Stable Isotope Probing and Viromics: Quantifying Virus-Host and Carbon Cycling Dynamics in Soil with Isotope-Targeted Metagenomics

Project Overview

Viruses are the most abundant biological entities on Earth. In the environment, viruses play a large but poorly understood role in microbial evolution and antibiotic resistance, soil carbon processes, and nutrient cycling. Due to remarkable advances in virology, molecular biology, and microbial ecology, we can now imagine controlling microbial populations in natural and engineered environments using the viruses that naturally infect and kill them. Currently, bacterial viruses (known as bacteriophages) are being used to control bacterial infections. If this approach can be extended to more complex systems, it may be able to target natural reservoirs of human pathogens, balance engineered microbial systems, and control carbon cycling. However, these applications are not possible without a better understanding of how bacteriophage species interact with their hosts in complex environments. Currently, this understanding is limited by the immense diversity of microbes and their viruses in the environment, as well as the difficulty cultivating them in the laboratory, which prevents the identification and study of specific microbe-virus pairings. Our goal was to develop advanced methods for characterizing and tracking virus activities and virus-host dynamics in complex systems and to apply these methods to quantify the role of viral lysis (i.e., a virus' ability to break down a cell's membrane) of bacterial cells in soil carbon cycling. Specifically, we used stable isotope probing (SIP) targeted metagenomics to develop and validate methods to characterize viruses and virus-host dynamics in soil. Our approach allowed us to move beyond a general catalogue of the genetic repertoire of these soil communities and expose the specific population-level dynamics and functional capacities of the active dsDNA viral community.

Mission Impact

This project supported the NNSA goal of expanding and applying our science and technology capabilities to deal with broad national security challenges. By providing an innovative capability to detect and characterize virus-host activities and data regarding biological pathogens and antibiotic-resistant bacterial pathogens, this research supports the Laboratory's research and development challenge to find chemical and biological countermeasures to address the Laboratory's mission in the threat reduction of weapons of mass destruction. This research enhances the Laboratory's core competencies in bioscience and bioengineering, as well as nuclear, chemical, and isotopic science and technology.

Publications, Presentations, and Patents

Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. 2021. "Active virus-host interactions at sub-freezing temperatures in Arctic peat soil," Microbiome. 9:208. LLNL-JRNL-814032.

ter Horst AM, Santos-Medellin C, Sorensen JW, Zinke LA, Wilson RM, Johnston ER, Trubl GG, Pett-Ridge J, Blazewicz SJ, Hanson PJ, Chanton JP, Schadt CW, Kostka JE, Emerson JB. 2021. "Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations," Microbiome. 9:233. LLNL-JRNL-818141.

Tas N, Jong A, Li Y, Trubl G, Xue Y, and Dove NC. 2021. "Metagenomic tools in microbial ecology research," Current Opinion in Biotechnology. 67:184-191. LLNL-JRNL-814338.

Trubl, G. 2021. "Combining stable isotope probing and metagenomic approaches to increase detection of viruses, characterize their activity, and increase virus-host linkages." JGI VEGA symposium. Berkeley, CA. LLNL-PRES-821698.

Trubl, G. 2021. "Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H₂¹⁸O stable isotope probing metagenomics." Firestone meeting. Berkeley, CA. LLNL-PRES-820800.

Trubl, G. 2021. "Unraveling The Hidden Potential of Viruses in Soil Ecosystems Using Stable Isotope Probing Metagenomics."LLNL PLS seminar. LLNL-PRES-818370.

Trubl, G. 2020. "Characterizing viruses for understanding ecology, biotechnology, and health benefits." Georgetown seminar, Washington, D.C. LLNL-PRES-814599.

Trubl, G. 2020. "Tracking active viral population dynamics and their impact on microbial biogeochemistry in Arctic peat soil via stable isotope probing metagenomics." National summer undergraduate research project BIPOC Seminar Series. LLNL-PRES-814031.

Trubl, G. 2019. "Tracking active viral population dynamics and their impact on microbial biogeochemistry in Arctic peat soil and tropical rainforest soil via stable isotope probing metagenomics." AGU 2019, San Francisco, CA. LLNL-PRES-809447.

Trubl, G. 2020. "Characterizing viruses for ecology, biotechnology, and health benefits." Georgetown seminar, Washington, D.C. LLNL-PRES-814030.

Trubl, G. 2019. "Characterizing Viral Impacts on Microbial Community Structure and Biogeochemistry via Stable Isotope Probing Metagenomics and Process Measurements." LLNL BBTD seminar. LLNL-PRES-809289.

Trubl, G. 2019. "Tracking the world's most deadly predator in soils." LLNL Research SLAM. LLNL-PRES-792699.

Trubl, G. 2019. "Using stable isotopes to track viruses in soils." NASA Astrovirology workshop without walls, Mountain View, CA. LLNL-PROC-791159.

Trubl, G. 2019. "Characterizing viruses in soils for understanding ecology, biotechnology, and health benefits." Washington, D.C. LLNL-PRES-787657.

Trubl, G. 2019. "Characterizing active soil viruses and virus-host dynamics in Arctic and Tropical soils using stable isotope probing targeted metagenomics." Evergreen Phage conference, Olympia, WA. LLNL-PROC-785858.

Trubl, G. 2021. Episode #93 - "Soil Microbes & Viral Ecology." Storytellers of STEMM podcast. LLNL-MI-819798.

Trubl, G. 2020. "Soil viruses in peatlands." JGI Genome Insider podcast. LLNL-MI-805972.

Trubl, G. 2019. "Viromes from Northern Minnesota Reveal Peatland Habitat Endemism of Globally Distributed Viral Population." Anneliek from Emerson Lab AGU 2019, San Francisco, CA. LLNL-POST-800299.

Trubl, G. 2019. "Applying Classic and Modern Techniques to Characterize Viruses in Soils." AGU 2019, San Francisco, CA. LLNL-POST-796680.

Trubl, G. 2019. "Characterizing active soil viruses and virus-host dynamics in arctic and tropical soils using stable isotope probing targeted metagenomics." LLNL postdoc symposium. LLNL-POST-785859.

Trubl, G. 2019. "Applying Classic and Modern Techniques to Characterize Viruses in Soils." Rylee ACP summer poster competition at LLNL. LLNL-POST-785001.