. nov., isolated from estuary sediment. | Jeong HI, Jin HM, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000913 | 2016 | ||
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 |
Phylogeny | 28853685 | Arenimonas soli sp. nov., isolated from saline-alkaline soil. | Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ, Wu XL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002026 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Transcriptome |
Phylogeny | 29745867 | Arenimonas halophila sp. nov., isolated from soil. | Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002801 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Transcriptome |
Phylogeny | 30040064 | Arenimonas caeni sp. nov., isolated from activated sludge. | Liu H, Ren L, Lu P, Sun L, Zhu G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002937 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7407 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18148) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18148 | ||||
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 | ||||
31832 | 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 | 28098 | 28776041 | ||
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) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
86440 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396980.1 | StrainInfo: A central database for resolving microbial strain identifiers |