The Vital Importance of Soil Health: from Laboratory Systems to Ecosystems

Healthy soil is an important resource in both natural and agricultural ecosystems.  It harbors both chemical and biological sources of nutrients that are required for plant growth, reproduction, insect and pathogen resistance, and response to changing environments.  However, current agricultural practices rely heavily on the meticulous management of chemical nutrients.  In natural ecosystems, nutrients are taken up by microorganisms and delivered to plants during interactions with plant roots in exchange for fixed carbon.  While such symbiotic relationships play an essential role in the regulation of soil nutrient cycling and subsequent carbon management, the complexity and variation of such natural systems has hindered the accurate assessment of the factors that signal, establish and maintain these interactions.  Thus, our lab has made use of simplified Populus-Laccaria-Pseudomonas laboratory systems and multiple "omics" approaches to integrate RNA-Seq, SWATH proteomics, ChIP-Seq, biochemical and FTIR imaging analyses to enhance our understanding of how atmospheric carbon is sequestered as plant and/or subsurface fungal biomass during symbiotic interaction and/or nutrient limitation.  Our results indicate that molecular events at the protein level are key in drawing conclusions for such processes.  We aim to make use of these laboratory systems to study natural ecosystems by providing a mechanism to probe how nature so effectively controls availability of soil nutrients through the activity of beneficial microbes.  We discuss how holistic system design approaches, combined with modern molecular techniques, provide technologies for the deep repair of ecosystems and the development of solutions for depleted topsoil, broken hydrological cycles, and falling soil fertility.