Methylobacterium oryzae (DSM 18207, KACC 11585, LMG 23582)

Name: Methylobacterium oryzae (DSM 18207, KACC 11585, LMG 23582)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7181

Type strain

Strain Designation CBMB20

Culture col. no. DSM 18207 KACC 11585 LMG 23582 CBMB20 JCM 16405

NCBI tax ID(s) 334852

Special Collections DSMZ JCM Literature strains

History <- T.-M. Sa, Chungbuk National University; CBMB20 <- M. Madhaiyan KACC 11585 <-- T.-M. Sa CBMB20.

Links

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

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 290811

LMG 23582,DSM 18207,KACC 11585,JCM 16405

@ref 20215

Last LPSN update 2026-02-09 11:19:24

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium oryzae

Full scientific name Methylobacterium oryzae Madhaiyan et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31890	negative	2.425 µm	0.7 µm	rod-shaped
125439	negative				96.3
125438	negative				97.802

Pigmentation

31890

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7431	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	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

@ref	Growth	Type	Temperature (°C)	Range
7431	positive	growth	28	mesophilic
31890	positive	growth	20-30
31890	positive	optimum	28	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31890	positive	optimum	6.8
31890	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31890	aerobe
125439	aerobe	92.2

Spore formation

@ref	Spore formation	Confidence
31890
125439		97

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31890	NaCl	positive	growth	<2.0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31890	28644 ChEBI	2-oxopentanoate	+	carbon source
31890	17128 ChEBI	adipate	+	carbon source
31890	22599 ChEBI	arabinose	+	carbon source
31890	22653 ChEBI	asparagine	+	carbon source
31890	35391 ChEBI	aspartate	+	carbon source
31890	16947 ChEBI	citrate	+	carbon source
31890	16236 ChEBI	ethanol	+	carbon source
31890	15740 ChEBI	formate	+	carbon source
31890	24148 ChEBI	galactonate	+	carbon source
31890	28260 ChEBI	galactose	+	carbon source
31890	24265 ChEBI	gluconate	+	carbon source
31890	29987 ChEBI	glutamate	+	carbon source
31890	17754 ChEBI	glycerol	+	carbon source
31890	21217 ChEBI	L-alaninamide	+	carbon source
31890	24996 ChEBI	lactate	+	carbon source
31890	25115 ChEBI	malate	+	carbon source
31890	15792 ChEBI	malonate	+	carbon source
31890	51850 ChEBI	methyl pyruvate	+	carbon source
31890	17632 ChEBI	nitrate	+	reduction
31890	17272 ChEBI	propionate	+	carbon source
31890	30031 ChEBI	succinate	+	carbon source
31890	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31890	acid phosphatase	+	3.1.3.2
31890	catalase	+	1.11.1.6
31890	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Stem (Branch)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
7431	stem tissues of rice (Oryza sativa L. 'Nam-Pyeoung')	Oryza sativa	Cheongwon (36° 58' N 127° 57' E), Chungbuk	Republic of Korea	KOR	Asia	36.9667	127.95 36.9667/127.95
67770	Stem tissues of rice (Oryza sativa L. 'Nam-Pyeoung')	Oryza sativa

Taxonmaps

69479

Global distribution of 16S sequence AY683045 (>99% sequence identity) for Methylobacterium from Microbeatlas

Aquatic Samples	3355
Soil Samples	2361
Animal Samples	6178
Plant Samples	2438
Total Samples	14332

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7431	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM75779v1 assembly for Methylobacterium oryzae CBMB20	complete	GCA_000757795	693986.4	2627854079	693986	99.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7431	Methylobacterium oryzae strain CBMB20 16S ribosomal RNA gene, partial sequence	AY683045	1416		693986

GC content

@ref	GC-content (mol%)	Method
7431	70.6
67770	70.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylobacterium oryzae CBMB20
NCBI: GCA_000757795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.00	no
125439	motility	BacteriaNetⓘ	yes	59.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	92.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium oryzae CBMB20 CBMB20
NCBI: GCA_000757795.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	yes
125438	anaerobic	anaerobicⓘ	no	95.56	yes
125438	aerobic	aerobicⓘ	yes	87.36	no
125438	spore-forming	spore-formingⓘ	no	87.92	yes
125438	thermophilic	thermophileⓘ	no	96.16	yes
125438	flagellated	motile2+ⓘ	yes	72.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Impact of Phyllosphere Methylobacterium on Host Rice Landraces.	Sanjenbam P, Shivaprasad PV, Agashe D.	Microbiol Spectr	10.1128/spectrum.00810-22	2022
Metabolism	A survey of Methylobacterium species and strains reveals widespread production and varying profiles of cytokinin phytohormones.	Palberg D, Kisiala A, Jorge GL, Emery RJN.	BMC Microbiol	10.1186/s12866-022-02454-9	2022
Stress	Label-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 T	Environ Microbiol	10.1111/1462-2920.15937	2022
Stress	Physiological 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 T	3 Biotech	10.1007/s13205-019-1923-1	2019
Metabolism	Methylobacterium 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 U	Planta	10.1007/s00425-019-03139-w	2019
	Assessment 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 T	AMB Express	10.1186/s13568-017-0518-7	2017
Genetics	Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.	Kwak MJ, Jeong H, Madhaiyan M, Lee Y, Sa TM, Oh TK, Kim JF	PLoS One	10.1371/journal.pone.0106704	2014
Metabolism	Development 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 T	J Appl Microbiol	10.1111/jam.12384	2013
Metabolism	Aggregation of selected plant growth promoting Methylobacterium strains: role of cell surface components and hydrophobicity.	Joe MM, Saravanan VS, Sa T	Arch Microbiol	10.1007/s00203-013-0866-x	2013
Metabolism	Thiosulfate oxidation and mixotrophic growth of Methylobacterium oryzae.	Anandham R, Indiragandhi P, Madhaiyan M, Kim K, Yim W, Saravanan VS, Chung J, Sa T	Can J Microbiol	10.1139/W07-057	2007
Pathogenicity	Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato (Lycopersicon esculentum L).	Madhaiyan M, Poonguzhali S, Sa T	Chemosphere	10.1016/j.chemosphere.2007.04.017	2007
Phylogeny	Methylobacterium 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 SH	Int J Syst Evol Microbiol	10.1099/ijs.0.65047-0	2008
Phylogeny	Methylobacterium 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 TM	Int J Syst Evol Microbiol	10.1099/ijs.0.64603-0	2007

References

#7431	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18207
#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#28149	IJSEM 326 2007 ( DOI 10.1099/ijs.0.64603-0 , PubMed 17267973 )
#31890	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28149
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João 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 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Methylobacterium oryzae (DSM 18207, KACC 11585, LMG 23582)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000757795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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