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Systems Biology for Energy and the Environment

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Genomic Science Program

Science Focus Area: Oak Ridge National Laboratory

SEED: Secure Ecosystem Engineering and Design

SEED ecosystem engineering diagram
The SEED SFA led by Oak Ridge National Laboratory (ORNL) focuses on ecosystem engineering to promote or limit microbial invasions. Natural microbial communities (black) face many potential microbial invaders (shown in green, blue, pink, and yellow). A successful invader must sequentially establish, spread, and produce a functional impact. Invaders have different traits (keys) that potentially allow them to proceed through barriers (locks) at each stage. By manipulating the invader (e.g., providing keys to an engineered strain) or the ecosystem (e.g., changing the locks at a given stage), an ecosystem engineer can control the outcome of potential invasions. In this example, the engineered strain (green) has the necessary traits to successfully deliver its payload and improve tree health while the undesired invaders (blue, pink, and yellow) are blocked. [Courtesy ORNL]

  • Principal Investigator and Laboratory Research Manager: Paul E. Abraham1
  • Scientific Co-Managers: Melissa Cregger1 and Joshua Michener1
  • Co-Investigators: Daniel Jacobson1, David Kainer1, Jessy Labbé1, Wellington Muchero1, Xiaohan Yang1, Carrie Eckert2
  • Participating Institutions: 1Oak Ridge National Laboratory; 2University of Colorado–Boulder
  • Project Website:

Human-mediated microbial dispersal, both intentional and unintentional, is occurring at unprecedented levels. The establishment, spread, and impact of microorganisms into new terrestrial and aquatic systems presents an emerging challenge to understanding the interplay between biodiversity, the environment, and ecosystem function.

The movement or invasion of a microorganism into a new system can threaten both ecosystems and the economy. For example, a fungus native to Asia was accidentally introduced into North America during the 19th century and decimated chestnut tree populations. This had devastating economic and social impacts on communities in the eastern United States. However, targeted application or manipulation of microbes associated with plants can also benefit plant health and productivity. For example, many off-the-shelf plant probiotic products contain microbes capable of increasing plant root surface area, boosting water and nutrient update, and maximizing plant yield.

Currently, the knowledge needed to successfully and safely introduce beneficial microbial alterations into systems is insufficient, as is the understanding required to prevent undesired modifications and assess the risks of proposed ecosystem biodesign efforts. To address these knowledge gaps, the Secure Ecosystem Engineering and Design (SEED) Science Focus Area (SFA), led by Oak Ridge National Laboratory, 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 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.

The first major research objectives include:

  • Identify, quantify, and manipulate biotic and abiotic factors that alter the establishment of introduced genes, pathways, organisms, or communities in managed ecosystems.
  • Investigate factors that influence the spread of genes, pathways, organisms, or communities through managed ecosystems.
  • Quantify and manipulate the impact of a microbial invasion across space and time.

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