Strain identifier

BacDive ID: 7617

Type strain: Yes

Species: Arthrobacter humicola

Strain Designation: KV-653

Strain history: NRRL B-24479 <-- S. ?mura KV-653.

NCBI tax ID(s): 409291 (species)

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General

@ref: 18053

BacDive-ID: 7617

DSM-Number: 25587

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, motile, rod-shaped

description: Arthrobacter humicola KV-653 is an aerobe, Gram-positive, motile bacterium that was isolated from paddy soil.

NCBI tax id

  • NCBI tax id: 409291
  • Matching level: species

strain history

@refhistory
18053<- NRRL; NRRL B-24479
67770NRRL B-24479 <-- S. ?mura KV-653.

doi: 10.13145/bacdive7617.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter humicola
  • full scientific name: Arthrobacter humicola Kageyama et al. 2008

@ref: 18053

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter humicola

full scientific name: Arthrobacter humicola Kageyama et al. 2008

strain designation: KV-653

type strain: yes

Morphology

cell morphology

  • @ref: 32047
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

  • @ref: 18053
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
18053positivegrowth28
32047positivegrowth04-34
67770positivegrowth28

culture pH

  • @ref: 32047
  • ability: positive
  • type: growth
  • pH: 06-10
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 32047
  • oxygen tolerance: aerobe

halophily

  • @ref: 32047
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3204717234glucose+carbon source
3204729864mannitol+carbon source
3204728053melibiose+carbon source
3204716634raffinose+carbon source
3204726546rhamnose+carbon source
3204717992sucrose+carbon source
3204718222xylose+carbon source

enzymes

@refvalueactivityec
32047acid phosphatase+3.1.3.2
32047alpha-galactosidase+3.2.1.22
32047catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
18053paddy soilJapanJPNAsia
67770Paddy soilJapanJPNAsiaSaitama Pref.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)
#Condition#Humid

taxonmaps

  • @ref: 69479
  • File name: preview.99_625.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_386;99_625&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: AB279890
  • Sequence Identity:
  • Total samples: 5810
  • soil counts: 2849
  • aquatic counts: 364
  • animal counts: 580
  • plant counts: 2017

Safety information

risk assessment

  • @ref: 18053
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18053
  • description: Arthrobacter humicola gene for 16S rRNA, partial sequence
  • accession: AB279890
  • length: 1463
  • database: nuccore
  • NCBI tax ID: 409291

GC content

@refGC-contentmethod
1805367
6777067high performance liquid chromatography (HPLC)

External links

@ref: 18053

culture collection no.: DSM 25587, JCM 15921, NBRC 102056, NRRL B-24479

straininfo link

  • @ref: 77061
  • straininfo: 396638

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175682Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov.Kageyama A, Morisaki K, Omura S, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.64875-02008Arthrobacter/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/analysis, Genes, rRNA, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny28853684Micrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria.Toth A, Baka E, Bata-Vidacs I, Luzics S, Kosztik J, Toth E, Keki Z, Schumann P, Tancsics A, Nagy I, Sos E, Kukolya JInt J Syst Evol Microbiol10.1099/ijsem.0.0020182017Animals, Animals, Zoo/microbiology, Arthrobacter/classification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Glycolipids/chemistry, Hungary, Micrococcaceae/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Porcupines/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18053Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25587)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25587
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
32047Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2829728776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
77061Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396638.1StrainInfo: A central database for resolving microbial strain identifiers