Environmental Biology Group
The Environmental Biology Group develops and deploys capabilities to sample, detect, and respond to biological threats in the environment. Our diverse group includes expertise in the areas of environmental sampling, molecular biology, microbiology, ecology, chemistry, quality assurance, and population genetics. We strive to improve the time-to-detect, efficiency, sensitivity, and specificity of analytical tools used for counterterrorism (ie. BioWatch), food safety, and response/recovery efforts. Our current research projects involve developing rapid viability methods for select agents, fielding a mobile biological laboratory for special event monitoring, and developing methods for detecting biothreats in complex environmental samples.
Research Areas
- Biosurveillance through Environmental Monitoring
- Biothreat Response Vehicle: A Field Deployable Laboratory
- COVID-19 Testing
- Rapid Viability—Polymerase Chain Reaction (RV-PCR)
Biosurveillance through Environmental Monitoring
Contact: Thomas Bunt
There is a critical time between exposure and the onset of symptoms during a biological attack, where early detection and warning could save many lives. Over the past 15 years, members of the Environmental Biology Group in BBTD, along with colleagues across LLNL and federal agencies, have been developing and fielding laboratory diagnostics to scan the environment to detect and respond to a biological attack as early as possible. Our Biological Aerosol Sentry and Information System (BASIS) deployable laboratory, which incorporated highly-specific DNA signatures and real-time Polymerase Chain Reaction (PCR) assays was deployed shortly after the events of 9/11 to protect the National Capital Region (NCR). We have continued to expand and improve upon methods, assays, and laboratories for environmental biothreat monitoring, which have been utilized in programs such as the Department of Homeland Security (DHS) BioWatch Program. We’ve supported the DHS BioWatch Program since it started in 2003 by providing subject matter expertise, reach-back support, data management systems, hands-on training, and even setting up and operating laboratories. Our current research is focusing on improving and developing methods for characterizing the public health risk of environmental contamination following an initial biothreat detection.
Biothreat Response Vehicle: A Field Deployable Laboratory
The Biothreat Response Vehicle (BRV) is a mobile BioSafety Level 2+ laboratory designed by LLNL to be a rapidly deployable asset for biothreat countermeasures. For example, it’s anticipated that thousands of environmental samples would be collected in a short period of time to characterize a biological event (ex. bioterrorism attack), so the BRV was designed to be one of the resources that could assist in screening such a high volume of samples. The robotic liquid handling systems onboard the BRV make it a unique asset, since it allows us to screen hundreds to thousands of environmental samples per day. Members of the Environmental Biology Group in BBTD maintain and operate the BRV and have deployed with the BRV to support National Special Security Events (NSSEs), such as major political conventions. The BRV was also strategically designed with a flexible infrastructure that could be adapted to a wide spectrum of uses, so our group has also partnered with EPA and FDA for joint exercises related to decon clean-up efforts and food emergency response, respectively.
Rapid Viability—Polymerase Chain Reaction
Contact: Staci Kane
Dr. Staci Kane, Teneile Alfaro, and Julie Avila in partnership with EPA’s National Homeland Security Research Center (NHSRC) are developing rapid methods for analysis of viable pathogen cells or spores in surface and environmental samples. The RV-PCR method was successfully transitioned to the EPA Environmental Response Laboratory Network (ERLN) allowing EPA to be in a better position to make response and remediation decisions. After a bio-attack, a large number of samples of diverse type will need to be analyzed in a short timeframe to determine the efficacy of decontamination and to clear the site for re-use and re-entry. Routine methods including real-time PCR do not provide information on whether the decontamination efforts have killed the pathogen. The RV-PCR method is an innovative integration of high-throughput sample processing, short-incubation broth culture, and highly sensitive and specific real-time PCR assays to detect low levels of viable pathogen cells or spores. This RV-PCR method addresses limitations of the traditional culture method (e.g., time for analysis, cost, labor demand, incubator space), and has a lower limit of detection (LOD) since the entire sample is used for analysis. The method is also semi-automated, and less prone to inhibition by environmental matrices and to interference by outgrowth of other microbes. The method was field-tested in 2011 with Bacillus globigii (a surrogate for B. anthracis) during the interagency Bio-response Operational Testing and Evaluation (BOTE) that tested various decontamination approaches in a mock-contaminated building. RV-PCR successfully detected live B. globigii spores even for < 10-spore levels with a 98% agreement with the split samples run using the traditional culture-based analyses. Follow-on studies with virulent B. anthracis spores showed 10-spore level LODs for samples treated with either bleach disinfection or fumigation with chlorine dioxide or vaporous hydrogen peroxide showing utility for real-world post-decontamination samples.
