Ensure the availability of biocontainment approaches for engineered organisms.

Engineering Biology for Climate & Sustainability

Conservation of Ecosystems and Biodiversity Goal:

Ensure the availability of biocontainment approaches for engineered organisms.

Current State-of-the-Art

Biocontainment of engineered organisms is a critical concern for engineering biology applications in the environment; the introduction of a new living organism to an ecosystem has the potential to cause adverse environmental impacts that are perpetuated by organism reproduction, out-crossing, persistence, and/or movement. Even though this Goal exists as a subsection of this theme, it is intended to inform all parts of the roadmap where engineered organisms might be released into the environment. Furthermore, though this Goal approaches biocontainment from an engineering biology perspective, there are significant overlaps with active research in ecology and other environmental sciences.

Before an engineered organism is released into the environment, researchers should be able to articulate mechanisms by which an organism could escape containment and what the consequences of that escape might be.¹^, ² To accomplish this, tools are needed to model and understand any potential impacts engineered organisms might have on the environment.³ There is ongoing research to examine how different engineered organisms interact with native populations and ecosystems, and how they will react to different climate change factors, over different time periods (see for example Allainguillaume et al., 2009⁴, Rinkevich, 2015⁵, and Lu et al., 2016⁶), but more work is needed to model and study these interactions in simulated environments. Environmental release should be accompanied by means to monitor the organism(s) post-release, processes to collect evidence and inform risk assessment, strategies to contain the organisms in intended environments, and fail safes for eliminating the organisms in the event of a containment breach. Approaches to promoting resilience within existing populations will likely require the use of gene drive technologies, thus fundamentals of gene drive consequences, impacts, and control must be well understood. Additionally, means for detecting biocontainment breaches are needed, for example through the ubiquitous sensing and monitoring of unique biomarkers associated with an engineered organism. Furthermore, approaches are needed that confer lethality upon engineered organisms that escape biocontainment, such as auxotrophic bacterial strains with reliance on nutrients specific to an intended environment.⁷^, ⁸

Social and regulatory uncertainties exist regarding affected communities’ interests in the deployment of engineering biology tools. Coordination is also necessary to work directly with communities to find solutions that suit their needs and improve local economic conditions. Potential social, economic, and ethical implications—and how researchers can engage with such non-technical considerations—are discussed in more detail in the Social and Nontechnical Dimensions Case Studies.

Breakthrough Capabilities & Milestones

Understand and model the potential and realized impacts of engineered organisms on the environment.

Develop integrated field biosensors for detection and monitoring of engineered organisms.

Bottleneck/Challenge: Engineering sensors that are robust to horizontal gene transfer of engineered genetic material.

Potential Solution: Engineer multi-component biosensors that can sense and report the presence of engineered sequences and the abundance of microbial genera.

Bottleneck/Challenge: Incorporation of biosensors at a density that is useful for detection and monitoring without negatively impacting field ecology.

Potential Solution: Engineer quantitative cell-free biosensors that provide more information at lower density.

Design and carry out environmental case-control studies comparing engineered biomes with control biomes in simulated environments to assess the impacts of engineered organisms on biodiversity.

Bottleneck/Challenge: Determining genetic systems responsible for environmental persistence of engineered organisms released to the environment (e.g., soil, waterways, animal gut).

Potential Solution: Specific tests of diversity maintenance, productivity maintenance/improvement and resilience for plant/microbe systems in environmental ‘twin’ formats such as EcoPODS.

Potential Solution: Identify relative genetic components of native organisms that are adaptive and resilient to climate stresses to incorporate into engineered systems.

Bottleneck/Challenge: Tracking and reporting (remotely, such as by release of detectable volatile compounds) of location and spread of engineered vs. native organisms within the study environment.

Potential Solution: Develop applicable biosensors.

Bottleneck/Challenge: Integrated risk-return models for releasing bioengineered organisms and systems into the field, including risk of dispersal and adverse ecological impacts, are needed.

Potential Solution: Environmental case studies deployed and standardized across a network of laboratories and centers to allow for comparative studies of ecosystem function and effects of intervention.

Model and predict the dispersal of hyper-cultivated organisms and engineered biology (e.g., gene drives) and their impact on ecosystem diversity.

Bottleneck/Challenge: Dispersal indicators for key species, and the evidence backing the biotic and abiotic mechanisms of their constraint, are needed (currently under-developed).

Potential Solution: Develop open and integrated data and analysis systems for search and inferred relationships among biological data focused on prediction of key biological mechanisms most affecting key ecosystem health and productivity and pointing to engineering interventions.

Potential Solution: Identify the ecological impacts of gene drives, such as any adverse effects the gene drive might have on non-target populations.

Bottleneck/Challenge: Demonstrated effectiveness of deployment approaches.

Potential Solution: Scaled solutions (pilot and 1-2 years of field data) and assessments of risk criteria/considerations for deployment.

Potential Solution: Biodiversity tracking programs for the migration of hyper-cultivated and engineered biology to support studies of their impact on ecosystem function.

Develop robust strategies for biocontainment.

Demonstrate successful biocontainment of engineered organisms in conditions identical to or closely approximate the intended environment of release.

Bottleneck/Challenge: Escaped cells could find an ecological niche in the natural environment where conditions allow the organisms to proliferate.

Potential Solution: Test biocontainment in conditions that simulate realistic environmental release.

Potential Solution: Develop growth conditions that simulate a worst-case scenario (for example, containing alternative nutrients the engineered organism could utilize that would enable its escape).

Potential Solution: Minimize the number of genes required for survival in broad conditions, so that the engineered host can only survive in the intended environment.

Bottleneck/Challenge: Small reactor sizes and short time-course measurements impose limits on approximating real-world conditions.

Potential Solution: Develop computer models that simulate industrial scale growth and/or environmental release of engineered organisms.

Develop methods to remove engineered species from ecosystems in the event of a containment breach.

Develop approaches for tracing engineered organisms in the environment and measuring their persistence.

Develop strategies to better understand the impacts of biocontainment breaches for different organisms in specific environments so that appropriately strong and/or layered biocontainment measures can be implemented (see Ellstrand, 2018*).

Synthesize complementary biocontainment strategies (e.g., reliance on non-canonical amino acids, genetic recoding schemes, kill switches, genome reduction, synthetic speciation) to achieve standards for low-risk/high-containment** environmental release.

Bottleneck/Challenge: Containment strategies might need to be used in parallel to sufficiently decrease risk, which might decrease organism fitness and create pressure for escape (see Gallagher et al., 2015⁹; Moe-Behrens et al., 2013¹⁰).

Potential Solution: Improve containment using individual strategies and identify determinants of any fitness costs associated with using multiple biocontainment strategies.

*Ellstrand, N. C. (2018). “Born to Run”? Not Necessarily: Species and Trait Bias in Persistent Free-Living Transgenic Plants. Frontiers in Bioengineering and Biotechnology, 6. https://doi.org/10.3389/fbioe.2018.00088

**Guidelines issued by the National Institutes of Health in 2019 stipulate that systems wherein recombinant or synthetic nucleotides escape at a rate of less than 1/10⁸ may be deemed to have a high level of biological containment (National Institutes of Health, 2019).

Footnotes

Ellstrand, N. C. (2018). “Born to Run”? Not Necessarily: Species and Trait Bias in Persistent Free-Living Transgenic Plants. Frontiers in Bioengineering and Biotechnology, 6. https://doi.org/10.3389/fbioe.2018.00088
Mackelprang, R., & Lemaux, P. G. (2020). Genetic Engineering and Editing of Plants: An Analysis of New and Persisting Questions. Annual Review of Plant Biology, 71(1), 659–687. https://doi.org/10.1146/annurev-arplant-081519-035916
Arnolds, K. L., Dahlin, L. R., Ding, L., Wu, C., Yu, J., Xiong, W., Zuniga, C., Suzuki, Y., Zengler, K., Linger, J. G., & Guarnieri, M. T. (2021). Biotechnology for secure biocontainment designs in an emerging bioeconomy. Current Opinion in Biotechnology, 71, 25–31. https://doi.org/10.1016/j.copbio.2021.05.004
Allainguillaume, J., Harwood, T., Ford, C. S., Cuccato, G., Norris, C., Allender, C. J., Welters, R., King, G. J., & Wilkinson, M. J. (2009). Rapeseed cytoplasm gives advantage in wild relatives and complicates genetically modified crop biocontainment. New Phytologist, 183(4), 1201–1211. https://doi.org/10.1111/j.1469-8137.2009.02877.x
Rinkevich, B. (2015). Climate Change and Active Reef Restoration—Ways of Constructing the “Reefs of Tomorrow.” Journal of Marine Science and Engineering, 3(1), 111–127. https://doi.org/10.3390/jmse3010111
Lu, B.-R., Yang, X., & Ellstrand, N. C. (2016). Fitness correlates of crop transgene flow into weedy populations: A case study of weedy rice in China and other examples. Evolutionary Applications, 9(7), 857–870. https://doi.org/10.1111/eva.12377
Torres et al. (2016). Synthetic biology approaches to biological containment: Pre-emptively tackling potential risks. Portland Press. https://portlandpress.com/essaysbiochem/article/60/4/393/78400/Synthetic-biology-approaches-to-biological
Rottinghaus, A. G., Ferreiro, A., Fishbein, S. R. S., Dantas, G., & Moon, T. S. (2022). Genetically stable CRISPR-based kill switches for engineered microbes. Nature Communications, 13(1), 672. https://doi.org/10.1038/s41467-022-28163-5
Gallagher, R. R., Patel, J. R., Interiano, A. L., Rovner, A. J., & Isaacs, F. J. (2015). Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Research, 43(3), 1945–1954. https://doi.org/10.1093/nar/gku1378
Moe-Behrens, G., Davis, R., & Haynes, K. (2013). Preparing synthetic biology for the world. Frontiers in Microbiology, 4. https://doi.org/10.3389/fmicb.2013.00005