APPLIED AND ENVIRONMENTAL MICROBIOLOGY,0099-2240/01/$04.0010 DOI: 10.1128/AEM.67.9.4324–4328.2001

Sept. 2001, p. 4324–4328 Vol. 67, No. 9

Copyright © 2001, American Society for Microbiology. All Rights Reserved.

Mapping Microbial BiodiversityDAPHNE 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. ROPE5

Biotechnology Department,1 Applied Geosciences Department,2 Software Development Department,3 andIntegrated 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, Wyoming4

Received 15 December 2000/Accepted 30 May 2001

We report the development of a prototype database that “maps” microbial diversity in the context of thegeochemical and geological environment and geographic location. When it is fully implemented, scientists willbe 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 con-tains microbiological diversity that has the potential for re-markable scientific, social, and economic impact. In spite ofthese recent research activities, microbiological diversity re-mains largely undiscovered, and an understanding of its globaldistribution and temporal variability remains elusive. Recog-nized is the need to integrate microbiological data with envi-ronmental parameters, ecological data, and geographical loca-tion in order to improve our understanding of the spatial andtemporal patterns of microbial diversity and the relationshipbetween population structure and function (1–3; http://www2.ocean.washington.edu/lexen/). With the development of Geo-graphic Information System (GIS) software, a meaningful ap-proach to cataloging microorganisms in the context of theirgeographical position and geological and geochemical habitatsis now possible. The ability to display information in map formwill enable investigators to discern the spatial and temporalpatterns that arise from the distribution and activity of micro-organisms and to visualize these trends at greater spatialscales. In addition, the ready access to information that is madepossible with the Internet will benefit scientific research andsupport resource management and policy decisions regardingthe identification, sustainable use, and protection of criticalmicrobial biodiversity resources.

To demonstrate several of the data accession and displayfeatures that are possible with Internet-based GIS applica-tions, we have developed a prototype system using microbio-logical, geochemical, and geographic data and maps from Yel-lowstone National Park. Examples with active links weredeveloped for Octopus Spring, which is located in the LowerGeyser Basin. The demonstration system was constructed us-ing Microsoft Access database software, which was linked toArc Internet Map Server software (ESRI, Inc., Redlands, Cal-if.). The map server is accessible via the Internet (http://remus.inel.gov/ynphome) using any computer system that has a com-patible Internet browser. When fully developed, the system will

have search and query capabilities, data entry forms, and theability to print or download files, photographs, and maps. Datacan be accessed by typed entries, pulldown menus, “point andclick” map features, and dialog boxes.

Because it is an interactive system, maps can be constructedcontaining the information that is of interest to the user. Forexample, by clicking on buttons, features such as roads andtrails, U.S. Geological Survey (USGS) topographical maps,springs can be added or removed from a map (Fig. 1). Knownlocations can be located via the feature name e.g., OctopusSpring or Ojo Caliente (Fig. 1). Once a site is selected, the mapserver launches a map with the feature of interest highlightedand a table of information (Fig. 2). Clicking on a feature lo-cation allows access to photographs, sampling points, generaland site-specific safety information, and references (Fig. 3).Spring locations can be identified and located using geograph-ical coordinates or by searching for physical-chemical charac-teristics such as pH and temperature (Fig. 4). When fullydeveloped, results for a query such as “Where have membersof the genus Thermus been detected?” would be displayed as alist of locations or as a map (Fig. 5). The display of geochemi-cal data in map form can facilitate the selection of areas ofinterest for scientific studies or bioprospecting activities. Fig-ure 6 depicts the pH data that were collected for springs in theHeart Lake area of Yellowstone National Park. Easily viewedis the range of pH measurements (pH 1.7 to 10.0) that wereobtained in this one area.

The Internet access point (http://remus.inel.gov/ynphome)provides links to the project description, the map server anddirections for use, a recommended set of field sampling anddata documentation protocols, and other relevant databases.The purpose of the field sampling and data documentationprotocols is to provide guidance for consistent collection ofsamples and data related to general water chemistry, environ-mental conditions, and location information at the time thesamples were collected. Standardization of field methods isessential to ensure reliable data and to promote uniformity inthe collection and reporting of data.

The intent of the database is to capture as much data aspossible from published and unpublished sources to provide acomprehensive source of microbial diversity information. It isour view that there is much valuable information in the un-

* Corresponding author. Mailing address: Biotechnology, Idaho Na-tional Engineering and Environmental Laboratory, P.O. Box 1625, MS2203, Idaho Falls, ID 83415-2203. Overnight street address: 2525 Fre-mont Ave., Idaho Falls, ID 83415. Phone: (208) 526-8786. Fax: (208)526-0828. E-mail: dstoner@inel.gov.

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FIG. 1. Map server with the “Find” feature and clickable options available for customizing the map display according to an individual user’sneeds. Depicted is a relief map of Yellowstone National Park.

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 Springand a portion of the Lower Geyser Basin topographical map.

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FIG. 3. Each site can be linked with information specific for that location. Photographs, such as this one showing Octopus Spring, are also asource of information.

FIG. 4. The query feature of the database, which searches for specific physicochemical characteristics, may identify locations of interest.

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published data that is scattered among individual investigator’srecords and in the archives of federal and state agencies. Thedatabase houses microbiological data, geochemical data, andgeneral field data, which include sampling information, sampletype, weather conditions, and methods information. The datatable architecture accommodates the range of monikers andapproaches used to detect, identify, and classify microorgan-isms. Image and spatial data include base maps, e.g., USGStopographical maps, GIS “polygons” derived from ground sur-veys, aerial imagery, photographs, and sample locations. Thedatabase was also designed to accommodate location-specificinformation. For Yellowstone National Park this includes ac-cess information (e.g., directions to backcountry locations andPark Ranger escort requirements), safety concerns (e.g., sea-sonal bear closures and unstable ground), and habitat protec-tion (e.g., stay on trail and watch for endangered vegetation).

The strategic goal of this project is to develop a globaldatabase that has application to fundamental research in mi-crobial biodiversity and biogeochemistry, the discovery of newbiological products, and resource management. Because of thiswide applicability, we are encouraging all potential users tobecome involved with the development of the fully functionalsystem. In the near term, the scientific community and re-source management personnel can assist by informing us oftheir scientific and information needs, sharing expertise in thedevelopment of the system, or writing complementary research

FIG. 5. Display that would result from the query “Where have members of the genus Thermus been detected?” Red dots indicate locations ofThermus species. The size of the dot is proportional to the number of species detected.

FIG. 6. Display generated from the pH data collected for the fea-tures in the Heart Lake area. Zooming (inset) allows a closer view ofthe spring data.

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proposals. When the database is fully developed, scientists cancontribute by organizing, notifying us, and entering their datainto the system. Meanwhile, anyone can begin to help by col-lecting accurate Geographic Position System (GPS) coordi-nates of their sampling locations; data; time; type of samplecollected, e.g., soil, water, mud, or roots; and, where applica-ble, the genus and species or at least the common name of abiological host. We suggest that GPS receiver units with sub-meter accuracy should be used when a significant feature is notavailable to identify and verify that someone is at the correctlocation at a later date. Photographs across a feature anddirected at four compass points and down are also recom-mended, as this might be the only way to capture the feature,or portion of it, so that others can find it. Additional key fielddata that will augment the microbial data include depth, pH,temperature, oxidation-reduction potential, conductivity forwater samples, and soil moisture, texture, and color. Equip-ment and methods used should be noted as well.

The prototype database is the first of its kind that linksmicrobiological data with geochemical and geographical infor-mation. While there are Internet-accessible databases that aredevoted to or include microbial diversity, they are limited inthe geographical and geochemical information that they con-tain. Traditional microbial diversity databases are not designedto display the information in map form and do not contain thecompilation of geochemical information needed for ecological

studies or the geographical information for discerning long-term trends in global distribution.

In summary, the GIS-based microbial-geochemical databaseand its Internet accessibility provide expanded capabilities forbasic and applied scientific research and natural resource man-agement. The access to information and the ability to visualizetrends will promote the understanding of microbial life andmicrobial activity within the environment and enable scientiststo identify gaps in our understanding of the distribution anddiversity of microorganisms.

We are grateful for the support from the Laboratory Research andDevelopment Program under contract DE-AC07-99ID13727 from theDepartment of Energy to the Idaho National Engineering and Envi-ronmental Laboratory.

Selected GIS coverages and spatial data were obtained from Yel-lowstone National Park. We appreciate the helpful discussions withcolleagues from the many technical disciplines that are required todevelop this database.

REFERENCES

1. Bull, A. T., A. C. Ward, and M. Goodfellow. 2000. Search and discoverystrategies for biotechnology: the paradigm shift. Microbiol. Mol. Biol. Rev. 64:573–606.

2. Staley, J. T. 1999. Bacterial biodiversity: a time for place. ASM News 65:681–687.

3. 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. 1997. The microbial world: foundationof the biosphere. A report from the American Academy of Microbiology.American Society for Microbiology, Washington, D.C.

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