Source: KANSAS STATE UNIV submitted to
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
Funding Source
Reporting Frequency
Accession No.
Grant No.
Project No.
Proposal No.
Multistate No.
Program Code
Project Start Date
Oct 1, 2012
Project End Date
Sep 30, 2017
Grant Year
Project Director
Garrett, K.
Recipient Organization
Performing Department
Plant Pathology
Non Technical Summary
We will provide improved strategies for mitigating pathogen invasions and evaluating future pathogen risk scenarios. And we will develop broader systems analysis approaches to evaluate resilience in linked agricultural disease systems. If we achieve our desired impact, mitigation of invasive pathogens by groups such as USDA APHIS will be more efficient and more likely to be successful; long-term research strategies for plant disease management by groups such as the CGIAR will be more likely to be appropriate for future scenarios; index insurance may be used to more efficiently support plant disease management for resource-poor farmers. Research teams with whom we collaborate will have greater efficiency for collecting and prioritizing information collection and dispersal; information about biofuel grass pathogens will support potential selection of resistant cultivars. End users include scientists, regulatory agencies, conservation biologists, grass-based biofuels developers, agricultural development groups, policy makers, and ultimately crop producers impacted by these groups. We will provide new models for disease ecology that incorporate the new types of microbial community data now available. If we achieve our desired impact, greater understanding of plant-associated microbial communities is likely to support new management strategies, in addition to opening new areas for scientific investigation. End users are primarily scientists in the short run, and ultimately crop producers as new management strategies are developed.
Animal Health Component
Research Effort Categories

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
Goals / Objectives
A. Our first goal is improvement to management of invasive pathogens and to adaptation of disease management under global change. Objectives within this goal are: Analysis of the performance of new mitigation strategies for invasive pathogens in terms of general outcomes and specific performance for test systems such as continental invasions of rusts and the spread of huanglongbing; A new research network for identifying climate change scenario analyses for plant disease and synthesizing the available data sets and parameter estimates; An analysis of the potential for index insurance to support adaptation of disease management to climate variability; A new information value network analysis to support research prioritization related to plant disease management; Analysis of plant disease ecology of tallgrass prairie, including identification of pathogens that may become important in new biofuels systems using switchgrass and/or big bluestem. B. Our second goal is the development of methods for using new types of information about soil microbial communities in disease epidemiology. Objectives within this goal are: Collection and analysis of new microbial community data sets from Kansas, Bolivia, and Zambia; A new conceptual framework to guide analysis of microbial communities in disease ecology. All the results of these research projects will be published in peer-reviewed journals. Activities will include conducting and analyzing experiments, teaching, and mentoring. Events will include meetings to address these topics. Products will include new frameworks for disease forecasting models based on weather and climate; R code for implementing models; scientific papers describing progress toward these goals; datasets with information about soil communities and plant disease epidemics; knowledge and skills for students participating in project; materials for incorporation in KSU teaching.
Project Methods
A.1.The complexity of pathogen invasions and pathogen responses to changing environmental conditions is a challenge for the development of predictive models to support mitigation and formulation of long-term strategies. Current data and models are scattered and often only relevant to specific cases. A stronger framework for forecasting, scenario analysis, and index insurance is needed and these three areas of research can provide important synergies if successfully synthesized. A.2. We have been developing systems for direct estimation of epidemic network parameters using available data sets for rust pathogens and, beginning in 2012, additional pathogen systems such as huanglongbing. Climate change poses another challenge for plant disease management. While climate change effects on drought stress may be relatively straightforward to evaluate, the effects of weather on plant disease risk are typically a function of many more factors. We are working to optimize the use of models for scenario analysis so that they incorporate an appropriate level of complexity. Index insurance is a promising technology which has been applied to mitigate the impacts of weather-based impacts on small farmers. Again, drought is easier to address than plant disease, though some preliminary tests of index insurance for plant disease have been implemented. A.3. For climate change scenario analyses we are rescaling disease forecasting models for application at regional and global scales. We are developing this general approach for other plant diseases, and evaluating the effects of climate variability and weather time series autocorrelation on plant disease risk. For index insurance programs, we are evaluating historical records of plant disease severity and yield loss to plant disease, in combination with expert opinion about disease, in simulations to optimize insurance programs. B.1. New sequencing tools have revolutionized approaches to studying microbial communities, including those associated with plants, but much work remains to figure out how best to use this new form and quantity of data. B.2. Pyrosequencing and newer generation sequencing tools have made whole new types of experiments possible. New conceptual frameworks are needed to evaluate how to use this type of information in important applications such as management strategies to support disease suppressive soils. B.3. We are collecting soils in replicated experiments, including 8 or more subsamples per sample, in two experiments in Kansas, in two experiments in Bolivia, and in one experiment in Zambia. We are evaluating bacterial and fungal communities in these soils using primers developed to facilitate taxonomic categorization. We are modeling the effects of management treatments such as choice of soil amendment on the microbial communities using generalized linear models and multivariate approaches such as nonmetric multidimensional scaling for summarizing community shifts. We are studying approaches to detect and isolate potential biases introduced by the methodologies, to reduce data variability, and to develop biologically meaningful and testable hypotheses.

Progress 01/01/12 to 12/31/12

OUTPUTS: We have completed several projects contributing to system optimization for management of plant pathogens under global change. For example, Garrett et al. (in press) evaluated the effects of climate variability and the color of weather time series on agricultural diseases and pests, and also evaluated the effects of these patterns on the efficacy of decision making for disease management. They also developed a computer program for evaluating the effects of these patterns. Garrett et al. (2012) evaluated the prospects for managing plant health under climate change and proposed new experimental options for designing research spillover from plant genomics to understand the role of microbial communities. Skelsey et al. (in review) have developed a new approach for evaluating climate change impacts in maps of plant disease risk. We have presented in a number of symposia and meetings on these topics. Most recently, Garrett co-organized a meeting for the CGIAR Climate Change, Agriculture and Food Security (CCAFS) program in Lima, Peru, to bring together an international team of scientists to address this topic. We have also engaged four statistics graduate students in projects related to this topic. PARTICIPANTS: These projects engaged students including the following: Xiuqin Bai, graduate student in Statistics Tennery Carrtar, undergraduate student Lorena Gomez-Montano, graduate student in Plant Pathology Girly Ramirez, graduate student in Statistics Bo Tong, graduate student in Statistics Lianqing Zheng, graduate student in Statistics Collaborators in other KSU departments include: Shawn Hutchinson, Geography Ari Jumpponen, Biology Bala Natarajan, ECE Caterina Scoglio, ECE Kim With, Biology Collaborators in other institutions include: Liz Borer, University of Minnesota Jorge Cusicanqui, Bolivia Andy Dobson, University of Oxford, UK Paul Esker, University of Wisconsin Greg Forbes, International Potato Center, China Miguel Angel Gonzales, FAO, Bolivia Bob Holt, University of Florida Scott Isard, Pennsylvania State University Jurgen Kroschel, International Potato Center, Peru Peter Motovalli, University of Missouri Simone Orlandini, University of Florence, Italy Adam Sparks, International Rice Research Institute, Philippines Henri Tonnang, International Potato Center, Peru Corinne Valdivia, University of Missouri Partner organizations include: Ceres Trust CGIAR Climate Change, Agriculture and Food Security program CGIAR Roots Tubers and Bananas program FAO International Food Policy Research Institute International Potato Center, Peru and China International Rice Research Institute Pennsylvania State University University of Florence, Italy University of Florida University of Minnesota University of Missouri University of Oxford University of Wisconsin TARGET AUDIENCES: We developed these projects to support US and international programs in improving plant disease management. We have engaged the international scientific community to increase the impact of the work. We have also provided training to students at KSU in research projects and through teaching a course in Ecology and Epidemiology of Plant Pathogens (PLPTH905). PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

We make it a priority to develop our outputs into publications. The outputs described above are published or in the process of being published. The new insights and models we have been developing have been adapted by CCAFS as part of their program for addressing climate change and plant disease, and we have been awarded research funds from CCAFS for new work in the area.


  • Borer, E. T., J. Antonovics, L. L. Kinkel, P. J. Hudson, P. Daszak, M. J. Ferrari, K. A. Garrett, C. R. Parrish, A. F. Read, and D. M. Rizzo. 2011. Bridging taxonomic and disciplinary divides in infectious disease. EcoHealth 8:261-267 [published 2012].
  • Cox, C. M., W. W. Bockus, R. D. Holt, L. Fang, and K. A. Garrett. 2013. The spatial connectedness of plant species: Potential links for apparent competition via plant diseases. Plant Pathology (in press).
  • Garrett, K. A. 2012. Information networks for plant disease: Commonalities in human management networks and within-host signaling networks. [Invited] European Journal of Plant Pathology 133:75-88.
  • Garrett, K. A., A. Dobson, J. Kroschel, B. Natarajan, S. Orlandini, H. E. Z. Tonnang, and C. Valdivia. 2013. The effects of climate variability and the color of weather time series on agricultural diseases and pests, and decision making for their management. Agricultural and Forest Meteorology (in press).
  • Garrett, K. A., G. A. Forbes, L. Gomez, M. A. Gonzales, M. Gray, P. Skelsey, and A. H. Sparks. 2012. Cambio climatico, enfermedades de las plantas e insectos plaga. In Cambio climatico en los Andes. E. Jimenez, ed. (in press)
  • Garrett, K. A., A. Jumpponen, C. Toomajian, and L. Gomez-Montano. 2012. Climate change and plant health: Designing research spillover from plant genomics for understanding the role of microbial communities. [Invited] Canadian Journal of Plant Pathology 34:349-361.
  • Sutrave, S., C. Scoglio, S. A. Isard, J. M. S. Hutchinson, and K. A. Garrett. 2012. Identifying highly connected counties compensates for resource limitations when evaluating national spread of an invasive pathogen. PLoS ONE 7:e37793.