Strain identifier

BacDive ID: 134290

Type strain: Yes

Species: Methylobacterium platani

Strain Designation: PMB02

Strain history: <- W Park, Korea Univ.

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

@ref: 32286

BacDive-ID: 134290

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

description: Methylobacterium platani PMB02 is an aerobe, Gram-negative, motile bacterium that was isolated from plant associated.

NCBI tax id

NCBI tax idMatching level
1295136strain
427683species

strain history

@refhistory
67770W. Park PMB02 <-- H.-D. Shin.
67771<- W Park, Korea Univ.

doi: 10.13145/bacdive134290.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Methylobacterium
  • species: Methylobacterium platani
  • full scientific name: Methylobacterium platani Kang et al. 2007

@ref: 32286

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium platani

strain designation: PMB02

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32286negative4.25 µm1.45 µmrod-shapedyes
67771negative
69480negative91.174

pigmentation

  • @ref: 32286
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32286positivegrowth20-30
32286positiveoptimum27.5mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
32286positivegrowth6.0-8.0
32286positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32286aerobe
67771aerobe

spore formation

@refspore formationconfidence
32286no
69480no99.995

halophily

  • @ref: 32286
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

observation

@refobservation
32286aggregates in clumps
67770quinones: Q-10
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3228630089acetate+carbon source
3228622599arabinose+carbon source
3228635391aspartate+carbon source
3228615740formate+carbon source
3228628757fructose+carbon source
3228624175galacturonate+carbon source
3228624265gluconate+carbon source
3228629987glutamate+carbon source
3228624996lactate+carbon source
3228651850methyl pyruvate+carbon source
3228626271proline+carbon source
3228617272propionate+carbon source
3228626490quinate+carbon source
3228630031succinate+carbon source
3228626986threonine+carbon source

enzymes

@refvalueactivityec
32286catalase+1.11.1.6
32286cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
32286plant associated
67770Leaf of Platanus orientalis tree at Korea UniversityPlatanus orientalisSeoulRepublic of KoreaKORAsia
67771From leaf, plane treesRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants

taxonmaps

  • @ref: 69479
  • File name: preview.99_1774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_262;97_289;98_1400;99_1774&stattab=map
  • Last taxonomy: Methylobacterium platani
  • 16S sequence: EF426729
  • Sequence Identity:
  • Total samples: 1659
  • soil counts: 351
  • aquatic counts: 302
  • animal counts: 744
  • plant counts: 262

Sequence information

16S sequences

  • @ref: 32286
  • description: Methylobacterium platani strain PMB02 16S ribosomal RNA gene, partial sequence
  • accession: EF426729
  • length: 1432
  • database: nuccore
  • NCBI tax ID: 427683

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium platani JCM 14648GCA_001312265contigncbi1295136
66792Methylobacterium platani JCM 146481295136.3wgspatric1295136
66792Methylobacterium platani JCM 146481295136.4wgspatric1295136
66792Methylobacterium platani JCM 146482728369717draftimg1295136
66792Methylobacterium platani PMB022855953901draftimg427683
66792Methylobacterium platani JCM 146482651869728draftimg1295136
67770Methylobacterium platani JCM 14648GCA_001043885contigncbi1295136
67770Methylobacterium platani PMB02GCA_001653715scaffoldncbi427683

GC content

@refGC-contentmethod
3228668.5
6777068.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno87no
motileyes91.895yes
gram-positiveno97.51yes
anaerobicno98.682no
aerobicyes94.13yes
halophileno91.786no
spore-formingno94.032yes
thermophileno99.225yes
glucose-utilyes93.416no
flagellatedno76.93no
glucose-fermentno86.251no

External links

@ref: 32286

culture collection no.: KCTC 12901, JCM 14648

straininfo link

  • @ref: 91874
  • straininfo: 323252

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048737Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis.Kang YS, Kim J, Shin HD, Nam YD, Bae JW, Jeon CO, Park WInt J Syst Evol Microbiol10.1099/ijs.0.65262-02007Aerobiosis, Bacterial Typing Techniques, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Magnoliopsida/*microbiology, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureEnzymology
Phylogeny23315404Methylobacterium tarhaniae sp. nov., isolated from arid soil.Veyisoglu A, Camas M, Tatar D, Guven K, Sazak A, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.049551-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nigeria, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny26776106Methylobacterium indicum sp. nov., a facultative methylotrophic bacterium isolated from rice seed.Chaudhry V, Baindara P, Pal VK, Chawla N, Patil PB, Korpole SSyst Appl Microbiol10.1016/j.syapm.2015.12.0062015Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/analysis, Methylobacterium/*classification/genetics/*isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seeds/*microbiology, Sequence Analysis, DNAEnzymology
Phylogeny29160200Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system.Lee Y, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0025002017*Air Conditioning, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Methylobacterium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny31463788Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo TJ Microbiol10.1007/s12275-019-9007-92019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genotype, Lipids/chemistry, Methylobacterium/*classification/genetics/*isolation & purification/radiation effects, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry, Whole Genome SequencingGenetics
Phylogeny32100693Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0040542020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Methylobacterium/*classification/isolation & purification/radiation effects, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny32207677Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing.Feng GD, Chen W, Zhang XJ, Zhang J, Wang SN, Zhu HInt J Syst Evol Microbiol10.1099/ijsem.0.0041122020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Methylobacterium/*classification/isolation & purification, *Mining, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Tungsten, Ubiquinone/analogs & derivatives/chemistryTranscriptome

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
32286Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172852628776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
91874Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID323252.1