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

Secure Ecosystem Engineering and Design (SEED) to Enable Safe Biodesign of Novel Plant-Microbe Interactions


Xiaohan Yang*, Yang Liu, Mengjun Shu, Joanna Tannous, Tomas Rush, Kuntal De, Wellington Muchero, Jay Chen, and Paul E. Abraham


Oak Ridge National Laboratory (ORNL)



The Secure Ecosystem Engineering and Design (SEED) Science Focus Area (SFA), led by ORNL, combines unique resources and expertise in the biochemistry, genetics, and ecology of plant-microbe interactions with new approaches for analysis and manipulation of complex biological systems. The long-term objective is to develop a foundational understanding of how non-native and engineered microorganisms establish, spread, and impact ecosystems critical to U.S. Department of Energy missions. This knowledge will guide biosystems design for ecosystem engineering while providing the baseline understanding needed for risk assessment and decision-making across biodefense enterprises.


Advancements made in plant engineering are necessary to address future challenges associated with climate change and food security. CRISPR/Cas9-based genome engineering now provides novel methods for accelerating high precision engineering in non-model plants. Yet nearly all genetic editing is created through tissue culture–based plant transformation systems, and these are often poorly developed in non-model plant species. Moreover, it is currently difficult to predict the activity of CRISPR using existing bioinformatic methods. Virus-mediated delivery of CRISPR/Cas systems has great potential to improve the delivery needed to expedite and maximize the usefulness of this technology. Because it is a challenge to deliver an entire CRISPR/Cas tool using RNA viruses, researchers recently developed an intein-mediated split-nCRISPR/Cas9 technology to deliver an entire based editing CRISPR/Cas system into plants (Yuan et al. 2021). Biocontainment of these advanced genome engineering tools is important to mitigate risks of unwanted genome engineering. Therefore, the team developed a biosensor for real-time detection of active CRISPR/Cas tools in planta and an anti-CRISPR (Acr) protein countermeasure to limit unwanted CRISPR/Cas9-based genome editing activity in planta (Yuan et al. 2022; Liu et al. 2023). These advancements are important steps towards safe, high-throughput plant biodesign and genome engineering.

Targeted genome editing of plants alone may not facilitate the advancements necessary to achieve the Department of Energy’s climate and economic competitiveness goals. Emerging research on plant holobiont theory and microbial invasion ecology emphasizes the importance of plant-microbe interactions. However, researchers currently lack the knowledge necessary to successfully introduce beneficial alterations, prevent undesired modifications, or assess the risks of proposed ecosystem engineering efforts. Therefore, advancements are being made to detect and control novel plant-microbe interactions for safe biodesign. Researchers are currently developing plant-based biosensors to detect the establishment of fungi on poplar, and the Plasminogen-Apple-Nematode (PAN) domain was recently recognized for its important role in plant host cell invasion, which will serve as a useful target for engineering plants to control microbial invasion. Lastly, plant-delivered in situ engineering is being developed to control root-associated microbes through the delivery of small-secreted proteins. Preliminary results indicate these advancements have potential for engineering plants to detect and control associated microbes and thus facilitating new opportunities of safe ecosystem engineering.


Liu, Y., et al. 2023. “Expanding the Application of Anti-CRISPR Proteins in Plants for Tunable Genome Editing,” Plant Physiology kiad076. DOI:10.1093/plphys/kiad076.

Yuan, G., et al. 2021. “Plant-Based Biosensors for Detecting CRISPR-Mediated Genome Engineering,” ACS Synthetic Biology 10(12), 3600–03.

Yuan, G., et al. 2022. “An Intein-Mediated Split–nCas9 System for Base Editing in Plants,” ACS Synthetic Biology 11(7), 2513–17.

Funding Information

The SEED SFA is sponsored by the Genomic Science program (GSP), U.S Department of Energy, Office of Science, Biological and Environmental Research (BER) Program, under FWP ERKPA17. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under contract no. DE-AC05-00OR45678. This program is supported by the U. S. Department of Energy, Office of Science, through GSP, BER Program, under FWP ERKP123.