Genome Information of Methylobacterium oryzae, a Plant-Probiotic Methylotroph in the Phyllosphere

Abstract

Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.

Plant Growth Promoting Activity of Pink Pigmented Facultative Methylotroph - Methylobacterium extorquens MM2 on Lycopersicon esculentum L.

“…The bacterium was investigated for the production of indole acetic acid and its relation with plant growth promotion was established. Microbes utilize methanol dehydrogenase (MDH) enzyme for the degradation of methanol encoded by mxaF gene which can be employed as marker gene for the identification of Methylobacterium [8].…”

“…are classified as biostimulator, biofertilizer and biocontroller as they directly influence the plant growth by producing phytohormones especially auxins, supply nutrients to the plants and induce systemic resistance in the plants against phytopathogens [8]. In recent years, Methylobacterium received considerable attention for industrial and agricultural applications [9].…”

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

“…Generally, the phyllosphere contains four major phyla of bacteria such as the Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria (Kembel et al 2014;Durand et al 2018). Methylotrophic bacteria are predominant in phyllosphere which includes genera such as Methylobacterium, Methylophilus, Methylibium, Hyphomicrobium, Methylocella, Methylocapsa, and Methylocystis (Mizuno et al 2013;Iguchi et al 2013;Kwak et al 2014;Krishnamoorthy et al 2018). Methylobacterium and Sphingomonas are the predominant genera belonging to the class alphaproteobacteria reported in several plant phyllospheres (Delmotte et al 2009;Kumar et al 2019a).…”

Endophytic bacteria isolated from ip mirim (Tecoma stans Bignoniaceae) and its application for plant growth promotion

“…Which was previously reported by other authors (Sy et al, 2001;Madhaiyan et al, 2006Madhaiyan et al, , 2007Bogas et al, 2016). The mechanisms involved are: (1) phytohormone production: Mainly auxin and cytokinines (Dourado et al, 2015;Kwak et al 2014); (2) Stress decrease: Heavy metal tolerance (Dourado et al, 2015) and ACC deaminase production (Bogas et al, 2016). Bacterial ACC deaminase uses the ethylene precursor: ACC (Aminocyclopropane-1-carboxylic acid) as source of nitrogen, decreasing the production of ethylene, increasing plant growth (Hardoim et al, 2008(Hardoim et al, , 2015; (3) Nutrient uptake: Phosphate solubilization (Glick, 1995), nitrogen fixation and plant nodulation (Sy et al, 2001).…”