Harnessing Metagenomics to Unveil the Underrepresented Fraction of the Soil Microbiome

Abstract

Soil ecosystem services such as nutrient cycling, maintenance of soil fertility, water purification and carbon sequestration depend on complex microbial communities. However, our ability to study microorganisms in the environment has been limited by the constraints in technological capabilities. Gene marker analyses have allowed us to taxonomically describe the diversity and composition of microbial communities and identify the factors shaping their population abundances. More recent advances in genomics have enabled the study of mobile genetic elements and viruses within the soil, which have important roles in bacterial host survival and function and overall soil processes. In this PhD thesis, I leveraged metagenomic analysis tools to explore two understudied fractions of the soil microbiome – phages and mobile genetic elements –, and their response to anthropogenic ecosystem changes that threaten soils globally. I observed that soil viruses and mobile genetic elements such as plasmids have unique responses at the community structure and functional level to anthropogenic changes in soil, both directly through land use practices, and through changes in ecosystem processes (drought) and climate. Furthermore, these responses can alter the structure and function of the overall microbial communities, making the study of these underrepresented fractions relevant to the prediction of soil microbial responses to global change and the development of strategies to maintain essential ecosystem services.