Colleges of Science and Agricultural Sciences Department of Microbiology Newsletter Editor Debbie Farris

Copy Editor 4 Katharine de Baun

Designer Sharon Betterton SPRING 2017 Department of Microbiology Jerri Bartholomew, Dept. Head 2 On the Move Publisher 10 Our amazing undergraduates balance academic Department of Microbiology life with transformative experiences Nash Hall 226 Oregon State University Corvallis, OR 97331 4 Bright Minds Updates from our graduate students and On the cover: This graphic postdoctoral researchers depicts zebrafish gut microbiota interacting with one another upon exposure 14 8 Help from Our Friends to the antibiotic triclosan. We are growing thanks to the generosity of our The circles represent alumni and friends! specific that are found in the microbiome and the lines indicate 10 News which bacteria ecologically Innovation, rejuvenation, hires, promotions interact with one another and awards (e.g., shared metabolism, competition). The large colored polygons represent highly 14 From Our Labs interconnected groups of Research gains momentum with fieldwork bacteria. Collectively, this worldwide network illustrates how gut bacteria influence one another upon triclosan exposure and 21 Alumni identifies potential keystone Congratulations to our recent microbiology species of bacteria. graduates and alumni! FROM THE HEAD EVENTS

Welcome to our annual newsletter! As New hires include Andrew Thurber, an APRIL 8 we move forward towards a new year, assistant professor for our new aquatic STUDENT SYMPOSIUM it is a good time to look back at all of the microbiology option; Emy Daniels, who 3rd Annual Microbiology Student accomplishments and changes of 2016. replaces Camille; and two professional Association Symposium—open to advisors, Alex Beck and Barbara Kessel. the public It was a great year in terms of student success. We graduated 216 Bachelors, We’ve also been busy with SPARK, a APRIL 13–MAY 27 one M.S. and eight Ph.D. students. We year-long, campus-wide collaboration MICROBIOME EXHIBIT launched new courses for our biohealth between art and science. Working with “Seeing the Unseen,” Collaboration sciences majors and received approval The Arts Center|Corvallis, we hosted with The Arts Center|Corvallis for a pre-med option for microbiology four workshops where visual artists, and part of SPARK, a yearlong majors. For a second year, our students writers, poets and musicians were celebration of the interplay hosted their own research symposium, challenged to translate our science into between art and science drawing speakers from across the their medium. Their work culminates Pacific Northwest. in a show, “The Microbiome: Seeing MAY 5 the Unseen,” as part of a campus- SCHOLARSHIP LUNCHEON It’s also been a banner year for faculty wide Microbiome Initiative this spring. Honoring Undergraduate travel and research funding. Our Meanwhile, student artists intern in our Microbiology scholarship faculty have conducted research in the labs and at sea, creating art that shines recipients North Atlantic, the Sargasso Sea, the a new lens on our research. Mediterranean and the South Pacific. MAY 11 & 12 They won four major National Science Finally, I want to thank our generous OSU MICROBIOME INITIATIVE (OMBI) Foundation awards on an array of alumni and donors. Limited budgets are Training Workshop (May 11, all day) topics from cheating in bacteria to always a challenge, but with the help of Ed Yong (May 11, 5:30 p.m.) the role of viruses in coral reef health. our donors our undergraduates benefit Horizon Room, Memorial Union Successful patents and new discoveries from new equipment, participate in Research Forum (May 12, all day) abound. Look for these stories in the research, and travel to conferences. research section (pages 14–20). Throughout these pages, we’ll share JUNE 16 many stories about how your support GRADUATION CELEBRATION We’ve had our share of goodbyes and has enhanced our students, our faculty Microbiology and BioHealth hellos, with three retirements and four and our work. Sciences Graduation Celebration new hires. Peter Bottomley retired after 37 years, and Bruce Geller after I look forward to meeting more of you 30 years. Both continue as emeritus in the upcoming year. faculty engaged in active research. Camille Partridge, hired to work in the media kitchen in 1980, also retired. Jerri Bartholomew, Head, Microbiology

Department of Microbiology 1 SMALL TALK: STUDENTS On the move Our amazing undergraduates balance academic life with transformative experiences

CONNECTING WITH THE PROFESSIONAL students I teach...to introduce them to Oregon and Washington to share their WORLD OF MICROBIOLOGY the wonders of microbes. research with us, on topics ranging from dengue fever to the innate The Microbiology Department is excited I truly enjoyed the conference and all immunity of the eye. With the support about the opportunities we are able to the fascinating presentations. I hope of the Department, MSA hosted a provide to our undergraduate students, that the students going to ASM Microbe successful symposium and we hope to due to generous gifts and strong next year enjoy it as much as I did, continue this tradition in future years. support. One highlight is the chance and that it opens up new avenues of to attend professional conferences. exploration for them, like it did for me.” Other events such as a Thanksgiving This gives students a glimpse into the —Ashley M social, a fieldtrip to 2 Towns Ciderhouse, professional world, with opportunities and a bake sale to benefit the Linn for networking and the chance to STUDENT CLUBS Benton Food Share helped MSA reach its explore new directions. The American goals for the 2015–16 school year. Society for Microbiology (ASM) meetings TheMicrobiology Student Association in Seattle and Boston were funded in (MSA) brings undergraduate students We are incredibly thankful for the part by generous donations from Joel interested in microbiology together to Department’s and MSA’s ability to use Peterson and Sheila Van Zandt. engage in microbiology-related events. microbiology to create a welcoming Our main goals during the 2015-16 community and facilitate lasting Here, in her own words, is how one school year were to provide students friendships. student benefited: with a platform to interact with each other, to help students deepen their —Emaan Khan & Vanlena Le, 2015–16 “I’ve never been to the East Coast passion for microbiology and to give MSA co-Presidents before, so when the opportunity was back to our community. We planned available to visit as part of the trip a variety of events this past year to TheBioHealth Sciences (BHS) Club to ASM, I decided to give it a shot. achieve these goals. was established in fall of 2015 with While I loved Boston, I was even more a mission to help prepare all BHS blown away by the conference itself. In the fall, club advisors Linda Bruslind students for post-baccalaureate health It was far more than even my wildest and Jeneva Anderson took a group of profession careers. We accomplish dreams could have imagined. The students to the American Society of this goal by providing volunteer sheer number of groups represented Microbiology Northwest Conference opportunities, coordinating training was unfathomable, making me realize (ASM NWC) in Seattle, where attendees sessions, inviting guest speakers to how many options I have with my networked with professionals and campus and organizing field trips. major beyond the medical track. I had, heard about a broad range of topics in We also provide space for students prior to the conference, started to feel microbiology. to socialize with like-minded people, disheartened with my major, realizing provide academic support and offer that I do not have the aptitude for MSA wanted to share what we learned a platform for upperclass students to medical school, but this opened my at the ASM NWC and other similar share their academic and out-of-the- mind to all the possibilities. Even better, conferences with the community here classroom experiences, and wisdom, to I was able to connect with a gentleman at Oregon State, so we planned our own new students. at the University of Washington about research symposium in the spring. We doing fluorescent microbial art with the invited 10 speakers from universities in Last fall, the officers of the BHS Club

2 Oregon State University Colleges of Science and Agricultural Sciences coordinated a field trip to PeaceHealth Medical Laboratory in Springfield, OR where they toured the microbiology, flow cytometry, urine analysis, blood bank and pathology departments. This trip was an applicable experience American Society of Microbiology Northwest Conference (ASM NWC) in Seattle for students who hope to work in a medical laboratory setting, and likewise for students who will be ordering diagnostic lab tests during their careers.

During spring term of last year, the officers of the club coordinated a CPR training session in collaboration with the American Heart Association and pre-professional clubs across campus to successfully certify more than 40 students. Certification allowed students to easily obtain jobs this past summer. The club is planning a similar event for this academic year.

The BHS Club hosted numerous Biohealth Sciences students practice taking Kelly Girouard and Hannah Mathews represent blood pressure Biohealth Sciences Club at the COS science fair professional guest speakers, including dentists, doctors, nurses, as well as representatives from graduate programs and student success centers across campus. This year, the club will kick off our speaker series with an osteopathic physician who will talk about the profession and his path as an undergraduate.

We continually strive to support and encourage students to work towards their career goals, while connecting with their fellow students and with faculty.

Wait, there’s more! Read about undergraduate research on page 16. American Society for Microbiology Conference (Boston): Emaan Khan, Vanlena Le, E. Seul (Elizabeth) Kim, Rachel Conover, Ilya Bobrovnikov, Elise Ewens, Aparna Govindan, Stephanie Mikkelsen, Eugenia (Jana) Rott

Department of Microbiology 3 SMALL TALK: STUDENTS Bright minds Updates from our graduate students and postdoctoral researchers

WELCOME NEW GRADUATE STUDENTS! function used in this process. the social behaviors of bacteria, focusing primarily on quorum sensing Damien Barrett (Bartholomew Grace Klinges (Vega-Thurber Lab): Coral in . I am Lab): I am interested in the genetic reefs occur in a wide array of hydrologic currently working on a project to architecture of disease resistance in settings throughout the Indian, Pacific determine the requirements for true salmonids. My research is focused on and Atlantic Oceans and are exposed to quorum sensing. identifying resistance genes in rainbow many different environmental stressors, trout (Oncorhynchus mykiss) to the so it is crucial that we understand how Quinn Washburn (Giovannoni Lab): myxozoan parasite Ceratonova shasta. biogeography and hydrology affect coral The goal of my research is to develop symbiont diversity and community throughput cultivation methods for Lindsay Collart (Dreher Lab): I am structure. My research will use understanding microbial communities. interested in cyanobacteria genetics innovative data visualization methods to and ecology. My project will be evaluate variation in the coral holobiont TRAVELS AND ADVENTURES focused on identifying drivers of at local and regional scales throughout population dynamics in freshwater the South Pacific. Last year, Ryan McMinds, a Ph.D. cyanobaterial blooms. student in the Vega-Thurber Lab, was Rebecca Maher (Vega-Thurber Lab): I am quoted as saying “Life as a graduate Jesse Coutu (Jin Lab): I am interested studying how environmental stressors student can be summed up best in studying viral latency and the alter the coral host and its associated with this statement: Well, I just hit development of novel antiviral therapies microbes. I will be conducting field and 50,000 miles that I’ve flown for this that combat this viral strategy of tank experiments at the Gump Research project.” Since then, Ryan has logged immune evasion. My current research Station on Moorea, French Polynesia, an additional 28,000 miles (plus or focuses on studying the molecular to investigate how parrotfish predation minus), with trips to French Polynesia, virology of a recently discovered latency and nutrient enrichment combine to Saudi Arabia, Hawaii, Panama and associated factor (ORF6) found in Koi cause coral mortality. Curacao. He now has his feet happily Herpesvirus. I will study ORF6’s function on the ground in data-processing and during viral latency with a particular Bryce Penta (Halsey Lab): I am interested paper-writing mode. focus on the role of ORF6 in apoptosis in the role of phytoplankton physiology (programmed death of cells). on marine biogeochemical cycles. Taking a different path, another student Currently, I am working on studying in the Vega-Thurber Lab,Stephanie Bailey Keefe (Bermudez Lab): My phytoplankton physiological responses Rosales, packed her bags for a land- research interests include learning during acclimation to seasonal deep locked location: Nepal! Through the NSF more about how pathogens cause mixing of the ocean. I plan to extend Graduate Research Internship Program disease in both humans and animals. my research to investigate the role of (GRIP), which seeks to expose graduate The project I will be working on various phytoplankton groups, such as students to research environments explores the host-microbe interaction mixotrophs (phytoplankton that can outside of academia, Stephanie’s between Mycobacterium avium and photosynthesize and consume organic first stop was the Smithsonian human respiratory epithelial cells. carbon) on ecosystem production. National Zoo (SNZ), Washington, Specifically, I am looking at their D.C. There she received training on ability to form microaggregates and Tanner Robinson (Schuster Lab): My diagnostic procedures for Elephant identifying the proteins and their research interests lie in understanding endotheliotropic herpesvirus (EEHV).

4 Oregon State University Colleges of Science and Agricultural Sciences “EEHV is a rapidly progressing disease in Asian elephants that presents characteristic symptoms, including lethargy, edema of the head, cyanosis of the tongue, oral ulcers, tachycardia and internal hemorrhaging. If left untreated, EEHV usually results in the death of the animal within 1–7 New Microbiology graduate students. L to R, Back Row: Quinn Washburn, Bryce Penta, Jesse Coutu, Damien Barrett. Middle: Lindsay Collart, Tanner Robinson, Becca Maher. Front: Bailey Keefe, Grace Klinges. days after clinical signs arise. So early detection is essential to increase survival rates.

“During my training at the SNZ, I learned to process trunk washes (saline wash from the trunk of elephants) and use PCR (polymerase chain reaction) for EEHV detection. The Zoo was an enriching, two-week experience where I had the opportunity to meet researchers outside my field and learn about the unique research opportunities that are made possible by the Smithsonian’s rich, historic datasets. It was also a plus that I could Stephanie Rosales collecting samples for Elephant Grad student Kelsey McBeain aboard the Endotheliotropic Herpesvirus in Nepal. R/V Atlantis retreat to the Orangutan or coral reef exhibits during breaks!

“The adventure continued in Nepal where I had to apply my new EEHV diagnostic skills. In Chitwan, Nepal, elephants have recently been diagnosed with EEHV, but the prevalence in the population is unknown. Although my supervisor at the Smithsonian and I planned this trip extensively with the Center of Molecular Disease-Nepal (CMDN), the logistics of the trip fell apart the day of my arrival. Luckily, Dr. Vega-Thurber had trained me to handle less-than- ideal fieldwork situations. Grad student Scott Klasek spent the summer sailing in the Arctic Ocean to study methane sediments. Core sampling (L) aboard the RV Helmer Hanssen (R).

Department of Microbiology 5 SMALL TALK: STUDENTS

“So with some perseverance and a last summer doing research at Kwansei lot of help from the National Trust Gakuin University in Sanda, Japan. The for Nature Conservation in Chitwan, work was funded by the NSF and The I was able to collect trunk washes Japan Society for the Promotion of and process the samples from a Science and focused on the application cohort of Asian elephants. However, of Raman microspectroscopy and this story is ‘to be continued’ as my stable isotopes to study amino acid samples are sitting in a freezer at utilization by microbial communities in Graduate student Brandon Kieft CMDN. In the future, I hope not only to Osaka Bay. examine EEHV prevalence, but also the microbiome of these samples.” Eric Moore and fellow Halsey Lab member Kelsey McBeain traveled to Kelsey McBeain (Kim Halsey Lab) had New Orleans last February for the the amazing opportunity last May to Ocean Sciences Meeting. “We both study the North Atlantic phytoplankton presented posters on our research bloom and all of its influences (as to marine scientists from around the many as we can measure, at least) on world, attended over 50 presentations, a month-long research cruise with toured two research vessels and the North Atlantic Aerosols and Marine enjoyed the famous sights, sounds and Ecosystems Study. tastes of vibrant New Orleans.”

Wei Wei (center right) in Singapore, on a NSF In summer 2016, Wei Wei (Walt Scott Klasek (Rick Colwell Lab) spent East Asia & Pacific Summer Institute fellowship Ream Lab) traveled to Singapore on three weeks last summer sailing in the a National Science Foundation East Arctic Ocean with scientists from the Asia and Pacific Summer Institute Arctic University of Norway Center for fellowship to conduct research on Arctic Gas Hydrate and Environment. plant metabolomics at the National University of Singapore. Wei is studying “The objective of the cruise was to the interactions between the bacterial use a remote-operated vehicle (ROV) plant pathogen Agrobacterium and to obtain detailed maps of seafloor its hosts. Agrobacterium species can communities where methane from genetically modify plants. sediments leaks into the overlying ocean. Using the ROV, we took samples Wei’s research focuses on identifying of sediments, water, rocks, gases and how an Agrobacterium virulence animals to investigate how carbon Graduate student Scott Klasek protein, GALLS-CT, alters plant gene and other nutrients are cycled in these expression during infection. She spent unique ecosystems.” 10 weeks in Singapore investigating how GALLS-CT expression changes the Courtney Armour (Tom Sharpton secondary metabolite profile of plants. Lab) was one of 14 graduate students Plant metabolites are the functional around the world awarded the products of genes that affect many Association for Computing Machinery essential plant processes. Her research Society Special Interest Group on aims to improve current methods of High Performing Computing/Intel Agrobacterium-mediated genetic Computational & Data Science technologies for plant modification. Fellowship. This three-year fellowship will help to support her large-scale Brandon Kieft (Ryan Mueller Lab) spent data analysis of the gut microbiome. Graduate student Courtney Armour (photo by An Vuong)

6 Oregon State University Colleges of Science and Agricultural Sciences POSTDOCTORAL RESEARCHERS BRINGING THE WORLD TO OSU

Dr. Gema Alama Bermejo The Department of Microbiology (Bartholomew Lab) began a hosts visiting professors from tenure-track position at the a variety of universities and National Scientific and Technical countries. These exchanges enrich Research Council in Argentina. She the department in so many ways, Dr. Gema Alama Bermejo is developing a research program fostering collaborations that have on marine parasites that will profound impact on our research. cultivate myozoans to myoliquefy This year saw the following commercial fish fillets using researchers in our laboratories: genomics and other molecular approaches she learned at OSU. Dorothee Huchon Pupko, Israel (Bartholomew Lab) Dr. Cleo Davie-Martin (Halsey Lab) received the OSU Postdoctoral Tamar Lotan, Israel Association’s Professional (Bartholomew Lab) Development Award, allowing her to attend a workshop and Chengzhong Yang, China conference on proton-transfer- (Bartholomew Lab) reaction mass spectrometry Dr. Cleo Davie-Martin (PTR-MS) in Austria last February. Choonbok Song, South Korea She then ventured into the North (Kent Lab) Atlantic Ocean in May 2016 to observe the spring bloom, once Qiao Yang, China (Giovannoni Lab) again taking with her our resident PTR-MS (James, Mr. 007) to Miwa Satoshi, Japan (Oregon measure the cycling of volatile Department of Fish and Wildlife) compounds by marine plankton. Joe Ortiz, Kent State University, OH Armanda Roco is a new postdoc (Dreher Lab) working with Professors Mueller, Myrold and Kleber in Crop and Anindo Choudhury, St. Norbert Soil Science. Her Ph.D. work at College, WI (Kent Lab) Armanda Roco Cornell University focused on soil denitrifier community ecology and she is currently working on a mass spectrometry-based proteomic project to understand how protein turnover affects organic nitrogen availability in soils.

Tim Otten, a postdoc in the Dreher Lab, started his own company, Bend Genetics LLC, in Sacramento, CA, using genetic and toxin analysis to monitor/research harmful cyanobacterial algal blooms. L to R: Connor Driscoll, Nathan Brown and Tim Otten

Department of Microbiology 7 SMALL TALK: ALUMNI Help from our friends We are growing thanks to the generosity of our alumni and friends!

UNDERGRADUATE SCHOLARSHIPS SHEILA VAN ZANDT RESEARCH receptors. The funding from the Sheila EXPERIENCE SCHOLARSHIP Van Zandt Student Research Experience At our annual undergraduate awards Scholarship has made it possible to luncheon in May 2016, 17 students were A new opportunity for students was collaborate with Amandip Singh, a presented with scholarships totaling unveiled this year: the Sheila Van Zandt motivated undergraduate who recently $26,000. These scholarships may Research Experience Scholarship, joined our lab. Amandip’s involvement be targeted to achievement, need or which was awarded to two graduate/ significantly improves the pace of lab discipline, but together they are critical undergraduate research teams. The work and facilitates the sharing of to our students’ success. And students students developed a proposal and ideas which guides our next steps. In are extremely appreciative. budget, then obtained the support of addition to providing an opportunity a faculty mentor for the project. This for Amandip to engage with scientific “This departmental scholarship will has been a tremendous opportunity to research, I am gaining important allow me to focus on my microbiology promote graduate student mentorship experience which will improve my skills classes to work towards my career of undergraduates and to allow them to as a mentor.” —Joe Sexton goal of going into the dental field. I also experience what it is like to administer want to conduct more microbiology- a small research project. It also helps Identification of Burkholderia species related research, possibly doing a dual the department to promote diversity associated with secondary infections graduate degree program. On behalf by providing minority students with in stranded harbor seals on the Pacific of my family and myself, thank you so research experiences. Coast. much for giving to the department.” —Aparna G. Impact of bacteriocins on siderophore “The Sheila Van Zandt Student diversity in Pseudomonas. Research Experience Scholarship “Thank you for your generous donation enriched my scientific knowledge in a making the Middlekauf Scholarship “I have been able to continue working variety of ways. I was able to practice possible. I am a junior in microbiology on a spring term project, thanks to essential lab skills and familiarize and am interested in food microbiology the Sheila Van Zandt Scholarship. I am myself with laboratory equipment, and quality assurance. This scholarship experiencing the highs and lows that while also applying the material I is a huge blessing to me as I would not come with research, while at the same learned from previous microbiology be able to afford tuition without your time gaining valuable insight into the classes, such as DNA cloning, gel help. I am honored to be receiving this field. As a microbiology major I believe it electrophoresis and data analysis. In award.” —Ryan W. is important to have a solid assessment my opinion, this was the best way to of what research is like before understand my topic of interest and “I’m so honored to be the recipient graduating. Working with a mentor is also gain insight on what happens of your scholarship. You have given allowing me to gain insights from the before a scientific journal article me the opportunity to pursue many perspective of a mentee, which will be gets published. Additionally, this opportunities due to this scholarship. I valuable in the future if I am mentoring opportunity allowed me to connect can continue to pursue microbiological someone else.” —Amandip S. with personnel and build a relationship research and spend my time helping with both my lab principal investigator with community services. With this “As a graduate student in the Schuster and graduate student mentors. award you are able to relieve some of Lab, I study the evolution of iron Although I have an interest in pursuing my financial burden.” Dang— D. chelating siderophores and their medicine, my lab research experience

8 Oregon State University Colleges of Science and Agricultural Sciences HONOR ROLL Recognizing the Department’s annual supporters who have made Ph.D. student Connor Driscoll is one of two outright gifts or pledge payments Mark H Middlekauf Outstanding Graduate totaling $1,000 or more between Achievement in Microbiology winners. July 1, 2015 and December 31, 2016. will open doors for future medical Scholarship was awarded to Connor Anonymous (1) research.” —Natalie L. Driscoll (Dreher Lab) and Omran Muslin Joy Asbury (Giovannoni Lab). Matthew A. Bacho ’92 “The Sheila Van Zandt Scholarship was Jerri Bartholomew ’85 a rewarding mentoring and training Harriet M. Winton Scholarship Mary E. & Michael J. Burke experience. The opportunity provided was awarded to Claire Howell Robert W. Foote ’83 a platform to advise and improve (Bartholomew Lab). Janna E. Ford ’99 my teaching skills. For instance, I William R. Ford ’65 was responsible for training Natalie Tartar Fellowship was awarded to Gregory D. Geist ’72 in laboratory skills, presentations, Eric Moore (Halsey Lab). Warren J. Groberg, Jr. ’73 writing and note taking. Also, it was Frances T. Hall ’52 a great chance to show Natalie the MICROSCOPE GIFTS Charles A. Hays ’85 dedication and time involved in the Karen S. & Ronald P. Hedrick ’75 scientific process. Overall, this was Alumnus Bob Foote (Geology, ’83; Linda L. & Richard A. Holt ’88 an educational experience that has Geophysics, ’85) made another generous Judith F. & Paul R. Kenis ’66 enhanced my training as a scientist and gift this year that was matched by his Scott E. LaPatra ’79 helped train a young microbiologist.” former employer, Chevron. This gift Joyce ‘78 & Thomas C. McLean ’75 —Stephanie Rosales enabled the purchase of additional new Cynthia & Michael M. Mueller microscopes for our teaching labs, so Madeleine C. Deininger & Joel E. GRADUATE SCHOLARSHIPS/FELLOWSHIPS now we have replaced nearly all of our Peterson ’69 older models with brand new ones! Matthew E. Stinson ’12 This year we presented six awards at our Joan Countryman Suit ’53 & first-ever graduate awards luncheon: JOHN L. FRYER FELLOWSHIP Herman D. Suit Sheila Griep Van Zandt ’59 Mark H. Middlekauf Outstanding As part of the 25th year celebration of Harriet M. Winton Fund of The Teaching & Service in Microbiology was the John L. Fryer Aquatic Animal Health Oregon Community Foundation awarded to Prabhat Talukdar. Lab, we reached out to former students, James R. Winton ’81 collaborators and friends, asking them Mark H Middlekauf Outstanding to consider donating to this fellowship. THANK YOU! Graduate Achievement in Microbiology Many stepped forward with generous If you notice any inaccuracies, was awarded to Connor Driscoll (Dreher gifts, and because of this we are able to please contact Penny Hardesty, Lab) and Eric Moore (Halsey Lab). offer several terms of full support each Director of Donor Relations, OSU year for a graduate student conducting Foundation, Penny.Hardesty@ Joan Countryman Suit Graduate research on infectious diseases of fish. oregonstate.edu or 541-737-1469.

Department of Microbiology 9 SMALL TALK: NEWS News Innovation, rejuvenation, hires, promotions and awards

“I have had a lifelong passion for and animals and how they move and fierce or innocuous. Her rich exterior art and science and feel that I was protect themselves. I am particularly color directs the focus of the lines of made for this show. I have a Ph.D. drawn to creatures in nature that her undulated appendages.” in molecular biology and was a walk the line between beguiling and — Kristin Levier molecular microbiologist for 20 years terrifying. I envision Endulata bas before starting my second career as a as a creature stolidly and gracefully sculptor. The majority of my sculptural navigating the currents of the deep Learn about Microbiology-inspired art work is inspired by microbes, plants ocean. It is unclear whether she is on the next few pages.

10 Oregon State University Colleges of Science and Agricultural Sciences CONGRATULATIONS! for students to work on in small groups, fostering cooperation and active learning Rebecca Vega-Thurber was promoted of the course concepts. The redesigned to associate professor this year. In course was well received by students and addition, she was selected by the Faculty resulted in the highest assessment scores Recognition and Awards Committee as to date. She plans to implement the new the 2016 recipient of the OSU Impact model for her spring term Microbiology Award for Outstanding Scholarship. 302, adding the use of undergraduate learning assistants to provide additional Ruth Milston-Clements, manager resources for the 200 students that WELCOME NEW FACULTY AND STAFF of the John L. Fryer Aquatic Animal typically take the course. Health Laboratory, was selected as Andrew Thurber (above), our newest the 2016 recipient of the Agricultural “I absolutely loved how MB 302 was faculty member, has a joint appointment Research Foundation Faculty Research taught during the summer! I felt like the with the College of Earth, Ocean, and Assistant Award. expectations of the class were really clear Atmospheric Sciences. He researches as the lectures, worksheets and textbook how microbial processes fit into the Jerri Bartholomew received the were all similar in style and information. overall ecosystem function of marine S.F. Snieszko Distinguished Service The class was really organized, with the systems. His current projects range from Award from the American Fisheries assignments in class ...[forcing] me to identifying how sulfide and changing Society (AFS) for her outstanding think about the concepts on my own food supply may impact the Manila accomplishments in the field of aquatic with the ability for Q&A time during class clam population, thus addressing a food animal health. This lifetime achievement rather than making time for teacher’s security issue of Native Americans in award is the highest honor presented office hours after individual study. The Washington state, to identifying factors by the Fish Health Section of the AFS. textbook was really easy to read (I ended that control the distribution of bacteria Jerri’s decades of research on salmon up reading other portions of the textbook and archaea in the deep-subsurface off parasites and her directorship of the J.L. for fun!). Dr. Bruslind is a fantastic of the South China Sea and India. Fryer Aquatic Animal Health Laboratory lecturer and really brought together all have deepened our understanding learning styles for a course that was This year he returns to Antarctica with his of how infectious organisms sicken focused on the success of its students!” graduate student to study how methane, salmonids and other freshwater fish, —Michelle M., undergraduate a potent greenhouse gas, is consumed generating forecast models of how in the cold and isolated waters of the climate change might affect the In building a unique curriculum for our southern continent. Thurber will share interaction. Her research has advanced biohealth sciences major, we developed his research with students in an aquatic the microbiological understanding of three new courses. Jeneva Anderson microbiology course. the host-pathogen dynamic, producing developed a new writing intensive practical recommendations for fisheries course, “Microbial Influences on Human Our biohealth sciences advising team that have already been put into use. Health,” which was taught for the first was completed this year with the hiring time last spring and will be offered of Alex Beck, who has worked at OSU for INNOVATIONS IN LEARNING online this spring. more than 13 years, and Barbara Kessel, who comes to us from Oregon Coast Dr. Linda Bruslind completely overhauled Thomas Sharpton introduced the Community College where she was an her “General Microbiology” course last “Human Microbiome” course, where advising specialist for six years. summer, to teach in a more engaging students learn about the biodiversity, and innovative way. Fundamental to function and medical importance of the Emy Daniels joined the department, this was her authoring of an open source communities of that replacing Camille Partridge in the textbook, with the help of experts at inhabit the human body. media kitchen. This position supports OSU Open Campus who are dedicated to our teaching laboratories. Emy providing free access to learning tools for Michael Kent taught “Mechanisms of previously worked for the Scripps students. Along with the textbook, Linda Disease,” which introduces students to Institution of Oceanography. designed a series of in-class activities the basic principles of disease.

Department of Microbiology 11 SMALL TALK: NEWS

four artist workshops in microbiology their interpretations of the microbial laboratories. The first workshop was world. The students’ artwork will be held at the John L. Fryer Aquatic Animal featured in The Corvallis Arts Center in Health Laboratory. Artists heard from the final art exhibit this spring. researchers and graduate students This year, OSU’s Division of Arts and about investigations into aquatic RESIDENT ARTISTS Sciences, which includes the College of microbiomes. They had the opportunity Science, launched a series of events to to culture organisms from different In addition to the microbiome art celebrate and highlight the relationship water sources and to examine these exhibit, researchers in the department between art and science. As part of environments more intimately under are hosting and collaborating with art this yearlong event, the Microbiology the microscope. Participants were students and artists in their laboratories Department is collaborating with provided nutrient agar plates to culture to help them interpret our discoveries The Corvallis Arts Center (TAC) on microbes from soil, water and even and to engage a broader audience in our a microbiology-based art show, their own bodies. research. Microbiomes: To See the Unseen. Subsequent workshops were held in Karl Payne: A senior in engineering The project focuses on microbial the microbiology teaching laboratory. minoring in fine arts, Karl is working in systems that affect human health, the Artists heard talks by microbiology the Bartholomew Lab on a sculpture biodiversity of animal species and air, graduate students about microbes that of the Willamette River that will find earth and water quality, asking both inhabit soil and aquatic environments, its home in the west patio of Nash artists and researchers, how can we the air and the human body. The artists Hall. This metal and glass sculpture is a see the unseen? Microbiology tries to toured working laboratories, explored collaboration with Jerri Bartholomew measure, visualize and understand microbiomes that they cultured and its design was influenced by complex microscopic systems in the themselves under microscopes, and discussions with scientists who have same way artists seek understanding even painted with bacteria. Since worked on the river. for life’s many questions. In the exhibit, different bacteria can produce a variety artists will document and interpret of pigments, the artists “painted” with Samm Newton: is pursuing an M.A. complex research concepts to bring a palette of Pseudomonas aeruginosa in OSU’s new Environmental Arts greater understanding to the public, (blue-green), Pseudomonas and Humanities Program. She is and offer a unique perspective to the aureofaciens (orange), Serratia currently spending time in Steve scientific community. marcescens (red), Micrococcus luteus Giovannoni’s lab examining microbial (yellow), (pale communities and how the metabolic The exhibition runs April 13—May 27, yellow) and Bacillus subtilis (white). processes of bacteria contribute to 2017, and includes invited and juried global biogeochemical cycles. Samm visual artists, musicians and poets. We MICROBIOLOGY-ART OUTREACH is working on a collection of paintings, plan to host several events, including prose, poetry and photography inspired a speaker, a music performance and As part of the exhibit Microbiomes: by ocean microbiomes. poetry readings. We are also producing To See the Unseen, graduate students an exhibit catalog and video to from the department are participating Brianna Leahy: An illustrator and expand the audience of this project. in a series of outreach activities with sculptor living in the Willamette Valley, For information and updates, visit local elementary schools. Between Brianna is currently working with the our website: microbiology.science. October 2016 and May 2017, graduate Vega-Thurber Lab to create scientific oregonstate.edu/spark. students are giving microbiology illustrations for textbook and journal lessons and leading hands-on demos publications. She is also collaborating Artist workshops: To help artists for more than 220 students in the with the lab to create a comic series for learn more about the science of schools. The students will then work web-based outreach. Their goal is to microbiology and to explore a with artists to take what they’ve inform and inspire children and youth microbiome themselves, we hosted learned and create artwork reflecting to get interested in science.

12 Oregon State University Colleges of Science and Agricultural Sciences “Dispersion” by Chi Meredeth portrays the Johanna Rotko’s “Yeastograms” are created movement of microbes from one area into another. by exposing to ultraviolet light.

Work by Diane English inspired by cell walls (right). “I love how cell walls when viewed through a microscope look very organic and at the same time very architectural.”

Laura Reichenbach’s fiber art Beyond the Naked Complex Communities by Laura and Tom Sharpton is an interactive artwork designed to aesthetically Eye makes use of diatomic forms (above) demonstrate this temporal change in microbiome biodiversity.

Department of Microbiology 13 SMALL TALK: SECTIONRESEARCH From our labs Research gains momentum with fieldwork worldwide

DREHER LAB. The Dreher Lab has seen blooms in Upper Klamath Lake, as the also actively exploring how changes in some major transitions this year, with primary producer. We have identified the operation of the gut microbiome two graduate students, Nathan Brown Anabaena as the producer of the influence human and animal health and Connor Driscoll, completing their unpleasant flavor product, geosmin, in and evolution. This includes a new Ph.D.s, and postdoc Tim Otten leaving a drinking water reservoir in Kansas, study of the salmon gut microbiome for the exciting work of starting his and we have tracked the Microcystis and the role it plays in salmon ecology. own company. They were all in the genotypes over an eight-year period in Our biggest research story of the year lab for a number of years, and have Copco and Iron Gate Reservoirs on the was work led by Christopher Gaulke, produced some excellent studies and Klamath River in Northern California. a postdoc in our lab, wherein we left a lot of fantastic groundwork for showed that exposure to triclosan, a future research on the cyanobacteria We also have a long-term dataset consumer-grade antibiotic, rapidly that occur in the Pacific Northwest. from Dexter Reservoir near Eugene, perturbs the gut microbiome. This story We have embraced the use of which will form the basis for the thesis was covered by many news agencies genomics to describe the genomes research of first-year graduate student including Fortune and TIME magazines. of the cyanobacteria that bloom in Lindsay Collart, who until recently lakes such as Upper Klamath Lake, worked on Microcystis blooms in Lake In addition, Tom was fortunate Dexter and Detroit Reservoirs in the Erie. Her research will seek to explain enough to participate in the rollout Cascade foothills and Anderson Lake why blooms disappear or transition of the National Microbiome Initiative in Washington State. These lakes are to a different species, so that we can at the White House in May. Several where the cyanobacteria are a problem predict such dynamics in the future. Ph.D. students in the lab were either because they disrupt the lake During collections to Oregon blooms awarded research fellowships. ecology or because they produce toxins this summer, recent microbiology We are also having a great time that are a public health concern. undergraduate Briana Bullington integrating computational and helped to recognize coordinated self- bioinformatic methods into graduate We have used to advantage a recently induced cell lysis, apparently triggered and undergraduate courses. In fact, developed DNA-sequencing technology by some stress signal, as a potential Tom developed an upper division (PacBio, produced by Pacific mechanism for bloom termination in microbiology course, “The Human Biosciences) which can produce much local cyanobacterial populations. Microbiome” that was offered for longer units of primary DNA sequencing the first time this year. The students data than the more commonly used SHARPTON LAB. We had a lot of fun this were enthusiastic and did great with Illumina technology. The longer “reads” past year. We graduated our first Ph.D. this new subject material. Our lab is have allowed us to determine the student, Melissa Conley, published equally excited about what the next complete genomes of several bacteria several manuscripts on microbiome year will bring! (every single nucleotide, which is health and received multiple grants, currently not the norm) and to show including a major award from the MUELLER LAB. We welcomed two that this is important because a few National Science Foundation. Thanks new members to the lab this year. key genes can be missed when other to this award, we are now working The first is second-year graduate technologies are used. We have applied to develop computational methods student Winni Wang, who joined us our genomic studies to examine that will reveal specific members of last summer to begin working on bacteria that form a community based the microbiome that are important to a new project examining nutrient on Aphanizomenon flos-aquae, which ecological and human health. We are cycling in seagrass meadows. Sampling

14 Oregon State University Colleges of Science and Agricultural Sciences This figure illustrates how ecological relationships among gut bacteria change upon exposure to the antibiotic triclosan (Sharpton Lab). for this project started last summer SCHUSTER LAB. The Schuster Lab in bacterial cell-cell signaling. FEMS with collections taken from Mallorca, studies the principles of cooperation Microbiol Rev. pii: fuw038, Epub ahead Crete, Valencia, Canary Islands and and conflict in bacteria. The evolution of of print. Sardinia. Also joining the lab as a new cooperation remains a central paradox postdoc is Armanda Roco, who comes in biology: Why should an individual VEGA-THURBER LAB. It’s been another to us from Cornell University where carry out a costly cooperative behavior wonderful year for the Vega-Thurber she completed a Ph.D. focused on for the benefit of others? To help Lab. We have continued to travel characterizing microbes that perform answer this question, we investigate the world to investigate the roles of denitrification reactions in forest soils. two tractable bacterial model systems, viruses and bacteria in the evolution, Armanda’s research will apply her skills cell–to–cell communication and ecology and health of threatened to a collaborative research project that cooperative iron acquisition. They species and ecosystems. First, Rory seeks to examine organic nitrogen are widespread and vitally important Welsh graduated with his Ph.D. last turnover across distinct soil types processes in many microbes, with December and received an Oak Ridge found throughout Oregon. implications in soil ecology, agriculture Institute for Science and Education and medicine. Both processes involve fellowship to work at the Center for Lastly, I am very pleased to say that the secretion of compounds that not Disease Control. His Ph.D. work on Sam Bryson’s first manuscript from only benefit the producing cell, but bacterial predators was highlighted in the lab was published this year in the neighboring cells as well. Intriguingly, ASM’s magazine, Microbe. journal mSystems. The quality of Sam’s some cells have the ability to steal work was recognized by its selection as these compounds from the producing Stephanie Rosales successfully the “Editor’s Choice” for that volume cells, thus saving on production costs. defended her Ph.D. in December. and through two short interviews that Her work on the viral and microbial Sam gave for a blog on the American Together with graduate students pathogens in stranded seals was Society for Microbiology (ASM) website Kyle Asfahl, Joe Sexton and Tanner recently published in PLoS One. and for The Scientist magazine. Bryson, Robinson, we aim to find out how and Stephanie also presented this work S., Li, Z., Pett-Ridge, J., Hettich, R.L., why these cooperative behaviors are at ASM this year and was featured in Mayali, X., Pan, C., and Mueller, R.S. nevertheless maintained. As part of ASM’s education magazine. Stephanie (2016). Proteomic Stable Isotope this effort, Kyle Asfahl has published also was awarded an NSF Graduate Probing Reveals Taxonomically Distinct a comprehensive review of recent Research Intern Program fellowship to Patterns in Amino Acid Assimilation by advances in the field. Asfahl KL and work with the Smithsonian in Nepal to Coastal Marine Bacterioplankton. Schuster M (2016) Social interactions study elephant viruses. Ryan McMinds

Department of Microbiology 15 SMALL TALK: RESEARCH

traveled around the world including collaborations this year. Gael Kurath Saudi Arabia, Hawaii and Panama to (United States Geological Survey, collect samples for his dissertation Seattle branch) and postdoc Rachel project on the co-evolution of Breyta will be using phylogenetic bacteria with corals, presenting to the modeling to better resolve patterns in International Coral Reef Symposium parasite genotype and spatial and host in July. Lastly, Vega-Thurber recently distribution. Dorothee Huchon (Tel Aviv sailed on the research vessel Tara to University, Israel) is spending a year collect and process coral samples from on sabbatical with us to work on the Easter Island to Tahiti. Her lab is leading elusive structure of the mitochondrial an international effort to understand genes of myxozoans. Chengzhong Yang the coral reef microbiome across the (Chongqing Normal University, China) entire Pacific Ocean. joined us last March to investigate host-parasite molecular evolution with BARTHOLOMEW LAB. The core a focus on myxozoans and fish. Closer research of our lab focusses on to home, we are working with Meghna an endemic myxozoan parasite of Babbar-Sebans (civil and construction salmonid fishes, Ceratonova shasta. engineering) and her Ph.D. student We use caged fish, field water sampling Amir Javaheri to model parasite and invertebrate host sampling transport under different flow regimes. to generate spatial and temporal Water sampling in the Mediterranean near parasite abundance data in three HALSEY LAB. While I stayed on land Majorca (Mueller Lab) major rivers in the Pacific Northwest. this year, two members of the lab (Dr. These data inform epidemiological Cleo Davie Martin and M.S. student, and predictive models to understand Kelsey McBeain) spent last May in the environmental variables linked to the North Atlantic aboard the R/V disease-related mortality in salmonids Atlantis studying the annual spring (Julie Alexander and Sascha Hallett, phytoplankton bloom and the volatile research associates). compounds released by plankton to the atmosphere (The North Atlantic Other C. shasta studies include Aerosols and Marine Ecosystems Study, investigation of fish mucosal immunity naames.larc.nasa.gov). and resistance mechanisms (Laura Taggart-Murphy, M.S. candidate) and In the lab, Eric Moore (Ph.D. student) identification of disease-resistance has made some exciting discoveries A methane-fueled habitat for Thurber Lab to genes (Damien Barrett, Ph.D. about diatom interactions and growth explore how microbes limit greenhouse gasses. candidate). Plus we have ongoing behaviors, for which he was awarded a studies using transcriptomics and departmental scholarship. Kelsey found genomics approaches to understand that as food sources, phytoplankton the structure and function of the can taste like a four-star meal or like parasite’s ‘stinging’ cells (equivalent cardboard depending on the species to cnidae in jellyfish), which initiate and environment. Her work has serious the infection process (Gema Alama implications for trophic interactions, Bermejo, postdoc; Stephen Atkinson, especially as nutrient-limited regions research associate; Tamar Lotan, of the ocean expand. collaborator, University of Haifa, Israel). Very tricky experiments conducted We embarked upon several new by Nerissa Fisher (M.S., 2015) showed Dr. Stephen Atkinson and graduate student Claire Howell (Bartholomew Lab)

16 Oregon State University Colleges of Science and Agricultural Sciences that diatoms are remarkably efficient bacteria to live. Because humans have at very low light. Her data suggest different genes than bacteria, PPMOs that diatoms can shift energy flow don’t attack human genes. through different metabolic pathways depending on light availability, and In a new twist, we have modified this “pathway gating” allows diatoms PPMOs so that they no longer kill to persist through the dark days of the bacteria, but instead prevent Theo Dreher’s Lab uses genomics to understand winter. This strategy may explain why the antibiotic-resistance genes the molecular biology of algal blooms. diatoms are commonly the first group from functioning. This restores the of phytoplankton to bloom in the effectiveness of formerly useless early spring (Halsey and Fisher, 2016. antibiotics, which can then be used in Photosynthesis Research). Finally, we combination with our compounds to welcome Bryce Penta (Ph.D. student), kill antibiotic-resistant bacteria. The who joined the lab this fall. technology discovered in this NIH- funded project has been patented GELLER LAB. Antibiotic resistance is an and licensed to Sarepta Therapeutics. escalating, world-wide problem that has Additional testing is underway, and it is gained urgency in the past decade. our hope that clinical trials required for Many strains of bacterial pathogens FDA approval will commence within a have become resistant to multiple couple of years. antibiotics, and some are now resistant Dr. Bruce Geller, professor of microbiology to all standard antibiotics, which makes KENT LAB. The zebrafish has become treatment difficult. Indeed the mortality a very important vertebrate model rate from infection with many strains of for biomedical research. The main multidrug-resistant bacteria is research focus of the Kent Lab is the estimated to be 50%. To make matters investigation of infectious diseases worse, it’s been decades since a single, using zebrafish. The research has new class of antibiotics has been two aims: study diseases that impact approved for many of these pathogens. zebrafish facilities, and study human A post-antibiotic era is no empty threat. pathogens or their surrogates using When physicians and research scientists the zebrafish model. consider the most urgent medical problems we face as a world-wide Important findings this past year community, antibiotic resistance is include documenting that Pseudoloma A nematode in the intestine of a zebrafish certainly among the top concerns. This neurophilia, a very common parasite (Kent Lab) is not only because of the pragmatic in zebrafish labs, causes behavioral consequences, but also because it changes. The parasite causes fish to be means the loss of one of the greatest “hypervigilant” and exhibit behaviors achievements in the history of medicine. consistent with those exposed to anxiety stressors (Spagnoli et al. 2015; Dr. Bruce Geller has been working on 2016). Zebrafish are now a common a new kind of antibiotic (called PPMO) model in behavior research, and that can kill multidrug-resistant given how common the parasite is, it bacteria. Compared to all of the other may be an important cause of non- antibiotics approved by the FDA to date, protocol induced variation in this type PPMOs have a unique ability to block of research, as recently reported in the expression of specific bacterial Nature News (Szilágyi 2016). Sean genes, making it impossible for the Spagnoli led this research in the Kent Patented biopolymer producing bacterial strain used as natural thickener agent (Trempy Lab)

Department of Microbiology 17 SMALL TALK: RESEARCH

Lab as a Ph.D. student, and he is now GIOVANNONI LAB. The Giovannoni on the faculty in the Department of Lab had a busy year of ocean cruises Biomedical Sciences here at OSU. and transitions. Graduate student Omran Muslin perfected technology We are also investigating the cause for measuring osmolyte compounds of a common intestinal cancer of in seawater. Postdoc Luis Bolanos zebrafish, in collaboration with moved to Corvallis from Universidad Karen Guillemin and her team at Nacional Autónoma de México to work University of Oregon through a joint on the North Atlantic phytoplankton NIH grant to Guillemin and Kent. bloom project. Luis spent last April Discovering the cause of this common on his first scientific voyage. Postdoc zebrafish cancer would benefit the Jimmy Saw joined us from Uppsalla, zebrafish research community and Sweden, where he co-discovered may lead to a useful model to study Lokiarchaeota. Jimmy is now working gastrointestinal cancers of humans, a on SAR11 genomics and dissolved leading cause of cancer deaths in the organic matter metabolism under the United States. auspices of BIOS-SCOPE, a new grant based in Bermuda. Through transmission studies in the Kent Lab we have shown that an Last fall, new graduate students Samm infectious agent is clarly causing the Newton and Quinn Washburn joined Undergraduate Michelle Michelson cancer. Study of the microbiome the lab. Samm, an environmental arts has consistently indicated that a and humanities student, is putting art Mycoplasma sp. is associated with the and science together to tell stories, and cancers, and may be the cause. We got her science initiation in September have cultured the Mycoplasma sp. for on board the research vessel Atlantic affected zebrafish, and experiments Explorer. Quinn is also working with the will soon be conducted to determine Sharpton Lab to develop automated, if this is truly the cause, rather than high-throughput culturing methods. simply a bacterium that happens to Zach Landry is finishing his research, proliferate in cancerous intestines. which may be the first to recognize an ancient metabolism that evolved to Another study on the zebrafish oxidize stable forms of organic matter. intestinal microbiome entails a Microbiology student Stephen Noell also collaboration with Tom Sharpton, went to sea and is busy optimizing tools Undergraduate Duncan Ocel who has joint appointments in the for measuring dissolved organic matter departments of microbiology and uptake by SAR11. The lab received a new statistics. With experiments led by grant from NSF to explore functional Chris Gaulke in the Sharpton Lab, we and genomic diversity in vitamin B1 discovered that a common nematode metabolism and impacts on plankton parasite profoundly alters the bacterial networks and productivity, and is microbiome of zebrafish (Gaulke et al. looking forward to an active year ahead 2016). These findings are important exploring this topic. for researchers studying the zebrafish microbiome and dysbiosis, and TREMPY LAB. With a focus on microbial perhaps will lead to a model to study applications, my research program parasite-bacteria interactions in the expanded efforts in technology gastrointestinal tract. transfer activities. This past year, I Undergraduate Ian Humphreys

18 Oregon State University Colleges of Science and Agricultural Sciences continued to seek opportunities to infection of host plants, including move patented technology discovered Arabidopsis thaliana. This effector “at the bench” in my research program protein appears to trigger expression to the commercial sectors. In 2016 of a microRNA that silences a family we learned that one of my patented of known defense genes, thereby biopolymer-producing bacterial strains increasing susceptibility to infection by was enjoying commercial success for Agrobacterium. Undergraduate Rosio Lopez-Arellano assisted use as a natural, organic and potentially by Jamie Graen probiotic thickening agent in fermented Also, we are collaborating with Jeff food products. The commercial global Chang, Marilyn Miller and other market for polymers, including bacterial colleagues from the Department of biopolymers, has an expected worth of Botany and Plant Pathology in an $7 billion dollars by 2018 through uses effort to sequence the genomes of 500 in the food, petroleum, biomedical and strains of Agrobacterium. This analysis pharmaceutical industries. And recent revealed an unexpected finding: most reports from other research programs strains isolated from woody species link biopolymer-producing probiotic are “nopaline-type” strains, whereas organisms with health benefits, with most of those isolated from herbaceous global demand for probiotic products plants are “octopine-type” strains. expected to reach $45 billion by 2018. In the laboratory, both types cause crown gall tumors on either woody or Undergraduate Madison Messmer We are replicating our commercial herbaceous hosts, so the preference success through the characterization of of a particular host in nature was other biopolymer-producing bacterial unexpected. Five of the strains from strains with probiotic potential. Marilyn’s collection comprise a new Discovered by my research program, species in the genus Agrobacterium, these new natural bacterial isolates, sharing ~86% sequence identity with novel combinations of phenotypic with their closest known relatives. In and genotypic traits, are commercially addition, Marilyn and I have sequenced desirable. Karen Dierksen continues to the genomes of several Pseudomonas serve as my senior scientist while I, too, strains isolated from crown gall tumors. still work at the lab bench. We recently We hope this analysis will help us characterized gene sequences of newly understand the microbial communities discovered, unique combinations of that inhabit crown gall tumors. genes responsible for the biopolymer phenotype desired in fermented food UNDERGRADUATE RESEARCH products. This past year I began a new position at OSU, serving as associate Michelle Michelson has been working in vice provost of academic affairs. the Giovannoni Lab since her freshman Although my departmental teaching year. She is studying the inhibition and service activities are reduced, I of Pelagibacter growth by organic continue to work with Karen and a few compounds. Michelle formed her own undergraduate students in the lab! hypothesis and is hoping to help solve the long-standing problem that a REAM LAB. Our laboratory studies an majority of the microbial cells in nature Agrobacterium rhizogenes effector can’t be grown in laboratory culture. protein that suppresses antibacterial defense responses that normally limit Duncan Ocel, (botany and plant Undergraduate Molly Unsworth

Department of Microbiology 19 SMALL TALK: RESEARCH

pathology) is quantifying the amount development for cancers that remain UNDERGRADUATES COMMUNICATE of primary production lost as volatile difficult to treat. THEIR SCIENCE organic carbon in a globally significant cyanobacterium in the Halsey Lab. Ian works with a cyanobacterial Students conducting compound called coibamide A that was undergraduate research present Kayla Stalheim, a senior microbiology discovered by College of Pharmacy their findings each term at our major, attended the Volcano collaborator Kerry McPhail in the department colloquia. Spring Conference in Chemical Biology in fast-moving waters off the Pacific term awards are given to the best Washington State last February to coast of Panama. This compound presentations as ranked by faculty. present her work in Sandra Loesgen’s cuts off the cancer cells’ ability to lab on fungal epigenetics. communicate with blood vessels and In 2015—2016, the following other cells, eventually starving the cell students received the departmental Jessica Hodgen spent last summer and triggering cell death. Ian works Undergraduate Awards for Best researching core circadian clock genes independently with a range of human Research Presentations: in Drosophila melongaster fruit flies, cancer cell types to understand the more specifically how the rhythmic signaling pathway that is responsible Senior Elyssa Armstrong expression of these genes influences for coibamdie-induced death. (Bermudez Lab, Veterinary the aging process. She learned Medicine), “Establishment of an in sophisticated laboratory techniques In the Bartholomew Lab, OSU STEM vitro model to study persistence in that allowed her to determine gene leader Rosio Lopez-Arellano learned Mycobacterium avium.” expression levels in various fly how to extract DNA from water genotypes and statistically analyze samples and to identify and isolate Senior Megan Huber (Robinson Lab, how the late-life rhythmic expression the invertebrate host of a salmon Wood Science and Engineering) of certain clock genes impacts the pathogen, Ceratonova shasta, from “Peruvian fungal pigment longevity, activity levels and stress sediment samples. These samples were production.” resilience of older flies. then used by Honors College student Madison Messmer to investigate Senior Amandip Singh (Schuster Jessica plans to continue conducting relationships between the invertebrate Lab, Microbiology) “Evolution research in the Giebultowicz Lab host genotype and parasite infection. of siderophore receptors in (integrative biology) this winter upon And Whitman College undergraduate Pseudomonas aeruginosa.” returning from studying abroad in student Molly Unsworth joined us for England and hopes that her research a summer internship to investigate Junior Zachary Konkel (Loesgen will contribute to better understanding why particular genotypes of C. shasta Lab, Chemistry), “Antibiotic of the roles of circadian clocks in have persisted above the dams in the activity against methicillin- healthy aging. Jessica’s research is Klamath River even though their fish resistant Staphylococcus aureus funded jointly by the Departments of host is no longer being stocked there. from an Oregonian Aspergillus.” Microbiology and Integrative Biology. Sophomore Bryna Rackerby (Crump Ian Humphreys, a Junior majoring Lab, Ocean Ecology), “Microbial in microbiology, is continuing his diversity in the Mekong River.” research in Jane Ishmael’s laboratory (Pharmacy) last fall with matching support from the Departments of Microbiology and Pharmaceutical Sciences. The Ishmael Lab studies mechanisms of cell stress and death in response to natural product cytotoxins with the goal of inspiring new drug

20 Oregon State University Colleges of Science and Agricultural Sciences Alumni Congratulations to our recent microbiology graduates and alumni!

Saeed Banawas (Ph.D. ’16)—Assistant Atlanta on an ORISE fellowship. He is before applying to graduate school. She professor, Medical Laboratories currently researching the origins of a is working with the Scripps Institute Department, College of Applied Medical newly discovered fungal pathogen that and focuses on raising antibodies Science, Majmaah University, Saudi has become antibiotic resistant and is against the Ebola virus. She is the Arabia. Dr. Banawas is working as a vice infecting patients across the country. second author on this Science paper, dean of scientific research at Majmaah her second paper: science.sciencemag. University and teaching applied clinical Steve Hubbs (B.S. ’16) is now in org/content/early/2016/02/17/ microbiology. “People here are happy graduate school studying clinical science.aad5788 that I graduated from OSU!” microbiology at Oregon Health & Science University (OHSU). Dr. Nitzan Soffer (Ph.D. ’14) is a research Lauren Brooks (Ph.D. ’16)— scientist at Intralytix in Baltimore, MD, Postdoctoral Scholar, Life and Aidan Maxwell (B.S. ’16) graduated where she studies phage therapy for Environmental Sciences, School and is working as a lab technician at human diseases. of Natural Sciences, University of OHSU at the Vaccine and Gene Therapy California, Merced. She is doing Institute in Beaverton where he works Paul Carini (Ph.D. ’13) just became an evolutionary and microbiome research on HIV therapies using a non-human assistant professor at the University of and having a blast! primate model system. Arizona.

Nathan Brown (Ph.D. ’16) is doing a Ariel Liberda (B.S. ’16) graduated and Hyatt Green (Ph.D. ’11 ) is an assistant postdoc at the University of Leicester is a histology lab technician at Bend professor of microbiology in the in the UK to work on the use of Dermatology. Department of Environmental and bacteriophages to treat bacterial Forest Biology at the State University infections. Lmar Babrak (Ph.D. ’15) is a postdoc of New York, College of Environmental at the Agricultural Research Service Science and Forestry. Michael Dobie (M.S. ’16)—Bacteriologist where he makes monoclonal antibodies for Oregon Freeze Dry Foods. to deploy onto immunoassays to detect pathogens. Connor Driscoll (Ph.D. ’16) is finishing publications and interviewing for jobs Nerissa Fisher (M.S. ’15) is now a Ph.D. in Seattle. student at the University of Technology in Sydney, Australia. Zach Landry (Ph.D. ’16)—Postdoc in the Giovannoni Lab. Marius Ibuye (B.S. ’15 Biohealth Sciences) is now in the OSU Pharm. D. Sasha Rose (Ph.D. ’16)—Postdoc in the program. Bermudez Lab. Hannah Turner (B.S. ’14) just had her Dan Tanaree (Ph.D. ’16). second paper published in Science on the Ebola vaccine. She was Valerian’s Rory Welsh (Ph.D. ’15) is now working undergraduate researcher for a while at the Center for Disease Control in and then worked with Vega-Thurber

Department of Microbiology 21 Department of Microbiology Nash Hall 226 Oregon State University Corvallis, OR 97331

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