Nitzan Soffer [email protected] 609-658-8413 ------Education
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Alex Vompe ~ [email protected] (614)531-4955
Alex Vompe ~ [email protected] (614)531-4955 Areas of Interest: marine microbiology, metagenomics, marine disease ecology, coral reef conservation, molecular biology, marine microbial ecology, marine virology Current Research Projects: 2019 – Present Microbial communities and coral resilience 2019 – Present Near shore microbial communities and human pathogens before and after a rain event 2018 – Present Ecology of Labyrinthula zosterae, the causative agent of Eelgrass Wasting Disease 2018 – Present Development of machine learning systems for seagrass data analysis Education: 2019 – Present Oregon State University | PhD, Microbiology College: College of Science Cumulative GPA: 4.0 2015 – 2019 Cornell University | BA, Biological Sciences: Microbiology College: Arts and Sciences Cumulative GPA: 3.8 Grants, Honors, and Awards: 2019 – 2020 Provost Fellowship, College of Science, Oregon State University 2015 – 2019 Dean’s List, Cornell Arts and Sciences 2018 Best Undergraduate Poster (Sigma Xi) 2018 Best Research Methods (Cornell Undergraduate Research Board) 1 2018 CORALS/Betty Miller Intern 2017 Lynch Scholar 2015 IB Diploma Recipient 2015 AP Scholar with Honors Award 2015 Valedictorian from Dublin Coffman High School 2015 Senator’s Award for Community Service Published Work: McAndrew, C., Napolitano, N., Vompe, A., Wewers, M., Gavrilin, M. (2018). ASC phosphorylation at Y146 regulates inflammasome activation and pyroptosis. Journal of Immunology 200. Available: http://www.jimmunol.org/content/200/1_Supplement/115.2 Presentations: 2017 -
“-Omics” Complexity of Coral Reef Holobionts Across the Pacific Ocean
COMMUNITY PAGE The Tara Pacific expeditionÐA pan-ecosystemic approach of the ª-omicsº complexity of coral reef holobionts across the Pacific Ocean 1,2³ 3³ 4 1 Serge PlanesID *, Denis Allemand , Sylvain Agostini , Bernard Banaigs , 1 5 5,6 2,7 Emilie BoissinID , Emmanuel BossID , Guillaume Bourdin , Chris BowlerID , 8 9 10 10 a1111111111 Eric DouvilleID , J. Michel FloresID , Didier Forcioli , Paola FurlaID , Pierre 2,11 2,12 10 6 a1111111111 E. GalandID , Jean-FrancËois Ghiglione , Eric Gilson , Fabien Lombard , 13 14,15 16 3 CleÂmentine Moulin , Stephane PesantID , Julie Poulain , SteÂphanie Reynaud , a1111111111 2,17 18 19 20 Sarah Romac , Matthew B. SullivanID , Shinichi SunagawaID , Olivier P. ThomasID , a1111111111 2,13 2,17 21 Romain Trouble , Colomban de Vargas , Rebecca Vega ThurberID , Christian a1111111111 22 2,16 3 ¶ R. VoolstraID , Patrick Wincker , Didier ZoccolaID , the Tara Pacific Consortium 1 Laboratoire d'Excellence ªCORAIL,º PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Universite de Perpignan, Perpignan Cedex, France, 2 Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE, Paris, France, 3 Centre Scientifique de OPEN ACCESS Monaco, Monte Carlo, Principality of Monaco, 4 Shimoda Marine Research Center, Shimoda, Japan, 5 School of Marine Sciences, University of Maine, Orono, Maine, United States of America, 6 Sorbonne Citation: Planes S, Allemand D, Agostini S, Banaigs UniversiteÂ, Institut de la Mer de Villefranche sur mer, Laboratoire d'OceÂanographie de Villefranche, B, Boissin E, Boss E, et al. (2019) The Tara Pacific Villefranche-sur-Mer, France, 7 Institut de Biologie de l'Ecole Normale SupeÂrieure (IBENS), Ecole normale expeditionÐA pan-ecosystemic approach of the supeÂrieure, CNRS, INSERM, Universite PSL, Paris, France, 8 Laboratoire des Sciences du Climat et de ª-omicsº complexity of coral reef holobionts across l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Universite Paris-Saclay, Gif-sur-Yvette, France, the Pacific Ocean. -
Curriculum Vitae
Rory Welsh Curriculum Vitae Contact Information: Oregon State University [email protected] Department of Microbiology Work Tel: (541) 737-7793 Nash Hall, Office 452 Personal Tel: (770)846-8069 Corvallis OR 97331-3804 Fax: (541) 737-0496 Education: 2001-2005 B.S. Microbiology, University of Georgia 2010-2011 Ph.D Biology, Florida International University 2011-present Ph.D Microbiology, Oregon State University Employment and Positions: 2009- 2010 Research Technician, Florida International University 2007-2009 Research Technician, Monterey Bay Aquarium Research Institute 2005-2007 Research Associate II, Marine Biology and Fisheries Division, Rosenstiel School of Marine & Atmospheric Science, University of Miami 2004-2005 Undergrad Researcher, Marine Microbiology Lab, University of Georgia Summer 2003 Lifeguard Manager, Peachtree Stations Swimming Pool, Dunwoody, Ga Summer 00’ 02’ Construction worker, ABCO, Atlanta, Ga Field Work: 2012 National Science Foundation Polar Programs, McMurdo Station, Antarctica 2009 Herbivore Exclusion Project, Key Largo, FL (long-term time series) 2009 Acropora millepora Virome, Australia, Great Barrier Reef (3 weeks) Oceanographic Cruises: R/V Western Flyer, Eastern North Pacific, Oct 2007, (one and a half weeks) R/V Walton Smith, Straits of Florida, Sep 2007 R/V Kilo Moana, South Pacific, March 2007, (two weeks) R/V Seward Johnson, Equatorial Atlantic, 2006, (four weeks) R/V Walton Smith, Straits of Florida, 2006 R/V Walton Smith, Straits of Florida, Two Expeditions in 2005 Honors and Awards: 2011 Honorable Mention. National Science Foundation (NSF) Graduate Research Fellowship Program. 2011 Travel award to attend and present at the American Society of Limnology and Oceanography international meeting in Puerto Rico. 2010 Travel award to attend and present at the International Society of Microbial Ecology meeting in Seattle. -
2014 Newsletter
December 2014 RESEARCH AND HIGHER EDUCATION OBSERVE W O N D DISCOVER FROM THE CHAIR: Out with the old, and in with the new! Dear Friends of Microbiology, with 2014 closing, it's my pleasure to once again provide you with some of the latest news from Microbiology and Nash Hall. And first on the list is to say that, as I come to the end of ten years as Department Chair, I'm delighted to welcome our colleague, Prof. Jerri Bartholomew, as the next Head of the Department of Mi- crobiology. Jerri will take over department leadership on January 1, when I step down to return to my cyanobacterial bloom research and Virology teaching. Jerri has led a distinguished research program focused on diseases of native fish, particularly para- sites afflicting salmon, and is the Director of the John L. Fryer Salmon Disease Laboratory (see article on page 9). It has been a privilege for me to lead the department over the last years. We are a small but productive department. Each tenure-stream professor conducts research that has been consistently funded by external grants and contracts sup- porting world-class research: no dead wood here! For well over a decade, we have involved numerous undergraduate students in integral roles in the research enterprise, alongside graduate students, post-doctorals and other research staff. Such experience, together with required Microbiology lab classes, produces students with practical skills that remain ad- vantageous for job placement after graduation or for successful transition to graduate school. Our Instructors are dedi- cated teachers whose impact has been great in making Microbiology a highly sought-after major: between 2009 and 2014, our major count rose from about 140 to 325, far higher than overall OSU enrolment growth. -
Fioblockgrantsfinaltechnicalre
Gulf of Mexico Research Initiative – Year 1 Block Grants - Final Technical Report RESEARCH INSTITUTION: :”BASELINE AND OIL SPILL IMPACTED MARINE SPONGE MICROBIAL COMMUNITIES AND GENE EXPRESSION ANALYSIS WITH METAGENOMICS” Jose V Lopez1, Rebecca Vega Thurber, Peter McCarthy, Patricia Blackwelder, Marie Cuvelier 1- Nova Southeastern University Oceanographic Center 8000 North Ocean Drive Dania Beach, FL 33004 SCIENCE ACTIVITIES 1) General Summary Narrative (1 pages maximum): Please provide a brief overview of the project and goals supported during the conduct of this project. Be sure to highlight any ‘lessons learned’ that could be applied to the conduct of RFP-I and RFP-II projects (e.g., management, data support, logistics, etc.). Listing accomplishments against project activities, objectives and milestones in bulleted form is acceptable. The central aim of this proposal was to develop and characterize “sentinel” sponge species and their associated microbiota along with advanced molecular and genomic tools to assess the impact of oil contamination on Western Florida shelf reefs. Marine sponges and their associated microbes are excellent environmental sentinels. Using next generation transcriptomics and metagenomics we can simultaneously trace the direct impact of crude oil (and byproducts) and dispersants on both sponge physiology (a general marker of reef health) and microbial community dynamics (a general marker of regional seawater quality). Evaluating shifts in the composition and function of these organisms and their resident microbes will allow us to determine the overall effects of hydrocarbon loading in the water column that have resulted from the Deepwater Horizon oil spill. Our primary approach was the application of modern “next generation” DNA sequencing and electron microscopic methods. -
Different Nitrogen Sources Speed Recovery from Corallivory and Uniquely Alter the Microbiome of a Reef-Building Coral
Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral Mallory M. Rice1,*, Rebecca L. Maher2,*, Rebecca Vega Thurber2 and Deron E. Burkepile1,3 1 Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA 2 Department of Microbiology, Oregon State University, Corvallis, OR, USA 3 Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, USA * These authors contributed equally to this work. ABSTRACT Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 C, warming: 29 C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of Submitted 6 March 2019 higher temperatures on would healing rates. -
Phage-Bacteria.Pdf
bs_bs_banner Environmental Microbiology (2014) doi:10.1111/1462-2920.12553 Phage–bacteria network analysis and its implication for the understanding of coral disease Nitzan Soffer,*† Jesse Zaneveld and Veron et al., 2009). Scleractinian (stony) corals generate Rebecca Vega Thurber the physical structure of coral reefs, and thus are ecologi- Department of Microbiology, Oregon State University, cally important members of many tropical marine eco- 220 Nash Hall, Corvallis, OR 97331, USA. systems. In addition to supporting macroscopic reef communities, corals also host diverse microbial consortia that include Symbiodinium dinoflagellates, bacteria, Summary archaea, fungi and other microbial eukaryotes (Knowlton Multiple studies have explored microbial shifts in dis- and Rohwer, 2003; Cróquer et al., 2006). Culture-based eased or stressed corals; however, little is known studies have demonstrated that these coral-associated about bacteriophage interactions with microbes in microbes (the coral microbiota) take on a variety of roles this context. This study characterized microbial 16S ranging from mutualistic to pathogenic (Rohwer et al., rRNA amplicons and phage metagenomes associated 2001; Ritchie, 2006; Mouchka et al., 2010; Rosenberg with Montastraea annularis corals during a concur- and Kushmaro, 2011; Cook et al., 2013). For example, rent white plague disease outbreak and bleaching while bacteria such as Serratia marcescens, Vibrio shiloi event. Phage consortia differed between bleached and Vibrio coralliilyticus have been shown to cause and diseased tissues. Phages in the family Inoviridae disease signs (Ben-Haim, 2003; Rosenberg and were elevated in diseased or healthy tissues com- Falkovitz, 2004; Sutherland et al., 2011), Photobacterium pared with bleached portions of diseased tissues. spp. cultured from coral mucus secrete antibiotics that Microbial communities also differed between dis- can reduce pathogen growth (Ritchie, 2006). -
Scientists Shed New Light on Viruses' Role in Coral Bleaching 14 October 2020
Scientists shed new light on viruses' role in coral bleaching 14 October 2020 species. A complex composition of dinoflagellates—including the algae symbiont—fungi, bacteria, archaea and viruses make up the coral microbiome, and shifts in microbiome composition are connected to changes in coral health. The algae the corals need can be stressed by warming oceans to the point of dysbiosis—a collapse of the host-symbiont partnership. To better understand how viruses contribute to making corals healthy or unhealthy, Oregon State Ph.D. candidate Adriana Messyasz and microbiology researcher Rebecca Vega Thurber of the OSU College of Science led a project that Pocillopora corals from Mo'orea. Credit: Andrew compared the viral metagenomes of coral colony Thurber, OSU pairs during a minor 2016 bleaching event in Mo'orea, French Polynesia. Also known as environmental genomics, Scientists at Oregon State University have shown metagenomics refers to studying genetic material that viral infection is involved in coral recovered directly from environmental samples, in bleaching—the breakdown of the symbiotic this case samples taken from a coral reef. relationship between corals and the algae they rely on for energy. For this study, scientists collected bleached and non-bleached pairs of corals to determine if the Funded by the National Science Foundation, the mixes of viruses on them were similar or different. research is important because understanding the The bleached and non-bleached corals shared factors behind coral health is crucial to efforts to nearly identical environmental conditions. save the Earth's embattled reefs—between 2014 and 2017 alone, more than 75% experienced "After analyzing the viral metagenomes of each bleaching-level heat stress, and 30% suffered pair, we found that bleached corals had a higher mortality-level stress. -
Seeking Student Success During a Pandemic
COLLEGES OF SCIENCE & AGRICULTURAL SCIENCES DEPARTMENT OF MICROBIOLOGY Seeking student success during a pandemic Contents Winter 2020 Bright minds, bold moves Department of 2 2 Students persevere through a challenging year Microbiology Steve Giovannoni, Head Mary Fulton, Sascha Hallett, Making waves Newsletter Committee 6 Faculty news Editors Cari Longman Big discoveries Mary Hare 8 Research funding and highlights Designer Sharon Betterton In memoriam 10 Remembering Thomas Aspitarte Publisher Department of Microbiology Nash Hall 226 8 Supporting student success Oregon State University 12 Teaching and field work during a pandemic Corvallis, OR 97331 Alumni and friends 16 Making a difference Stay connected Please volunteer as a way of giving back. Mentor students, give a lecture on campus, coach 18 Department news students about career paths or hire an intern. Contact us at: Stepping up 20 Our COVID-19 heroes [email protected] 12 On the cover — Microbiology faculty, OSUScience / OSUAgSci staff and students are getting creative and finding new ways to connect, teach, work and learn during a pandemic. College of Science science.oregonstate.edu College of Agricultural Sciences agsci.oregonstate.edu 20 took a campus leadership role in removing barriers that were slowing the advancement of underrepresented groups, and our faculty partnered with students to gain grants that increase underrepresented minorities among our undergraduate and graduate student populations. As the new Department Head, I opened our all-department meetings to all faculty, staff and students and shared more widely information about our department to promote open discourse, participation and fact-based planning. Our Core Values Committee has been a champion of these causes and is promoting the implementation of codes of conduct aimed at making our department a more just and equitable place. -
Different Nitrogen Sources Speed Recovery from Corallivory and Uniquely Alter the Microbiome of a Reef-Building Coral
UC Santa Barbara UC Santa Barbara Previously Published Works Title Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral. Permalink https://escholarship.org/uc/item/8811n2ps Authors Rice, Mallory M Maher, Rebecca L Vega Thurber, Rebecca et al. Publication Date 2019 DOI 10.7717/peerj.8056 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral Mallory M. Rice1,*, Rebecca L. Maher2,*, Rebecca Vega Thurber2 and Deron E. Burkepile1,3 1 Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA 2 Department of Microbiology, Oregon State University, Corvallis, OR, USA 3 Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, USA * These authors contributed equally to this work. ABSTRACT Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. -
Different Nitrogen Sources Speed Recovery from Corallivory and Uniquely Alter the Microbiome of a Reef-Building Coral
Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral Mallory M. Rice1,*, Rebecca L. Maher2,*, Rebecca Vega Thurber2 and Deron E. Burkepile1,3 1 Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA 2 Department of Microbiology, Oregon State University, Corvallis, OR, USA 3 Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, USA * These authors contributed equally to this work. ABSTRACT Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals’ response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 C, warming: 29 C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of Submitted 6 March 2019 higher temperatures on would healing rates.