Strain identifier

BacDive ID: 133492

Type strain: Yes

Species: Rhodoplanes pokkaliisoli

Strain Designation: JA415

Strain history: <- Ch Sasikala, Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT Univ., India

NCBI tax ID(s): 551546 (species)

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General

@ref: 29186

BacDive-ID: 133492

keywords: 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Rhodoplanes pokkaliisoli JA415 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 551546
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Ch Sasikala, Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, JNT Univ., India

doi: 10.13145/bacdive133492.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Rhodoplanes
  • species: Rhodoplanes pokkaliisoli
  • full scientific name: Rhodoplanes pokkaliisoli Lakshmi et al. 2009

@ref: 29186

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Hyphomicrobiaceae

genus: Rhodoplanes

species: Rhodoplanes pokkaliisoli

strain designation: JA415

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
29186negative4 µm1.1 µmrod-shapedyes
67771rod-shapedyesmonotrichous, polar
67771negative

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29186positivegrowth25-30mesophilic
29186positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
29186positivegrowth6-7.5
29186positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29186facultative aerobe
67771anaerobe

halophily

@refsaltgrowthtested relationconcentration
29186NaClpositivegrowth0-2.5 %
29186NaClpositiveoptimum1.5 %

observation

@refobservation
29186aggregates in chains
67771quinones: Q-10, RQ-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2918630089acetate+carbon source
2918616947citrate+carbon source
2918617754glycerol+carbon source
2918624996lactate+carbon source
2918625115malate+carbon source
2918615361pyruvate+carbon source
2918630031succinate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29186soil
67771From soil sample of a pokkali rice field(pH7)Vypeen Islands, Emakulam, Kerala, the west coast of India(1°N 7°E)IndiaINDAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5126.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_2492;97_3043;98_3821;99_5126&stattab=map
  • Last taxonomy: Rhodoplanes pokkaliisoli subclade
  • 16S sequence: FM202448
  • Sequence Identity:
  • Total samples: 1599
  • soil counts: 929
  • aquatic counts: 417
  • animal counts: 172
  • plant counts: 81

Sequence information

16S sequences

  • @ref: 29186
  • description: Rhodoplanes sp. JA415T partial 16S rRNA gene
  • accession: FM202448
  • length: 1404
  • database: nuccore
  • NCBI tax ID: 551546

GC content

@refGC-contentmethod
2918667.2
6777167.2high performance liquid chromatography (HPLC)

External links

@ref: 29186

culture collection no.: KCTC 5711, NBRC 104972

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19605702Rhodoplanes pokkaliisoli sp. nov., a phototrophic alphaproteobacterium isolated from a waterlogged brackish paddy soil.Lakshmi KV, Sasikala Ch, Ramana ChVInt J Syst Evol Microbiol10.1099/ijs.0.008185-02009Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fermentation, Flagella, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, India, Locomotion, Molecular Sequence Data, Organelles/ultrastructure, Organic Chemicals/metabolism, Oryza, Photosynthesis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thiosulfates/metabolism, Xanthophylls/analysisGenetics
Phylogeny24695055Rhodoplanes oryzae sp. nov., a phototrophic alphaproteobacterium isolated from the rhizosphere soil of paddy.Srinivas A, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.063347-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, India, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
29186Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172561028776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/