Methylobacterium nodulans (CNCMI 2342, LMG 21967, ORS 2060)

Name: Methylobacterium nodulans (CNCMI 2342, LMG 21967, ORS 2060)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133674

Type strain

Culture col. no. CNCMI 2342 LMG 21967 ORS 2060

NCBI tax ID(s) 460265 114616

Special Collections Literature strains

Links

Methylobacterium nodulans CNCMI 2342 is an aerobe, Gram-negative, motile bacterium that was isolated from plant endophyte.

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

Name and taxonomic classification

SI-ID 21083

VKM B-3209,LMG 21967

@ref 20215

Last LPSN update 2026-05-29 08:38:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylobacterium

Species Methylobacterium nodulans

Full scientific name Methylobacterium nodulans Jourand et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30069	negative	1.25 µm	0.9 µm	rod-shaped
125439	negative					93.352

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30069	positive	growth	30-37
30069	positive	optimum	33.5

Culture pH

@ref	Ability	Type	PH
30069	positive	optimum	7.15
30069	positive	growth	6.8-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30069	aerobe
125439	obligate aerobe	95.492

Spore formation

@ref	Spore formation	Confidence
125439		98.689

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30069	30089 ChEBI	acetate	+	carbon source
30069	16947 ChEBI	citrate	+	carbon source
30069	28757 ChEBI	fructose	+	carbon source
30069	17234 ChEBI	glucose	+	carbon source
30069	29987 ChEBI	glutamate	+	carbon source
30069	17632 ChEBI	nitrate	+	reduction
30069	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30069	catalase	+	1.11.1.6
30069	cytochrome oxidase	+	1.9.3.1
30069	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Other
#Host	#Plants

Isolation

30069

Sample typeplant endophyte

Taxonmaps

69479

Global distribution of 16S sequence AF220763 (>99% sequence identity) for Methylobacterium nodulans from Microbeatlas

Aquatic Samples	77
Soil Samples	257
Animal Samples	191
Plant Samples	24
Total Samples	549

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM2208v1 assembly for Methylobacterium nodulans ORS 2060	complete	GCA_000022085	460265.11	643348564	460265	97.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30069	Methylobacterium nodulans strain ORS 2060 16S ribosomal RNA gene, partial sequence	AF220763	1435		460265
124043	Methylobacterium nodulans gene for 16S rRNA, partial sequence, strain: LMG 21967.	AB252199	1434		114616

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2208v1 assembly for Methylobacterium nodulans ORS 2060
NCBI: GCA_000022085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.49	no
125439	motility	BacteriaNetⓘ	yes	51.20	no
125439	gram_stain	BacteriaNetⓘ	negative	93.35	no
125439	spore_formation	BacteriaNetⓘ	no	98.69	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genetic evidence for algal auxin production in Chlamydomonas and its role in algal-bacterial mutualism	Calatrava V, Hom E, Guan Q, Llamas A, Fernandez E, Galvan A.	iScience		2023
	Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales.	Antonets KS, Kliver SF, Nizhnikov AA.	Evol Bioinform Online	10.1177/1176934318768781	2018
Enzymology	The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases.	Cerda-Costa N, Guevara T, Karim AY, Ksiazek M, Nguyen KA, Arolas JL, Potempa J, Gomis-Ruth FX.	Mol Microbiol	10.1111/j.1365-2958.2010.07434.x	2011
Metabolism	Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.	Shen YQ, Bonnot F, Imsand EM, RoseFigura JM, Sjolander K, Klinman JP.	Biochemistry	10.1021/bi201763d	2012
	Engineered Methylobacterium extorquens grows well on methoxylated aromatics due to its formaldehyde metabolism and stress response.	Seriki AL, Alleman AB, Ticak T, Baugh AC, Creagh JW, Marx CJ.	mSphere	10.1128/msphere.00171-25	2025
	New evidence supports the prophage origin of RcGTA.	Xu Y, Liu B, Jiao N, Liu J, Chen F.	Appl Environ Microbiol	10.1128/aem.00434-24	2024
	Exploring diazotrophic diversity: unveiling Nif core distribution and evolutionary patterns in nitrogen-fixing organisms.	Nichio BTL, Chaves RBR, Pedrosa FO, Raittz RT.	BMC Genomics	10.1186/s12864-024-10994-9	2025
Enzymology	The more we learn, the more diverse it gets: structures, functions and evolution in the Phosphofructokinase Superfamily.	Compton JA, Patrick WM.	Biochem J	10.1042/bcj20253024	2025
Phylogeny	Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus.	Alleman AB, Stolyar S, Marx CJ, Leducq JB.	ISME J	10.1093/ismejo/wraf011	2025
Genetics	Genomic and Physiological Investigation of Heavy Metal Resistance from Plant Endophytic Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum.	Photolo MM, Sitole L, Mavumengwana V, Tlou MG.	Int J Environ Res Public Health	10.3390/ijerph18030997	2021
	Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis.	Nisrina L, Effendi Y, Pancoro A.	Heliyon	10.1016/j.heliyon.2021.e07636	2021
	XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium.	Mineo CR, Jiang J, Martinez-Gomez NC.	Appl Environ Microbiol	10.1128/aem.01304-25	2025
Enzymology	Diversity and distribution of the lanthanome in aerobic methane-oxidising bacteria.	Dandare SU, Allenby A, Silvano E, Nockemann P, Chen Y, Smith TJ, Kumaresan D.	Environ Microbiome	10.1186/s40793-025-00776-5	2025
Enzymology	[Properties of modified amperometric biosensors based on methanol dehydrogenase and Methylobacterium nodulans cells].	Kuznetsova TA, Beschastnyi AP, Alferov SV, Trotsenko IuA.	Prikl Biokhim Mikrobiol	10.1134/s0003683813060100	2013
	Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta.	de Freitas STF, Silva FG, Bessa LA, de Souza UJB, Augusto DSS, de Faria GS, Vitorino LC.	Sci Rep	10.1038/s41598-024-66161-3	2024
	Rhizobial, passenger nodule endophytes and phyllosphere bacteria in combination with acyl homoserine lactones enhances the growth and yield of groundnut.	Madhan S, Arunan YE, Rangasamy A, Dananjeyan B, Iruthayasamy J, Gajendiran M, Ramasamy K, Rajasekaran R, Saminathan V.	Biotechnol Rep (Amst)	10.1016/j.btre.2025.e00893	2025
	Application and effectiveness of Methylobacterium symbioticum as a biological inoculant in maize and strawberry crops.	Torres Vera R, Bernabe Garcia AJ, Carmona Alvarez FJ, Martinez Ruiz J, Fernandez Martin F.	Folia Microbiol (Praha)	10.1007/s12223-023-01078-4	2024
Enzymology	[Purification and characteristics of methanol dehydrogenase of Methylobacterium nodulans rhizosphere phytosymbionts].	Kuznetsova TA, Beschastnyi AP, Ponomareva ON, Trotsenko IuA.	Prikl Biokhim Mikrobiol	10.1134/s0003683812060063	2012
	Five copper homeostasis gene clusters encode the Cu-efflux resistome of the highly copper-tolerant Methylorubrum extorquens AM1.	Davalos A, Garcia-de Los Santos A.	PeerJ	10.7717/peerj.14925	2023
	Effects of foliar-sprayed bio-fertilizer with N-fixing Methylobacterium symbioticum on morpho-physiological traits of maize under varying N fertilization rates.	Bolla PK, Panozzo A, Minozzi E, Valente F, Potestio S, Visioli G, Martinez-Sanudo I, Vamerali T.	Front Plant Sci	10.3389/fpls.2025.1661290	2025
	Symbiotic properties of Methylobacterium nodulans ORS 2060T: A classic process for an atypical symbiont	Renier A, Jourand P, Rapior S, Poinsot V, Sy A, Dreyfus B, Moulin L.	Soil Biol Biochem	10.1016/j.soilbio.2007.12.020	2008
Enzymology	Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy.	Le TK, Lee YJ, Han GH, Yeom SJ.	Front Bioeng Biotechnol	10.3389/fbioe.2021.787791	2021
	Nodulation of Crotalaria podocarpa DC. by Methylobacterium nodulans displays very unusual features.	Renier A, De Faria SM, Jourand P, Giraud E, Dreyfus B, Rapior S, Prin Y.	J Exp Bot	10.1093/jxb/err083	2011
	The Biosynthesis of 1-octene-3-ol by a Multifunctional Fatty Acid Dioxygenase and Hydroperoxide Lyase in Agaricus bisporus.	Su T, Chen Y, Liu H, Gao Y, Guo J, Li Y, Qi Y, Qiu L.	J Fungi (Basel)	10.3390/jof8080827	2022
Enzymology	Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase.	Hying ZT, Miller TJ, Loh CY, Bazurto JV.	Appl Environ Microbiol	10.1128/aem.02090-23	2024
Phylogeny	Groundnut harbours non-nodulating non-rhizobial plant growth-promoting bacterial endophytes.	Rana AK, Vyas P, Sharma S, Sardana V.	3 Biotech	10.1007/s13205-023-03837-z	2023
	Proteomic analysis of the earthworm Eisenia fetida exposed to oxytetracycline in soil.	Zhao H, Shi S, Zhao H, Guo J, Yang Z, Gao H, Lu F.	RSC Adv	10.1039/c9ra06004a	2019
Enzymology	Isolation and Characterization of Homologically Expressed Methanol Dehydrogenase from Methylorubrum extorquens AM1 for the Development of Bioelectrocatalytical Systems.	Karaseva T, Fedorov D, Baklagina S, Ponamoreva O, Alferov S, Ekimova G, Abdullatypov A, Trubitsina L, Mustakhimov I.	Int J Mol Sci	10.3390/ijms231810337	2022
	Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae.	Lee JA, Stolyar S, Marx CJ.	Front Microbiol	10.3389/fmicb.2022.849573	2022
Genetics	Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment.	Henriques AC, Azevedo RM, De Marco P.	PeerJ	10.7717/peerj.2498	2016
Genetics	Harnessing Novel Soil Bacteria for Beneficial Interactions with Soybean.	Goncalves OS, Souza TS, Goncalves GC, Fernandes AS, Veloso TGR, Tupy SM, Garcia EA, Santana MF.	Microorganisms	10.3390/microorganisms11020300	2023
Phylogeny	Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tallgrass prairie of northern Oklahoma.	Bahulikar RA, Torres-Jerez I, Worley E, Craven K, Udvardi MK.	Appl Environ Microbiol	10.1128/aem.02091-14	2014
	Design and Control of Extrachromosomal Elements in Methylorubrum extorquens AM1.	Carrillo M, Wagner M, Petit F, Dransfeld A, Becker A, Erb TJ.	ACS Synth Biol	10.1021/acssynbio.9b00220	2019
Phylogeny	From genome to evolution: investigating type II methylotrophs using a pangenomic analysis.	Samanta D, Rauniyar S, Saxena P, Sani RK.	mSystems	10.1128/msystems.00248-24	2024
	Induction of endophytic colonization in rice (Oryza sativa L.) tissue culture plants by Azorhizobium caulinodans	Senthilkumar M, Madhaiyan M, Sundaram SP, Sangeetha H, Kannaiyan S.	Biotechnol Lett		2008
	Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0.	Mahadevan P, Seto D.	BMC Res Notes	10.1186/1756-0500-3-41	2010
	Induction of endophytic colonization in rice (Oryza sativa L.) tissue culture plants by Azorhizobium caulinodans.	Senthilkumar M, Madhaiyan M, Sundaram SP, Sangeetha H, Kannaiyan S.	Biotechnol Lett	10.1007/s10529-008-9693-6	2008
	Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production.	Mazoyon C, Hirel B, Pecourt A, Catterou M, Gutierrez L, Sarazin V, Dubois F, Duclercq J.	Microorganisms	10.3390/microorganisms11010199	2023
Genetics	Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species.	Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A.	Front Microbiol	10.3389/fmicb.2021.740610	2021
	Insights into origin and evolution of alpha-proteobacterial gene transfer agents.	Shakya M, Soucy SM, Zhaxybayeva O.	Virus Evol	10.1093/ve/vex036	2017
Metabolism	Root nodule bacteria isolated from South African Lotononis bainesii, L. listii and L. solitudinis are species of Methylobacterium that are unable to utilize methanol.	Ardley JK, O'Hara GW, Reeve WG, Yates RJ, Dilworth MJ, Tiwari RP, Howieson JG.	Arch Microbiol	10.1007/s00203-009-0456-0	2009
Genetics	Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria.	Zhang X, Xia L, Liu J, Wang Z, Yang Y, Wu Y, Yang Q, Huang L, Shen P.	Int J Mol Sci	10.3390/ijms24087521	2023
	Lotononis angolensis forms nitrogen fixing, lupinoid nodules with phylogenetically unique, fast-growing, pink-pigmented bacteria, which do not nodulate L. bainesii or L. listii	Yates RJ, Howieson JG, Reeve WG, Nandasena KG, Law IJ, Brau L, Ardley JK, Nistelberger HM, Real D, O'Hara GW.	Soil Biol Biochem	10.1016/j.soilbio.2007.01.025	2007
Enzymology	Culture-independent assessment of Rhizobiales-related alphaproteobacteria and the diversity of Methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus.	Andreote FD, Carneiro RT, Salles JF, Marcon J, Labate CA, Azevedo JL, Araujo WL.	Microb Ecol	10.1007/s00248-008-9405-8	2009
	A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria.	Islam T, Hernandez M, Gessesse A, Murrell JC, Ovreas L.	Microorganisms	10.3390/microorganisms9030477	2021
Metabolism	Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.	Peng T, Lin J, Xu YZ, Zhang Y.	ISME J	10.1038/ismej.2015.246	2016
	Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the Southern African crotalarioid clade Lotononis s.l.	Ardley JK, Reeve WG, O'Hara GW, Yates RJ, Dilworth MJ, Howieson JG.	Ann Bot	10.1093/aob/mct095	2013
	Salt tolerant Methylobacterium mesophilicum showed viable colonization abilities in the plant rhizosphere.	Egamberdieva D, Wirth S, Alqarawi AA, Abd Allah EF.	Saudi J Biol Sci	10.1016/j.sjbs.2015.06.029	2015
Metabolism	Characterization of pigmented methylotrophic bacteria which nodulate Lotononis bainesii.	Jaftha JB, Strijdom BW, Steyn PL.	Syst Appl Microbiol	10.1078/0723-2020-00124	2002
Genetics	The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method.	Narihiro T, Suzuki A, Yoshimune K, Hori T, Hoshino T, Yumoto I, Yokota A, Kimura N, Kamagata Y.	Microbes Environ	10.1264/jsme2.me14002	2014
	In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria.	Rajput A, Kumar M.	Sci Rep	10.1038/s41598-017-07241-5	2017
Genetics	Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges.	Pimentel-Elardo SM, Grozdanov L, Proksch S, Hentschel U.	Mar Drugs	10.3390/md10061192	2012
Phylogeny	Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts.	Sawada H, Kuykendall LD, Young JM.	J Gen Appl Microbiol	10.2323/jgam.49.155	2003
Metabolism	Widespread soil bacterium that oxidizes atmospheric methane.	Tveit AT, Hestnes AG, Robinson SL, Schintlmeister A, Dedysh SN, Jehmlich N, von Bergen M, Herbold C, Wagner M, Richter A, Svenning MM.	Proc Natl Acad Sci U S A	10.1073/pnas.1817812116	2019
	Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum.	Elliott GN, Chen WM, Bontemps C, Chou JH, Young JP, Sprent JI, James EK.	Ann Bot	10.1093/aob/mcm227	2007
	Herbaceous Legume Encroachment Reduces Grass Productivity and Density in Arid Rangelands.	Wagner TC, Hane S, Joubert DF, Fischer C.	PLoS One	10.1371/journal.pone.0166743	2016
	Origin and evolution of group XI secretory phospholipase A₂ from flax (Linum usitatissimum) based on phylogenetic analysis of conserved domains.	Gupta P, Saini R, Dash PK.	3 Biotech	10.1007/s13205-017-0790-x	2017
Metabolism	SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in *Staphylococcus aureus*.	Verstraete MM, Perez-Borrajero C, Brown KL, Heinrichs DE, Murphy MEP.	J Biol Chem	10.1074/jbc.ra118.001875	2018
	Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.	Asplund-Samuelsson J, Bergman B, Larsson J.	PLoS One	10.1371/journal.pone.0049888	2012
Phylogeny	Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter.	Lu L, Cai L, Jiao N, Zhang R.	Virol J	10.1186/s12985-017-0773-x	2017
	Domain annotation of trimeric autotransporter adhesins--daTAA.	Szczesny P, Lupas A.	Bioinformatics	10.1093/bioinformatics/btn118	2008
Enzymology	Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.	Wang Q, Quensen JF, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR.	mBio	10.1128/mbio.00592-13	2013
Phylogeny	A comprehensive phylogenetic analysis of copper transporting P_1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes.	Cubillas C, Miranda-Sanchez F, Gonzalez-Sanchez A, Elizalde JP, Vinuesa P, Brom S, Garcia-de Los Santos A.	Microbiologyopen	10.1002/mbo3.452	2017
Metabolism	A distinct pathway for tetrahymanol synthesis in bacteria.	Banta AB, Wei JH, Welander PV.	Proc Natl Acad Sci U S A	10.1073/pnas.1511482112	2015
Metabolism	Identification of two nickel ion-induced genes, NCI16 and PcGST1, in Paramecium caudatum.	Takenaka Y, Haga N, Inoue I, Nakano T, Ikeda M, Katayama S, Awata T.	Eukaryot Cell	10.1128/ec.00112-14	2014
Transcriptome	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
	Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.	Ardley J, Tian R, Howieson J, Yates R, Brau L, Han J, Lobos E, Huntemann M, Chen A, Mavromatis K, Markowitz V, Ivanova N, Pati A, Goodwin L, Woyke T, Kyrpides N, Reeve W.	Stand Genomic Sci	10.1186/1944-3277-9-5	2014
	Transfer of a Catabolic Pathway for Chloromethane in Methylobacterium Strains Highlights Different Limitations for Growth with Chloromethane or with Dichloromethane.	Michener JK, Vuilleumier S, Bringel F, Marx CJ.	Front Microbiol	10.3389/fmicb.2016.01116	2016
	South african papilionoid legumes are nodulated by diverse burkholderia with unique nodulation and nitrogen-fixation Loci.	Beukes CW, Venter SN, Law IJ, Phalane FL, Steenkamp ET.	PLoS One	10.1371/journal.pone.0068406	2013
Phylogeny	Shear rate moderates community diversity in freshwater biofilms.	Rickard AH, McBain AJ, Stead AT, Gilbert P.	Appl Environ Microbiol	10.1128/aem.70.12.7426-7435.2004	2004
Genetics	New Genomic Insights into "Entotheonella" Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction.	Liu F, Li J, Feng G, Feng G, Li Z.	Front Microbiol	10.3389/fmicb.2016.01333	2016
Phylogeny	Impact of plants on the diversity and activity of methylotrophs in soil.	Macey MC, Pratscher J, Crombie AT, Murrell JC.	Microbiome	10.1186/s40168-020-00801-4	2020
Metabolism	Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.	Vilar-Sanz A, Puig S, Garcia-Lledo A, Trias R, Balaguer MD, Colprim J, Baneras L.	PLoS One	10.1371/journal.pone.0063460	2013
	Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents.	Kogay R, Wolf YI, Koonin EV, Zhaxybayeva O.	mBio	10.1128/mbio.01206-20	2020
	NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient.	Penton CR, Yang C, Wu L, Wang Q, Zhang J, Liu F, Qin Y, Deng Y, Hemme CL, Zheng T, Schuur EA, Tiedje J, Zhou J.	Front Microbiol	10.3389/fmicb.2016.01894	2016
Enzymology	Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases.	da Fonseca RR, Johnson WE, O'Brien SJ, Vasconcelos V, Antunes A.	BMC Evol Biol	10.1186/1471-2148-10-281	2010
Metabolism	Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501.	Yan Y, Ping S, Peng J, Han Y, Li L, Yang J, Dou Y, Li Y, Fan H, Fan Y, Li D, Zhan Y, Chen M, Lu W, Zhang W, Cheng Q, Jin Q, Lin M.	BMC Genomics	10.1186/1471-2164-11-11	2010
	Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.	Popa O, Landan G, Dagan T.	ISME J	10.1038/ismej.2016.116	2017
	Housekeeping genes essential for pantothenate biosynthesis are plasmid-encoded in Rhizobium etli and Rhizobium leguminosarum.	Villasenor T, Brom S, Davalos A, Lozano L, Romero D, Los Santos AG.	BMC Microbiol	10.1186/1471-2180-11-66	2011
Metabolism	Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes.	Lin J, Peng T, Jiang L, Ni JZ, Liu Q, Chen L, Zhang Y.	Genome Biol Evol	10.1093/gbe/evv022	2015
	Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae.	Estrada-de Los Santos P, Palmer M, Chavez-Ramirez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Dos Reis Junior FB, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK.	Genes (Basel)	10.3390/genes9080389	2018
Genetics	An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.	Thiergart T, Landan G, Schenk M, Dagan T, Martin WF.	Genome Biol Evol	10.1093/gbe/evs018	2012
Metabolism	Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum.	Sudtachat N, Ito N, Itakura M, Masuda S, Eda S, Mitsui H, Kawaharada Y, Minamisawa K.	Appl Environ Microbiol	10.1128/aem.00755-09	2009
Enzymology	Isolation of optically targeted single bacteria by application of fluidic force microscopy to aerobic anoxygenic phototrophs from the phyllosphere.	Stiefel P, Zambelli T, Vorholt JA.	Appl Environ Microbiol	10.1128/aem.01087-13	2013
	Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.	Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ, Li DF, Wang S, Wang J, Gilbert LB, Li YR, Chen WX.	Proc Natl Acad Sci U S A	10.1073/pnas.1120436109	2012
	Genetic and phenotypic diversity in Burkholderia: contributions by prophage and phage-like elements.	Ronning CM, Losada L, Brinkac L, Inman J, Ulrich RL, Schell M, Nierman WC, Deshazer D.	BMC Microbiol	10.1186/1471-2180-10-202	2010
Metabolism	Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants.	Bao Z, Okubo T, Kubota K, Kasahara Y, Tsurumaru H, Anda M, Ikeda S, Minamisawa K.	Appl Environ Microbiol	10.1128/aem.00969-14	2014
	Molecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.	Lafay B, Burdon JJ.	PLoS One	10.1371/journal.pone.0000277	2007
Enzymology	Improved prediction of malaria degradomes by supervised learning with SVM and profile kernel.	Kuang R, Gu J, Cai H, Wang Y.	Genetica	10.1007/s10709-008-9336-9	2009
Phylogeny	Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes.	Wolinska A, Kuzniar A, Zielenkiewicz U, Banach A, Izak D, Stepniewska Z, Blaszczyk M.	Microb Ecol	10.1007/s00248-016-0837-2	2017
Phylogeny	Web-based software for rapid top-down proteomic identification of protein biomarkers, with implications for bacterial identification.	Fagerquist CK, Garbus BR, Williams KE, Bates AH, Boyle S, Harden LA.	Appl Environ Microbiol	10.1128/aem.00079-09	2009
	Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.	Diouf F, Diouf D, Klonowska A, Le Quere A, Bakhoum N, Fall D, Neyra M, Parrinello H, Diouf M, Ndoye I, Moulin L.	PLoS One	10.1371/journal.pone.0117667	2015
Genetics	Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes.	Gelencser Z, Choudhary KS, Coutinho BG, Hudaiberdiev S, Galbats B, Venturi V, Pongor S.	Sensors (Basel)	10.3390/s120505432	2012
	Leaf-residing Methylobacterium species fix nitrogen and promote biomass and seed production in Jatropha curcas.	Madhaiyan M, Alex TH, Ngoh ST, Prithiviraj B, Ji L.	Biotechnol Biofuels	10.1186/s13068-015-0404-y	2015
Phylogeny	Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees.	Stepkowski T, Hughes CE, Law IJ, Markiewicz L, Gurda D, Chlebicka A, Moulin L.	Appl Environ Microbiol	10.1128/aem.02125-06	2007
Metabolism	Elucidation of the 3-O-deacylase gene, pagL, required for the removal of primary beta-hydroxy fatty acid from the lipid A in the nitrogen-fixing endosymbiont Rhizobium etli CE3.	Brown DB, Muszynski A, Salas O, Speed K, Carlson RW.	J Biol Chem	10.1074/jbc.m113.470484	2013
Genetics	Pheno- and Genotyping of Hopanoid Production in Acidobacteria.	Damste JSS, Rijpstra WIC, Dedysh SN, Foesel BU, Villanueva L.	Front Microbiol	10.3389/fmicb.2017.00968	2017
Metabolism	Osmotically induced synthesis of the dipeptide N-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria.	Sagot B, Gaysinski M, Mehiri M, Guigonis JM, Le Rudulier D, Alloing G.	Proc Natl Acad Sci U S A	10.1073/pnas.1003063107	2010
Metabolism	Identification and functional analysis of secreted effectors from phytoparasitic nematodes.	Rehman S, Gupta VK, Goyal AK.	BMC Microbiol	10.1186/s12866-016-0632-8	2016
Metabolism	Methylotrophic autotrophy in Beijerinckia mobilis.	Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA.	J Bacteriol	10.1128/jb.187.11.3884-3888.2005	2005
Enzymology	Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus.	Beasley FC, Cheung J, Heinrichs DE.	BMC Microbiol	10.1186/1471-2180-11-199	2011
Genetics	Information theoretic perspective on genome clustering.	Veluchamy A, Mehta P, Srividhya KV, Vikram H, Govind MK, Gupta R, Aziz Bin Dukhyil A, Abdullah Alharbi R, Abdullah Aloyuni S, Hassan MM, Krishnaswamy S.	Saudi J Biol Sci	10.1016/j.sjbs.2020.12.039	2021
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Enzymology	Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme.	Carretero-Paulet L, Lipska A, Perez-Gil J, Sangari FJ, Albert VA, Rodriguez-Concepcion M.	BMC Evol Biol	10.1186/1471-2148-13-180	2013
Metabolism	Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions.	Sy A, Timmers AC, Knief C, Vorholt JA.	Appl Environ Microbiol	10.1128/aem.71.11.7245-7252.2005	2005
Metabolism	Outer and inner membrane proteins compose an arginine-agmatine exchange system in Chlamydophila pneumoniae.	Smith CB, Graham DE.	J Bacteriol	10.1128/jb.00652-08	2008
Phylogeny	Legume symbiotic nitrogen fixation by beta-proteobacteria is widespread in nature.	Chen WM, Moulin L, Bontemps C, Vandamme P, Bena G, Boivin-Masson C.	J Bacteriol	10.1128/jb.185.24.7266-7272.2003	2003
Metabolism	Evolution of mitochondria reconstructed from the energy metabolism of living bacteria.	Degli Esposti M, Chouaia B, Comandatore F, Crotti E, Sassera D, Lievens PM, Daffonchio D, Bandi C.	PLoS One	10.1371/journal.pone.0096566	2014
	Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.	Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin EG.	PLoS One	10.1371/journal.pone.0050875	2012
Metabolism	Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine by a phytosymbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoides x nigra DN34).	Van Aken B, Yoon JM, Schnoor JL.	Appl Environ Microbiol	10.1128/aem.70.1.508-517.2004	2004
Metabolism	Gene duplications in prokaryotes can be associated with environmental adaptation.	Bratlie MS, Johansen J, Sherman BT, Huang da W, Lempicki RA, Drablos F.	BMC Genomics	10.1186/1471-2164-11-588	2010
Pathogenicity	Genome-wide transcriptional responses of two metal-tolerant symbiotic Mesorhizobium isolates to zinc and cadmium exposure.	Maynaud G, Brunel B, Mornico D, Durot M, Severac D, Dubois E, Navarro E, Cleyet-Marel JC, Le Quere A.	BMC Genomics	10.1186/1471-2164-14-292	2013
	The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s.	Nelson DR, Goldstone JV, Stegeman JJ.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2012.0474	2013
Metabolism	tRNA is the source of low-level trans-zeatin production in Methylobacterium spp.	Koenig RL, Morris RO, Polacco JC.	J Bacteriol	10.1128/jb.184.7.1832-1842.2002	2002
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Enzymology	1-Aminocyclopropane-1-carboxylate (ACC) deaminases from Methylobacterium radiotolerans and Methylobacterium nodulans with higher specificity for ACC.	Fedorov DN, Ekimova GA, Doronina NV, Trotsenko YA	FEMS Microbiol Lett	10.1111/1574-6968.12133	2013
Metabolism	TonB-dependent receptors in nitrogen-fixing nodulating bacteria.	Lim BL	Microbes Environ	10.1264/jsme2.me10102	2010
Phylogeny	Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.	Sy A, Giraud E, Jourand P, Garcia N, Willems A, de Lajudie P, Prin Y, Neyra M, Gillis M, Boivin-Masson C, Dreyfus B	J Bacteriol	10.1128/JB.183.1.214-220.2001	2001
Metabolism	Characterization of recombinant PPi-dependent 6-phosphofructokinases from Methylosinus trichosporium OB3b and Methylobacterium nodulans ORS 2060.	Rozova ON, Khmelenina VN, Trotsenko YA	Biochemistry (Mosc)	10.1134/S0006297912030078	2012
Metabolism	Nodulation and plant-growth promotion by methylotrophic bacteria isolated from tropical legumes.	Madhaiyan M, Poonguzhali S, Senthilkumar M, Sundaram S, Sa T	Microbiol Res	10.1016/j.micres.2006.08.009	2006
	Role of methylotrophy during symbiosis between Methylobacterium nodulans and Crotalaria podocarpa.	Jourand P, Renier A, Rapior S, Miana de Faria S, Prin Y, Galiana A, Giraud E, Dreyfus B	Mol Plant Microbe Interact	10.1094/MPMI-18-1061	2005
Phylogeny	Methylobacterium oryzisoli sp. nov., a novel methylotrophic methanol-utilizing bacterium isolated from the paddy soil.	Liu L, Zhang SY, Gao P, Shen HC, Rensing C, Liu GH, Zhou SG.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006805	2025
Phylogeny	Foliimonas ilicis gen. nov., sp. nov., a carbon monoxide-oxidizing bacterium belonging to a novel genus of the family Phyllobacteriaceae isolated from leaves of Ilex aquifolium.	Banerjee S, Tancsics A, Wu Z, Stafioiu T, Gao J, Toth E, Baka E, Bending G, Schafer H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006953	2025
Enzymology	Methylobacterium isbiliense sp. nov., isolated from the drinking water system of Sevilla, Spain.	Gallego V, Garcia MT, Ventosa A.	Int J Syst Evol Microbiol	10.1099/ijs.0.63773-0	2005
Genetics	Microvirga massiliensis sp. nov., the human commensal with the largest genome.	Caputo A, Lagier JC, Azza S, Robert C, Mouelhi D, Fournier PE, Raoult D.	Microbiologyopen	10.1002/mbo3.329	2016
	Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov.	de Lajudie P, Willems A, Nick G, Moreira F, Molouba F, Hoste B, Torck U, Neyra M, Collins MD, Lindstrom K, Dreyfus B, Gillis M.	Int J Syst Bacteriol	10.1099/00207713-48-2-369	1998
Phylogeny	Methylobacterium crusticola sp. nov., isolated from biological soil crusts.	Jia LJ, Zhang KS, Tang K, Meng JY, Zheng C, Feng FY	Int J Syst Evol Microbiol	10.1099/ijsem.0.004020	2020
Phylogeny	Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria.	Jourand P, Giraud E, Bena G, Sy A, Willems A, Gillis M, Dreyfus B, de Lajudie P	Int J Syst Evol Microbiol	10.1099/ijs.0.02902-0	2004

References

#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 )
#26429	IJSEM 2269 2004 ( DOI 10.1099/ijs.0.02902-0 , PubMed 15545469 )
#30069	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 #26429
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 nodulans (CNCMI 2342, LMG 21967, ORS 2060)

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