Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems

Authors:

Kathleen L. Arnolds1* (katie.arnolds@nrel.gov), Natalie A. Lamb1, Riley C. Higgins1, Kimberly A. Rosenbach1, Thomas J. Musselwhite1, Gabriela Li1, Jeffrey G. Linger2, Karsten Zengler3, Yo Suzuki4, Michael T. Guarnieri1

Institutions:

1Biosciences Center, National Renewable Energy Laboratory; 2Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory; 3University of California–San Diego; 4J. Craig Venter Institute

URLs:

Goals

The Integrative Modeling and Genome-scale Engineering for Biosystems Security (IMAGINE BioSecurity) Science Focus Area seeks to establish an understanding of the behavior of engineered microbes in controlled versus environmental conditions to predictively devise new strategies for responding to biological escape. To this end, the IMAGINE Team has established a plant-soil mesocosm platform to track and quantify the fate of industrial microbes in environmental systems and assess the efficacy of biocontainment constraints upon genetically engineered microbe escape frequency and the impact of industrial microbes upon native ecological microbiomes.

Abstract

Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect complexities found in natural environments, necessitating an environmentally relevant–analysis pipeline that allows for the detection of rare escapees, the effect of associated bioproducts, and the impact on native ecologies. To this end, the team has developed an approach that utilizes soil mesocosms and integrated systems analyses to evaluate the efficacy of novel biocontainment strategies and assess the impact of production systems upon terrestrial microbiome dynamics. The project demonstrates the utility of this approach by modeling a contamination with industrial microbial chasses versus their biocontained counterparts. Here, researchers demonstrate the broad utility of this system by highlighting findings from both strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system and strains of Escherichia coli that are contained via genomic recoding. The resultant data demonstrate that this system has broad utility across diverse microbial chassis and biocontainment strategies. The data also enable tracking the fate of the contaminating microbe with high sensitivity in the soil and monitoring broader impacts of the perturbation on the underlying soil system. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

Funding Information

This research was supported by the DOE Office of Science, BER program, GSP, Secure Biosystems Design Science Focus Area, IMAGINE BioSecurity: Integrative Modeling and Genome-scale Engineering for Biosystems Security, under contract number DE-AC36-08GO28308.