Designing secure biosystems to protect environmental microorganisms.
Genetically engineered microorganisms (GEMs) play an important role in building and maintaining a sustainable bioeconomy. To reduce the risk of unintended ecological consequences from environmentally deployed GEMs, the Secure Biosystems Design Scientific Focus Area (SFA) at LLNL is developing built-in security mechanisms that ensure GEMs function where and when needed.
Our security mechanisms will help safeguard the deployment of engineered microbes in the rhizosphere (the narrow region of soil directly influenced by root secretions and associated soil microorganisms known as the root microbiome). Additionally, layered containment strategies at the sequence, cellular, and population levels are expected to increase the overall system robustness to environmental fluctuations.
By stabilizing GEMs and preventing the transfer of potentially invasive traits to native microbiomes, our ultimate objective is to control the niche-specific function of GEMs for safer and more effective environmental applications.
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With vast potential for use in large-scale applications, GEMs are critical in building and maintaining a sustainable bioeconomy. The need for biocontainment strategies is particularly relevant for the sustainable development of bioenergy crops and carbon sequestration. The microbiota colonizing the rhizosphere of plant roots, especially plant-benefiting microorganisms (PBMs), contribute to plant growth and modulate soil carbon input, release, and storage. Genetic engineering approaches have been used to enhance the beneficial traits of PBMs, such as nutrient acquisition and drought resistance.
Our work focuses on establishing robust biocontainment strategies in soil microbes at the DNA sequence, cellular, and population levels without sacrificing microbial fitness. Leveraging LLNL’s high-performance computing (HPC) and high-throughput gene-editing capabilities, we will advance a synthetic gene entanglement strategy for containment. In this method, two genes are encoded as overlapping sequences within the same DNA molecule to protect engineered functions against mutational inactivation and mitigate the potential transfer of engineered genes to naturally occurring microbes.
Building on this layer of genetic stability, our team will incorporate additional strategies that control cellular physiology and direct population coordination to increase the overall system robustness to environmental fluctuations. With the help of the “Microbes Persist” Soil Microbiome SFA at LLNL and their rich experience in soil microbial ecology, we will evaluate the ecological benefits of these containment mechanisms in soil and rhizosphere environments. Ultimately, our biosystem designs—created to improve gene fitness, function, and evolutionary stability—will provide a knowledge base to enable safer use of GEMS in distinct applications like plant probiotics, carbon sequestration, metal recovery, nuclear-activity detection, and biomaterial production.
Our multi-institutional team includes experts in bioscience and biotechnology.