Metabolomic analysis of maize (Zea mays&nbsp L.) seedlings treated with selected plant growth promoting rhizobacteria

Abstract

Global food production has significantly increased mainly due to the use of high-yield crop varieties, fertilisers, fungicides and pesticides, and improved irrigation methods. Despite the increase in production, there has been a significant cost to the environment in the form of pollution, and to farmers in the form of rising fertiliser and pesticide costs. The impacts on the environment include but are not limited to groundwater contamination, declining soil health and increased pest and pathogen resistance, all which increase the financial cost to farmers. To reverse or rather salvage the situation, more sustainable agricultural practices need to be employed that will maintain high productivity with little to no damage to the environment, and will reduce agrochemical use, thus, reducing the financial strain on farmers. A potential solution would be to exploit soil dwelling rhizospheric microorganisms to improve plant growth with little to no application of agrochemicals. The rhizosphere refers to the region of soil directly influenced by plant roots and is home to microorganisms known as plant growth promoting rhizobacteria (PGPR). These PGPR have been found to stimulate plant growth via numerous mechanisms, which directly affect the plant metabolome and in turn translates into observable effects in the plant phenotype. The plant metabolome has been described as the bridge between the genotype and phenotype, thus metabolomics acts as a useful tool to evaluate the contribution of external influences on the plant phenotype based on metabolic changes. The effect of PGPR on the plant metabolome is vital in understanding their mode of action, which will further validate their use in farming. The overall aim of this project was to assess the effect of selected PGPR strains with known plant growth promoting activity on the metabolic profile of maize seedlings; and to evaluate if these changes in the metabolic profile directly correlate with the observable effects on the growth of the seedlings. To achieve this aim, firstly, the effect of Lysinibacillus sphaericus (T19), Paenibacillus sp. (T29) and Bacillus megaterium (A07) on early maize growth, i.e., the effects on dry root and shoot biomass, leaf chlorophyll content, stem diameter and shoot length, was assessed. Secondly, the effect of single strain PGPR inoculation on the metabolic profile of maize was evaluated. Finally, metabolomics analysis was conducted on the roots and shoots of the maize seedlings inoculated with strains T29 and T19 respectively. Statistical analysis of the metabolomics results was conducted to find significant pathways and discriminating metabolites between the control and inoculated plants. To assess the effects of the PGPR strains on early maize growth, a greenhouse trial was first conducted. Non-invasive techniques were used to measure the growth parameters that could be recorded prior to harvest. Next an untargeted metabolomics approach was used to analyse the metabolome of harvested roots and shoots. Metabolomics data acquisition was achieved using ultra-performance liquid chromatography hyphenated to quadrupole time of flight mass spectrometry detection (UPLC/QTOF-MS). Finally, to evaluate the effect of single strain inoculation on the maize root and shoot metabolome, univariate and multivariate methods were applied. The results of the greenhouse trial showed a tendency of strains T19 and T29 in stimulating shoot growth and root growth respectively in the maize seedlings. Pathway analysis using results from univariate analysis revealed a number of pathways affected by T19 and T29 in the shoots and roots respectively. Multivariate statistical analysis also showed that the inoculated samples differed from the control samples, albeit with varying trends, which indicates differing metabolic states. Some of the metabolic pathways deemed significant in the inoculated shoots and roots were amino acid, nucleotide metabolism or carbon fixation related. A number of discriminating features were found to be differentially regulated in the inoculated roots and shoots. Overall, the results showed that T19 and T29 inoculation stimulated metabolic responses in maize shoots and roots linked to plant growth and development.