Waad S. AlHarbi



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:  Ph.D. candidate; Nash 528; 541-737-9664;



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 the microbial diversity of the subsurface within glacial outwash ponds, and the role the microbes play in global element cycling.  My aim is to strengthen our understanding of the link between iron redox processes and anaerobic oxidation of methane.

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 356; 541-737-5079;



My research interests center on microbial ecology, especially in the ocean, and I would like to explore the specific interactions microbes have with other microbes and the environment.  I will be rotating in my first year through the Thurber, Sharpton, and Giovannoni Labs.

Dr. Thurber:  Ph.D. candidate; Burt 222; 541-737-3649;



I am interested in the interactions between microbial communities in the gut and behavioral outcomes.  These interactions are studied in a mouse model of Autism Spectrum Disorder, focusing on the effects elicited by the addition of Clostridium celatum, a species found to be enriched in the stool of children with ASD.  I am interested in identifying key microbial meta-bolites that may be associated with behavioral changes.  I also collaborate with researchers in the Honey Bee Lab to study the gut microbiome of honey bees in response to probiotic treatment as well as infection by the pathogen Nosema.

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



I am working to develop probiotics that improve the survival of oyster larvae.  My research will use 16S community analysis to examine how the oyster microbiome changes with the addition of probiotics.

Dr. Mueller:  M.S. candidate; Nash 446; 541-737-8605;



My research interests lie in marine microbiomes and microbial ecology. My graduate work focuses on analyzing data collected from bleached corals surrounding the island of Mo'orea, which is located near Tahiti. Using three years of data collected from over 300 corals, I will test whether certain microbiomes impact the ability of corals to resist and recover from bleaching; this will advance our understanding of how the interplay between various coral reef components impacts the ecosystem services of a marine system.

Dr. Andrew Thurber:  M.S. candidate; Burt 222; 541-737-3649;


This year I am rotating through three labs that perform microbiome and microbial ecology research.  I am broadly interested in using integrated "omic" and bioinformatic techniques to examine microbial diversity and link microbial community function to ecological processes or host-associated traits.

Dr. Sharpton:  Ph.D. 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; 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;



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;



I am studying Puffy Snout Syndrome (PSS), which is a lethal disease prevalent in various species of fish in aquaculture and aquarium settings.  I am interested in discovering the etiological agent or agents that cause disease as well as disease mitigation techniques to reduce the spread of PSS.

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



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, additively, 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;



My research focuses on determining the patho-physiological changes associated with senescence and pathogen burdens between the parasite Ceratonova shasta and a novel enteric microsporidium in pre-spawning mortality in Chinook salmon.

Dr. Kent:  M.S. candidate; Nash 514; 541-737-1858;



My research will investigate microalgal production of biogenic volatile organic compounds (BVOCs). Little is known about the range of BVOCs produced by different algae and how their production is altered depending on the growth environment and the presence of bacteria. A broad goal of this project is to understand how algal-bacterial interactions control sea-air emissions of BVOCs.

Dr. Halsey; pH.D. candidate; Nash



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 356; 541-737-5079;


I am interested in studying the connection between the microbiome-gut-brain axis, specifically in Autism Spectrum Disorder. My research aims to learn in vivo, in vitro, and bioinformatic approaches to understand the impact of the gut microbiota on behavior, unravel specific biomarkers, and identify microbial and host pathways involved in the modulation of peripheric and central neurological circuits.

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



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.  I spend my time doing a combination of fieldwork, labwork, and programming and bioinformatics to analyze both high-throughput metagenomics and amplicon data.

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;


The habitats of beavers in the Arctic is highly dependent on climate. As global temperatures warm, especially in the far North, beavers have expanded their range. My research will be centered around the biogeochemical effect that beaver ponds have on Arctic permafrost. When standing water exists over permafrost soil, as when beavers dam a river, it can lead to an increase in the depth of the soil active layer. This means previously frozen microorganisms can begin to metabolize ancient stores of thawed organic and inorganic carbon. As a result, carbon in the forms of CO2 and methane is liberated from this once permanently-frozen source. I aim to characterize the microbes found in this unique environmental niche.

Dr. Colwell; Weniger 537; 541-514-8586;


My research involves developing novel molecular and computational methods to further elucidate the underlying mechanisms to better understand how host-gut microbiome interactions impact health and how this knowledge can be used to treat disease.  Specifically, I am interested in using zebrafush as a model vertebrate organism to study these interactions.

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


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;



My research interest is exploring the concept of microbial degradation of plastic compounds, specifically how microbial consortia coordinate to co-metabolize highly complex com-pounds. This will be studied by identifying which organisms play functional roles in each metabolic step of decomposition as well as what metabolites are produced.

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



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 418; 541-737-4305;



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;



My research uses in situ sampling and bioinformatics to examine the association between environmental stressors and phase shifts in corals and their microbiomes.  My graduate work will inform coral conservation strategies and consider the importance of microbial communities in coral resilience.

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



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.  I am studying marine bacterial communities in the deep ocean as well as the zebrafish gut microbiome using this approach.  The goal 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;


Dr. Giovannoni:  M.S. candidate, Nash     ;



My research focuses on the microbiology and biochemistry of shallow marine ecosystems entering hypoxic states.  In conjunction with Dr. Francis Chan (Integrative Biology), we are performing experiments to test mechanistic models that will help us understand the rate of oxygen loss in systems experiencing oxygen stress.

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



I am interested in the effects of climate change on Ceratonova shasta, a myxozoan parasite that infects salmoids on the Pacific Coast of North America.  Specifically, my research will focus on relationships between river temperature and the dynamics of genetic variants of C. shasta, and how their phenologies may change under future climate contexts.

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








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 446; 541-737-7793;



I am studying the broad topic of how bacteria in the ocean interact with dissolved organic matter. I am 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,