I am interested in the conservation of wild salmon stocks and the proliferation of sustainable aquaculture.  While sometimes conflicting, these two goals can be pursued simultaneously through the careful anticipation of increased competition, genetic introgression, and disease transmission.  My research investigates two parasites, Myxobolus cerebralis and Ceratomyxa shasta which are transmissible between cultured and wild stocks of salmonids and responsible for extensive mortality among both populations.  I am analyzing gene expression of these parasites during infection in order to develop treatments which will allow aquaculturists to better manage disease.

Dr. Bartholomew:  M.S. candidate; Nash 528; 541-737-9664;



My research will use omics to study microbial communities in lagoons on the northern coast of Alaska. Seasonal shifts in salinity, temperature, freshwater runoff, and increasing permafrost thaw are all potential factors in shaping these communities. This is part of a larger, Long Term Ecological Research (LTER) study aimed at understanding how these changing factors affect the estuarine food webs.

Dr. Crump:  Ph.D. candidate; Weniger 537, 541-737-2359;



I am interested in studying the genetic architecture of disease resistance in Salmonids. My research is focused on identifying resistance genes in rainbow trout (Oncorhynchus mykiss) to the myxozoan parasite Ceratonova shasta.  

Dr. Bartholomew: Ph.D. candidate; Nash 514; 541-737-9664;



High-latitude aquatic microbiomes are particularly dynamic and responsive due to climate change and yet we do not understand, and cannot predict, how crucial aspects of this system will change.  My research will focus on defining functional diversity of northern wetland metagenomes and the role they play in global element cycling, more specifically iron.

Dr. Colwell:  Ph.D. candidate; Weniger 537; 541-514-8584;



My project will be centered on volatile organic compounds in cyanobacterial blooms, specifically for freshwater lakes in the Northwest.

Dr. Halsey:  Ph.D. candidate; Nash 352; 541-737-1806;



I am interested in studying viral latency and the development of novel antiviral therapies that combat this viral strategy of immune evasion. My current research focuses on studying the molecular virology of a recently discovered latency associated factor (ORF6) found in Koi Herpesvirus. I will study ORF6’s function during viral latency with a particular focus on the role of ORF6 in apoptosis.

Dr. Jin: Ph.D. candidate; Dryden Hall 105B; 541-737-6540;



I am rotating through three labs this year, beginning with a project investigating the impact of the gut microbiota on autism spectrum disorder.  I am also interested in learning and utilizing computational methods to explore large data sets.  I am also interested in microbial ecology and microbiome research.

 Dr. David: Ph.D. candidate; Nash 554; 541-737-8630;



In collaboration with the Confederated Tribes of the Warm Springs of Oregon Reservation, USFWS, and ODFW, our goal is to discover the role of pathogens (such as the parasitic myxozoan, Ceratonova shasta) in juvenile and pre-spawn mortalities of adult Spring Chinook salmon.   We will use qPCR analyses of both bi-weekly and longitudinal water samples, conduct sentinel fish exposures, and perform necropsies. 

Dr. Bartholomew:  M.S. candidate; Nash 528; 541-737-2977;



I am interested in leveraging computational techniques to improve our understanding of microbial evolution.  My work currently focuses on assessing the accuracy of 165 phylogenetic trees which are an integral tool used to infer evolutionary relationships between members of microbial communities.

Dr. Sharpton:  M.S. candidate; Nash 554; 541-737-8630;



I am investigating the pathogenesis of Mycobacterium avium and related species. I am interested in intracellular survival mechanisms and host response.

Dr. Bermudez:  Ph.D candidate; Dryden106; 541-737-6532;



My research interests include learning more about how pathogens cause disease in both humans and animals. The project I will be working on is looking at the host-microbe interaction between Mycobacterium avium and human respiratory epithelial cells. Specifically, I am looking at their ability to form microaggregates and identifying the proteins and their function used in this process.

Dr. Bermudez:  M.S. candidate; Dryden 106; 541-737-6532;



I am interested in the ecology and evolution of Vibrio bacteria, particularly those associated with shellfish, as Vibrio species can cause disease in shellfish. In one project, I am investigating the dynamics of Vibrio populations and the overall microbial communities within shellfish hatcheries in relation to disease events and changes in abiotic factors. In another project, I am sequencing draft genomes of Vibrio isolates and conducting comparative genomic analysis to understand gene differences between isolates.

Dr. Mueller:  Ph.D. candidate;  Nash 446; 541-737-8605;



I am interested in how matter and energy flow through large biological systems, namely the microbial systems that connect the continents to the seas.  I am using -omics to study the turnover of terrestrially-derived organic matter by bacterial communities in estuaries and coastal oceans.  Findings from this research should provide a better understanding of the composition and function of heterotrophic bacterial communities that "eat" and respire all the carbon that is produced on land but washes to the sea.

Dr. Mueller:  Ph.D. candidate;  Nash 446; 541-737-8605;



Microorganisms that occupy the vertebrate gastrointestinal tract play an important role in determining their vertebrate host's health.  However, it is unclear how the influence of microbes on host health is related to the ecological success of vertebrates.  I use a salmonid model (i.e., rainbow trout) to quantify the contribution of gut bacteria to the ecological fitness of fishes and how climate change perturbs these contributions.  Ultimately, my work will improve the management and conservation practices of fisheries.

Dr. Sharpton:  Ph.D. candidate; Nash 514; 541-737-9664;



Marine sediments are one of the earth’s largest sources of methane, a greenhouse gas.  Consortia of methanotrophic archaea and sulfate-reducing bacteria in marine sediments consume up to 90% of this methane, so comparatively little reaches the overlying ocean.  The microbial community response to methane flux from the subsurface is largely uncharacterized.  I am using high-pressure enrichments and analyzing microbial communities in Arctic sediment samples to investigate how and where these microbes consume methane and how their communities change over time.

Dr. Colwell:  Ph.D. candidate; Weniger 537; 608-609-2474;



Disruption of symbiosis by pathogens or abiotic stressors is correlated with disease events, which are a major cause of coral mortality in tropical reefs worldwide. I study an obligate intracellular parasite within Rickettsiales that is correlated with decreased coral health and stimulated by excess nitrogen in the form of nutrient pollution. By probing the newly-assembled genome of this organism, I hope to discover a genetic basis for these effects on coral health. Additionally, I will use transcriptomics to assess the effects of this parasite on the coral immune system during nutrient-enriched tank experiments.

Dr. Vega-Thurber: Ph.D. candidate; Nash 446; 541-737-8605;



Toxoplasma gondii is currently the second most common foodborne illness in the United States. Utilizing zebrafish as a high-throughput, biomedical model allows for future discovery of drugs to combat the chronic stage of toxoplasmosis. My research aims at improving the current zebrafish model by understanding immunological mechanisms within the organism. 

Dr. Kent:  M.S. candidate; Nash Hall 514; 541-737-9664;



I study how environmental stressors alter the coral host and its associated microbes.  I will be conducting field and tank experiments at the Gump Research Station on Moorea, French Polynesia to investigate how parrotfish predation and nutrient enrichment combine to cause coral mortality.

Dr. Vega-Thurber:  Ph.D. candidate; Nash Hall 446; 541-737-8605;



I am interested in the roles microbial communities play in ecosystems.  My work will focus on links between biogeochemical cycling, viral infection, and endosymbiotic dinoflagellates in overall coral physiology and reef health.

Dr. Andrew Thurber:  M.S. candidate; Burt Hall 124;



I am interested in the evolution of symbiosis and inter-individual cooperation.  More specifically, I study the interactions between corals and their microbial associates, an important and understudied facet of a globally endangered ecosystem, the coral reef.

Dr. Vega Thurber:  Ph.D. candidate;  Nash 446; 541-737-8605;



Diatoms are among the most important phytoplankton. My research is focused on the behavior of diatoms. Using a wide variety of techniques, I am working to understand the ecology of the diatom life cycle and how diatoms interact with other microbes in the ocean. 

Dr. Halsey:  Ph.D. candidate; Nash 352; 541-737-1806;



I am interested in the role of phytoplankton physiology on marine biogeochemical cycles. Currently I am studying phytoplankton physiological responses during acclimation to deep mixing events in the ocean. I plan to extend my research to investigate the contributions of various phytoplankton groups, such as mixotrophs (phytoplankton that can both photosynthesize and consume organic carbon), on ecosystem production. 

Dr. Halsey: Ph.D. candidate; Nash 352; 541-737-1806;



I am interested in the connections between phytoplankton physiology and gene expression and ocean biogeochemical cycles. My research will focus on the role of microbial communities in carbon sequestration to the deep ocean.

Dr. Halsey: M.S. candidate; Nash 352; 541-737-1806;



My research interests lie in marine microbial ecology on tropical coral reefs, specifically how coral-associated microbial communities from different coral host species respond to nutrient enrichment, coral bleaching events, predation pressures, and varying anthropogenic impacts.

Dr. Vega-Thurber:  Ph.D. candidate; Nash 446, 541-737-8605;



I am interested in utilizing zebrafish as a biomedical model to further investigate immunological mechanisms that occur when fish are exposed to parasites, such as Pseudoloma neurophilia, and other pathogenic organisms.

Dr. Kent:  Ph.D. candidate; Nash 526; 509-853-7864;


I am interested in studying the effects of certain microbes on human health.  My research will focus on the impact of gut microbiomes on behavior, as part of the major study area of the microbiome-gut-brain axis.

Dr. David:  M.S. candidate; Nash 554; 541-737-8630;



I am interested in studying quorum sensing, iron acquisition, and social cheating in Pseudomonas.

Dr. Schuster:  Ph.D. candidate; Nash 446; 541-737-8605;



I am investigating mucosal immunity and resistance mechanisms to the myxozoan parasite, Ceratonova shasta, in rainbow trout.  My focus is on the role of immunoglobin T (a mucosal immunoglobulin isotype unique to fish) during infection with C. shasta.  I am also interested in characterizing the early and ongoing inflammatory response to different C. shasta genotypes, ad determining if an adaptive immune response provides protection against reinfection.

Dr. Bartholomew:  M.S. candidate; Nash 528; 541-737-2977;



I am studying gut bacteria and their relationship to human health, focusing on the gut-brain axis.  There is evidence to suggest that gut flora may be intimately involved in phenomenon like stress and obesity immunity and depression.  In addition, they may be related as well to neurological disorders such as Parkinson's or autism.  By understanding the communities that take up residence in our bodies and our relationship with them, we can develop more sensitive and specific diagnostics, effective treatments and lifestyles conducive to healthy body and mind function.

Dr. David:  M.S. candidate; Nash 554; 541-737-8630;



Seagrasses are critical coastal ecosystems that provide goods and services including stabilizing sediments, serving as a habitat for coastal organisms and nursery fishes, and partaking in nutrient cycling and carbon sequestration. Seagrass-associated microbes play a direct role in regulating nutrient cycling and seagrass health. My research aims to elucidate changes in carbon cycling and shifts in the microbial communities of seagrasses in light of eutrophication and ocean acidification. 

Dr. Mueller:  Ph.D. candidate; Nash 446; 541-737-8605;



The goal of my research is to develop the next generation of high throughput cultivation methods for understanding microbial communities.  I am focusing on methods for quantifying enrichment culture composition in a high throughput format that can be automated and applied to very low cell density cultures.  I am hoping to study dark ocean bacterioplankton with this technology.

Dr. Giovannoni and Dr. Sharpton: Ph.D. candidate; Nash 254; 541-737-3189;



I am interested in microbial diversity, bioinformatics, and the roles that microorganisms play in various aquatic systems.  I will be rotating in the labs of Dr. Giovannoni, Dr. Vega-Thurber, and Dr. Bartholomew.

Dr. Giovannoni:  Ph.D. candidate; Nash 224; 541-737-8966;








Dengue virus is the most rapidly spreading arbovirus worldwide with over one-third of the world’s population living in areas at risk for contracting the virus. Early and rapid detection of dengue is crucial to lessening the burden of this significant pathogen. Early diagnosis allows for patients to receive appropriate care reducing the drain to health systems and the danger of progression to more severe disease. Previously, our lab has developed a rapid assay to detect dengue virus serotype 2. My project is to use reverse transcription recombinase polymerase amplification (RT-RPA) to detect other dengue virus types such as 1, 3, and 4. The RT-RPA assay is a sensitive and specific isothermal reaction capable of differential detection of dengue serotypes in less than 20 minutes with a sensitivity as low as 50 copies. We will use two detection formats to view RT-RPA products and highlight the dynamic nature of the RT-RPA assay. Later, we will use the RPA technology to detect influenza and respiratory syncytial virus in nasal samples.

Dr. Pastey:   M.S. candidate; Comparative Health Sciences, Dryden 106A, 541-777-0941;



The goal of my research is to understand how the complex community of microorganisms that inhabit the intestines, known as the gut microbiome, influence vertebrate health and evolution. The primary aims of my research are: to determine (1) which microbiome functions consistently stratify healthy and diseased humans, (2) which microbiome functions are conserved across mammals, and (3) whether evolutionarily conserved microbiome functions are critical to health. Overall, this research will provide insight into the importance of specific microbiome functions to maintaining host health and will highlight their potential contribution to the evolutionary fitness of vertebrates

Dr. Sharpton:  Ph.D. Candidate  Molecular and Cellular Biology; Nash 554; 541-737-8630;




Methane in the seafloor is constantly advecting upward from deep reservoirs towards the ocean floor, but very little of it ever reaches the ocean.  Instead, it is oxidized anaerobically in the sediment column by consortia of methanotrophic archaea and sulfate-reducing bacteria.  My research combines community ecology approaches with modeling of microbial metabolism to understand how this consortia survives on the low energy yield provided by this reaction and how anaerobic methane oxidation may be affected by climate change, which threatens to destabilize methane reservoirs in shallow sediments. 

Dr. Colwell:  Ph.D. candidate; Ocean Ecology and Biogeochemistry; Weniger 537; 732-977-3488;



I am interested in the role of viruses in coral reef health and disease.  More specifically, I want to conduct a time series analysis of viral production, prevalence, and severity in coral reefs and track viral expression levels to find any potential patterns that may aid in understanding corval disease.

Dr. Vega-Thurber:  Ph.D. candidate; Environmental Sciences; Nash; 541-737-7793;



My research is focused in the Arctic, where I have spent the summers of 2014 and 2015 doing fieldwork.  I am involved in long-term ecological research in the lakes and streams near Toolik Field Station, AK, but my thesis focuses on understanding the mechanisms of soil carbon degradation in the Arctic, which has important implications for carbon cycling and climate change.  Using metatranscriptomic techniques, I am investigating how soil carbon, once leached from soil and dissolved into surface water, is broken down by both microbes and sunlight.

Dr. Crump:  M.S. candidate; Ocean Ecology and Biogeochemistry; Weniger 529; 541-737-4369;;



My research is to evaluate the microbial and matrix regulators of protein degradation in soils as a controller of nitrogen turnover.  I am interested in learning how soil proteins break down under different environmental conditions.  Protein depolymerization was recently recognized as a critical rate-limiting step in the nitrogen cycle before any further mineralization or immobilizatin occurs.  Extracellular protease activity and mineral surface structures are predicted to play an imiportnat role in this process.  I hope to discover how foersted soil environments with wide ranges of mineralogy and microbial composioint, might contribute and characterize this bottle-neck in the nitrogen cycle.

Dr. David Myrold:  Ph.D. Candidate.  Soil Science, ALS 3110A.



I work with SAR11 bacteria, an ubiquitous group of marine bacteria.  Because of their large global population and the impact this has on the global carbon cycle, the ecology of SAR11 is of interest to me.  I am exploring what kinds of compounds they metabolize using a technique called metabolic footprinting, which employs mass spectrometry to analyze post-growth culture extracts.  I am also interseted in exploring the physiology of SAR11 to better understand how they are able to oxidize such a wide range of compounds, given that they have such microscopic genomes.

Dr. Giovannoni:   Ph.D. candidate; Molecular and Cellular Biology; Nash 250;  405-385-3750,