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

Developing a National Virtual Biosecurity for Bioenergy Crops Center


Paul Freimuth* (, Kerstin Kleese van Dam, John Shanklin, Alistair Rogers, Robert McGraw, Qun Liu, Shantenu Jha, and Martin A. Schoonen


Brookhaven National Laboratory


The goal of this 18-month pilot project is to develop a roadmap for a new U.S. Department of Energy (DOE) Office of Science Biological and Environmental Science capability to address biothreats to bioenergy crops. The main deliverable of this effort is a roadmap toward a new National Virtual Biosecurity for Bioenergy Crop Center (NVBBCC) based on community input as well as the experiences of conducting a limited study on anthracnose, a disease affecting Sorghum, one of the DOE’s leading biofuels feedstocks. A mature NVBBCC is envisioned to be a distributed, virtual center with multiple DOE laboratories at its core to maximize the use of unique facilities and expertise across the DOE complex. NVBBCC will support community-driven plant pathology research as well as broader BER-relevant plant biology research. The new NVBBCC capability could also support responses to biothreats to unmanaged ecosystems and techniques, workflows, and infrastructure could be readily pivoted to a wider range of biosecurity challenges.


Rationale: The development of resilient and sustainable bioenergy crops is an important part of U.S. government strategy to transition to a net-zero economy. An important consideration in developing the US bioeconomy is the biosecurity of crops grown for bioenergy production. The most likely biosecurity threats to bioenergy crops are either known pests or pathogens that emerge in new areas, possibly driven by climate change or new pests or pathogens that are genetically related to known ones. A robust biosecurity capability optimized to respond rapidly to biothreats to bioenergy crops requires an integrated and versatile platform that delivers rapid detection and targeted sampling, propagation prediction, and timely characterization of the interaction between a pest or pathogen and the bioenergy crop. These capabilities are needed to underpin the development of controls and solutions. Here the team reports on a new pilot study funded by the DOE to develop a roadmap for a National Virtual Biosecurity for Bioenergy Crops Center (NVBBCC) organized around four interconnected modules: detection and sampling, biomolecular characterization, assessment, and mitigation.

Approach: The team will use a series of community planning meetings and experimental work on a known disease in Sorghum to develop a roadmap for the development of NVBBCC. The roadmap planning meetings, conducted within the first nine months, will identify partnerships within and outside DOE necessary to establish the full capability required for an end-to-end biosecurity platform and develop a network of experts and facilities that the center can draw upon when faced with a biothreat. A study on a fungal disease, anthracnose, which affects Sorghum, a leading energy crop, will be used to develop material, experimental, and data workflows as well as guide future investments. Anthracnose is caused by Colletotrichum sublineola and can lead to significant reductions by up to 67% in crop yield (Stutts and Vermerris 2020). The team has established the capability to work with the disease to study pathogen-host interactions. Biomolecular imaging capabilities at Brookhaven National Laboratory will be used to advance understanding of the interaction of C. sublineola with Sorghum.

Informed by lessons learned from DOE’s National Virtual Biotechnology Laboratory (NVBL), the team will develop a dedicated computing platform to support the NVBBCC pilot study. Its backbone is an integrated and flexible computational science software and hardware system to support persistent data storage; advanced AI/ML-enabled data analysis; data fusion; data sharing; and near- real-time visualizations of the geographic localization of disease as well as computational simulations and predictions. The pilot study intends to stand up an initial prototype of a computational platform that can be scaled up if needed. A separate contribution to this meeting will focus on that component of the pilot study.

Results: The presentation will be a status review of the pilot study and a preliminary report from two community planning meetings that will have been held by mid-April. One planning meeting, held in February, will be focused on biomolecular characterization of biothreats to bioenergy crops. A second one will focus on atmospheric dispersion pathways of diseases relevant to bioenergy crops.


Stutts, L. R. and W. Vermerris, 2020. “Elucidating Anthracnose Resistance Mechanisms in Sorghum—A Review,” Phytopathology 110(12), 1863–76. DOI:10.1094/PHYTO-04-20-0132-RVW.

Funding Information

Brookhaven National Laboratory is managed by Brookhaven Science Associates, LLC for the U.S. Department of Energy under contract no. DE-SC0012704. This program is supported by the U. S. Department of Energy, Office of Science, through the Biological Systems Science, Office of Biological and Environmental Research, under FWP BI207.