Physiological and Genomic Diversity of Marine Nitrifiers
A major focus of our lab is the cultivation and characterization of previously uncultured marine nitrifiers. To us, they are the most exciting representatives of a broad metabolic group of microorganisms called chemolithoautotrophs--organisms that get their energy and carbon from inorganic compounds.
Enrichment cultures of archaea that can carry out the first step of nitrification by oxidizing ammonia (NH3) to nitrite (NO2-) are a powerful tool for learning about what controls this process in the environment, how ammonia-oxidizing archaea interact with other microorganisms, and understanding the evolution of ammonia oxidation. Our lab houses a unique culture collection of ammonia-oxidizing archaea from the open ocean. We have used the cultures to describe the stable isotopic signature of nitrite produced by archaea and to show that they can produce the greenhouse gas nitrous oxide (N2O). We are using a combination of molecular techniques (including genomics, transcriptomics, and proteomics) and traditional physiology to understand how these archaea have expanded to become such ubiquitous and abundant members of the microbial world.
We also study the organisms that carry out the second step of nitrification, the nitrite-oxidizing bacteria (NOB). Our lab houses a large collection of NOB isolated by Stan Watson and Frederica Valois at Woods Hole Oceanographic Institution over many years. Through an award from the DOE's Joint Genome Institute, we are sequencing the genomes of several strains in this collection.