RESEARCH ASSOCIATES, RESEARCH ASSISTANTS AND POSTDOCS

Dr. Julie Alexander, Research Associate

Web Sitehttp://microbiology.science.oregonstate.edu/content/julie-alexander
Phone:  541-737-1849
Emailalexanju@onid.orst.edu
Education:  Ph.D. Biology Montana State

Generally my research interests lie within the field of disease ecology.  I am fascinated by parasites that exploit multiple hosts during their life cycles as a means of ensuring their reproductive success.  I am interested in factors that drive and determine the outcomes of host-parasite interactions, how interactions may change under different environmental contexts, and how ecological and life history variables influence the evolution of host-parasite dynamics.

 

Dr. Stephen Atkinson, Research Associate

Websitehttp://microbiology.science.oregonstate.edu/dr-stephen-atkinson
Phone:  541-737-1849
Emailatkinsos@oregonstate.edu
Education: Ph.D. Parasitology, University of Queensland, Australia

I research myxozoans - a widespread group of parasitic Cnidaria.  Though they are related to corals and jellyfish, myxozoans are obligate parasites of fish and invertebrates.  My work includes describing new species, exploring the evolutionary relationships between hosts and parasites, and developing methods for detecting myxozoans in environmental samples.

Publications

 

Dr. Karen Dierksen, Research Associate

Websitehttp://microbiology.science.oregonstate.edu/content/dr-janine-trempy
Emailkaren.dierksen@oregonstate.edu
Education:  Postdoctoral Researcher, University of Otago, Dunedin, New Zealand
Ph.D., Microbiology, Oregon State University

My research in the Trempy Lab is focused on developing new strains of lactic acid bacteria of potential interest to the food, dairy and/or pharmaceutical industries.  Our original patent strain, Lactococcus lactis Ropy 352, which produces a unique exopolysaccharide, has been licensed commercially.

 

Dr. Sascha Hallett, Senior Research Associate

Websitehttp://microbiology.science.oregonstate.edu/content/dr-jerri-bartholomew
Emailsasha.hallett@oregonstate.edu
Phone:  541-737-4721
Education:Ph.D.  The University of Queensland, Australia

I find parasites fascinating organisms and have always been drawn to the aquatic environment. Thus, I am interested in parasites of marine and freshwater fish. Most of my research has focused on one phylum - the Myxozoa and I've never dissected a fish without encountering at least one of these microscopic, spore-forming, endoparasitic metazoans. Over 2000 are found in fish world-wide and most do not harm their host, but there are several that cause serious diseases (Ceratomyxa shasta, Parvicapsula minibicornis, Myxobolus cerebralis) in the Pacific Northwest of North America. My current research focuses on answering questions about these parasites so that we can make informed management decisions and reduce their impact on native fishes.

 
Dr. Richard Holt, Senior Research Associate

Websitehttp://microbiology.science.oregonstate.edu/aahl
Phone:  541-737-0743
Emailholtr@onid.orst.edu
Education:  Ph.D. Microbiology, Oregon State U.

Forty-two years of experience in the study of fish disease as Senior Fish Pathologist at the Oregon Department of Fish and Wildlife (Retired).  Previous activities include conducting research in the diagnosis and treatment of fish parasites, pathogens in hatchery fish, detection of pathogens in wild stocks of fish and determining causes of fish losses in Oregon.  Principal area of research and publications has been in studies of the yellow pigmented bacterial fish pathogens such as Flavobacterium psychrophilum agent of cold-water disease and F. columnare, agent of columnaris disease.  Currently participating on a project to study the occurrence of the myxosporean parasite, Ceratomyxa shasta, and its impact on wild salmonid stocks in the Klamath River watershed.

 

Dr. Anne Taylor, Research Associate

Websitehttp://microbiology.science.oregonstate.edu/content/dr-peter-bottomley
Phone:  541-737-4136
Emailanne.taylor@oregonstate.edu
Education: M.S. BioResource Research, Soil Science, Oregon State; Ph.D. Environ. Engr., Oregon State

Our lab studies the nitrogen cycle in soil, and specifically the oxidation of ammonia to nitrite. This process is known as nitrification and is carried out by ammonia oxidizing archaea and bacteria (AOA and AOB). Over the past few years my work has focused primarily on developing tools to distinguish the contributions to nitrification by AOA and AOB. Using these tools I am now investigating how different environmental conditions, such as temperature and soil water content, influence the ecology, physiology, and function of the two groups of nitrifiers in soil. This work has particular significance as global climate change becomes more pronounced. Changes in soil temperature and rainfall patterns will affect the contributions of the AOA and AOB to nitrification, and may have profound effects on nitrogen balance in agricultural and forest soils and the production of greenhouse gasses. 

 

POSTDOCS

 

Dr. Gema Alama Bermejo, Postdoc--NOW A TENURE TRACK FACULTY IN MARINE BIOLOGY AND FISHERIES INSTITUTE AT THE NATIONAL SCIENTIFIC AND TECHNICAL RESEARCH COUNCIL IN ARGENTINA

Website: http://microbiology.science.oregonstate.edu/content/gema-alama-bermejo
Phone:  541-737-9664
Emailgema.alama@gmail.com
Education:
Ms.C. Aquaculture & Ph.D. Marine Resources, University of Valencia, Spain; Postdoc Institute of Parasitology, Czech Academy of Sciences, Czech Republic.

I define myself as an aquatic parasitologist, with special focus on a group of microscopic cnidarian parasites, myxozoans. I study different aspects of their biology, with special interest in host-parasite interactions. I am currently studying virulence factors in the myxozoan Ceratonova shasta by using different virulent-level genotypes of this parasite affecting salmonids in the Pacific NW.

 

Dr. Luis Bolanos, Postdoc

Website:  http://microbiology.science.oregonstate.edu/dr-stephen-giovannoni
Phone:  541-737-3502
Emailbolanosl@oregonstate.edu
Education:  Ph.D. Biomedical Sciences, National Autonomous University of Mexico
My research interests lie in the understanding of the factors that shape the dynamics and interactions of microbial ecosystems.  I am currently investigating the diversity of marine plankton in the North Atlantic bloom and how it changes at different depths and cycle time points.

 

Dr. Cleo Davie-Martin, Postdoc     

Websitehttp://microbiology.science.oregonstate.edu/michael-kent
Phone:  541-737-1839
Email:cleo.davie-martin@oregonstate.edu      
Education: Postdoc Department of Microbiology, Oregon State U.
Ph.D. Environmental and Analytical Chemistry
University of Otago, Dunedin, New Zealand

My research investigates the microbial cycling of volatile organic compounds (VOCs) in the oceans under both controlled laboratory and field conditions using proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF/MS).  PTR-TOF/MS allows for real time detection of VOCs at trace levels, through which we can determine the production and consumption rates pf VOCs by marine plankton and explore how these change under various conditions and at different stages of the bloom cycle.

Dr. Tyrell DeWeber, Postdoc         

Website:https://sites.google.com/site/tyrelldeweber/
Phone:  541-737-1859
Emailjtdeweber@gmail.com         
Education: Postdoc Department of Microbiology, Oregon State U.
Ph.D. Wildlife and Fisheries Service, Penn State U.
M.S. Fisheries and Wildlife Service, Virginia Tech
B.S. Biology, Liberty U. 

I am interested in understanding the effects of human activities on river systems and fish populations to help guide management and conservation.  River system alteration and pollution can result in stressful conditions and increased disease, eventually leading to widespread mortality of wild adult and juvenile fish.  I am working with Dr. Michael Kent in the Microbiology Program at Oregon State University investigating causes of prespawn mortality in Spring Run Chinook salmon in the Willamette River Basin.                      

 

Dr. Christopher Gaulke, Postdoc 

Website:  http://sharptonlab.cgrb.oregonstate.edu/?=gaulkec
Phone:  541-737-8630
Email:  gaullkec@onid.oregonstate.edu
Education:  Postdoc, Department of Microbiology, Oregon State U.; Ph.D. University of California, Davis

A growing body of evidence has identified the gut microbiome as an important factor involved in the maintenance of gastrointestinal homeostasis.  However, relatively little is known about how routine environmental exposures might influence the structure and function of these microbial communities and how these shifts might alter host physiology.  My research employs high-throughput molecular and computational techniques to evaluate the impact of environmental exposures on microbial abundance, function, and host physiology.  These investigations aim to (1) identify potential microbial biomarkers of environmental exposure, (2) Define microbial functions that are associated with host health, and (3) Generate testable hypotheses about how microbial communities interact with their hosts.

 

Dr. Armanda Roco, Postdoc

Website
Phone:  541-737-8568
Emailarmanda.roco@oregonstate.edu
Education: Ph.D. Cornell, Microbiology; Postdoc Dept. of Microbiology, Oregon State U.

I am working on a collaborative project with Dr. Mueller (Microbiology) and Dr. Mryold and Dr. Kleber (Crop and Soil Science).  My Ph.D. research involved the characterization of microbial communities undertaking denitrification in soils under varying environmental conditions.  I employed the use of genome sequencing, metagenomics, metatranscriptomics, and gas analyses to complete the research.  At present, I am working on a mass spectrometry-based proteomic project with the ultimate goal of understanding the relative contributions, both physical and biological, of protein turnover in soils of varying nitrogen availability. 

 

Dr. Justin Sanders, Postdoc

Websitehttp://www.justinlsanders.com; https://www.researchgate.net/profile/Justin_Sanders
Phone:  541-737-1859
Emailjustin.sanders@oregonstate.edu   
Education: Postdoc Dept. of Microbiology, Oregon State U.
Ph.D. Microbiology, Oregon State University

As a public health microbiologist I learned firsthand the impacts of infectious diseases.  I came to OSU to study parasitology with Dr. Michael Kent.  I discovered the value of the zebrafish as an in vivo model to study numerous characteristics of pathogens, primarily the Microsporidia.  I am currently working with Dr. Brian Dolan to study the immunological effects of chronic infectious disease and further develop the tools available for immunological studies using zebrafish.  I am also working with several collaborators at OSU as well as nationally to develop a new in vivo model for Toxoplasma gondii, a parasite that infects an estimated one-third of the human population, with the goal of developing drugs to treat the chronic stage of the infection.

 

 

 

Dr. Jimmy Saw, Postdoc
Website: http://microbiology.science.oregonstate.edu/dr-stephen-giovannoni
Phone: 541-737-3189
Email: sawj@oregonstate.edu
Education: B.S., M.S., and Ph.D. in Microbiology, University of Hawaii at Manoa,
Marie-Curie Incoming International Postdoctoral Fellow (Uppsala University, Sweden)

My research project focuses on understanding the interaction of SAR11 bacterial clade with dissolved organic matter (DOM) in the ocean. I am particularly interested in analyzing the evolutionary ‘hotspots’ within the genomes of divergent SAR11 strains in the ocean to understand how these genomic regions may play a role in shaping their metabolic capabilities and ultimately on how they break down DOM. I am also interested in evolutionary forces shaping these regions. We plan to carry out deep sequencing of single-cell genomic and metagenomic libraries that will be generated from an upcoming cruise to Bermuda as part of the BIOS-SCOPE research collaboration.

 

 

Dr. Sean Spagnoli, DVM, DACVP, Postdoc COMPLETED PHD EMPLOYED AT OSU VET MED    

Website: http://microbiology.science.oregonstate.edu/michael-kent
Phone:  541-737-9664
Email: sean.spagnoli@oregonstate.edu      
Education:   Postdoc Department of Microbiology, Oregon State U.
Ph.D. Comparative Health Sciences, Oregon State U., in progress

The zebrafish is a rising star of the laboratory animal world whose popularity is rapidly approaching that of the mouse.  Unfortunately, since the zebrafish has only been used in comparative health science since approximately the mid-seventies, it has not been exposed to the rigorous biosecurity and “clean-up” measures that have benefited the mouse as a research animal. In the absence of rigorous screening and health programs, many facilities are plagued by subclinical infectious diseases from the zebrafish’s humble beginnings in commercial aquaculture that could potentially influence study results.  My research focuses on identifying the effects of the microsporidian parasite Pseudoloma neurophilia on various research topics including behavior, neurology, and immune suppression via gamma irradiation in order to warn the scientific community of the dangers involved with subclinical disease and to increase the rigor biosecurity and screening measures.

 

Dr. Erin Sully, Postdoc    PATENT WRITER FOR A LAW FIRM, SAN DIEGO

Website: http://microbiology.science.oregonstate.edu/content/bruce-geller
Phone:  541-737-1846

Emailsully@science.oregonstate.edu         
Education: Postdoc Department of Microbiology, Oregon State U.
Ph.D. Biomedical Sciences, University of New Mexico

My present research focuses on the efficacy of antisense of antibiotics against pathogenic antibiotic-resistant bacteria including Klebsiella penumonia, Escherichia coli, and Haemophilus influenza.  I use peptide-conjugated phosphorodiamidate morpholino oligomers (PMOs) targeted to essential or non-essential bacterial genes to reduce bacterial viability or inhibit a specific aspect of its pathogenicity both in vitro and in vivo. We have demonstrated protective efficacy of a PPMO against the NDM-1 carbapenemase in a mouse model of NDM-1 positive E. coli sepsis and are currently working to show protection in a pneumonia model with Acinetobacter baumannii.  I would like to continue work in the area of antibiotic resistance and the development of vaccines and therapeutics at a biomedical research institute or pharmaceutical company in the future.

 

Dr. Rory Welsh, Postdoc COMPLETED PHD EMPLOYED IN NORTH CAROLINA
 

Websitehttp://oregonstate.edu/microbiology/vegathurberlab/rory-welsh
Phone:  541  737  8605
Email:  rory.welsh@gmail.com
Education:  B.S. University of Georgia, Microbiology; Ph.D. Oregon State University, Microbiology

I employ a wide range of methods and technologies utilizing culture dependent and independent techniques to study how cell-cell interactions impact microbial comunity structure and function.  My doctoral research focused on the mechanisms and controls of bacterial population dynamics in the coral host microbiome with a special emphasis on predatory bacteria.  My postdoctoral research with Dr. Rebecca Vega Thurber involves the application of these methods as well as next generation sequencing for rapid detection of viral diseases and discovery of novel viral pathogens.  I use microscopy and metagenomic techniques to study the role of viruses in structuring coral reefs in the Red Sea, the world's northernmost tropical sea (in collaboration with Dr. Christian R. Voolstra).

Current Publications
 

 

Dr. Jesse Zaneveld, Postdoc  NOW ASSISTANT PROFESSOR, U OF W, BOTHELL

Website:http://microbiology.science.oregonstate.edu/content/dr-rebecca-vega-thurber
Phone:  541-737-2411
Email: zaneveld@gmail.com
Education: B.S. University of Oregon (Biology and Political Science); Ph. D. University of Colorado at Boulder  

I use a combination of computational and empirical methods to study the microbiome of humans and other animals.  My Ph.D. research in Rob Knight lab involved studying horizontal gene transfer and genome evolution in the human gut microbiome and developing software for large-scale microbial community analysis.  In my postdoctoral research with Dr. Rebecca Vega Thurber, I am applying these methods to to examine the ecology and evolution of threatened reef-building corals at greater temporal and spatial scales than has previously been possible.  Current projects include an analysis of multi-year field experiments in the Florida Keys tracking the microbial consequences of overfishing and nutrient pollution on benthic communities, coral health, and coral microbiomes (a collaboration with Deron Burkepile) and the Global Coral Microbiome Project, a world wide comparison of coral microbiology across phylogenetic diversity (a collaboration with Monica Medina and the Earth Microbiome Project).  I also develop software for microbial ecology, evolution, and comparative genomics, including the popular PICRUSt software package which uses evolutionary modeling of the genomes of all sequenced bacteria to predict the function of microbial communities from 16S rRNA data.

Current Papers

Coral Microbiomes Through Space and Time, presentation on coral microbiome work to the U.S. National Academy of Science Kavli Frontiers of Science Forum, is now available on line.

A short outreach video highlighting Global Coral Microbiome Project sampling in Saudi Arabia is online here.  This video is part of a larger effort by Dave Carter and Justin Smith of OSU, collaboration with the Global Coral Microbiome Project team to develop Saving Atlantis, a full-length documentary highlighting the connections between coastal communities, tropical, tropical reef conservation, and coral microbiology.

 

RESEARCH ASSISTANTS

 

Ryan Craig, Faculty Research Assistant

Website: http://microbiology.science.oregonstate.edu/aahlEmail:
Phone:  541-737-0743
Email:  ryan.craig@oregonstate.edu

Education:  B.S. Environmental Science, Oreogn State U.

As a research assistant at the JL Fryer Aquatic Animal Health Lab, I am responsible for the daily animal husbandry, maintenance of the facility, and assisting researchers with experimental design. In addition, I am involved in the field work for projects monitoring the prevalence of Ceratonova shasta, its invertebrate host, and the effect of the parasite on salmonids in the Klamath River.

Publications:

Bruce A. Menge, Sally D. Hacker, Tess Freidenburg, Jane Lubchenco, Ryan Craig, Gil Rilov, Mae Noble, Erin Richmond (2011). Potential impact of climate-related changes is buffered by differential responses to recruitment and interactions. Ecological Society of America 81(3) 493-509.

 

Dr. Lixin Li, Faculty Research Assistant   

Website: http://microbiology.science.oregonstate.edu/content/bruce-geller
Phone:  541-737-1846

Emaillili@oregonstate.edu 
Education: M.S. University of Southern China, School of Medicine
M.D. University of Southern China, School of Medicine

I am working on antisense effects on multi-drug resistance bacteria.  Basically, synthetic nucleotide analogs are utilized to target specific antibiotic resistant genes, and the effects are tested, using molecular and cellular biotechnology and rodent models.

 

Ruth Milston-Clements, Faculty Research Assistant   

Web Site: http://microbiology.science.oregonstate.edu/aahl
http://microbiology.science.oregonstate.edu/content/ruth-milston-clements-0
Phone: 541-737-8630
Emailaahl.manager@oregonstate.edu      
Education: B.S. Environmental Science, Lancaster University
M.S. Fisheries Science, Oregon State University Department of Fish and Wildlife

Worked for the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) at the OSU Department of Integrative Biology and the Crop and Food Research Institute in Nelson, New Zealand; before starting my current position in the J.L. Fryer Aquatic Animal Health Laboratory at OSU.  As Lab Manager, I am responsible for maintaing the research facility and physical plant; coordinating resarchers, and ensuring proper care and health of the aquatic animals.  My research interests are focused on the effect of environmental stressors such as temperature or pollutants on the immune systems of aquatic animals.

 

 Virginia Watral, Faculty Research Assistant

Website: http://microbiology.science.oregonstate.edu/michael-kent
Phone: 541-737-1858
Emailwatralv@oregonstate.edu
Education:

I have been involved with the study of the diseases of salmonids and zebrafish for the past 30 years.

Currently the focus of my research has been on the impacts of the diseases of zebrafish on experimental outcomes due to non-protocol induced variation and the development of specific pathogen free fish lines to aide in alleviating this problem.  I am also investigating various drug treatments and disinfectants for their potential to control zebrafish diseases. Most recently I have been working on transmitting and identifying the etiological agent causing intestinal tumors in zebrafish. In the past I have also conducted numerous field studies including studying the lifecycles and possible effects of parasites on endangered Klamath Lake suckers and determining a parasitic causation of skeletal deformities in Willamette River fishes. Most of these studies necessitate the need for a zebrafish disease facility which I maintain and manage.

 

Dr. Xie Zhangxian, Research Assistant

Website:  http://microbiology.science.oregonstate.edu/dr-stephen-giovannoni
Phone:  541 737 3502
Emailxiezh@oregonstate.edu
Education:  B.S. Marine Science, Xiamen University, China; Ph.D. Environmental Science, Xiamen University, China

Dissolved organic matter (DOM) in the ocean contains as much carbon as CO2 in the atmosphere (700 vs 750 billion tons).  Marine microbes are greatly involved in the carbon cycling of marine DOM.  My research in the Giovannoni Lab is on the metabolism of DOM by marine microbes, particularly the most abundant SAR11 bacteria.  Applying mass spectrometry, we can determine DOM produced and/or consumed by marine bacteria which will improve our understanding of the roles of marine microbes in the carbon cycle.