Publications

Browse through all available publications made public by the SEED SFA team and retrieve additional information.

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Tools

Browse through available public tools that were made public by the SEED SFA team. Here, you will also find additional public tools that we find useful towards accomplishing our objectives.  

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Data Catalog

Browse through data products made public by the SEED SFA team and retrieve additional information.

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Our mission

Human-mediated microbial dispersal, both intentional and unintentional, is occurring at unprecedented levels. The movement or invasion of a microorganism into a new system can have diverse and widespread impacts and is known to be a major threat to ecosystems and the US economy. Therefore, improving our understanding of the complex and interconnected relationships governing how microbes establish, spread, and impact terrestrial and aquatic systems presents an emerging challenge.

Today, there is a growing appreciation of the relationships between microbial communities and plant health. Fully realizing the potential of microbes and how they interact with plant systems and related ecosystems has been recognized as a key research challenge to maintaining an efficient, resilient, and sustainable bioeconomy when faced with the negative impacts of climate change (e.g., shortages of arable land and water, degradation of ecosystems, loss of biodiversity, etc.) (Science Breakthrough by 2030).

Microbial interactions with plants have wide-ranging outcomes that are often difficult to predict. On one side of the spectrum, invasive disease-causing microbes can cost around $23.5 billion USD yearly in crop yield losses and pesticide resistance populations are becoming more prevailing. On the other side, beneficial microbes have become an integral part of plant pest management strategies and serve as active ingredients in a growing market of commercial plant probiotics, where they improve plant health and productivity in natural and stress-induced environments.

These interactions can be redesigned through genome editing — aided by scientific and technical advances in functional genomics (i.e., transcriptomics, proteomics, and metabolomics) and computational sciences — and offers exciting advances in biotechnology.  Yet, plant-microbe interactions are vast, complex, highly interconnected system with many interdependent factors that remain difficult to predict.

Currently, the knowledge and tools needed to successfully and safely introduce beneficial microbial alterations (natural or engineered) into systems is insufficient, as is the understanding required to prevent undesired modifications and assess the risks of proposed ecosystem biodesign efforts. Addressing this research challenge is the long-term objective of the Secure Ecosystem Engineering and Design (SEED) Science Focus Area (SFA).

At Oak Ridge National Laboratory, our team cuts across disciplinary boundaries to integrate knowledge, tools, and ways of thinking from experts in life sciences and computational sciences to solve complex problems associated biosystems design and ecosystem engineering. Combining expertise in microbiology and plant biology, ecology, genetic engineering, analytical technologies, and computational sciences, our goal is to build a foundational knowledge base of factors that influence microbial invasions success using a suite of laboratory and field experiments. We will then use this knowledge to design new engineering strategies to detect, promote and limit microbial invasions while also improving biological risk assessment.

Achieving the goals of the SEED SFA will advance methods to improve the security, reliability, and productivity of DOE mission-critical ecosystems. Fundamental science will lead to innovative biodesign strategies and tools to successfully introduce beneficial alterations, prevent undesirable changes, and overcome uncertain ecological risks from introducing nonnative or genetically engineered microorganisms into the environment. Scientific breakthroughs and new technologies are expected to benefit other DOE genomic science programs and other agency stakeholders in the US bioeconomy (e.g., US Department of Agriculture, US Department of Defense, and Advanced Research Projects Agency–Energy). Within the larger framework of national security, these advancements can offer national biodefense solutions to ensure a prosperous and secure domestic bioeconomy. an operational goal of this SFA will be to make our scientific knowledge, technologies, and data readily available to the research community and to the public as possible to enable knowledge and technology transfer.

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 the engineered green strain) or ecosystem (e.g. changing the locks at a given stage), an ecosystem engineer can control the outcome of these 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.

Latest News

October 11, 2022 - DOE highlights research by Xiaohan Yang: Watching Plants Switch on Genes

Recent research by Xiaohan Yang was highlighted by DOE showcasing a novel technique for screening molecular characteristics in plants. Read more about it here.

May 10, 2022 - Hiring Fungal Geneticist

The SEED-SFA is hiring a fungal geneticist. Join our amazing team!

December 10, 2021 - Active detection of CRISPR-based editing tools

Xiaohan Yang and his team recently published a manuscript where they described a new approach to actively detect CRISPR-based editing tools in organisms. Read more about the article here. Additionally, you can watch short video describing the work.

December 7, 2021 - Graduate Student Cole Sawyer Receives Fellowship for SEED Work

University of Tennessee, Knoxville has awarded graduate student Cole Sawyer with a fellowship for the 2021-2022 school year. The fellowship is funded by the UT-Oak Ridge Innovation Institutes EERE Workforce Development Project under the Predictive Systems Biology for Circular and Sustainable Economies sub-field.

Latest Publications

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools ...

An Intein-Mediated Split–nCas9 System for Base Editing in Plants

Virus-assisted delivery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system represents a promising approach for editing plant genomes. Among the CRISPR/Cas systems, CRISPR/Cas9 is most widely us...

Precision genome editing in plants using gene targeting and prime editing: existing and emerging strategies

Precise modification of plant genomes, such as seamless insertion, deletion, or replacement of DNA sequences at a predefined site, is a challenging task. Gene targeting (GT) and prime editing are currently the best approaches for this purpose. How...

Reflection on the challenges, accomplishments, and new frontiers of gene drives

Ongoing pest and disease outbreaks pose a serious threat to human, crop, and animal lives, emphasizing the need for constant genetic discoveries that could serve as mitigation strategies. Gene drives are genetic engineering approaches discovered d...