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

2023 Abstracts

Secure Ecosystem Engineering and Design (SEED) to Mitigate the Impacts of Non-Native Fungal Pathogens on Managed Ecosystems


Joanna Tannous1* ([email protected]), Tomas Rush1, Dana Carper1, Alyssa Carrell1, Cole Sawyer1, Miranda Clark1, Wellington Muchero1, Jared LeBoldus2, David Kainer1, Daniel A. Jacobson1, and Paul E. Abraham1


1Oak Ridge National Laboratory (ORNL); and 2Oregon State University



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.


Invasion of non-native fungal species is acknowledged as one of the major external drivers altering the structure, biodiversity, and function of ecosystems (Pyšek and Richardson 2010). Understanding the mechanisms of establishment of these invaders and developing mitigation approaches to manage them is a critical aspect of sustaining native biodiversity and normal ecosystem functions. The fungal pathogen Sphaerulina musiva is a well-characterized example of an invasive species spread unintentionally by human activities (Abraham et al. 2018). Originally native to Eastern North America, S. musiva was only recently introduced and established into the Pacific Northwest of North America, resulting in deleterious effects on susceptible Populus species/genotypes, a foundational bioenergy crop, and a keystone tree species in forested ecosystems (Herath et al. 2016; Sakalidis et al. 2016).

Within the SEED SFA, a goal is to identify genetic determinants that alter S. musiva establishment, spread, and overall impact in DOE-managed Populus ecosystems to guide engineering and risk mitigation strategies for more sustainable and productive systems. As a critical first step, researchers are developing an S. musiva pangenome representing isolates collected across the U.S. and generating genome-wide association study resources for high-throughput genotype-to-phenotype discovery. These resources have already uncovered genetic associations for several important establishment and pathogenicity traits that can be exploited by developed genomic engineering approaches, such as CRISPR-enabled gene drives. To enable future biodesign on S. musiva, the team developed the first transformation system using a protein-based version of the CRISPR-Cas9 genome editing system.

Ultimately, the ongoing research will address fundamental knowledge gaps related to anthropogenic-assisted microbial invasions and guide future biosystems design strategies that safely prevent undesired modifications in DOE-managed ecosystems.


Abraham, N. D., et al. 2018. “Multiplex qPCR for Detection and Quantification of Sphaerulina musiva in Populus Stems,” Plant Pathology 67, 1874–82.

Herath, P., et al. 2016. “Anthropogenic Signature in the Incidence and Distribution of an Emerging Pathogen of Poplars,” Biological Invasions 18, 1147–61.

Pyšek, P., and D. M. Richardson. 2010. “Invasive Species, Environmental Change and Management, and Health,” Annual Review of Environment and Resources 35, 25–55.

Sakalidis, M. L., et al. 2016. “Genetic Patterns Reveal Historical and Contemporary Dispersal of a Tree Pathogen,” Biological Invasions 18, 1781–99.

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.