We are using state of the art Genomics and Bioinformatics tools to study problems in Molecular Ecology and Evolution. We are developing molecular techniques for the high throughput characterization of the interactions of bacteria, fungi, archae, protists in microbial communities, molecular systematics, and population genetics. We have recently developed a Multitag Pyrosequencing methodology that allows us to profile dozens of samples at one time. We are using this technology to reconstruct evolutionary histories of organisms, characterize microbial communities of aquatic and terrestrial ecosystems, and analyze human and environmental diseases.