Plant Interaction with Methylotrophic Communities

  • Manish KumarEmail author
  • Raghvendra Saxena
  • Rajesh Singh Tomar
  • Pankaj Kumar Rai


Methylotrophs are a diverse group of bacterial community utilizing a number of C1 carbon compounds as a source of carbon and energy. This peculiar group of microorganisms has capability to enhance plant growth by solubilizing phosphates, by producing siderophores, by inhibiting ethylene accumulation in plants in adverse conditions, by fixing atmospheric nitrogen, by producing phytohormones such as auxins and cytokinins, and by degrading various harmful and toxic compounds. The plant roots are colonized by different types of methylotrophic bacteria, and solubilized essential elements are provided to the plants making them healthier and strong. There are a number of beneficial biological interactions of methylotrophs with the plants. Interaction of methanotrophs with plants leads to the reduction in greenhouse effects in the environment. The interaction of methylotrophic bacteria with plants as endophytes, epiphytes, plant colonizers, phytohormone producers, and other types of beneficial association makes them very peculiar group of microbes interacting natural flora. Apart from higher plants, methylotrophic interaction was observed with bryophytes also as epiphytic as well as endophytic bacteria.


Methylotrophs PGPRs Endophyte Bacterial community Phytohormone 



Manish Kumar, Raghvendra Saxena, and Rajesh Singh Tomar wish to express their sincere gratitude to Dr. Ashok Kumar Chauhan, President, RBEF parent organization of Amity University Madhya Pradesh (AUMP) for providing necessary facilities, as well as valuable support.


  1. Aken BV, Peres CM, Doty SL, Yoon JM, Schnoor JL (2004) Methylobacterium populi sp. nov., a novel aerobic, pink-pigmented, facultatively methylotrophic, methane-utilizing bacterium isolated from poplar trees. Int J Syst Evol Microbiol 54:1191–1196CrossRefPubMedGoogle Scholar
  2. Anitha KG (2010) Enhancing seed germination of mono and dicotyledons through IAA production of PPFM. Trends Soil Sci Plant Nutr J 1:14–18Google Scholar
  3. Barraquio WL, Watanabe I (1981) Occurrence of aerobic nitrogen-fixing bacteria in wetland and dryland plants. Soil Sci Plant Nutr Tokyo 27:121–125CrossRefGoogle Scholar
  4. Basile DV, Slade LL, Corpe WA (1969) An association between a bacterium and a liverwort, Scapania nemorosa. Bull Torrey Bot Club 96(6):711–714CrossRefGoogle Scholar
  5. Chauhan PS, Lee GS, Lee MK, Yim WJ, Lee GJ, Kim YS, Chung JB, Sa TM (2010) Effect of Methylobacterium oryzae CBMB20 inoculation and methanol spray on growth of red pepper (Capsicum annuum L.) at different fertilizer levels. Korean J Soil Sci Fert 43:514–521Google Scholar
  6. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Mering CV, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. PNAS 10b(38):16428–16433CrossRefGoogle Scholar
  7. Dourado MN, Ferreira A, Araújo WL, Azevedo JL, Lacava PT (2012) The diversity of endophytic methylotrophic bacteria in an oil-contaminated and an oil-free mangrove ecosystem and their tolerance to heavy metals. Biotechnol Res Int 2012:759865CrossRefPubMedPubMedCentralGoogle Scholar
  8. Dourado MN, Neves AAC, Santos DS, Araújo WL (2015) Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. Biomed Res Int.
  9. Dubey SK, Singh JS (2001) Plant-induced spatial variation in the size of methanotrophic population in dryland and flooded rice agroecosystems. Nutr Cycl Agroecosyst 59:161–167CrossRefGoogle Scholar
  10. Fedorov DN, Ekimova GA, Doronina NV, Trotsenko YA (2013) 1-Aminocyclopropane-1-carboxylate (ACC) deaminases from Methylobacterium radiotolerans and Methylobacterium nodulans with higher specificity for ACC. FEMS Microbiol Lett 343(1):70–76CrossRefPubMedGoogle Scholar
  11. Ferreira A, Quecine MC, Lacava PT et al (2008) Diversity of endophytic bacteria from Eucalyptus species seed and colonization of seedlings by Pantoea agglomerans. FEMS Microbiol Lett 287:8–14CrossRefPubMedGoogle Scholar
  12. Figueira MM, Laramee L, Murrell JC, Groleau D, Miguez CB (2000) Production of green fluorescent protein by the methylotrophic bacterium methylobacterium extorquens. FEMS Microbiol Lett 193:195–200CrossRefPubMedGoogle Scholar
  13. Glick BR (1995) The enhancement of plant growth by free-living bacteria. Can J Microbiol 41(2):109–117CrossRefGoogle Scholar
  14. Hardoim PR, Overbeek LSV, Elsas JDV (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16(10):463–471CrossRefPubMedGoogle Scholar
  15. Holland MA, Polacco JC (1992) Urease-null and hydrogenase- null phenotypes of a phylloplane bacterium reveal altered nickel metabolism in two soybean mutants. Plant Physiol 98:942–948CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hornschuh M, Grotha R, Kutschera U (2002) Epiphytic bacteria associated with the bryophyte Funaria hygrometrica: effects of methylobacterium strains on protonema development. Plant Biol 4:682–687CrossRefGoogle Scholar
  17. Iguchi H, Yurimoto H, Sakai Y (2015) Interactions of methylotrophs with plants and other heterotrophic bacteria. Microorganisms 3:137–151CrossRefPubMedPubMedCentralGoogle Scholar
  18. Irvine IC, Brigham CA, Suding KN, Martiny JBH (2012) The abundance of pink-pigmented facultative methylotrophs in the root zone of plant species in invaded coastal sage scrub habitat. PLoS One 7(2):e31026CrossRefPubMedPubMedCentralGoogle Scholar
  19. Ivanova EG, Doronina NV, Shepelyakovskaya AO et al (2000) Facultative and obligate aerobic methylobacteria synthesise cytokinins. Mikrobiologiya 69:764–769Google Scholar
  20. Ivanova EG, Pirttila AM, Fedorov DNF et al (2008) Association of methylotrophic bacteria with plants: metabolic aspects. In: Sorvari S, Pirttila AM (eds) Prospects and applications for plant associated microbes. A laboratory manual, part A: bacteria. Biobien innovations, Turku, pp 225–231Google Scholar
  21. Kalyuzhnaya MG, Beck DAC, Vorobev A, Smalley N, Kunkel DD, Lidstrom ME, Chistoserdova L et al (2011) Novel methylotrophic isolates from lake sediment, description of Methylotenera Versatilis sp. nov. and emended description of the genus Methylotenera. Int J Syst Evol Microbiol 62(Pt 1):106–111PubMedGoogle Scholar
  22. Keerthi MM, Babu R, Joseph M, Amutha R (2015) Optimizing plant geometry and nutrient management for grain yield and economics in irrigated green gram. Am J Plant Sci 6:1144–1150CrossRefGoogle Scholar
  23. Koenig RL, Morris RO, Polacco JC (2002) tRNA is the source of low level trans-zeatin production in Methylobacterium spp. J Bacteriol 184:1832–1842CrossRefPubMedPubMedCentralGoogle Scholar
  24. Kumar M, Srivastava AK, Pandey AK (2015) Biocontrol activity of some potent Methylotrophs isolated from Bhitarkanika mangrove sediment. Int J Curr Res Biosci Plant Biol 2:101–106Google Scholar
  25. Kumar M, Tomar RS, Lade H, Paul D (2016) Methylotrophic bacteria in sustainable agriculture. World J Microbiol Biotechnol 32:120CrossRefPubMedGoogle Scholar
  26. Larmola T, Leppänenb SM, Tuittilaa ES, Aarvab M, Meriläc P, Fritzed H, Tiirolab M (2014) Methanotrophy induces nitrogen fixation during peatland development. PNAS 111:734–739CrossRefPubMedGoogle Scholar
  27. Laukkanen H, Soini H, Kontunen-Soppela S et al (2000) A mycobacterium isolated from tissue cultures of mature Pinus sylvestris interferes with growth of Scots pine seedlings. Tree Physiol 20:915–920CrossRefPubMedGoogle Scholar
  28. Lee HS, Madhaiyan M, Kim CW, Choi SJ, Chung KY, Sa TM (2006) Physiological enhancement of early growth of rice seedlings (Oryza sativa L.) by production of phytohormone of N2-fixing methylotrophic isolates. Biol Fertil Soil 42:402–408CrossRefGoogle Scholar
  29. Limtong S, Kaewwichian R, Groenewald M (2013) Ogataea kanchanaburiensis sp. nov. and Ogataea wangdongensis sp. nov., two novel methylotrophic yeast species from phylloplane in Thailand. Antonie Van Leeuwenhoek 103:551–558CrossRefPubMedGoogle Scholar
  30. Madhaiyan M, Poonguzhali S, Senthilkumar M, Seshadri S, Chung H, Yang J, Sundaram S, Sa T (2004) Growth promotion and induction of systemic resistance in rice cultivar Co-47 (Oryza sativa L.) by Methylobacterium spp. Bot Bull Acad Sin 45:315–325Google Scholar
  31. Madhaiyan M, Poonguzhali S, Sa T (2007) Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium oryzae and interactions with auxins and ACC regulation of ethylene in canola (Brassica campestris). Planta 226(4):867–876CrossRefPubMedGoogle Scholar
  32. Madhaiyan M, Poonguzhali S, Senthilkumar M, Sundaram SP, Sa T (2009a) Nodulation and plant-growth promotion by methylotrophic bacteria isolated from tropical legumes. Microbiol Res 164:114–120CrossRefPubMedGoogle Scholar
  33. Madhaiyan M, Poonguzhali S, Kwon S-W, Sas T-M (2009b) Methylobacterium phyllosphaerae sp. nov., a pink pigmented, facultative methylotroph from the phyllosphere of rice. Int J Syst Evol Microbiol 59:22–27CrossRefPubMedGoogle Scholar
  34. Madmony A, Chernin L, Pleban S et al (2005) Enterobacter cloacae, an obligatory endophyte of pollen grains of Mediterranean pines. Folia Microbiol 50:209–216CrossRefGoogle Scholar
  35. McGiffen ME, Manthey JA Jr (1996) The role of methanol in promoting plant growth: a current evaluation. Hortscience 31(7):1092–1096Google Scholar
  36. Meena KK, Kumar M, Kalyuzhnaya MG, Yandigeri MS, Singh DP, Saxena AK, Arora DK (2012) Epiphytic pink-pigmented methylotrophic bacteria enhance germination and seedling growth of wheat (Triticum aestivum) by producing phytohormone. Antonie Van Leeuwenhoek 101:777–786CrossRefPubMedGoogle Scholar
  37. Mizuno M (2013) Studies on distribution and colonization of facultative methylotrophic bacteria Methylobacterium spp. on the perilla plant. Kyoto University Research Information RepositoryGoogle Scholar
  38. Omer ZS, Tomboloni R, Broberg A, Gerhardson B (2004) Indole-3-acetic acid production by pink-pigmented facultative methylotrophic bacteria. Plant Growth Regul 43:93–96CrossRefGoogle Scholar
  39. Pirttila AM, Laukkanen H, Pospiech H et al (2000) Detection of intracellular bacteria in the buds of Scotch pine (Pinus sylvestris L.) Microb Ecol 45:53–62CrossRefGoogle Scholar
  40. Pirttilä AM, Pospiech H, Laukkanen H et al (2003) Two endophytic fungi in different tissues of scots pine buds (Pinus sylvestris L.) Microb Ecol 45:53–62Google Scholar
  41. Pirttila AM, Laukkanen H, Hohtola A (2002) Chitinase production in pine callus (Pinus sylvestris L.): a defense reaction against endophytes? Planta 214:848–852CrossRefPubMedGoogle Scholar
  42. Pirttila AM, Pospiech H, Laukkanen H et al (2005) Seasonal variation in location and population structure of endophytes in bus of Scots pine. Tree Physiol 25:289–297CrossRefPubMedGoogle Scholar
  43. Podolich O, Laschevskyy V, Ovcharenko L, Kozyrovska N, Pirttila AM (2008) Methylobacterium sp. resides in unculturable state in potato tissues in vitro and becomes culturable after induction by Pseudomonas fluorescens IMGB163. J Appl Microbiol 106:728–737CrossRefGoogle Scholar
  44. Prasad SN, Ramachandra TV, Ahalya N, Sengupta T, Kumar A, Tiwari AK, Vijayan VS, Vijayan L (2002) Conservation of wetlands of India-a review. Trop Ecol 43(1):173–186Google Scholar
  45. Raghoebarsing AA, Smolders AJP, Schmid MC, Rijpstra WIC, Wolters-Arts M, Derksen J, Jetten MSM, Schouten S, Damste JSS, Lamers LPM et al (2005) Methanotrophic symbionts provide carbon for photosynthesis in peat bogs. Nature 436:1153–1156CrossRefPubMedGoogle Scholar
  46. Rajan SA, Devi TS, Maina CC, Prathibaha K, Sundaram SP (2012) Methylotrophs – a novel bioinoculant for sustainable agriculture. 6(3&4):141–144Google Scholar
  47. Rekadwad BN (2014) Growth promotion of crop plants by Methylobacterium organophilum: efficient bio-inoculant and biofertilizer isolated from mud. Res Biotechnol 5:1–6Google Scholar
  48. Sy A, Timmers AC, Knief C, Vorholt JA (2005) Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol 71:7245–7252CrossRefPubMedPubMedCentralGoogle Scholar
  49. Tanaka S, Walter KS, Schnoor JL (2008) Methods to investigate the role of endophytes in phytoremediation. In: Sorvari S, Pirttila AM (eds) Prospects and applications for plant associated microbes. A laboratory manual, Part A: Bacteria. Biobien Innovations, Turku, pp 325–332Google Scholar
  50. Ulrich K, Ulrich A, Ewald D (2008) Paenibacillus- a predominant endophytic bacterium colonizing tissue cultures of woody plants. Plant Cell Organ Cult 93:347–351CrossRefGoogle Scholar
  51. Verma P, Yadav AN, Kazy SK, Saxena AK, Suman A (2014) Evaluating the diversity and phylogeny of plant growth promoting bacteria associated with wheat (Triticum aestivum) growing in central zone of India. Int J Curr Microbiol App Sci 3(5):432–447Google Scholar
  52. Wang YN, Tian WY, He WH, Chen GC, An ML, Jia B, Liu L, Zhou Y, Liu SJ (2015) Methylopila henanense sp. nov., a novel methylotrophic bacterium isolated from tribenuron methyl-contaminated wheat soil. Antonie Van Leeuwenhoek 107(2):329–336CrossRefPubMedGoogle Scholar
  53. Wartiainen I, Hestnes AG, McDonald IR, Svenning MM (2006) Methylocystis rosea sp. nov., a novel methanotrophic bacterium from Arctic wetland soil, Svalbard, Norway (78° N). IJSEM 56:541–547PubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Manish Kumar
    • 1
    Email author
  • Raghvendra Saxena
    • 1
  • Rajesh Singh Tomar
    • 1
  • Pankaj Kumar Rai
    • 2
  1. 1.Amity Institute of BiotechnologyAmity UniversityGwaliorIndia
  2. 2.Department of Biotechnology and Bioinformatics CentreBarkatullah UniversityBhopalIndia

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