Strain identifier

BacDive ID: 158542

Type strain: Yes

Species: Rurimicrobium arvi

Strain Designation: J107-1

Strain history: J. Kim; Kyonggi Univ., South Korea; J107-1.

NCBI tax ID(s): 2049916 (species)

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General

@ref: 65590

BacDive-ID: 158542

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Rurimicrobium arvi J107-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from farmland soil.

NCBI tax id

  • NCBI tax id: 2049916
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. Kim; Kyonggi Univ., South Korea; J107-1.

doi: 10.13145/bacdive158542.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Rurimicrobium
  • species: Rurimicrobium arvi
  • full scientific name: Rurimicrobium arvi Dahal et al. 2017

@ref: 65590

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Chitinophagales

family: Chitinophagaceae

genus: Rurimicrobium

species: Rurimicrobium arvi

strain designation: J107-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
65590negative0.5-0.65 µm0.4-0.55 µmrod-shapedno
65590coccus-shaped

colony morphology

  • @ref: 65590
  • colony size: 1-2 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A

pigmentation

  • @ref: 65590
  • production: no
  • name: flexirubin-type pigments

Culture and growth conditions

culture medium

@refnamegrowth
65590Reasoner's 2A agar (R2A)yes
65590Nutrient agar (NA)yes
65590tryptone soy agaryes
65590sorbitol MacConkey agarno
65590brain heart infusion agarno
65590veal infusion agaryes
65590LB (Luria-Bertani) MEDIUMno
65590PDAno
65590MCAno
65590sulphide indole motility mediumyes

culture temp

@refgrowthtypetemperaturerange
65590positivegrowth15-42
65590positiveoptimum20-37
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65590positivegrowth5.5-9alkaliphile
65590positiveoptimum7-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65590
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65590
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65590NaClpositiveoptimum0 %
65590NaClpositivegrowth0-0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6559085146carboxymethylcellulose-hydrolysis
65590casein+hydrolysis
6559017029chitin-hydrolysis
6559016991dna-hydrolysis
65590esculin ferric citrate-hydrolysis
655905291gelatin-hydrolysis
6559017234glucose-fermentation
6559017368hypoxanthine-hydrolysis
6559017632nitrate-reduction
6559028017starch-hydrolysis
6559027897tryptophan-energy source
6559053423tween 40-hydrolysis
6559053425tween 60-hydrolysis
6559053426tween 80-hydrolysis
6559018186tyrosine+hydrolysis
6559015318xanthine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6559015688acetoinno
6559016136hydrogen sulfideno
6559035581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
6559017234glucose-
6559015688acetoin-
6559035581indole-

enzymes

@refvalueactivityec
65590urease-3.5.1.5
65590tryptophan deaminase-4.1.99.1
65590alkaline phosphatase+3.1.3.1
65590esterase Lipase (C 8)+
65590leucine arylamidase+3.4.11.1
65590valine arylamidase+
65590acid phosphatase+3.1.3.2
65590naphthol-AS-BI-phosphohydrolase+
65590esterase (C 4)+
65590cystine arylamidase+3.4.11.3
65590lipase (C 14)-
65590trypsin-3.4.21.4
65590alpha-chymotrypsin-3.4.21.1
65590alpha-galactosidase-3.2.1.22
65590beta-galactosidase-3.2.1.23
65590beta-glucuronidase-3.2.1.31
65590beta-glucosidase-3.2.1.21
65590alpha-glucosidase-3.2.1.20
65590N-acetyl-beta-glucosaminidase-3.2.1.52
65590alpha-mannosidase-3.2.1.24
65590alpha-fucosidase-3.2.1.51
65590catalase+1.11.1.6
65590cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65590C14:00.3
    65590C16:01.5
    65590C18:00.2
    65590C10:0 iso0.1
    65590C13:0 iso2
    65590C15:0 iso33.8
    65590C17:0 iso8.8
    65590C17:0 anteiso0.2
    65590C16:0 3OH0.3
    65590iso-C14:0 3-OH0.3
    65590iso-C15:0 3-OH3.9
    65590iso-C16:0 3-OH0.2
    65590iso-C17:0 3-OH15.6
    65590iso-C15:1 G28.7
    65590iso-C15:1ω9c3
    65590C17:1 iso ω10c0.3
    65590C16:1ω7c and/or C16:1ω6c0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
65590farmland soilSuwon, Gyeonggi-DoRepublic of KoreaKORAsia37.2772126.996R2A broth
67770Farmland soil at SuwonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field

taxonmaps

  • @ref: 69479
  • File name: preview.99_80737.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4656;96_33901;97_42990;98_56185;99_80737&stattab=map
  • Last taxonomy: Rurimicrobium arvi subclade
  • 16S sequence: KY233200
  • Sequence Identity:
  • Total samples: 1357
  • soil counts: 421
  • aquatic counts: 507
  • animal counts: 114
  • plant counts: 315

Sequence information

16S sequences

  • @ref: 65590
  • description: 16S rRNA gene sequence
  • accession: KY233200
  • database: nuccore

GC content

  • @ref: 65590
  • GC-content: 47.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65590

culture collection no.: KEMB 9005-549, KACC 19167, JCM 31921

literature

  • topic: Phylogeny
  • Pubmed-ID: 29072559
  • title: Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil.
  • authors: Dahal RH, Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002452
  • year: 2017
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
65590Ram Hari Dahal, Dhiraj Kumar Chaudhary, Jaisoo KimRurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil10.1099/ijsem.0.002452IJSEM 67: 5235-5243 201729072559
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/