Joint USGS/USEPA Pathogens in Soils Geographic Information Systems Project

Science Center Objects

Studies determine background concentrations of select pathogens in soils of the contiguous U.S. and the influences of geochemistry, weather and climate on these populations. 

In order to protect the environment from current and potential threats posed by uncontrolled intentional releases of hazardous substances, pollutants, and contaminants, the biothreat research community recognizes the needs to be able to detect threats in the appropriate matrices and also consider whether a detected constituent is naturally occurring or a contaminant associated with an accidental or purposeful release. Therefore, sensitive and specific methods for processing and analyzing environmental samples as well as methods to determine the existing risk to the public from endemic microorganisms are needed.

U.S. Environmental Protection Agency (USEPA) has collaborated with the USGS to analyze soil samples collected during the USGS North American Soil Geochemical Landscapes Project (NASGLP) for the presence of Bacillus anthracis (Ba), Yersinia pestis (Yp), and Francisella tularensis (Ft). The NASGLP collected over 4800 soil samples across the lower 48 states and analyzed them for more than 40 major and trace elements from 2007 to 2010 (see U.S. Geological Survey Open-File Report 2014-1082, "Geochemical and mineralogical maps for soils of the conterminous United States").

The USEPA/USGS interagency agreement will expand microbial assessment capabilities for determining background levels of high priority biothreat agents. It is desired to improve upon the microbial processing and analytical methods used to analyze these samples in order to developed methods with lower limits of detection. Reanalysis of a subset of the archived samples will be completed to see if detection has been improved. Select sites may be resampled to evaluate spatio-temporal differences in environmental concentration.

It is also desired to know the relationship between the presence/absence of these biothreat agents and environmental variables such as (but not limited to): geochemical make-up of the soil, ambient meteorological conditions, soil moisture content, land use, past animal outbreaks, etc., to help predict persistence and natural occurrence of these agents in the environment. In order to do so, an interactive GIS model will be developed to map these variables for use as an investigative tool. Being able to analyze samples with confidence and to predict areas where naturally occurring organisms may or may not be located will help decision makers be better prepared in the event of contamination.

Map showing Calcium, Manganese, Phosphorous, and Strontium values

Map showing tentative threshold values (Calcium >= 13000 ppm, Manganese >= 463 ppm, Phosphorus >= 580 ppm, and Strontium >= 170 ppm) used to identify where naturally occurring outbreaks are "more likely" to occur than in other locations, with all other variables held constant. (Public domain.)

Development of a Sampling Protocol for Bacterial Pathogens in Surface Soil

The USGS and USEPA developed a protocol based on the protocol used by the NASGLP project, which describes the procedures for collecting, handling, and shipping soil samples for the detection of naturally occurring bacterial microorganisms, specifically residing within the top 0-5 cm layer of soil. This protocol has components for two different types of sampling applications: (1) typical sampling, when there is no suspicion of contamination (e.g., surveillance or background studies); and (2) in response to known or suspected contamination (e.g., the presence of animal carcasses).

For more details, see USEPA/USGS collection protocol for bacterial pathogens in surface soil

Method Development for Bacillus anthracis

The USGS collaborated with USEPA to make improvements in processing and analytical methods for detection of B. anthracis spores in soil (loam and sandy soils). This effort included optimization of a processing protocol for soil samples contaminated with B. anthracis spores and will also look at demonstrating the method followed by DNA extraction and qPCR analysis.

Interactive GIS Model for Pathogen and Outbreak Investigations

Along with microbial presence/absence data for the soil samples collected during this study, several variables related to microbial survival were mapped using GIS and include: geochemical make-up of the soil, percent slope, area drainage class, ambient meteorological conditions, soil moisture content, land use, and land cover. In addition, variables related to potential natural outbreaks were included, such as available inventory of livestock and past animal outbreaks by county.