Holistic sequencing: moving forward from plant microbial proteomics to metaproteomics

In natural environments, plant and microbial communities continuously interact with each other as well as with the environment. Plant-associated microbial communities are critical to plant growth and health. However, the biological impact of microbial communities within natural habitats is not only attributed to the biological activities of a specific microbe, but are also impacted by the microbial communities as a whole. Hence, a deep understanding of the complexity of microbial systems cannot be achieved solely by monitoring certain microbes in isolation. The integration of omics data provides a unique opportunity to tackle long-term problems in the area of plant and microbial ecology. Environmental proteomics or metaproteomics provides a practical tool for a better understanding of the function, structure, dynamics and significance of plant-associated microbial communities in both natural and man-made environments. To begin this chapter, we will present the importance of plant associated microbial communities and their impact on plant growth and health. We will then progress to the application of different omics approaches, especially proteomics for large-scale protein analysis, in order to dissect the molecular basis of plant-microbial interactions in a post genomic era. Next we will examine the advantages of integrating omics data to give a comprehensive understanding of plant microbial communities toward the development of efficient management strategies that reduce the impact of environmental stress and control plant disease epidemiology. We will conclude with a real application of metaproteomics to manage a plant phytobiome, thereby promoting agricultural sustainability.