Mapping Microbial Biodiversity

Transcription

1 APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2001, p Vol. 67, No /01/$ DOI: /AEM Copyright 2001, American Society for Microbiology. All Rights Reserved. Mapping Microbial Biodiversity DAPHNE L. STONER, 1 * MICAH C. GEARY, 2 LUKE J. WHITE, 3 RANDY D. LEE, 3 JULIE A. BRIZZEE, 3 ANN C. RODMAN, 4 AND RONALD C. ROPE 5 Biotechnology Department, 1 Applied Geosciences Department, 2 Software Development Department, 3 and Integrated Environmental Analysis Department, 5 Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho 83415, and Geographic Information System Laboratory, Yellowstone Center for Resources, Yellowstone National Park, Wyoming 4 Received 15 December 2000/Accepted 30 May 2001 We report the development of a prototype database that maps microbial diversity in the context of the geochemical and geological environment and geographic location. When it is fully implemented, scientists will be able to conduct database searches, construct maps containing the information of interest, download files, and enter data over the Internet. In recent years, research has indicated that the earth contains microbiological diversity that has the potential for remarkable scientific, social, and economic impact. In spite of these recent research activities, microbiological diversity remains largely undiscovered, and an understanding of its global distribution and temporal variability remains elusive. Recognized is the need to integrate microbiological data with environmental parameters, ecological data, and geographical location in order to improve our understanding of the spatial and temporal patterns of microbial diversity and the relationship between population structure and function (1 3; With the development of Geographic Information System (GIS) software, a meaningful approach to cataloging microorganisms in the context of their geographical position and geological and geochemical habitats is now possible. The ability to display information in map form will enable investigators to discern the spatial and temporal patterns that arise from the distribution and activity of microorganisms and to visualize these trends at greater spatial scales. In addition, the ready access to information that is made possible with the Internet will benefit scientific research and support resource management and policy decisions regarding the identification, sustainable use, and protection of critical microbial biodiversity resources. To demonstrate several of the data accession and display features that are possible with Internet-based GIS applications, we have developed a prototype system using microbiological, geochemical, and geographic data and maps from Yellowstone National Park. Examples with active links were developed for Octopus Spring, which is located in the Lower Geyser Basin. The demonstration system was constructed using Microsoft Access database software, which was linked to Arc Internet Map Server software (ESRI, Inc., Redlands, Calif.). The map server is accessible via the Internet ( using any computer system that has a compatible Internet browser. When fully developed, the system will * Corresponding author. Mailing address: Biotechnology, Idaho National Engineering and Environmental Laboratory, P.O. Box 1625, MS 2203, Idaho Falls, ID Overnight street address: 2525 Fremont Ave., Idaho Falls, ID Phone: (208) Fax: (208) dstoner@inel.gov. have search and query capabilities, data entry forms, and the ability to print or download files, photographs, and maps. Data can be accessed by typed entries, pulldown menus, point and click map features, and dialog boxes. Because it is an interactive system, maps can be constructed containing the information that is of interest to the user. For example, by clicking on buttons, features such as roads and trails, U.S. Geological Survey (USGS) topographical maps, springs can be added or removed from a map (Fig. 1). Known locations can be located via the feature name e.g., Octopus Spring or Ojo Caliente (Fig. 1). Once a site is selected, the map server launches a map with the feature of interest highlighted and a table of information (Fig. 2). Clicking on a feature location allows access to photographs, sampling points, general and site-specific safety information, and references (Fig. 3). Spring locations can be identified and located using geographical coordinates or by searching for physical-chemical characteristics such as ph and temperature (Fig. 4). When fully developed, results for a query such as Where have members of the genus Thermus been detected? would be displayed as a list of locations or as a map (Fig. 5). The display of geochemical data in map form can facilitate the selection of areas of interest for scientific studies or bioprospecting activities. Figure 6 depicts the ph data that were collected for springs in the Heart Lake area of Yellowstone National Park. Easily viewed is the range of ph measurements (ph 1.7 to 10.0) that were obtained in this one area. The Internet access point ( provides links to the project description, the map server and directions for use, a recommended set of field sampling and data documentation protocols, and other relevant databases. The purpose of the field sampling and data documentation protocols is to provide guidance for consistent collection of samples and data related to general water chemistry, environmental conditions, and location information at the time the samples were collected. Standardization of field methods is essential to ensure reliable data and to promote uniformity in the collection and reporting of data. The intent of the database is to capture as much data as possible from published and unpublished sources to provide a comprehensive source of microbial diversity information. It is our view that there is much valuable information in the un- 4324

2 VOL. 67, 2001 MAPPING MICROBIAL BIODIVERSITY 4325 FIG. 1. Map server with the Find feature and clickable options available for customizing the map display according to an individual user s needs. Depicted is a relief map of Yellowstone National Park. Downloaded from on December 26, 2018 by guest FIG. 2. Once a site is selected, the map server displays a map and information for the location. Depicted are a data table for Octopus Spring and a portion of the Lower Geyser Basin topographical map.

3 4326 STONER ET AL. APPL. ENVIRON. MICROBIOL. FIG. 4. The query feature of the database, which searches for specific physicochemical characteristics, may identify locations of interest. FIG. 3. Each site can be linked with information specific for that location. Photographs, such as this one showing Octopus Spring, are also a source of information.

4 VOL. 67, 2001 MAPPING MICROBIAL BIODIVERSITY 4327 FIG. 5. Display that would result from the query Where have members of the genus Thermus been detected? Red dots indicate locations of Thermus species. The size of the dot is proportional to the number of species detected. published data that is scattered among individual investigator s records and in the archives of federal and state agencies. The database houses microbiological data, geochemical data, and general field data, which include sampling information, sample type, weather conditions, and methods information. The data table architecture accommodates the range of monikers and approaches used to detect, identify, and classify microorganisms. Image and spatial data include base maps, e.g., USGS topographical maps, GIS polygons derived from ground surveys, aerial imagery, photographs, and sample locations. The database was also designed to accommodate location-specific information. For Yellowstone National Park this includes access information (e.g., directions to backcountry locations and Park Ranger escort requirements), safety concerns (e.g., seasonal bear closures and unstable ground), and habitat protection (e.g., stay on trail and watch for endangered vegetation). The strategic goal of this project is to develop a global database that has application to fundamental research in microbial biodiversity and biogeochemistry, the discovery of new biological products, and resource management. Because of this wide applicability, we are encouraging all potential users to become involved with the development of the fully functional system. In the near term, the scientific community and resource management personnel can assist by informing us of their scientific and information needs, sharing expertise in the development of the system, or writing complementary research FIG. 6. Display generated from the ph data collected for the features in the Heart Lake area. Zooming (inset) allows a closer view of the spring data.

5 4328 STONER ET AL. APPL. ENVIRON. MICROBIOL. proposals. When the database is fully developed, scientists can contribute by organizing, notifying us, and entering their data into the system. Meanwhile, anyone can begin to help by collecting accurate Geographic Position System (GPS) coordinates of their sampling locations; data; time; type of sample collected, e.g., soil, water, mud, or roots; and, where applicable, the genus and species or at least the common name of a biological host. We suggest that GPS receiver units with submeter accuracy should be used when a significant feature is not available to identify and verify that someone is at the correct location at a later date. Photographs across a feature and directed at four compass points and down are also recommended, as this might be the only way to capture the feature, or portion of it, so that others can find it. Additional key field data that will augment the microbial data include depth, ph, temperature, oxidation-reduction potential, conductivity for water samples, and soil moisture, texture, and color. Equipment and methods used should be noted as well. The prototype database is the first of its kind that links microbiological data with geochemical and geographical information. While there are Internet-accessible databases that are devoted to or include microbial diversity, they are limited in the geographical and geochemical information that they contain. Traditional microbial diversity databases are not designed to display the information in map form and do not contain the compilation of geochemical information needed for ecological studies or the geographical information for discerning longterm trends in global distribution. In summary, the GIS-based microbial-geochemical database and its Internet accessibility provide expanded capabilities for basic and applied scientific research and natural resource management. The access to information and the ability to visualize trends will promote the understanding of microbial life and microbial activity within the environment and enable scientists to identify gaps in our understanding of the distribution and diversity of microorganisms. We are grateful for the support from the Laboratory Research and Development Program under contract DE-AC07-99ID13727 from the Department of Energy to the Idaho National Engineering and Environmental Laboratory. Selected GIS coverages and spatial data were obtained from Yellowstone National Park. We appreciate the helpful discussions with colleagues from the many technical disciplines that are required to develop this database. REFERENCES 1. Bull, A. T., A. C. Ward, and M. Goodfellow Search and discovery strategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64: Staley, J. T Bacterial biodiversity: a time for place. ASM News 65: Staley, J. T., R. W. Castenholz, R. R. Colwell, J. G. Holt, M. D. Kane, N. R. Pace, A. A. Salyers, and J. M. Tiedje The microbial world: foundation of the biosphere. A report from the American Academy of Microbiology. American Society for Microbiology, Washington, D.C. Downloaded from on December 26, 2018 by guest