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

2023 Abstracts

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


Kathleen L. Arnolds, Riley C. Higgins1, Gabriela Li, Jeffrey G. Linger, and Michael T. Guarnieri* ([email protected])


National Renewable Energy Laboratory


The Integrative Modeling and Genome-scale Engineering for Biosystems Security (IMAGINE BioSecurity) Science Focus Area project 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 integrates core capabilities in synthetic and applied systems biology to develop a high-throughput platform for the design, generation, and analysis of biocontainment strategies in industrially relevant and emerging, next-generation microbes.


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 bio-products, and the impact on native ecologies. To this end, researchers have developed an approach that utilizes soil mesocosms and integrated systems analyses to evaluate the efficacy of novel biocontainment strategies and to assess the impact of production systems upon terrestrial microbiome dynamics. Researchers demonstrate the utility of this approach by modeling a perturbation event by contaminating the mesocosms with the industrial microbial chassis, Saccharomyces cerevisiae. The resultant data demonstrate that researchers can track the fate of the contaminating microbe with high sensitivity in the soil, as well as monitor broader impacts of the perturbation on the underlying soil microbiome with a high degree of spatial and temporal resolution. 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.


Arnolds K. L., et al. 2021. “Biotechnology for secure biocontainment designs in an emerging bioeconomy.” Current Opinion in Biotechnology 71, 25–31.

Funding Information

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