Linking Resource and Stress Gradients to Microbial Community Composition and Function through the Soil Profile of a California Annual Grassland at the Sedgwick Reserve

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Despite recent advances in environmental microbiology, our understanding of the factors that control microbial community composition and dynamics is still limited, and of the links between community composition and functioning not well understood. Developments in this direction will come from blending top-down (process) and bottom-up (molecular diversity) approaches, and tying into existing ecological theory. The intermediate disturbance & resource supply hypotheses from plant ecology should apply to microbial communities through the soil profile, as both resource availability and stress are high at the soil surface but decline with depth. Stress and disturbance may also partially explain why linking soil diversity to function has been difficult in studies that rarely sample below 10 centimeters. Soils are much deeper, with significant microbial populations at depth accounting for a substantial amount of whole-profile activity. The central hypothesis of this Microbial Observatory is that the gradients of resources and stress are the primary drivers of the size, diversity, dynamics, activity, and growth strategies (biofilm formation) of the microbial community throughout the soil profile. This project will be carried out at the Sedgwick Reserve, a site of active collaborative work on landscape processes, soil dynamics, plant community structure, and soil microbial processes in the California annual grassland/oak savanna ecosystem. Work will couple extensive sampling across the reserve to intensive manipulative studies at two core sites, where monitoring of soil climate, chemistry, and communities down to at least 4 meters depth and manipulative studies will be established. Soil moisture and temperature will be monitored to evaluate stress gradients, while substrate gradients will be assayed through a combination of physical soil organic matter fractionation and bioassay approaches. Microbial biomass will be measured, as will total and active numbers and biovolumes of bacteria and fungi. Bacterial community structure and composition will be assayed by pairing DGGE (denaturing gradient gel electrophoresis) and t-RFLP (terminally labeled restriction fragment length polymorphism). DGGE has the advantage that individual bands may be characterized and specific probes developed, while t-RFLPs provides cleaner analysis of complex DNA mixes. These fingerprinting approaches will be followed up by developing probes for specific bacteria and quantifying their population dynamics through the profile and under experimental manipulations. This project will also examine how the microbial microhabitat changes along the stress and resource gradients by examining the extent of biofilm formation and extracellular polysaccharide production, which appear to be central components of bacterial stress responses. Biofilm extent will be evaluated both by environmental electron microscopy and chemical analysis of polysaccharides. Microbial process dynamics will be measured by a suite of C and N turnover processes on intact soil samples. These include net and gross N turnover rates, maximum consumption rates for a variety of 14 C substrates (a range of monomers, cellulose, wood), the substrate use efficiency on those substrates, the growth rate of microbes using them, and the biomass of the populations capable of using each substrate. This integration of studies on resource and stress gradients, community composition, biofilms, and community functioning will greatly increase our understanding of microbial community ecology and its links to ecosystem processes.