User:Gareth Trubl

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Gareth (Gary) Trubl

Updated 10/2020

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
  • Web of Science ResearcherID: L-7977-2019
  • Twitter: @gtrubl

About Me

SFA team 2020 (location UC Berkeley)
2019 LLNL Research Slam Finalist
USDA lab (location U. Arizona)

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. I am currently interested in viruses that infect bacteria and archaea in soil systems. Previously this was limited to dsDNA viruses, but has expanded to include ssDNA viruses and hopefully soon RNA viruses.

Hear more about my previous and current work:

Genome Insider Podcast episodes by The Joint Genome Institute

Thawing permafrost, microbes, and viruses: Gary Trubl — episode 1

Thawing permafrost, microbes, and viruses: Gary Trubl — episode 2

MicroSeminar

Tracking active viral population dynamics and their impact on microbial biogeochemistry in Arctic peat soil and tropical rainforest soil via stable isotope probing metagenomics

Abisko, Sweden
Stordalen mire field site (May 2014)
Stordalen mire field site (July 2014)

Current Projects

Postdoc at Lawrence Livermore National lab

I am working on three projects with a diverse team from many Universities and National Labs.

1. Quantitative Viral Assessments for Improved Biomonitoring

LLNL LW-LDRD awarded to Gary Trubl

The goals of the LDRD are to (1) create a quantitative SIP-meta-omics pipeline to characterize single-stranded and double-stranded DNA and RNA viruses from a single soil sample and (2) use radioactive phosphate to quantitate and track virions persistence in soil.

2. Sip-viromics: quantifying virus-host and carbon cycling dynamics in soil with isotope-targeted metagenomics

LLNL ER-LDRD awarded to Steve Blazewicz

My role is using stable isotope probing and nano-scale secondary ion mass spectroscopy techniques with metagenomes and viral metagenomes (SIP-Viromics) to characterize soil viruses and virus-host linkages. I am most interested in characterizing the roles viruses play in carbon cycling, especially in soil ecosystems.

3. Microbes persist: systems biology of the soil microbiome

DOE SFA; project lead Jennifer Pett-Ridge. Collaborators from Lawrence Berkeley National Lab, University of California Berkeley, Northern Arizona University, The Ohio State University, and Environmental and Molecular Sciences Laboratory/Pacific Northwest National Lab 

The ultimate goal is to determine how microbial soil ecophysiology, population dynamics,
         and microbe-mineral-organic matter interactions regulate the persistence
                 of microbial residues under changing moisture regimes

Objectives include:

  • Apply SIP-metagenomics to delineate how changing water regimes shape activity of individual microbial populations and expression of ecophysiological traits that affect the fate of microbial and plant C
  • Identify and quantify mechanisms of mortality in the soil microbiome (focusing on phage lysis and water stress) and their contribution to C turnover and the biochemistry of microbial residues
  • Measure how the soil microbiome and its products (cell envelope, extracellular polymeric substances, exo-enzymes) interact with contrasting mineral assemblages to control both short- and long-term soil C persistence
  • Synthesize genome-scale ecophysiological trait data, population-specific growth and mortality, and SOM chemistry to build models of microbial functional guilds and SOM turnover, to predict the long-aspired connection between soil microbiomes and fate of soil C

My role is to characterize soil viruses and virus-host linkages from SIP-metagenomics and track the phage impact from wet-up.

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, Virology, Environmental Science, Biogeochemistry, Astrobiology, 
 Geobiology, Environmental Microbiology, Meta-omics, Climate Change, and Biotechnology
Virus Lab, 2016

Publications

  • Taş, N., Jong, A., Li, Y., Trubl, G., Xue, Y., and Dove, N.C. Metagenomic tools in microbial ecology research (in review at Current Opinion in Biotechnology)
  • Hyman, P., Trubl, G. and Abedon, S.T., 2020. Virus-Like Particle: Evolving Meanings in Different Disciplines. PHAGE 10.1089/phage.2020.0026.
  • Bolduc B, Hodgkins SB, Varner RK, Crill PM, McCalley CK, Chanton JP, Tyson GW, Riley WJ, Palace M, Duhaime MB, Hough MA, IsoGenie Project Coordinators, IsoGenie Project Team, A2A Project Team, Saleska SR, Sullivan MB, Rich VI. 2020. The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ 8:e9467 https://doi.org/10.7717/peerj.9467
  • Trubl, G., Stedman, K., Bywaters, K., & Boston, P. Astrovirology: Expanding the Search for Life. White paper submitted to The National Academies’ Planetary Science and Astrobiology Decadal Survey 2023-2032.
 *Top 5 most viewed Computational Biology article published in PeerJ in 2019

  *Featured by US Dept. of Energy Joint Genome Institute At the Forefront of Terrestrial Virus Research

 *Part of figure 4 was a featured image in volume 3, issue 5
 *Top Cited article from the Editors of mSystems
 *Featured in How Viruses Secretly Control the Planet
  • 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.
 *Featured in How Viruses Secretly Control the Planet
 *Featured by the US Dept. of Energy Getting To Know the Microbes that Drive Climate Change
 *Featured in Bacteria, Viruses and Carbon: how microorganisms in arctic soils can alter our climate
 *Behind the paper Soil viruses: unlocking the secret garden

Conference Proceedings/Seminars

Drs. Rachel Hestrin, Noah Sokol, and Gary Trubl at AGU 2019

Oral presentations

  • MicroSeminar 2020
  • LLNL Biosciences & Biotechnology Division Seminar Series 2020
  • American Geophysical Union (AGU) 2019
  • Georgetown Biotechnology Seminar Series 2019
  • NASA Astrovirology Workshop 2019
  • Evergreen Phage Meeting 2019
  • DOE IsoGenie consortium meeting 2019
  • University of California, Berkeley, Firestone lab 2019
  • Joint Genome Institute Metagenome Program 2018
  • Lawrence Berkeley National Lab BioSciences annual meeting 2018
  • AGU 2017
  • OSU Department of Microbiology symposium 2017
  • DOE IsoGenie consortium meeting 2017
  • Nevada Board of Regents meeting 2013
LBNL BioSciences annual meeting (summer 2018)
IsoGenie3 team

Employment

  • Postdoc at LLNL, Physical & Life Sciences Directorate, Livermore, California (Dec. 2018 – 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.
Mentors: Steve Blazewicz, Jennifer Pett-Ridge
  • Graduate Research Assistant, The Ohio State University (OSU), Columbus, Ohio (June 2015 – Dec. 2018); Previously at the University of Arizona (July 2013 – June 2015).
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, Michael Wilkins, Matthew Anderson
  • Graduate Research Assistant, Desert Research Institute (DRI)/University of Nevada, Reno (UNR), Nevada System of Higher Education, Reno, Nevada (Aug. 2011 – Aug. 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
Jose Liquet, M.S. (Jan. 2020–current), post college appointee, Livermore, California
Rylee Genner, M.S. (May 28–August 9; 11 weeks), summer ACP student at LLNL, Livermore, California
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)
Olivia Rassuchine (Aug-Dec 2012), undergraduate student, UNR/DRI, Reno, Nevada
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.
DOE-SCGSR fellowship at JGI (summer 2018)
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 bioinformatic tools. With iVirus we learned how to quality check metagenomics sequences, assembly, VirSorter, and mapping the reads to contigs for coverage.
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)
2019 Best poster award at LLNL postdoc symposium
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