Towards Understanding the Ecophysiology and Genome of the Novel Freshwater Ammonia-oxidizing Archaea That Originated from Biofilters

Nitrogen compounds such as ammonia, nitrate and nitrous oxide are environmental pollutants of concerns as they can degrade soil, water and air quality. Of particular interest in this study is the nitrification reaction within the nitrogen cycle where ammonia is oxidized to nitrite and subsequently to nitrate. Historically, nitrification is thought to be only catalyzed by ammonia-oxidizing bacteria but recent studies have indicated that members in the archaeal domain, particularly those within theThaumarchaeotaphylum, can also oxidize ammonia. The discovery of this new group of archaea is significant as their activities in different ecosystems can alter the nitrogen budget.Since ammonia-oxidizing archaea are a newly emerging group of organisms, our knowledge of their biology is still at its infancy and much remains to be learned. In our previous work, we have identified a novel group of ammonia-oxidizing archaea that are important in freshwater biofilters, and we have successfully cultured these ammonia-oxidizers in the laboratory. In order to gain further insights into the physiology and genome of the identified freshwater ammonia-oxidizing archaea, here we propose an innovative research plan that uses culturing approaches and advanced molecular techniques to study their biology. Specifically, using the established cultures, we will characterize the physiology of the freshwater ammonia-oxidizing archaea under environmentally-relevant conditions such as different temperature, pH and concentrations of ammonia, oxygen, salinity, carbon dioxide, and organic carbons. Furthermore, the genomes of the ammonia-oxidizing archaea will be sequenced and annotated using high-throughput sequencing approaches in order to determine their gene contents. Once the genomes are available, genome-wide transcriptomic and proteomic analyses will be conducted to query the metabolism of the ammonia-oxidizing archaea under different environmental conditions. Overall, the proposed research will provide new scientific knowledge of freshwater ammonia-oxidizing archaea and further our understanding of the nitrification reactions in freshwater environments.