My research interests focus on the fundamental and applied study of extremophiles. Current projects include optimizing the production of commercially relevant biomolecules using haloalkaliphiles, and characterizing the role of Acidithiobacillus caldus,an acidophilic thermophile, to the leaching and remediation of acid mine environments.

My project involves the syntrophic interaction of a sulfate-reducing bacterium, Desulfovibrio vulgaris,and a methanogen, Methanococcus maripaludis,with a focus on physiological responses to various stresses. Methane is both a valuable source of energy as well as a notoriously potent greenhouse gas, thus an understanding of microbial communities involved in methane cycling is essential. As natural microbial communities are likely to interact in a biofilm, this growth state and its regulation, formation and structure are of primary interest.

Currently, I‘m investigating the phylogenetics of the dimethylsulfoxide (DMSO) reductase family of molybdopterin enzymes, specifically the minimally characterized sulfur reductases. These enzymes generate energy for microorganisms by reducing elemental sulfur (So) or other sulfur species (e.g. polysulfides) to hydrogen sulfide (H2S) in concert with an electron donor complex (e.g. hydrogenase). Sulfur has been shown to be an important element in certain hot springs in Yellowstone National Park (YNP) providing thermophilic microorganisms a source of energy. I have also been working on annotating and analyzing the recently sequenced genomes of two phylogenetically novel, thermophilic Crenarchaeota: an Acidilobus-like and a Metallosphaera-like organism, both isolated from thermal features in YNP. Finally, a project that was catalyzed by the NSF Research Coordination Network (RCN, www.rcn.montana.edu), of which I am the current Program Coordinator, involves the metagenomic sequencing of 20 diverse thermal features distributed throughout YNP. While those sites are being sequenced, I’m currently using bioinformatics to characterize and analyze sequences from 5 preliminary sites. This project promises to be a source of continued research and interest, specifically to my Ph.D program. Of note, my previous research has involved pathogen genetics, specifically genotyping bioterror agents.

The filamentous anoxygenic phototrophs (FAPs) of the Bacterial family Chloroflexaceae are dominant members of the microbial communities of alkaline siliceous hot spring microbial mats in Yellowstone National Park. The model organism of this group, Chloroflexus aurantiacus, has the capability of fixing carbon using a unique autotrophic pathway known as the 3-hydroxypropionate pathway. Metagenomic and in situ physiological studies are being used to explore whether the resident Chloroflexaceae in these mats are capable of using this autotrophic pathway in order to understand their relevance in the carbon cycling dynamics of the mat ecosystem.

Physical Properties of Biomineralized Biofilms. Focus on the fundamental properties of biofilms with and without biomineralization, and renewable sources of energy.

Protein bound metals and metal clusters are ubiquitous in biology where they occupy key positions in metabolic pathways functioning as catalysts in a wide spectrum reactions. One family of metal cluster containing enzymes, the [FeFe] hydrogenases, contain a distinct ligand modified iron sulfur cluster capable of supporting reversible hydrogen oxidation and reduction respectively and thus posess intriguing questions as to the nature of the biological evolution, usage, and modification of metal cluster motifs to bring about physiologically relevant catalytic abilities. The bio-assembly of this unique cluster is being investigated within the context of an overall effort to explore biosynthetic and functional relationships between extant metal clusters in biology and possible geologically relevant cluster precursors.

I am a Ph.D. student in the Department of Earth Sciences at Montana State University and a second year trainee in our Geobiological Systems IGERT. I obtained my M.Sc. from MSU, under the direction of Dr. Mark Skidmore. This work utilized various field and laboratory experiments to demonstrate that microbes present in subglacial sediment at the bed of the Haut Glacier d’Arolla, Switzerland, enhance the magnitude of subglacial mineral weathering. The focus of my doctoral research is on the geomicrobiology of the basal ice zone of Taylor Glacier, an outlet glacier from the East Antarctic Ice Sheet. This work includes (a) complete geochemical (e.g., solid phase, aqueous, gas, and isotopic) analysis of ice and geologic debris from the basal zone to identify chemical signatures that correlate with in situ microbial activity, and (b) determination of chemical constituents important to microbes living in the basal ice of Taylor Glacier.

My current work is focused on carbon metabolism and energy conservation in sulfur-metabolizing thermoacidophilic archaea from the order Sulfolobales, particularly Sulfolobus solfataricusand Sulfolobus acidocaldarius. I use published data and genome information to build network models of each organism’s metabolism. The modeling approach, known as elementary mode analysis, provides the entire set of irreducible steady state flow patterns through a given network. In the case of cellular metabolic networks, linear combinations of that set describe all the long-term continuous chemical transformations available to the cell. This output is useful (in concert with experimental data) for validation of the assumed network structure, as well as rational design of knockout and recombination experiments. In the past, I have worked on biofilm-resistant surface coatings, visualization of spatial heterogeneity of gene expression in biofilms, and laboratory-scale chemical reactors based on biofilm catalysis.

Yellowstone National Park (YNP) terrestrial hot springs provide an excellent environment to study microbial life in geothermal systems because they are relatively simple (few dominant community members as compared to soils), closed systems. Hydrous ferric oxyhydroxide (HFO) mats in acid-sulfate-chloride (ASC) springs of YNP are habitats for diverse microbial populations of Archaea that have yet to be isolated or characterized. These groups are of primary interest because while their physiologies remain unknown, they likely play an important role in biogeochemical cycling within the systems they reside. These novel groups are not only found in YNP terrestrial hot springs but they also reside in deep sea hydrothermal vents and other terrestrial hot springs around the globe. Thus, they may possibly be linked to the global biogeochemical cycle as well. Currently, I am utilizing metagenomic and geochemical data from HFO mats in ASC springs to describe these populations. The use of culture-independent methods such as metagenomics will provide insights into their potential physiologies. Geochemical data provides possible electron donor/acceptor pairs which lend evidence to what types of physiologies may exist in these springs. Quantitative PCR (qPCR) will also be employed to describe and locate these archaeons in the springs. Metagenomic and qPCR data in concert with geochemical data will provide clues to the metabolic strategies they utilize (i.e. aerobic versus anaerobic respiration). Future work will involve the isolation and characterization of these novel archaeons.

I am interested in the microbial community temporal and spatial dynamics during biostimulation. I am studying the 100-H site in Hanford, Washington, a chromium contaminated environment, before and after nutrient addition to stimulate chromium reduction. My current work includes clonal libraries of soil and water samples, pyrosequencing, and enrichments of acetoclastic and hydrogenotrophic methanogens.

Increased necessity to limit dependence on foreign fossil fuels along with elevated concerns involving increasing carbon dioxide levels have intensified the search for carbon neutral renewable fuels. Biodiesel consisting of methyl esters of fatty acids, produced from microalgae, has the economic potential to replace petroleum based fuel utilized within the current national infrastructure. Rob’s research is focusing on isolation, and optimization, of algal strains which produce elevated levels of Triacylglyerol, composed of fatty acids chains esterified to glycerol, that can be extracted and transesterified with alcohol to produce biodiesel. Rob’s background includes a BS and MS in Biological Engineering from Utah State University and industrial work with ATK Launch Systems, Promontory UT.

The emergence of diazotrophy and chlorophototrophy are two important events in the evolution of life on earth. Interestingly, many of the essential iron-sulfur containing enzymes involved in nitrogen fixation have homologs that are involved in (bacterio)chlorophyll biosynthesis. These homologs are thought to have diverged from a common ancestor; however, little is known concerning the selective pressures which might have led to this divergence in sequence, structure, and functionality. PCR-based molecular methods will enable examination of the diversity and ecological distribution of the Fe protein (NifH) involved in nitrogen fixation and its homolog, the protochlorophyllide reductase protein (BchL) involved in bacteriochlorophyll biosynthesis in environments where deeply-branching lineages are predominant. Furthermore, determining the ecological constraints of these two processes will enable a better understanding of environments wherein their divergence from a common ancestor may have occurred. Ensuing directed evolution of BchL to a NifH complement will enable biochemical characterization of the key residue differences that have evolved to confer the catalytic efficiency and specificity of each of these homologous proteins.

I am studying existing archaeal viruses and trying to discover new ones using molecular biology, metagenomics, and bioinformatics. I am also interested in virus-host interactions and how the hot spring environments affect the different organisms in a system.

archaea, carbon fixation, metagenomics, ncRNAs, RNA processing and bioinformatiocs

Microbial dissimilatory iron reduction is an important anaerobic lithotrophic metabolism found in both autotrophs (Gao et al., 2006; Yoshida et al., 2006) and heterotrophs (Bowman et al. 1997) that results in the reduction of ferric iron (Fe(III)) to ferrous iron (Fe(II)). This redox transformation is biologically important because ferrous iron is much more soluble (and therefore bioavailable) at neutral pH than most forms of ferric iron (Kappler and Straub, 2005). Recent studies have demonstrated that net community production (NCP) in the Southern Ocean is positively correlated with the level of soluble iron input from sources including melting sea ice and coastal sediments (see Cassar et al., 2007 for review). For example, a naturally iron-fertilized region of the sub-Antarctic Southern Ocean was found to have a carbon flux three times higher than adjacent, non-iron-fertilized areas (Pollard et al., 2009). This increase in production can have far-reaching effects, including the removal of CO2 from surface waters, thereby potentially influencing atmospheric CO2 concentration over even anthropogenic time scales. While iron reduction is a common metabolic strategy in psychrophilic microorganisms living in cold environments, such as glaciers and the polar oceans (Roh et al., 2006; Stapleton et al. 2005; Vandieken et al., 2006; Zhang et al., 1999), little is currently known about the overall contribution of psychrophilic iron-reducing microorganisms to the total soluble iron input of the Southern Ocean. The study of dissimilatory iron reduction in psychrophilic microorganisms at cold temperatures will lead to a better understanding of how this important nutrient is cycled in the Antarctic environment. This increased understanding may ultimately provide additional insight into factors controlling global CO2 concentration, which is an important factor effecting global climate change.

Structural and biochemical studies of Crenarcheal CRISPR-Cas systems with specific focus on Sulfolobus solfataricus. Specifically I focus on the heterologous expression of the CRISPR associated proteins in Escherichia coli, purification, crystallization, and structure determination. The crystal structures are used to predict specific molecular functions for the proteins and to design molecular and biochemical experiments to confirm the predicted function.