Strain identifier
BacDive ID: 140489
Type strain:
Species: Kocuria pelophila
Strain Designation: RS-2-3
NCBI tax ID(s): 1638993 (species)
version 8.1 (current version)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
43101 | positive | optimum | 7 | psychrophilic |
43101 | positive | growth | 6-9 | psychrophilic |
43101 | positive | optimum | 28 | mesophilic |
43101 | positive | growth | 15-37 |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43101 | 17234 | glucose | + | builds acid from |
43101 | 28087 | glycogen | + | builds acid from |
43101 | 65327 | D-xylose | + | builds acid from |
43101 | 17716 | lactose | - | builds acid from |
43101 | 17306 | maltose | - | builds acid from |
43101 | 16899 | D-mannitol | - | builds acid from |
43101 | 16988 | D-ribose | - | builds acid from |
43101 | 17992 | sucrose | - | builds acid from |
43101 | 5291 | gelatin | + | hydrolysis |
43101 | 16199 | urea | + | hydrolysis |
43101 | 4853 | esculin | - | hydrolysis |
43101 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43101 | catalase | + | 1.11.1.6 |
43101 | cytochrome oxidase | + | 1.9.3.1 |
43101 | acid phosphatase | + | 3.1.3.2 |
43101 | esterase (C 4) | + | |
43101 | esterase Lipase (C 8) | + | |
43101 | alpha-glucosidase | + | 3.2.1.20 |
43101 | leucine arylamidase | + | 3.4.11.1 |
43101 | phosphohydrolase | + | |
43101 | pyrazinamidase | + | 3.5.1.B15 |
43101 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
43101 | trypsin | + | 3.4.21.4 |
43101 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43101 | alkaline phosphatase | - | 3.1.3.1 |
43101 | chymotrypsin | - | 3.4.4.5 |
43101 | cystine arylamidase | - | 3.4.11.3 |
43101 | alpha-fucosidase | - | 3.2.1.51 |
43101 | alpha-galactosidase | - | 3.2.1.22 |
43101 | beta-galactosidase | - | 3.2.1.23 |
43101 | beta-glucosidase | - | 3.2.1.21 |
43101 | beta-glucuronidase | - | 3.2.1.31 |
43101 | lipase (C 14) | - | |
43101 | alpha-mannosidase | - | 3.2.1.24 |
43101 | valine arylamidase | - |
fatty acid profile
fatty acids
@ref fatty acid percentage 43101 C15:0 anteiso 71.4 43101 C15:0 iso 14.2 43101 C17:0 anteiso 4 43101 C18:3ω6c 3.3 43101 C16:0 iso 2.2 43101 C16:0 2 43101 C17:0 iso 1.2 43101 C14:0 iso 1.1 43101 C12:0 anteiso 0.8 - 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
43101 | Moriyuki Hamada, Chiyo Shibata, Tomohiko Tamura, Arif Nurkanto, Shanti Ratnakomala, Puspita Lisdiyanti, Ken-ichiro Suzuki | Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove | 10.1099/ijsem.0.001186 | IJSEM 66: 3276-3280 2016 | 27221097 |