Goals of the database
What is the Phytophthora Database?
Phytophthora, an oomycete plant pathogen, is more closely related to brown algae and diatoms than true fungi and has been placed in a separate kingdom, the Stramenopiles (Gunderson et al., 1987; Förster et al., 1990; Leipe et al., 1994). Due to their high virulence and ability to spread rapidly throughout the world, Phytophthora is one of the most important groups of plant pathogens. The destructive potential of Phytophthora diseases is well illustrated by late blight (P. infestans), which was responsible for the Irish potato famine and has again become globally problematic due to the introduction of new, fungicide-resistant lineages (Fry and Goodwin, 1997). Sudden oak death in the US (Rizzo et al., 2002) and diseases on ornamental plants in Europe (Werres et al., 2001), caused by P. ramorum, are examples of the threat to forest ecosystems and the nursery industry.
Toward the goal of enhancing our ability to detect, diagnose, monitor, and manage Phytophthora diseases, we have been systematically cataloging genotypic and phenotypic data of Phytophthora spp. in a web-based database that can be easily accessed and utilized by the global community of plant health professionals. Although we are currently focusing on the genotypic characterization of the isolates archived in the World Phytophthora Collection (WPC; Phytophthora.ucr.edu) at UC-Riverside and in the Pennsylvania Department of Agriculture (PDA), we plan to include Phytophthora collections throughout the world in order to create a global atlas of the diversity and distribution of Phytophthora species. This project has been mainly supported by the NRI-Plant Biosecurity program (2005-35605-15393 and 2008-55605-18773) and currently involves the following principal investigators, including Seogchan Kang, David Geiser, and Scott Isard (Penn State), Mike Coffey (UC-Riverside), Joe Russo (ZedX, Inc.), Kelly Ivors (NC State), Frank Martin and Nik Grunwald (USDA-ARS). Grants from the Pennsylvania Department of Agriculture (ME442316 and ME 445580) and a cooperative agreement with USDA-ARS (59-1920-3-304) have also been used to support parts of this project.
Figure 1. Organization and functionality of the GPN.
Because of the global nature of Phytophthora problems, we need to network human and information resources on a global scale so that stakeholders impacted by the pathogen can make decisions based on the best available information. In the long run, this project will evolve to virtually linked global human and information resources, tentatively termed the Global Phytophthora Network (GPN). The GPN will weave together the following threads (Fig. 1): (i) a database archiving the global genotypic and phenotypic diversity within the genus; (ii) detailed global distribution maps of genotypes and populations of well characterized species; (iii) versatile molecular diagnostic tools; (iv) informatics tools supporting the use of archived data for Phytophthora detection and identification; (v) a Geographic Information Systems (GIS) platform for visualizing the distribution and change of Phytophthora in environmental and geospatial contexts; and (vi) a globally-linked network of scientists working together in monitoring and managing Phytophthora diseases.
A description of the data content and functionality of the Phytophthora Database can be found in a paper published in Plant Disease (Park et al., 2008).
Why was this project initiated?
This project was initiated to address a number of challenges we face in protecting agricultural production and environmental systems from devastating diseases. Crop loss from disease poses a serious threat to global food/fiber/feed security (Strange and Scott, 2005). Worldwide crop loss due to diseases, insects, and weeds accounts for 31- 42% of the potential crop production capacity; without protective measures, this loss would be much greater (Agrios, 2005). Pathogens can be equally catastrophic in natural landscapes, as illustrated by chestnut blight and Dutch elm disease (Liebhold et al., 1995). Besides production losses, some diseases (e.g., karnal bunt of wheat) incur huge indirect costs due to trade restrictions. After the September 11 attacks and the subsequent anthrax release, it became apparent that the threat to US agriculture and economy from the deliberate release of pathogens should not be underestimated (Council, 2003). Because the volume and variety of global agricultural commodities has been steadily increasing, disruption of agriculture in the US and major trading partners by the intentional release of pathogens could potentially be catastrophic to the US and global economic stability. Such events likely cause the erosion of public confidence in food safety and destabilization of the international commodity market by triggering fear-driven responses.
To enhance our preparedness, a number of measures have been recommended by scientific organizations and various federal agencies (Beale et al., 2002; Council, 2003; Madden and Wheelis, 2003), some of which have been implemented. One example is the establishment of the National Plant Diagnostic Network (NPDN), a nation-wide disease monitoring system set up by the USDA through the linking and upgrading of regional disease diagnostic labs in land-grant institutions. The USDA has also been supporting the development of new and improved diagnosis and disease management technologies (e.g., projects supported by the Plant Biosecurity program). Other federal agencies are also developing programs and initiatives that address agricultural biosecurity concerns as directed in the Homeland Security Presidential Directive 9. However, considering the need for monitoring vast and diverse agricultural production and environmental systems, current infrastructures are insufficient to deal effectively with both intentional and natural outbreaks of diseases. Because there are many worthy competing needs under severe budget constraints, creating a significant resource for setting up new infrastructures for agricultural biosecurity would be difficult. We believe that better utilization of existing human and information resources deserves a serious consideration as part of the solution (Kang et al., 2006). To this end, we need to establish mechanisms that will promote and support more unified cooperation and exchange of information in a timely manner within the US and with other countries.
The unintentional introduction of pathogens and pests has been an ongoing problem throughout human history. Pathogens do not carry passports and frequently migrate from one country to another through various means, including trade, human travel, and weather-related events. In recent years, the expanding volume of trade and the increasing numbers of entry points have greatly accelerated establishments of non-indigenous pathogens/pests. Ecological and economic consequences of such introductions can be catastrophic (Liebhold et al., 1995); the elimination of the American chestnut as a dominant species in eastern forests and the tremendous reduction of the importance of elms in the landscape can be attributed directly to unknowingly introduced fungi (Gibbs, 1978; Liebhold et al., 1995). There are numerous historical and contemporary examples of major crop loss caused by introduced pathogens (Agrios, 2005). Early detection, accurate identification, and the ability to trace pathogens back to their likely origin and entry point(s) will significantly increase the probability of achieving containment and preventing further introduction of exotic pathogens. Besides enhancing our capability of accurate diagnosis, global cooperation in mapping and documenting the known pathogen diversity and distribution in geospatial contexts is essential for implementing regulatory measures to mitigate the movement and introduction of exotic pathogens
Because many high risk pathogens threatening US agriculture and natural ecosystems (Hawks, 2002; Madden and Wheelis, 2003) are not currently present in the US, we do not have adequate knowledge of their biology, ecology, and epidemiology. Addressing this deficiency is a difficult task because research on such topics is severely restricted in the US due to the requirement of high-level containment facilities and strict regulatory compliance. Although USDA-ARS, particularly the Foreign Disease-Weed Science Research Unit at Ft. Detrick, in collaboration with USDA-APHIS has performed an excellent job in generating knowledge necessary for dealing with exotic pathogens (e.g., plum pox, soybean rust and P. ramorum), available resources (both human and facility) are vastly insufficient to adequately address other needs. This quandary highlights the importance of cooperation with scientists in countries in which target pathogens are endemic. Establishing a global database of the biology, ecology, and epidemiology of known pathogens worldwide, shared and curated by an international community of plant pathologists, will contribute to this goal (Kang et al., 2006).
Because plant disease results from complex interactions among host, pathogen, and the environment (a.k.a., the disease triangle), identifying the cause(s) of disease outbreaks, forecasting their spread, and implementing appropriate disease management strategies require the integration of disparate data sets, ranging from pathogen ecology to geospatial, agronomic and environmental contexts. However, tools supporting the integration of such disparate data sets are lacking. This problem impedes efforts to fully utilize available data to achieve a broader understanding of the role of individual epidemiological factors, as well as synergistic and/or antagonistic interactions among them, thus significantly diminishing the value of existing data and fragmenting research and regulatory activities. Establishing a user-friendly informatics platform that supports the integration and use of available data and cooperation within and between countries in disease monitoring and management should be considered as important as collecting new data for agricultural biosecurity. In this age of information overflow, the importance of data mining tools will continue to grow. Another critical aspect in enhancing agricultural biosecurity is the development of effective communication tools and protocols that enable researchers and regulators at multiple levels, ranging from individual disease diagnostic labs and field inspectors to state and federal agencies, to share information in a rapid manner, thus facilitating timely decision making and efficient resource allocation.
Although we focus on Phytophthora, the impacts of this project will go beyond a better control of Phytophthora problems; it can also serve as a model for dealing with other pathogen groups of national significance and help researchers and regulators work more closely and make better use of available data for advancing the objective of agricultural biosecurity. This research and development methodology can be applied to any pathogen groups. The informatics platform derived from the project can easily be adapted with minimal modification to establish new global networks against different pathogens. In the long run, the possible applications will reach a wider audience than those interested in plant disease. Information on the diversity and dynamics of plant pests and pathogens affecting human/animal health can be cataloged and analyzed in a similar manner. All the tools and scripts developed in this project will be freely available to others working on projects requiring similar tools.
Agrios GN (2005) Plant Pathology, Ed 5. Academic Press, San Diego
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National Research Council (2003) Countering Agricultural Bioterrorism. The National Academies Press, Washington, D.C.
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Park J, Park B, Veeraraghavan N, Blair JE, Geiser DM, Isard S, Mansfield MA, Nikolaeva E, Park SY, Russo J, Kim SH, Greene M, Ivors KL, Balci Y, Peiman M, Erwin DC, Coffey MD, Jung K, Lee YH, Rossman A, Farr D, Cline E, Grünwald NJ, Luster DG, Schrandt J, Martin F, Ribeiro OK, Makalowska I, Kang S (2008) Phytophthora Database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Dis. 92: 966-972
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