Projects
Amazon Rainforest Microbial Observatory: Functional Diversity, Taxonomic Diversity, and Response to Ecosystem Conversion.
The Amazon Forest is the largest terrestrial ecosystem, yet the least understood regarding microbial diversity. The increasing demand for food, fiber, and biofuels has caused an shift in forest to agriculture. In this research project, we ask: (1) What are the bacterial taxa present in the Amazon rainforest soils?, (2) How are these taxa present in space and time?, and (3) What are the taxa alterations due to forest-to-agriculture conversion? A combination of high throughput sequencing of the 16S rRNA gene (454 pyrosequencing) and cultivation will be used to a proxy for group-level genetic diversity.
Collaborators: Dr. Brendan Bohannan (Univ. of Oregon), Dr. Brigitte Feigl (Univ. of Sao Paulo), Dr. Klaus Nüsslein (Univ. Massachusetts), Dr. Vivian Pellizari (Univ. of Sao Paulo), and Dr. James M. Tiedje (Michigan State University).
Functional Genomics of a Verrucomicrobium Population for Cellulose Degradation.
Wood-feeding termites are model bioconverters, harboring an entire microbial community orchestrated to transform cellulose, hemicellulose and lignin into soluble oligosaccharides, H2, and methane, among other intermediates of interest for biofuel production. Earlier, a proposal submitted to the Department of Energy/Joint Genome Institute was approved for genome sequencing of one strain of the phylum Verrucomicrobia (TAV2) isolated from the termite gut. The genome revealed important physiological and ecological attributes relevant to the ecosystem functioning for cellulose degradation. We are interested in the carbohydrate utilization profiles of strain TAV2 under defined O2 conditions. In addition, we aim to extend the genomic and physiological characterization to the other members of the Verrucomicrobium population using the TAV2 genome as a guide. We hypothesize that intraspecies variation is as an essential component of ecotypic differences and a stabilizing force in ecosystem resilience.
Whole Cell Transcriptional Variation of a Shewanella baltica Population.
This research project asks if differences in whole cell transcriptional patterns rather than gene content drive speciation in early stages. We take advantage of four fully sequenced genomes of Shewanella baltica, representing three different ecological zones: oxic, transition, and anoxic environments. Because microbial processes in the environment are carried out by a mixed population rather than a single genotype, results from this research have wide applications such as the understanding of population diversity, microbial activity modeling, genomic response to environmental perturbations, raise of new species, among others.