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.
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.
Below are other science projects associated with this project.
USGS SCoRR Project: Antibiotic Resistance Genes in Microbial Communities in Soils and Sediments of the United States
Below are publications associated with this project.
Processing protocol for soil samples potentially contaminated with Bacillus anthracis spores [HS7.52.02 - 514]
Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil
Observations on the migration of bacillus spores outside a contaminated facility during a decontamination efficacy study
Anthrax and the geochemistry of soils in the contiguous United States
USGS/EPA collection protocol for bacterial pathogens in soil
A survey of the occurrence of Bacillus anthracis in North American soils over two long-range transects and within post-Katrina New Orleans
- Overview
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.
Presence of Microbes and the Distribution of Climatic, Environmental, and Geochemical Variables 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.
Development of a Sampling Protocol for Bacterial Pathogens in Surface Soil
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.) 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.
- Science
Below are other science projects associated with this project.
USGS SCoRR Project: Antibiotic Resistance Genes in Microbial Communities in Soils and Sediments of the United States
The primary objective of the SCoRR Project is to assess the ability of wastewater sources emanating from septic tank systems, wastewater treatment plant outfalls, combined stormwater/sewer overflow outfalls and overflow events to affect genetic change in residential microbial communities that may present health risks to wildlife, livestock, pets and humans. - Publications
Below are publications associated with this project.
Processing protocol for soil samples potentially contaminated with Bacillus anthracis spores [HS7.52.02 - 514]
This protocol describes the processing steps for 45 g and 9 g soil samples potentially contaminated with Bacillus anthracis spores. The protocol is designed to separate and concentrate the spores from bulk soil down to a pellet that can be used for further analysis. Soil extraction solution and mechanical shaking are used to disrupt soil particle aggregates and to aid in the separation of spores fAuthorsErin E. Silvestri, Dale W. GriffinOptimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil
Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities thatAuthorsErin E. Silvestri, David Feldhake, Dale Griffin, John T. Lisle, Tonya L. Nichols, Sanjiv Shah, A Pemberton, Frank W Schaefer IIIObservations on the migration of bacillus spores outside a contaminated facility during a decontamination efficacy study
The potential for an intentional wide-area or indoor release of Bacillus anthracis spores remains a concern, but the fate and transport of B. anthracis spores in indoor and outdoor environments are not well understood. Some studies have examined the possibility of spore transport within ventilation systems and in buildings and transport into a building following an outdoor release. Little researchAuthorsErin E. Silvestri, Sarah Perkins, Robert Lordo, William Kovacik, Tonya L. Nichols, Charlena Yoder Bowling, Dale W. Griffin, Frank W. SchaeferAnthrax and the geochemistry of soils in the contiguous United States
Soil geochemical data from sample sites in counties that reported occurrences of anthrax in wildlife and livestock since 2000 were evaluated against counties within the same states (MN, MT, ND, NV, OR, SD and TX) that did not report occurrences. These data identified the elements, calcium (Ca), manganese (Mn), phosphorus (P) and strontium (Sr), as having statistically significant differences in coAuthorsDale W. Griffin, Erin E. Silvestri, Charlena Y. Bowling, Timothy Boe, David B. Smith, Tonya L. NicholsUSGS/EPA collection protocol for bacterial pathogens in soil
This Sample Collection Procedure (SCP) describes the activities and considerations for the collection of bacterial pathogens from representative surface soil samples (0-5 cm). This sampling depth can be reached without the use of a drill rig, direct-push technology, or other mechanized equipment. This procedure can be used in most soil types but is limited to sampling at or near the ground surfaceAuthorsDale W. Griffin, F.L. Shaefer, Charlena Bowling, Dino Mattorano, Tonya Nichols, Erin SilvestriA survey of the occurrence of Bacillus anthracis in North American soils over two long-range transects and within post-Katrina New Orleans
Soil samples were collected along a north-south transect extending from Manitoba, Canada, to the US-Mexico border near El Paso, Texas in 2004 (104 samples), a group of sites within New Orleans, Louisiana following Hurricane Katrina in 2005 (19 samples), and a Gulf Coast transect extending from Sulphur, Louisiana, to DeFuniak Springs, Florida, in 2007 (38 samples). Samples were collected from the tAuthorsDale W. Griffin, T. Petrosky, S.A. Morman, V.A. Luna