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;



The parasite Ceratonova shasta is a major cause of mortality in Pacific salmon and trout.  Resistance to this important pathogen varies markedly among fish populations.  My work is aimed at finding the genetic loci responsible for resistance and determining if the resistance mechanism is conserved among different species of salmon and trout.  I am currently employing a combination of transcriptomics, genetic mapping, and population genetics to accomplish this goal.

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



My research focuses on defining functional diversity of northern wetland microbiomes and the role they play in global element cycling, more specifically iron and carbon cycling.

Dr. Colwell:  Ph.D. candidate; Weniger 537; 541-514-8586;



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 behavior.  I am also interested in learning and utilizing computational methods to explore large data sets in microbial ecology and microbiome research in general.

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



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;



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;



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;



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 am an NSF Graduate Research Fellow studying how local and global stressors alter the coral host and its associated microbial community.  I investigate how stressors such as fish predation, thermal stress, and nutrient enrichment act synergistically, additvely, or antagonistically to alter the coral microbiome.  In particular, I am interested in using multivariate statistical techniques to describe changes in the ecology of microbial communities.

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;



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;



Phytoplankton are key drivers of ocean biogeochemical cycling and form the base of the marine food web.  I am using RNA-Seq to explore how the model diatom Thalassiosira pseudonana differentially allocates photosynthetic energy under different light-mediated growth rates.  A better understanding of these organisms’ metabolic strategies may lead to more refined climate change models and increase the feasibility of metabolic engineering for production of biofuels and other natural products.

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 focuses on the microbiome-gut-brain axis, and more specifically on the impact of the gut microbiome on behavior.

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



To overcome the unique challenges of surviving as single celled organisms, microbes perform a variety of cooperative, multicellular behaviors, including biofilm formation, quorum sensing, nutrient acquisition, and dispersal.  I study the dynamics of these social interactions in the opportunistic pathogen Pseudomonas aeruginosa, a gram negative bacterium that exhibits a wide range of social behaviors.  I am specifically interested in cooperation, competition, and cheating in iron acquisition, and plan to study these interactions using competition experiments, single celled analysis, and mathematic modeling.

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



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 phenomena like obesity and depression, as well as neurological disorders such as Parkinson's or Autism Spectrum Disorder.  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.  I am currently focusing on developing biocomputing methods to study these interactions.

Dr. David:  Ph.D. 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;



I use next generation high throughput culturing to study bacterial community dynamics.  Specifically, I am interested in investigating microbial interactions with co-cultures that form from community subsamples.  Using this approach, I am studying marine bacterial communities in the deep ocean as well as the zebrafish gut microbiome.  The goal of the research is to provide insights into the interactions of microorganisms in their natural environments.

Dr. Giovannoni and Dr. Sharpton: Ph.D. candidate; Nash 250; 541-737-3502;



I am interested in marine microbiology.  Specifically, the physiological microbial processes that contribute to biogeochemical cycling.

Dr. Giovannoni:  Ph.D. candidate; Nash 250; 541-737-3502;




 Dr. Bartholomew:  M.S. candidate; Nash









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;



I am interested in the role of viruses in coral reef health and disease. I will be using bioinformatics to identify changes in viral diversity and abundance in both healthy, bleached, and nutrient-enriched corals. I will also be identifying viruses present in algae and tropical fish (S. nigricans) and studying which viruses are shared between coral, fish, and algae. Overall I want to know what kinds of viruses are transmitted around the coral ecosystem and the types of viruses that play important roles in coral health. 

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



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 immobilization occurs.  Extracellular protease activity and mineral surface structures are predicted to play an imiportant role in this process.  I hope to discover how forested soil environments with wide ranges of mineralogy and microbial composition, might contribute and characterize this bottle-neck in the nitrogen cycle.

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



I am studying the broad topic of how bacteria in the ocean interact with dissolved organic matter. I'm specifically interested in studying the metabolism, substrate range, and transport kinetics of the most abundant group of marine bacteria, SAR11. I am doing this using a range of techniques, from radiolabelled uptake experiments to mass spectrometry. I am also looking at differences in gene regulation strategies between groups of bacteria in the ocean, as well as why these bacteria employ the strategies they use.

Dr. Giovannoni:   Ph.D. candidate; Molecular and Cellular Biology; Nash 250;  541-737-3502,