Strain identifier

BacDive ID: 140489

Type strain: Yes

Species: Kocuria pelophila

Strain Designation: RS-2-3

NCBI tax ID(s): 1638993 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 43101

BacDive-ID: 140489

keywords: 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, coccus-shaped, colony-forming

description: Kocuria pelophila RS-2-3 is an aerobe, psychrophilic, Gram-positive bacterium that forms circular colonies and was isolated from rhizosphere of a mangrove.

NCBI tax id

  • NCBI tax id: 1638993
  • Matching level: species

doi: 10.13145/bacdive140489.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Kocuria
  • species: Kocuria pelophila
  • full scientific name: Kocuria pelophila Hamada et al. 2016

@ref: 43101

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Micrococcaceae

genus: Kocuria

species: Kocuria pelophila

strain designation: RS-2-3

type strain: yes

Morphology

cell morphology

  • @ref: 43101
  • gram stain: positive
  • cell length: 1 µm
  • cell width: 1 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 43101
  • colony size: 0.5-1 mm
  • colony color: orange-yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: NBRC medium 802

Culture and growth conditions

culture medium

  • @ref: 43101
  • name: NBRC medium 802
  • growth: yes
  • composition: 1.0 % (w/v) polypeptone, 0.2 % (w/v) yeast extract, 0.1 % (w/v) MgSO4x7H2O, 1.5 % (w/v) agar, pH 7.0

culture temp

@refgrowthtypetemperaturerange
43101positiveoptimum7psychrophilic
43101positivegrowth6-9psychrophilic
43101positiveoptimum28mesophilic
43101positivegrowth15-37

Physiology and metabolism

oxygen tolerance

  • @ref: 43101
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43101
  • spore formation: no

halophily

  • @ref: 43101
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-15 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4310117234glucose+builds acid from
4310128087glycogen+builds acid from
4310165327D-xylose+builds acid from
4310117716lactose-builds acid from
4310117306maltose-builds acid from
4310116899D-mannitol-builds acid from
4310116988D-ribose-builds acid from
4310117992sucrose-builds acid from
431015291gelatin+hydrolysis
4310116199urea+hydrolysis
431014853esculin-hydrolysis
4310117632nitrate+reduction

enzymes

@refvalueactivityec
43101catalase+1.11.1.6
43101cytochrome oxidase+1.9.3.1
43101acid phosphatase+3.1.3.2
43101esterase (C 4)+
43101esterase Lipase (C 8)+
43101alpha-glucosidase+3.2.1.20
43101leucine arylamidase+3.4.11.1
43101phosphohydrolase+
43101pyrazinamidase+3.5.1.B15
43101pyrrolidonyl arylamidase+3.4.19.3
43101trypsin+3.4.21.4
43101N-acetyl-beta-glucosaminidase-3.2.1.52
43101alkaline phosphatase-3.1.3.1
43101chymotrypsin-3.4.4.5
43101cystine arylamidase-3.4.11.3
43101alpha-fucosidase-3.2.1.51
43101alpha-galactosidase-3.2.1.22
43101beta-galactosidase-3.2.1.23
43101beta-glucosidase-3.2.1.21
43101beta-glucuronidase-3.2.1.31
43101lipase (C 14)-
43101alpha-mannosidase-3.2.1.24
43101valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43101C15:0 anteiso71.4
    43101C15:0 iso14.2
    43101C17:0 anteiso4
    43101C18:3ω6c3.3
    43101C16:0 iso2.2
    43101C16:02
    43101C17:0 iso1.2
    43101C14:0 iso1.1
    43101C12:0 anteiso0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy agar (TSA, Difco)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 1
  • software version: Sherlock 6.2
  • system: MIS MIDI
  • instrument: 6890N; Agilent Technologies

Isolation, sampling and environmental information

isolation

  • @ref: 43101
  • sample type: rhizosphere of a mangrove
  • geographic location: Rambut Island, DKI Jakarta
  • country: Indonesia
  • origin.country: IDN
  • continent: Asia
  • latitude: -6
  • longitude: 106

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Mangrove
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Sequence information

16S sequences

  • @ref: 43101
  • description: Kocuria sp. RS-2-3 gene for 16S ribosomal RNA, partial sequence
  • accession: LC042214
  • length: 1490
  • database: nuccore
  • NCBI tax ID: 1638993

GC content

  • @ref: 43101
  • GC-content: 71.8

External links

@ref: 43101

culture collection no.: NBRC 110990, InaCC A704

literature

  • topic: Phylogeny
  • Pubmed-ID: 27221097
  • title: Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.
  • authors: Hamada M, Shibata C, Tamura T, Nurkanto A, Ratnakomala S, Lisdiyanti P, Suzuki KI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001186
  • year: 2016
  • mesh: Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indonesia, Islands, Micrococcaceae/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/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
43101Moriyuki Hamada, Chiyo Shibata, Tomohiko Tamura, Arif Nurkanto, Shanti Ratnakomala, Puspita Lisdiyanti, Ken-ichiro SuzukiKocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove10.1099/ijsem.0.001186IJSEM 66: 3276-3280 201627221097