User:Gareth Trubl

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Gareth (Gary) Trubl

Updated 12/2018

Contact Info

  • Gareth (Gary) Trubl, Ph.D.
  • Livermore, CA 94550
  • Trubl.1@OSU.edu or Trubl1@llnl.gov
  • orcid.org/0000-0001-5008-1476
  • Scopus Author ID: 56178224700
  • Twitter: @gtrubl

About Me

USDA lab

I am a proud father and husband. I have always had a love for the environment and have been interested in how science and policy can shape our future. I love outreach and believe it is our duty as scientists to shape the next generation.

Image credit: NASA
Abisko, Sweden
Stordalen mire field site (May 2014)
Stordalen mire field site (July 2014)

Current Project

Postdoc at Lawrence Livermore National lab

Using stable isotope probing and nano-secondary ion mass spectroscopy techniques with viral metagenomes (SIP-Viromics) to characterize soil viruses and virus-host linkages.

Education

  • 2015–Dec. 2018, Ph.D. in Microbiology, The Ohio State University
Advisers Drs. Virginia Rich and Matthew Sullivan
   half-time 1/15–8/15, for medical leave, birth of child, & lab relocation
  • 2013–2015, Ph.D. in Soil, Water, and Environmental Science, University of Arizona
Minors in Astrobiology and Global Change
Advisers Dr. Virginia Rich and Matthew Sullivan
  • 2011–2013, M.S. in Environmental Science and Health, University of Nevada, Reno/Desert Research Institute
Adviser Dr. Alison Murray
  • 2007–2011, B.S. in Environmental Microbiology, University of Arizona
Minor in Chemistry
Adviser Dr. Peter Cotty

Research Interests

 Microbial Ecology, Polar Microbiology, Environmental Science, Biogeochemistry, Astrobiology, 
 Geobiology, Environmental Microbiology, Soil Microbiology, Meta-omics, Climate Change, and Biotechnology
When you do research, think something viral
Virus Lab, 2016

Publications

  • Towards optimized viral metagenomes from challenging soils. (submitted at PeerJ). Trubl G., Roux S., Solonenko N., Li Y-F., Bolduc B., Rodríguez-Ramos J., Eloe-Fadrosh E.A., Rich V.I., & Sullivan M.B.
  • Optimizing de novo genome assembly from PCR-amplified metagenomes. (In revision at PeerJ). Roux S., Trubl G., Goudeau D., Nath N., Couradeau E., Ahlgren N.A., Zhan Y., Marsan D., Chen F., Fuhrman J.A., Northen T.R., Coleman M.L., Sullivan M.B., Rich V.I., Malmstrom R.R., & Eloe-Fadrosh E.A. .
      *Part of figure 4 was a featured image in volume 3, issue 5
  • Host-linked soil viral ecology along a permafrost thaw gradient (2018). Emerson J.B., Roux S., Brum J.R., Bolduc B., Woodcroft B.J., Jang H-B., Singleton C.M., Solden L.M., Naas A.E., Boyd J.A., Hodgkins S.B., Wilson R.M., Trubl G., Li C., Frolking S., Pope P.B., Wrighton K.C., Crill P.M., Chanton J.P., Saleska S.R., Tyson G.W., Rich V.I., & Sullivan M.B. Nature Microbiology, 3(8), p.870.

Conference Proceedings

Oral presentations

  • Joint Genome Institute Metagenome Program 2018
  • Lawrence Berkeley National Lab BioSciences annual meeting 2018
  • American Geophysical Union (AGU) 2017
  • OSU Department of Microbiology symposium 2017
  • DOE IsoGenie consortium meeting 2017
  • Nevada Board of Regents meeting 2013

Poster presentations (conference, date, location, and authors):

  • VEGA, 2018, San Francisco, CA. Trubl G., Emerson J.B., Roux S., Jang H-B, Bolduc B., Solonenko N., Li Y-F., Eloe-Fadrosh E.A., Rich V.I., & Sullivan M.B.
  • Midwest Geobiology Conference, 2017, IUPUI, IN. Trubl G., Roux S., Bolduc B., Jang H-B, Emerson J.B., Solonenko N., Sullivan M.B., & Rich V.I.
  • AbSciCon, 2017, Mesa, AZ. Trubl G., Roux S., Emerson J.B., Bolduc B., Jang H-B, Solonenko N., Rich V.I., & Sullivan M.B.
  • AGU, 2016, San Francisco, CA. Trubl G., Roux S., Jang HB., Solonenko N., Sullivan M.B., & Rich V.I.
  • AGU, 2016, San Francisco, CA. *Emerson J.B., Roux S., Bolduc B., Brum J.R., Woodcroft B.J., Boyd J.A., Hodgkins S.B., Wilson R.M., Trubl G., Chanton J.P., Saleska S.R., Tyson G.W., Rich V.I., and Sullivan M.B.
  • International Society for Microbial Ecology (ISME), 2016, Montréal, Canada. Trubl G., Roux S., Jang H-B., Ellenbogen J., Emerson J.B., Solonenko N., Sullivan M.B., & Rich V.I.
  • ISME, 2016, Montréal, Canada. *Emerson J.B., Roux S., Bolduc B., Brum J.R., Woodcroft B.J., Boyd J.A., Hodgkins S.B., Wilson R.M., Trubl G., Chanton J.P., Saleska S.R., Tyson G.W., Rich V.I., and Sullivan M.B.
  • 11th Annual DOE-JGI, Genomics of Energy & the Environment Meeting, 2016, CA. *Brum, J.R., Roux, S., Rich, V.I., Sullivan, M.B., and collaborators.
  • AGU, 2014, San Francisco, CA. Trubl G., Solonenko N., Moreno M., Phu D., Sullivan M.B., & Rich V.I.
  • AGU, 2014, San Francisco, CA. *Niu D., Ciscato E., Trubl G., Maldonado J.G., Berelson W.M., Johnson H.A., Stevenson B.S., Stamps B.W., Corsetti F.A., Spear J.R., and Geobiology 2014.
  • UA Institute of the environment Grad Blitz, Tucson, AZ. Trubl G., Solonenko N., Moreno M., Phu D., Sullivan M.B., & Rich V.I.
  • Arizona-Nevada Academy of Sciences (ANAS), 2014, Flagstaff, AZ. Kim E-H., Trubl G., Ignacio-Espinoza J.C., Jones R., VerBerkmoes N., Rich V.I., & Sullivan M.B.
  • DRI Graduate Student poster competition, 2013, Reno, NV. 1st Place Trubl G., Kuhn E., Ostrom N.E., Fritsen C.H., Murray A.E. UNR * * * Graduate Student Association’s graduate poster competition, 2013, Reno, NV.Trubl G., Kuhn E., Ostrom N.E., Fritsen C.H., Murray A.E.
  • AGU, 2012, San Francisco, CA.Trubl G., Kuhn E., Ichimura A.S., Fritsen C.H., Madigan M.T., Murray A.E.
  • International Symposium on Isotopomers, 2012, Washington, DC. *Ostrom N.E., Murray A.E., Trubl G., Kuhn E
  • ANAS, 2012, Microbial denitrification in Lake Vida cryobrine. Trubl G., Kuhn E., Ostrom N.E., Murray A.E.

Employment

  • Postdoc at LLNL, Physical & Life Sciences Directorate, Livermore, California (Dec. 2015 – present
My research is advancing our understanding of soil viruses. Current work is applying SIP and NanoSIMS techniques with viromics to characterize soil viruses and virus-host linkages.
Mentor: Steve Blazewicz
  • Graduate Research Assistant, The Ohio State University (OSU), Columbus, Ohio (2015 – Dec. 2018). Previously the University of Arizona.
Overall project focus is to quantify and predict thawing permafrost response to a changing climate, scaling from genes to ecosystem processes in Abisko, Sweden. My role is to help examine the viral ecology and the viruses’ metabolic potential and quantitatively relate it to biogeochemical fluxes
Committee: Virginia Rich (adviser), Matthew Sullivan (co-adviser), Kelly Wrighton, and Michael Wilkins
  • Graduate Research Assistant, Desert Research Institute (DRI)/University of Nevada, Reno (UNR), Nevada System of Higher Education, Reno, Nevada (2011 – 2013)
Project focus was to better understand the microbial diversity, biogeochemistry, and specifically the nitrogen cycle physiology of bacteria in brine from Lake Vida, Antarctica. This work :used microbial culture techniques (aerobically and anaerobically) using isolates from this habitat to then study their roles in biogeochemical cycling, with a focus on N2O production. To :do this, I screened cultivars for genes and proteins of interest, quantified their biogeochemistry and used stable isotope techniques to identify isotopomers and isotopologues of N2O to :determine the source (abiotic or biological) and pathways involved in its cycling.
Adviser: Dr. Alison Murray
  • Biological Aid, United States Department of Agriculture-Agricultural Research Service (USDA-ARS; 2009 – 2011)
The laboratory leads aflatoxin management through improved understanding of aflatoxin-producing fungi and the aflatoxin contamination process. Responsibilities included studies of the :etiology and epidemiology of contamination as well as adaptation, divergence, dispersal, pathogenicity, morphogenesis, and cellular regulation of fungi. Experiments included (1) :extraction and analysis of B1 toxin and cyclopiazonic acid, (2) seed coating, and (3) fungal isolate diversity.
Adviser: Dr. Peter Cotty
  • Lab Technician, UA, Tree Ring Research Lab (2008)
Received, labeled, and sorted cross sections and core samples. Sanded, analyzed, and photographed samples to support graduate student research.
Supervisor: Dr. Ramzi Touchan

Teaching, Outreach, & other experiences

  • Mentorship
Lennel Camuy-Velez (Jan–March 2018; 7 weeks), graduate student, OSU, Columbus, Ohio
Josue Ramos Rodriguez (Aug–Oct 2017; 7 weeks), graduate student, OSU, Columbus, Ohio
Dylan Cronin (Aug–Oct 2017; 7 weeks), graduate student, OSU, Columbus, Ohio
Emma Hans (Sept 2016–June 2017), high school senior, OSU, Columbus, Ohio
Alex Runyon (Aug–Oct 2016; 7 weeks), graduate student, OSU, Columbus, Ohio
Jared Ellenbogen (Aug–Oct 2015; 7 weeks), graduate student, OSU, Columbus, Ohio
David Phu (Sept–Dec 2014), undergraduate student, UA, Tucson, Arizona
Darya Anderson, Krystalle S. Diaz, Maya Sederholm, & Morgan O. Binder (full-time Jan.–April 2014 for poster preparation and presentation at The Arizona-Nevada Academy of Sciences meeting; sporadically May 2014–Dec. 2014)
  • DOE-SCGSR fellow, Joint Genome Institute, Walnut Creek, California (June 4 – November 1, 2018).
My proposal "Pioneering soil viromics to elucidate virus impacts on soil ecosystem services" was funded to characterize 20 deeply-sequenced viromes. The viromes were generated in fall 2017 and the fellowship period was used to bioinformatically process the viromes.
Theme-"Earth Analog Environments and the Search for Life Beyond the Earth"
Interdisciplinary examination of the chemical, physical, and geological properties of potential extraterrestrial habitats and an in-depth description and analysis of sites on Earth with similar characteristics. In particular, lectures and activities considered icy satellites, rocky planets in the Solar System, extreme Earth environments, and terrestrial exoplanets.
NASA-ESA 2016 summer group
Zumaia Flysch, Spain
I evaluated talks and posters for the biological sciences section of the undergraduate forum March 30, 2016. Prior to this, judges attended a two-hour training session. Applicants were rated on (1) poster presentation (if applicable) :including research content, visual graphics, grammar, and conclusions; (2) oral presentation including appropriate terminology, poise/presentation, knowledge of work, and organization/flow.
  • The Ohio State University Viromics training course, Columbus, OH
The course was held Feb. 8-9 and training included the iVirus pipeline part of the CyVerse infrastructure and MetaVir. With iVirus we learned how to quality check metagenomics sequences, assembly, VirSorter, and mapping the reads to contigs for coverage. MetaVir is a web server designed to annotate viral metagenomic sequences. With these tools, we were able to give our data ecological meaning.
Directors: Drs. Matthew Sullivan, Simon Roux, and Ben Bolduc
Sky school Fellowship
Sky School is 1-5 day Science programs for Arizona K-12 students at the 25-acre Mt. Lemmon campus. My fellowship was for the 2014-2015 school year. Programs focus on core UA science areas :such as sky island ecology, biology, geology, and astronomy and have been developed in collaboration with local school districts to meet Arizona State and Next Generation Science :Standards. I specifically bridge biology and astronomy and share the field of astrobiology with the students. Fellowship Responsibilities include participating in at least 4-5 Sky School :events in during each semester, in which leading daytime activities and participating in evening activities. Daytime activities are for a group of 5-10 students and include sample :collection, learning projects, and demonstrations. 3+ day trips include a science inquiry project, which is presented before they leave, and an in-depth learning experience on the :graduate fellows field of study.
Director Dr. Alan Strauss
Sky school
March 14-15, 2015 I was a co-exhibitor for the Sky School booth at Science City part of the Tucson Festival of Books. It is the 2nd largest book festival and largest book and science :festival. Our booth had several meteorite samples and thin sections that students could view under the microscopes. We also had some neat giveaways to encourage and promote STEM :education. We also had material on the OSIRIS-Rex mission led by NASA. This huge festival draws a diverse group of people from all over the world. This year we got a special visit from :former Arizona congresswoman Gabrielle Giffords.
On Feb. 23, 2015 from 7:30-3:30 I was a co-exhibitor for the Sky School both at Sahuarita middle school SciTech festival. There were 480 6th-8th graders that participated and went to each :booth to answer questions in their “passport”. The Shy School booth question was: How can meteorites give us information on the formation of the solar system. Our booth had several :meteorite samples and thin sections that students could view under the microscopes. We also had material on the OSIRIS-Rex mission led by NASA.
Contact: Rebecca Lipson (rlipson@email.arizona.edu)
October 4 and 18, 2014, I led an Earth Sciences outreach event for visitors of B2 from 4-8pm. Each event incorporated geology and microbiology and was catered to that date’s theme.
Contact: Dr. Pacifica Sommers (psommers@email.arizona.edu)
I reviewed and evaluated travel grant applications submitted to UA GPSC for the Nov. 1, 2014 deadline. Applicants were rated on four topics: (1) professional development, (2) description :of their work, (3) description of the event and the student’s efforts to secure funding, and (4) their proposed budget for the event.
On September 5, 2014 I led an Earth Sciences day outreach event for all the 3rd-grade classes (44 students) at Lake Pleasant Elementary. We taught each object of strand 6: Earth and Space :Science from the Arizona Science Standards. The day started with learning about the layers of the Earth, then minerals, the three rock types, the rock cycle, fossils, and fossil fuel. :Songs, activities, and demonstrations were incorporated, including my famous Cheetos fossil experiment.
Contact: Mrs. Michelle Kist (mkist@peoriaud.k12.az.us)
A 5-week intense course. The first two weeks involved traveling around Southern California and Nevada collecting stromatolites, environmental, and microbial samples. Sample sites included :Walker Lake, Mt. Dunfee, Rowlands Reef, and Little Hot Creek. Weeks 3 and 4 were at CSU-Fullerton processing samples and coming up to speed on modern geological and biological techniques. :The final week was at the USC Wrigley institute for environmental studies on Catalina Island, where we pulled data and analyses to write and present a final report.
Dates: June 8-July 10, 2014
Final project and presentation: How do microbial mats become stromatolites?
Directors: Dr. Frank Corsetti (fcorsett@usc.edu) and Dr. John Spear (jspear@mines.edu)
GeoBiology 2014
School of Earth & Environmental Sciences (SEES) hosted EarthWeek at UA. The SWES department had their own designated day full of oral presentations by undergraduate and graduate students. :In 2014, I was in charge of student recruitment for presentations for the SWES department. I reviewed oral & poster abstracts that were submitted, ordered food, created sessions, reserved :rooms, and judged posters. For 2015 I was chair of the SWES department and a member of the UA SEES EarthWeek. I continued my previous year's duties, along with acting as social chair for :the University; this included planning several trivia nights to encourage city-wide participation in EarthWeek.
  • La Cima Middle School Career Shadow Day, Tucson, Arizona
I hosted four students for two hours interested in marine microbiology. For the first hour, I led a discussion about aspects of the field, necessary education, and career options. The :second hour involved a tour of the laboratory involving a discussion of equipment and methods.
La Cima coordinator: Vaughn Croft (vaughn.croft@schools.pima.gov)
As the event coordinator I confirmed logistics for the event with Arizona MESA (a university-based outreach program). I planned the activity schedule, recruited activity leaders, :identified keynote speakers, arranged for activity supplies and student prizes, organized volunteers, taught activities to volunteers, ordered snacks for students, provided feedback to :volunteers, and led the event. The goal was to excite ~80 underrepresented middle school students about STEM fields, college, and sponsor future science-related events. In February 2014 :the theme was "Astonishing Astrobiology" and in November 2014, the theme was "A Geological Perspective on Life".
March 1-3, 2013 a festival celebrating extreme environments was held at Death Valley National Park to get the public involved in STEM activities. The agenda included presentations, booth :expositions, and field trips (Badwater basin and other park sites). I presented posters to the public, showcased DRI, and collected samples on field trips with youth for viewing under a :microscope. Attendees also camped at the park overnight and participated in astrological activities.
  • Graduate outreach aid, University of Nevada, Reno for George L. Dilworth Middle School
We visited weekly through the fall and episodically through the spring. Topics and activities included microbiology mysteries (e.g., 1854 cholera outbreak, 1993 Milwaukee Cryptosporidium :outbreak), chemistry demonstrations (e.g., vinegar and baking soda, Coke and Mentos), and math lessons (e.g., calculating how much water we use in a year). Primary activities included :interacting with students to solve science problems, working with students to develop STEM research projects, and participating in career day.
Stable Isotope Biogeochemistry 2012
Dates: May 7-11 2012
Instructors: Dr. Nathaniel Ostrom (ostromn@msu.edu) and
Dr. Peggy Ostrom (ostrom@msu.edu)
www.zoology.msu.edu/news/6/164/Short-Course-Stable-Isotope-Biogeochemistry-ZOL-824.html
  • Preceptor, University of Arizona, NATS 101: A Geological Perspective
Class was three units with a mandatory discussion session. I co-taught the discussion for a semester with a graduate student; taught the discussion session independently for next three :semesters (25-30 students). The focus was on a single geological topic with a group assignment. I graded all the assignments and submitted the scores. Professor: :Dr. Jessica Kapp

Awards

UNR CABNR Award Ceremony April 2013. Dr. Glenn Miller and me
  • National Society of Collegiate Scholars
  • National Scholars Honor Society
  • Phi Kappa Phi honor society
  • Golden Key International Honour Society
  • National Blue Key Honorary (UA, 2009-2011)
  • Hope L. Jones Scholarship (2008)
  • W.H. Fuller Scholarship (2009)
  • T. F. Buehrer Scholarship (2010)
  • George L. Jones Scholarship (2010)
  • Great Lakes National Scholarship Program recipient (2013, $2,500)
  • UNR Graduate Student Association (GSA) travel grants (Fall 2011 for AGU, $500; Spring 2012 ASM, $500; Fall 2012 for AGU, $500)
  • UNR GSA’s poster competition 3rd place (2013, $650)
  • DRI poster competition 1st place (2013, $200)
  • Graduate student representative for the Division of Earth and Ecosystems at DRI (Fall 2011- Spring 2013)
UNR GSA Award night with fellow grads
  • College of Agriculture, Biotechnology, and Natural Resource’s Outstanding Graduate Student 2013
  • SWES graduate student representative (Fall 2013- Spring 2015)
  • Student Representative for UA Global Change minor committee (Fall 2014- Spring 2015)
  • SWES 2013-2014 excellent graduate student ($5,000)
  • SWES 2014-2015 excellent graduate student ($1,000)
  • H. E. Carter Travel Award ($600; 2014)
  • GPSC Travel Award ($750; 2014)
  • SWES Travel Award ($300; 2014)
  • Sky School fellowship ($4,000; 2014–2015)
  • United States Permafrost Association Travel Award ($500; 2014)
  • Great Lakes National Scholarship Program recipient (2015, $2,500)
  • Full scholarship to the 2016 Nasa astrobiology institute summer school in Santander, Spain (2016, ~$3,000)
  • Great Lakes National Scholarship Program recipient (2016, $2,500)
  • Travel award to attend Astrobiology Science Conference 2017 (AbSciCon, $500)
  • DOE-SCGSR fellowship ($18,000; June 4–November 1, 2018)
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