Strain identifier

BacDive ID: 17444

Type strain: Yes

Species: Arenimonas donghaensis

Strain Designation: HO3-R19

Strain history: <- B.-Y. Kim; HO3-R19

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
1121014strain
375061species

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

@refgrowthtypetemperaturerange
7407positivegrowth28mesophilic
31832positivegrowth04-37
31832positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
31832positivegrowth07-09alkaliphile
31832positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 31832
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31832
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31832NaClpositivegrowth0-3 %
31832NaClpositiveoptimum1.5 %

metabolite utilization

  • @ref: 31832
  • Chebi-ID: 5291
  • metabolite: gelatin
  • utilization activity: +
  • kind of utilization tested: carbon source

enzymes

@refvalueactivityec
31832acid phosphatase+3.1.3.2
31832alkaline phosphatase+3.1.3.1
31832catalase+1.11.1.6
31832gelatinase+
31832cytochrome 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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenimonas donghaensis DSM 18148 = HO3-R19GCA_000743535contigncbi1121014
66792Arenimonas donghaensis DSM 18148 = HO3-R191121014.3wgspatric1121014
66792Arenimonas donghaensis DSM 18148, HO3-R192597489983completeimg1121014
66792Arenimonas donghaensis DSM 18148, HO3-R192574179743draftimg1121014

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473240Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand.Kwon SW, Kim BY, Weon HY, Baek YK, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.64457-02007Bacterial 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, TemperatureGenetics
Phylogeny18048725Arenimonas 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 PDInt J Syst Evol Microbiol10.1099/ijs.0.64975-02007Bacterial 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 & purificationGenetics
Phylogeny22493175Arenimonas 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 HMInt J Syst Evol Microbiol10.1099/ijs.0.035410-02012Bacterial 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 & purificationGenetics
Phylogeny25731739Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.Zhang SY, Xiao W, Xia YS, Wang YX, Cui XL, Zhang NMAntonie Van Leeuwenhoek10.1007/s10482-015-0409-32015Bacterial 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/metabolismMetabolism
26380644High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T).Chen F, Wang H, Cao Y, Li X, Wang GStand Genomic Sci10.1186/s40793-015-0055-42015
Phylogeny26801058Arenimonas aestuarii sp. nov., isolated from estuary sediment.Jeong HI, Jin HM, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0009132016
Phylogeny28456894Arenimonas 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 ZYAntonie Van Leeuwenhoek10.1007/s10482-017-0876-92017Bacteria/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, *DNA, Bacterial, Fatty Acids, Phospholipids, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome
Phylogeny28853685Arenimonas soli sp. nov., isolated from saline-alkaline soil.Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ, Wu XLInt J Syst Evol Microbiol10.1099/ijsem.0.0020262017Bacterial 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 & purificationTranscriptome
Phylogeny29745867Arenimonas halophila sp. nov., isolated from soil.Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0028012018Bacterial 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 & purificationTranscriptome
Phylogeny30040064Arenimonas caeni sp. nov., isolated from activated sludge.Liu H, Ren L, Lu P, Sun L, Zhu GInt J Syst Evol Microbiol10.1099/ijsem.0.0029372018Bacterial 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 & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7407Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18148)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18148
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31832Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2809828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69479João 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
86440Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396980.1StrainInfo: A central database for resolving microbial strain identifiers