Strain identifier

BacDive ID: 7181

Type strain: Yes

Species: Methylobacterium oryzae

Strain Designation: CBMB20

Strain history: KACC 11585 <-- T.-M. Sa CBMB20.

NCBI tax ID(s): 334852 (species)

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General

@ref: 7431

BacDive-ID: 7181

DSM-Number: 18207

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

description: Methylobacterium oryzae CBMB20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stem tissues of rice .

NCBI tax id

  • NCBI tax id: 334852
  • Matching level: species

strain history

@refhistory
7431<- T.-M. Sa, Chungbuk National University; CBMB20 <- M. Madhaiyan
67770KACC 11585 <-- T.-M. Sa CBMB20.

doi: 10.13145/bacdive7181.20230509.8.1

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 oryzae
  • full scientific name: Methylobacterium oryzae Madhaiyan et al. 2007

@ref: 7431

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium oryzae

full scientific name: Methylobacterium oryzae Madhaiyan et al. 2007

strain designation: CBMB20

type strain: yes

Morphology

cell morphology

  • @ref: 31890
  • gram stain: negative
  • cell length: 2.425 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31890
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7431
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Methanol Distilled water

culture temp

@refgrowthtypetemperaturerange
7431positivegrowth28mesophilic
31890positivegrowth20-30
31890positiveoptimum28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31890positivegrowth05-10alkaliphile
31890positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

  • @ref: 31890
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31890
  • spore formation: no

halophily

  • @ref: 31890
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2.0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3189017128adipate+carbon source
3189021217L-alaninamide+carbon source
31890286442-oxopentanoate+carbon source
3189022599arabinose+carbon source
3189022653asparagine+carbon source
3189035391aspartate+carbon source
3189016947citrate+carbon source
3189016236ethanol+carbon source
3189015740formate+carbon source
3189024148galactonate+carbon source
3189028260galactose+carbon source
3189024265gluconate+carbon source
3189029987glutamate+carbon source
3189017754glycerol+carbon source
3189024996lactate+carbon source
3189025115malate+carbon source
3189015792malonate+carbon source
3189017272propionate+carbon source
3189051850methyl pyruvate+carbon source
3189030031succinate+carbon source
3189018222xylose+carbon source
3189017632nitrate+reduction

enzymes

@refvalueactivityec
31890acid phosphatase+3.1.3.2
31890catalase+1.11.1.6
31890cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
7431stem tissues of rice (Oryza sativa L. 'Nam-Pyeoung')Oryza sativaCheongwon (36° 58' N 127° 57' E), ChungbukRepublic of KoreaKORAsia36.9667127.95
67770Stem tissues of rice (Oryza sativa L. 'Nam-Pyeoung')Oryza sativa

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Stem (Branch)

taxonmaps

  • @ref: 69479
  • File name: preview.99_422.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_285;97_315;98_350;99_422&stattab=map
  • Last taxonomy: Methylobacterium
  • 16S sequence: AY683045
  • Sequence Identity:
  • Total samples: 14332
  • soil counts: 2361
  • aquatic counts: 3355
  • animal counts: 6178
  • plant counts: 2438

Safety information

risk assessment

  • @ref: 7431
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7431
  • description: Methylobacterium oryzae strain CBMB20 16S ribosomal RNA gene, partial sequence
  • accession: AY683045
  • length: 1416
  • database: ena
  • NCBI tax ID: 693986

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium oryzae CBMB20GCA_000757795completencbi693986
66792Methylobacterium oryzae CBMB20693986.4completepatric693986
66792Methylobacterium oryzae CBMB202627854079completeimg693986

GC content

@refGC-contentmethod
743170.6
6777070.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.204yes
flagellatedno78.203no
gram-positiveno97.17no
anaerobicno98.571yes
aerobicyes90.278yes
halophileno89.649no
spore-formingno93.703yes
glucose-utilyes89.645no
thermophileno99.592yes
glucose-fermentno88.179no

External links

@ref: 7431

culture collection no.: DSM 18207, KACC 11585, LMG 23582, JCM 16405

straininfo link

  • @ref: 76634
  • straininfo: 290811

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267973Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice.Madhaiyan M, Kim BY, Poonguzhali S, Kwon SW, Song MH, Ryu JH, Go SJ, Koo BS, Sa TMInt J Syst Evol Microbiol10.1099/ijs.0.64603-02007Amino Acids, Cyclic/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carbon-Carbon Lyases/*biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Methylobacterium/*classification/enzymology/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, Pigments, Biological/biosynthesis, Plant Stems/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidMetabolism
Pathogenicity17512031Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato (Lycopersicon esculentum L).Madhaiyan M, Poonguzhali S, Sa TChemosphere10.1016/j.chemosphere.2007.04.0172007*Adaptation, Physiological, Cadmium/*toxicity, Lycopersicon esculentum/*growth & development/*microbiology, Methylobacterium/drug effects/*metabolism/physiology, Nickel/*toxicityMetabolism
Metabolism17898842Thiosulfate oxidation and mixotrophic growth of Methylobacterium oryzae.Anandham R, Indiragandhi P, Madhaiyan M, Kim K, Yim W, Saravanan VS, Chung J, Sa TCan J Microbiol10.1139/W07-0572007Autotrophic Processes, Gram-Negative Bacterial Infections/*microbiology, Heterotrophic Processes, Methanol/metabolism, Methylobacterium/enzymology/*growth & development/*metabolism, Oryza, Oxidoreductases/genetics/*metabolism, Plant Diseases/*microbiology, Sulfite Oxidase/metabolism, Thiosulfate Sulfurtransferase/metabolism, Thiosulfates/*metabolismEnzymology
Phylogeny18175690Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea.Weon HY, Kim BY, Joa JH, Son JA, Song MH, Kwon SW, Go SJ, Yoon SHInt J Syst Evol Microbiol10.1099/ijs.0.65047-02008*Air Microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Metabolism23354325Aggregation of selected plant growth promoting Methylobacterium strains: role of cell surface components and hydrophobicity.Joe MM, Saravanan VS, Sa TArch Microbiol10.1007/s00203-013-0866-x2013Hydrogen-Ion Concentration, *Hydrophobic and Hydrophilic Interactions, Membrane Proteins/metabolism, Methylobacterium/metabolism/*physiology/ultrastructure, Microscopy, Electron, Scanning, Plants/microbiology, Species Specificity, Time FactorsPhylogeny
Metabolism24188110Development of alginate-based aggregate inoculants of Methylobacterium sp. and Azospirillum brasilense tested under in vitro conditions to promote plant growth.Joe MM, Saravanan VS, Islam MR, Sa TJ Appl Microbiol10.1111/jam.123842013Alginates/*chemistry, Azospirillum brasilense/enzymology/*physiology/ultrastructure, Biofilms/*growth & development, Dehydration/prevention & control, Droughts, Ethylenes/metabolism, Glucuronic Acid/chemistry, Hexuronic Acids/chemistry, Hydrolysis, Lipid Peroxidation, Lycopersicon esculentum/*growth & development/microbiology, Malondialdehyde/metabolism, Methylobacterium/enzymology/*physiology/ultrastructure, Microscopy, Electron, Scanning, Microspheres, Peroxidase/metabolism, Soil/chemistryEnzymology
Genetics25211235Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.Kwak MJ, Jeong H, Madhaiyan M, Lee Y, Sa TM, Oh TK, Kim JFPLoS One10.1371/journal.pone.01067042014Chromosomes/genetics, DNA, Bacterial/genetics, *Genome, Bacterial, Methylobacterium/*genetics, *Molecular Sequence Annotation, Oxidative Stress, Phylogeny, Plant Stems, Probiotics, *Sequence Analysis, DNAPhylogeny
29164352Assessment of Methylobacterium oryzae CBMB20 aggregates for salt tolerance and plant growth promoting characteristics for bio-inoculant development.Chanratana M, Han GH, Roy Choudhury A, Sundaram S, Halim MA, Krishnamoorthy R, Kang Y, Sa TAMB Express10.1186/s13568-017-0518-72017
Metabolism30877435Methylobacterium oryzae CBMB20 influences photosynthetic traits, volatile emission and ethylene metabolism in Oryza sativa genotypes grown in salt stress conditions.Chatterjee P, Kanagendran A, Samaddar S, Pazouki L, Sa TM, Niinemets UPlanta10.1007/s00425-019-03139-w2019Amino Acid Oxidoreductases/genetics/metabolism, Carbon-Carbon Lyases/genetics/metabolism, Endophytes, Ethylenes/*metabolism, Genotype, Methylobacterium/*physiology, Oryza/enzymology/genetics/*microbiology/physiology, Phenotype, *Photosynthesis, Plant Growth Regulators/*metabolism, Plant Proteins/genetics/metabolism, Salinity, Salt Stress, Stress, Physiological, Vacuolar Proton-Translocating ATPases/genetics/metabolism, Volatile Organic Compounds/*metabolismGenetics
Stress31656735Physiological response of tomato plant to chitosan-immobilized aggregated Methylobacterium oryzae CBMB20 inoculation under salinity stress.Chanratana M, Joe MM, Roy Choudhury A, Anandham R, Krishnamoorthy R, Kim K, Jeon S, Choi J, Choi J, Sa T3 Biotech10.1007/s13205-019-1923-12019
Stress35191581Label-free proteomics approach reveals candidate proteins in rice (Oryza sativa L.) important for ACC deaminase producing bacteria-mediated tolerance against salt stress.Roy Choudhury A, Roy SK, Trivedi P, Choi J, Cho K, Yun SH, Walitang DI, Park JH, Kim K, Sa TEnviron Microbiol10.1111/1462-2920.159372022

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7431Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18207)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18207
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31890Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2814928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76634Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290811.1StrainInfo: A central database for resolving microbial strain identifiers