Microbes dominate planetary biomass, play essential roles in nutrient recycling, can cause disease, and are an integral part of the healthy human body. Their genomes contain records of past evolutionary events, from which we can decipher how microbes evolve and adapt to their environments. Recent advances in DNA sequencing technologies brought us an avalanche of data: thousands of genomes and terabases of environmental DNA (metagenomes). We mine these data sets (1) to assess the impact of horizontal gene transfer on microbial populations; (2) to find new ways to characterize microbial communities; and (3) to track down genomic signatures of microbial adaptations.
We are actively investigating the following questions:
Gene transfer agents: their origin and role in evolution of microorganisms
Gene Transfer Agents (GTAs) are virus-like entities with their genes encoded in a host cell genome and controlled by the host and environmental factors. Expression of GTA genes results in production of small particles that package random pieces of host DNA (in contrast to a virus, which would preferentially package its own DNA). The particles are subsequently released into the environment and can deliver the DNA to other cells. We are interested in understanding where GTAs came from, why and how they are maintained in bacteria, how widespread they are in different lineages, and what their function is in microbial populations. To address these questions, we utilize comparative sequence analysis and data mining approaches. We recently showed that GTAs evolved under positive selection for the reduction of the energy cost of a GTA particle production. We hypothesize that GTAs are dedicated devices for the survival of bacteria under the conditions of nutrient limitation. The possible benefits conferred by GTAs under nutritional stress include horizontal dissemination of genes that could provide bacteria with enhanced capabilities for nutrient utilization and the increase of nutrient availability through the lysis of GTA-producing bacteria.
Genomic signatures of thermoadaptation
Microbes can occupy a diverse range of environments. The bacterial phylum Thermotogota once thought to be made up exclusively of organisms growing optimally at temperatures above 80°C. However, we now know that as a group, Thermotogota can grow between 20 and 90°C, occupying a variety of anaerobic environments rich in hydrocarbons and various pollutants. Adaptation for dramatically different thermal niches requires changes in genes and their protein products. With hundreds of Thermotogota genomes in hand we are hunting for clues of such adaptations.