CAREER: Elucidating Niche Diversification in Nonthermophilic Crenarchaeota Colonizing Freshwater Sediments

Oregon Health & Science University, Portland OR

Investigators

Abstract

Recent discoveries of novel microorganisms have transformed paradigms in biological research. One example involves the remarkable change in our understanding of prokaryotic contributions to global biogeochemical cycles, based on the discovery of ubiquitous and abundant mesophilic members of the division Crenarchaeota. This group was previously thought to be comprised exclusively of thermophilic and hyperthermophilic archaea, but is now known to include a broad membership of mesophilic and low-temperature archaea living in non-extreme habitats. Currently, there is only one representative of this important group in pure culture: a marine isolate that fixes inorganic carbon into cellular biomass under aerobic conditions, using ammonia for energy. The ammonia oxidation process is the first step in microbially mediated nitrification, which links the mineralization of organic matter (formation of NH4+) to the recycling of N to the atmosphere (denitrification of NO3-). The metabolism of this isolate, together with results from environmental studies, suggest that autotrophic ammonia oxidation in archaea, rather than bacteria, may be responsible for the majority of nitrification in both marine and soil ecosystems. The diversity of habitats colonized by nonthermophilic crenarchaeotes and results from in situ metabolic studies suggest these organisms possess additional metabolic capabilities that may further impact elemental cycling on Earth. This project is a first step in understanding niche diversification in nonthermophilic crenarchaeotes. Fine-scale microbiological and geochemical analyses will be coupled with genome mining, gene expression studies and laboratory cultivation to test the hypothesis that aerobic chemoautotrophic ammonia oxidation is an important metabolic strategy for nonthermophilic crenarchaeotes in freshwater sediments, while also investigating the importance of a suite of other metabolic strategies for these archaea. This work is expected to broaden our understanding of the genomics and ecological properties of these enigmatic archaea in significant ways. Situated at the crossroads of microbiology, genomics, ecology and geochemistry, the research in this project will involve students from high school, undergraduate, graduate and postdoctoral levels in department- and university-wide efforts to forge new, interdisciplinary scientific partnerships. Three specific objectives will be addressed in the development of the education components of the project: (i) Creation of an interdisciplinary graduate curriculum emphasizing molecules to global ecosystems; (ii) Development of an EBS degree program focused on interfaces between environmental systems and human health; and (iii) Integration of high school and undergraduate students into the research goals of the project. The development of the EBS graduate degree program (Objectives i and ii) will help Oregon to become a leader in cross-scale, interdisciplinary research on environmental systems and human health. Addressing the latter objective, a collaborative program for undergraduate research experience in genomics is proposed between OHSU and Pacific University, a 4-year undergraduate institution. The goals of this program are to provide undergraduates with hands-on experience in genomics through the annotation and analysis of emergent crenarchaeal genome sequence data. The development of research and education programs that seek to identify novel metabolic properties of nonthermophilic crenarchaeotes will help elucidate the ecological roles and importance in global elemental cycles of members of this recently-discovered archaeal group.