Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Abstract

: Plants do not grow in isolation, rather they are also hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their sole benefit, others may have a direct bearing on plants in a symbiotic manner. Unravelling plant-microbe interactions is a crucial component to recognize the beneficial and detrimental impact of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence the plants. The progress in sequencing technologies in the genomics era and several omics tool has grown in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plantmicrobiome. At the same time, this study further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation. This work also provides a better intelligence about metabolic interactions between the microbe and the plant through omics approaches. The review explores advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between the plant and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions. This review will bring forth recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

The cypsela (achene) of Echinacea purpurea as a diffusion unit of a community of microorganisms

“…The presence of endophytes is considered useful for the plants, by mean of several direct and indirect interaction mechanisms, including hormones-mediated stimulation of plant growth, improvement of mineral nutrition, increase of abiotic stress resistance, and defense from phytopathogens (Lugtenberg and Kamilova 2009 ; Liu et al 2017a ). Modern “omics” technologies have demonstrated that such beneficial interactions depend on specific genetic traits of these microorganisms (Sharma et al 2020 ), including genes involved in mineral nutrient metabolisms, antibiotic production/resistance, and sporulation: interestingly, such traits differ between beneficial microbes co-inoculated in plants (Gamez et al 2020 ).…”

Plant–Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

“…Through the advent of the genomic tools, a better understanding of the interactions between plant and pathogens is obtained. Transcriptomics have enabled us to identify genes that are enhanced or inhibited in the plant-microbe interaction, providing a clearer picture of what may be happening in the regulation at the molecular level [ 25 , 138 , 139 , 140 ]. These studies also implied important roles for microRNAs in plant response against the pathogens, the plants innate immunity, as well as the triggered defenses in plants [ 141 , 142 , 143 ].…”

The Lack of Knowledge on the Microbiome of Golf Turfgrasses Impedes the Development of Successful Microbial Products

“…Microbiomes of many plants, including model organisms like Arabidopsis thaliana or important crops like rice, have been studied in great detail [34,35], but holistic, state-of-theart research on microbial communities associated with turfgrasses, especially those used on golf courses, are lagging far behind (Figure 1). The lack of knowledge is even deeper as implied by the figure, considering that golf turfgrasses are highly diverse and include a multitude of different species and cultivars.…”