IMPACTS OF ANTHROPOGENIC STRESSORS ON MICROBIAL COMMUNITY STRUCTURE AND FUNCTION.

Microbial communities in soils and waters perform critical roles in maintaining ecosystem function, in addition to directly impacting human and plant health. Human impacts, including pollution and sea level rise, can effect both the structure and function of these communities in nature. This project will investigate the complex structures of microbial communities in soils and waters, and link these structures with critical ecosystem services. A clearer understanding of the impacts of human activities on microbial community structure and function will provide a mechanistic insight into impacts of pollution on our environment.

Identification of interactive networks within peatland microbial communities: The study sites for this objective will include established stations in Panama (Changiunola River, Bocas del Toro state, Panama; Cheesman et al., 2007) and the Florida Everglades (Water Conservation Areas). The primary approach will be metagenomic, and Small Subunit rRNA genes in DNA extracted from the samples will be sequenced via platforms available at the UF ICBR, such as the Illumina MiSeq or Life Technologies Ion Torrent systems (Degnan and Ochman, 2012). These data will be combined with previously obtained sequences for functional genes, such as mcrA (methanogenesis), dsrB (sulfate reduction), and nifH (nitrogen fixation) and organized into interaction networks. Bioinformatics will be a critical part of this objective. We will work in close association with specialists in the UF ICBR and with colleagues in the UF Computer & Information Science and Engineering Department.Characterization of the roles of interactive networks and environmental controls: The stability and controls of interactive networks defined in Objective 1 will be tested through analysis of samples collected across years and seasons. Controls on the networks and their impacts on specific processes will be tested in manipulative experiments, that include impacts on decomposition of plant material and methane production. This will include both SSU sequence analysis and RNA Seq approaches to define the response in expression of critical genes. General expression patterns will be defined through RNA Seq analysis and targeted gene expression will be monitored through RT-qPCR of specific genes of interest. Appropriate procedures will be used test correlations between activities of the genes of interest and the processes of interest, such as methane production and mercury transformation.Analysis of the impacts of sea level rise on the distribution of microbial groups and the processes: This work is currently in its beginning stages, and is being conducted in collaboration with colleagues in the UF Geology Department. Study sites include well defined sites in the Indian River Lagoon, Florida, and in the Yucatan Peninsula, Mexico. DNA extracted from water and sediment samples and characterized from coastal regions associated with submarine groundwater discharge, and analyzed for distribution and activities of genes specifically involved in sulfur and nitrogen cycling. SSU rRNA genes from selected samples are currently being sequenced via the Ion Torrent platform. Column experiments will be conducted to test hypotheses related to impacts of sea level rise on nitrogen cycling.Analysis of rhizosphere dynamics in citrus trees effected by huanglongbing Rhizosphere community functional diversity will be assessed in rhizopsheres of trees symptomatic of HLB infection and those not symptomatic. Ammendments intended to improve rhizosphere function will be tested. Functional diversity will be evaluated by Community Level Physiological Profiling (Weber and Legge, 2010), and the relative impact of the ammendents on mycorrhizal fungi will be investigated by monitoring spore numbers and percentage of mycorrhizal colonization of tree roots.