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Optimized Approaches Coupled with Interactive Mapping Application Provide a Tool to Visualize the Occurrence of Soil Pathogens

Colonies of the bacteria Bacillus globigii on a petri dish
Bacillus globigii colony forming units recovered from a seeded soil sample growing on a petri dish containing tryptic soy agar. Photo Credit: Dale W. Griffin, USGS.

Scientists optimized existing methods to collect and identify microorganisms including Bacillus anthracis, a pathogenic microorganism, in 4,800 soil samples across the United States, and developed a geographic information system (GIS)-based application to visualize microorganism occurrence throughout the United States.

Bacillus anthracis, the organism that causes the noncontagious infectious disease anthrax, is found naturally in soil and commonly affects domestic and wild animals in the United States and around the world. Domestic and wild animals such as cattle, sheep, goats, antelope, and deer can become infected when they breathe in or ingest spores in contaminated soil, plants, or water. Although it is rare in the United States, people can become infected with anthrax if they come in contact with infected animals or contaminated animal products.

The U.S. Geological Survey (USGS) and the U.S. Environmental Protection Agency (USEPA) collaborated through a series of studies to determine background concentrations of Bacillus anthracis and other pathogenic microorganisms in soils of the contiguous United States The joint research effort optimized existing methods for the collection and identification of pathogenic microorganisms in soils.

The optimized method showed an improved limit of detection (14 spores per gram of soil) over a previously used protocol (104 spores per gram of soil). This method is being further optimized through coupling with molecular assays for the purpose of conducting rapid large scale surveys at outbreak or occurrence locations.

A GIS decision support tool was created to enable rapid large-scale visualizations of Bacillus species detections at the time of data collection along with various other data related to microbial survival (geochemistry, outbreaks, precipitation, temperature change, slope, land cover, land use, and wildlife and livestock census data).

This joint research is part of ongoing efforts by the USGS Environmental Health Mission Area to understand the occurrence and transport of pathogens.

The USGS Toxic Substances Hydrology Program, the USGS Contaminant Biology Program, and the USGS Geochemical Landscapes Project, with long-term support from the USEPA, funded this project.

More Information


Bowling, C., Griffin, D., Mattorano, D., Silvestri, E., Schaefer, F., and Nichols, T., 2014, USEPA/USGS collection protocol for bacterial pathogens in surface soil: U.S. Environmental Protection Agency, EPA/600/R-14/027, 41 p.

Griffin, D.W., 2016, Experimental PCR data on soil DNA extracts: U.S. Geological Survey Data Release, doi:10.5066/F7WW7FRJ.

Griffin, D.W., Luna, V., Petrosky, T., and Morman, S.A., 2009, A survey of the occurrence of Bacillus anthracis in North American soils over two long-range transects and within post-Katrina New Orleans: Applied Geochemistry, v. 24, p. 1464–1471, doi:10.1016/j.apgeochem.2009.04.016.

Griffin, D.W., Silvestri, E., Bowling, C.Y., Boe, T., Smith, D.B., and Nichols, T.L., 2014, Anthrax and the geochemistry of soils in the contiguous United States: Geosciences, v. 4, no. 3, p. 114–127, doi:10.3390/geosciences4030114.

Silvestri, E.E., Feldhake, D., Griffin, D., III, Lisle, J., Nichols, T., Shah, S., Pemberton, A., and Schaefer, F.W., 2016, Optimizing recovery of Bacillus anthracis spores from soil: Journal of Microbiological Methods, v. 130, p. 6–13, doi:10.1016/j.mimet.2016.08.013.

Silvestri, E. and Griffin, D. 2017, Processing procedure for soil samples potentially contaminated with B. anthracis spores [HS7.52.02-514]: U.S. Environmental Protection Agency, Office of Research and Development, Homeland Security Research Program, EPA/600/R-17/028 I.

Silvestri, E.E., Perkins, S., Lordo, R., Kovacik, W., Nichols, T., Bowling, C.Y., Griffin, D., and Schaefer, F.W.,III, 2015, Assessing the potential for Bacillus spore transport from an indoor release to external environments: Biosecurity and Bioterrorism, v. 6, no. 2, p. 1–7, doi:10.4172/2157-2526.1000135.

Smith, D.B., Cannon, W.F., Woodruff, L.G., Solano, Federico, and Ellefsen, K.J., 2014, Geochemical and mineralogical maps for soils of the conterminous United States: U.S. Geological Survey Open-File Report 2014–1082, 386 p., doi:10.3133/ofr20141082.

U.S. Environmental Protection Agency, 2013, Literature review of protocols for processing soils contaminated with Bacillus anthracis spores: U.S. Environmental Protection Agency, EPA/600/R-13/185, 64 p.

U.S. Environmental Protection Agency, 2014, Literature review on mechanisms that affect persistence of Bacillus anthracis in soils: U.S. Environmental Protection Agency, EPA/600/R-14/216, 32 p.

U.S. Environmental Protection Agency, 2015, Literature review on processing and analytical methods for Francisella tularensis in soil and water: U.S. Environmental Protection Agency, EPA/600/R-15/118, 53 p.


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