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Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.

Drought stress is an alarming constraint to plant growth, development, and productivity worldwide. However, plant-associated bacteria, fungi, and viruses can enhance stress resistance and cope with the negative impacts of drought through the induction of various mechanisms, which involve plant biochemical and physiological changes. These mechanisms include osmotic adjustment, antioxidant enzyme enhancement, modification in phytohormonal levels, biofilm production, increased water and nutrient uptake as well as increased gas exchange and water use efficiency. Production of microbial volatile organic compounds (mVOCs) and induction of stress-responsive genes by microbes also play a crucial role in the acquisition of drought tolerance. This review offers a unique exploration of the role of plant-associated microorganisms?plant growth promoting rhizobacteria and mycorrhizae, viruses, and their interactions?in the plant microbiome (or phytobiome) as a whole and their modes of action that mitigate plant drought stress. Made available in DSpace on 2022-03-14T19:00:25Z (GMT). No. of bitstreams: 1 Mendes-Role-plant-associated-2021.pdf: 1525557 bytes, checksum: 34b9473fed0ef5b89fdb89a111478274 (MD5) Previous issue date: 2021

It is well documented that rice paddy fields act as agricultural wetlands that remove or retain nutrients; however, their associated effects on soil microbial communities are rarely reported. The present study evaluates the impact of rice variety on nutrient removal via plant uptake, nutrient retention in the soil, and bacterial associations in rice paddy fields, using a network analysis that compares the soil bacterial communities of two rice varieties. We found that the high-straw rice variety (YD-1) allows uptake of a high amount of nitrogen (N) and phosphorus (P) from paddy rice fields via harvesting, but causes less residual total N and P to remain in the soil. However, both rice varieties (YD-1 and XS-134 (Xiushui-134)) had non-significant effects on the dominant bacterial taxa. The short-term response of bacterial community diversity to rice variety is found to be mainly due to less frequently recovered species. A network analysis that incorporates soil nutrients as nodes, along with bacterial taxa, found that only one node representing the total P related to the non-dominant species had an indirect association with the rice straw biomass. The observed short-term impact of the two rice varieties (XS-134 and YD-1) on soil bacterial diversity and nutrient surplus in these agricultural wetlands is limited under a high level of fertilization.

CONTEXT: Studies in the Andes have demonstrated that seed degeneration of potato occurred in experimental conditions, but was negligible in farmers' conditions. There are two hypotheses for this difference: (1) farmers cultivate resistant varieties, or (2) they use on-farm practices that can manage seed degeneration. Farmers may replace some of the seed saved from their fields with outside seed, but it is an open question what level of benefit farmers experience from partial replacement. OBJECTIVES: The objective of this study was to investigate the role of the cultivated varieties, the on-farm seed management practices, and seed replacement in potato seed degeneration. Moreover, this study evaluated the potential effect of partial replacement of the farmers' seed lot each season with healthy seed, compared to less frequent nearly full replacement, in simulations. METHODS: We surveyed farmers in the Cotopaxi province, Ecuador, in 2008, 2010, and 2018, and performed a study on the incidence of pathogens and pests in farmers' seed lots in 2018. We also evaluated the potential effects of the timing of replacement of farmers' seed lots by healthy seed to manage degeneration, applying the seedHealth model. RESULTS AND CONCLUSIONS: We found that farmers experience no or only slow degeneration in their varieties. Analysing yield data reported by farmers to detect degeneration, we did not detect yield declines. The type of variety and year of data collection explained the variation in yield. These results seem to confirm the hypothesis that varieties cultivated in the Andes are resistant to the impact of seed degeneration on yield, and that seed degeneration depends on the agroecological conditions present within a cropping season or year. Because we did not find an impact on yield, we hypothesized that on-farm practices affect seed-borne pathogens and pests causing seed degeneration. We identified multiple on-farm practices playing a role in the process of seed degeneration: they either slowed down or accelerated this process depending on the seed-borne pathogen and pest causing seed degeneration. Our scenario analyses using the seedHealth model showed how replacing farmers' seed lots by healthy seed could usefully reduce seed degeneration compared to using the same amount of seed to periodically replace nearly all seed in a season. Our results showed that on-farm practices are also critical drivers in the process of seed degeneration. SIGNIFICANCE: This study demonstrated the importance of considering on-farm seed management practices (i.e., use of cultivated varieties) to strengthen seed systems interventions aiming to manage potato seed degeneration. Additionally, this study showed the potential of partially replacing farmers' seed with healthy seed as an alternative when complete seed replacement is not an option.

Climate change represents an unprecedented challenge to the world?s biosphere and to the global community. It also represents a unique challenge for plant health. Human activities and increased market globalization, coupled with rising temperatures, has led to a situation that is favourable to pest movement and establishment. This scientific review assesses the potential effects of climate change on plant pests and consequently on plant health. The evidence assessed strongly indicates that climate change has already expanded some pests? host range and geographical distribution, and may further increase the risk of pest introduction to new areas. This calls for international cooperation and development of harmonized plant protection strategies to help countries successfully adapt their pest risk management measures to climate change.

Seedborne pathogens and pests limit production in many agricultural systems. Quarantine programs help prevent the introduction of exotic pathogens into a country, but few regulations directly apply to reducing the reintroduction and spread of endemic pathogens. Use of phytosanitary thresholds helps limit the movement of pathogen inoculum through seed, but the costs associated with rejected seed lots can be prohibitive for voluntary implementation of phytosanitary thresholds. In this paper, we outline a framework to optimize thresholds for seedborne pathogens, balancing the cost of rejected seed lots and benefit of reduced inoculum levels. The method requires relatively small amounts of data, and the accuracy and robustness of the analysis improves over time as data accumulate from seed testing. We demonstrate the method first and illustrate it with a case study of seedborne oospores of Peronospora effusa, the causal agent of spinach downy mildew. A seed lot threshold of 0.23 oospores per seed could reduce the overall number of oospores entering the production system by 90% while removing 8% of seed lots destined for distribution. Alternative mitigation strategies may result in lower economic losses to seed producers, but have uncertain efficacy. We discuss future challenges and prospects for implementing this approach.

Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Tallgrass prairie species have evolved with regular exposure to fire. However, burning has been used as a management tool for reducing plant disease in agricultural systems, posing the question of how plant pathogens of tallgrass prairie would be affected by burning. The rust fungus Puccinia dioicae, infecting Erigeron strigosus (Asteraceae), was studied for 8 years in long-term experiments to evaluate the effects of burning in native tallgrass prairie. This experiment also allowed evaluation of the effects of nutrient additions, although E. strigosus was rare in the plots with added nutrients in most years. Burning reduced rust severity in most years, but effects from additions of nutrients were rarely observed. There was high interannual variation in rust severity within a location, suggesting that weather may be the most important of these three abiotic factors in determining infection. An analysis of weather variables associated with disease severity found that solar radiation in the month prior to sampling was associated with severity in unburned plots; temperature approximately 2 months prior to sampling was also associated with severity in burned plots. High interannual variation also suggests that the effects of this pathogen on its host would be sporadic and difficult to study in short-term experiments.

The grasses Sorghastrum nutans (Indian grass), Schizachyrium scoparium (little bluestem), Panicum virgatum (switchgrass), and Andropogon gerardii (big bluestem) are four of the most common plant species present in a tallgrass prairie (1). Infection with barley yellow dwarf virus (BYDV, family Luteoviridae) is of interest in these species because of the potential effects of the virus on tallgrass prairie plant communities and the potential for tallgrass prairie to function as a reservoir of the virus for infection in wheat or barley fields. In a previous inoculation experiment, an unidentified strain of BYDV transmitted by the aphid species Rhopalosiphum padi was reported to infect S. scoparium but none of the other three grass species (2). We sampled for the presence of five virus strains in at least 50 blooming plants of each grass species in a natural tallgrass prairie stand in August 2000. Samples were collected in watersheds that were designated 1B, 1D, K1A, 20B, and 20C at Konza Prairie Biological Station in the Flint Hills near Manhattan, KS. To detect the virus, we used enzyme-linked immunosorbent assay (ELISA) with antibodies purchased from Agdia (Elkhart, IN). For the PAV, MAV, RMV, and SGV strains, we used double-antibody sandwich ELISA with alkaline phosphatase label. For Cereal yellow dwarf virus (RPV), we used compound direct ELISA with alkaline phosphatase label. The scoring of ELISA results was based on comparison with infected and uninfected control plants of the same species. Symptoms of infection in the field were difficult to interpret visually, since plants in this natural environment often showed multiple symptoms of stress. None of the five strains were detected in 51 individuals of S. nutans. For 50 individuals of S. scoparium, the incidence of infection by the different strains was 4% for MAV, 0% for PAV, 2% for RMV, 0% for RPV, and 58% for SGV. For 51 individuals of P. virgatum, the incidence of infection was 31% for MAV, 0% for PAV, 0% for RMV, 0% for RPV, and 4% for SGV. For 64 individuals of A. gerardii, the incidence of infection was 59% for MAV, 0% for PAV, 0% for RMV, 0% for RPV, and 3% for SGV. The impact of BYDV on these tallgrass prairie species remains to be determined. The PAV strain is the most commonly reported strain in wheat in Kansas but was not recovered from these grass species. References: (1) C. C. Freeman. The flora of Konza Prairie: A historical review and contemporary patterns. Pages 69–80 in: Grassland Dynamics. A. K. Knapp et al., eds. Oxford, 1998. (2) W. N. Stoner. Plant Dis. Rep. 60:593, 1976.

Climate change has a number of observed, anticipated, or possible consequences on crop health worldwide. Global change, on the other hand, incorporates a number of drivers of change, including global population increase, natural resource evolution, and supply–demand shifts in markets, from local to global. Global and climate changes interact in their effects on global ecosystems. Identifying and quantifying the impacts of global and climate changes on plant diseases is complex. A number of nonlinear relationships, such as the injury (epidemic)–damage (crop loss) relationship, are superimposed on the interplay among the three summits of the disease triangle (host, pathogen, environment). Work on a range of pathosystems involving rice, peanut, wheat, and coffee has shown the direct linkage and feedback between production situations and crop health. Global and climate changes influence the effects of system components on crop health. The combined effects of global and climate changes on diseases vary from one pathosystem to another within the tetrahedron framework (humans, pathogens, crops, environment) where human beings, from individual farmers to consumers to entire societies, interact with hosts, pathogens, and the environment. This article highlights international phytopathological research addressing the effects of global and climate changes on plant diseases in a range of crops and pathosystems.

Virus-related degeneration constrains production of quality sweet potato seed, especially under open field conditions. Once in the open, virus-indexed seed is prone to virus infection leading to decline in performance. Insect-proof net tunnels have been proven to reduce virus infection under researcher management. However, their effectiveness under farmer-multiplier management is not known. This study investigated the ability of net tunnels to reduce degeneration in sweet potato under farmer-multiplier management. Infection and degeneration were assessed for two cultivars, Kabode and Polista, grown in net tunnels and open fields at two sites with varying virus pressures. There was zero virus incidence at both sites during the first five generations. Sweet potato feathery mottle virus and sweet potato chlorotic stunt virus were present in the last three generations, occurring singly or in combination to form sweet potato virus disease. Virus infection increased successively, with higher incidences recorded at the high virus pressure site. Seed degeneration modelling illustrated that for both varieties, degeneration was reduced by the maintenance of vines under net tunnel conditions. The time series of likely degeneration based on a generic model of yield loss suggested that, under the conditions experienced during the experimental period, infection and losses within the net tunnels would be limited. By comparison, in the open field most of the yield could be lost after a small number of generations without the input of seed with lower disease incidence. Adopting the technology at the farmer-multiplier level can increase availability of clean seed, particularly in high virus pressure areas.

Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. “General network analysis” identifies candidate taxa for maintaining an existing microbial community. “Host-focused analysis” includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. “Pathogen-focused analysis” identifies taxa with direct or indirect associations with taxa known a priori as pathogens. “Disease-focused analysis” identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.

Plantain and banana, both Musa spp. hybrids, constitute a major component of domestic food production in Haiti. In response to grower reports (Faculty of Agronomy and Veterinary Medicine, Port-au-Prince, personal communication) of up to 60% incidence of “toppling disease”, we conducted a preliminary study in July 2018 at four plantain farms in Arcahaie, Haiti. Symptoms observed on up to 30% of plants (n = ∼100) included a brown necrotic soft rot lesion on pseudostems extending up to 1 m in length and several centimeters deep. Toppling occurred at fruit onset, with plants folding over at the point of the soft rot. Six plants representing the four farms were sampled: 6-cm² sections were excised from the lesion edge, surface sterilized with 0.6% sodium hypochlorite, rinsed, and macerated with sterile tap water, and then the suspension was streaked onto nutrient agar (NA) and Miller-Schroth medium agar (MSM) plates, yielding six bacterial isolates. Colonies were round, glossy, convex, translucent gray-white on NA, produced a transient red-orange color change on MSM, and were aerobic, gram-negative, oxidase-negative and hypersensitive response negative on ‘Bonnie Best’ tomato and ‘Hicks’ tobacco (Schaad et al. 2001); all the above tests were repeated twice. All six isolates were identical in initial 16S rDNA sequencing, so pathogenicity of two randomly chosen isolates (G18-1365 and G18-1376) was tested on disease‐free ‘Dwarf Cavendish’ banana plantlets by drilling a 2.5-cm hole into the pseudostem, inserting sterile cotton-tipped swabs drawn through 48-h cultures on NA (negative control was dipped in sterile water) into the drilled incision, and sealing with Parafilm. Each plant was wounded once, with five plants per isolate or control. Rotting symptoms consistent with the field observations were observed 4 weeks after inoculation for all isolate inoculations; control plants remained symptomless. Reisolation and identification to fulfill Koch’s postulates were completed with results identical to the first isolations and tests. Genomic DNA was boil-extracted as previously described (Dashti et al. 2009) from the two isolates grown 24 h on NA. The amplification and sequencing of 16S rDNA, rpoB, phoE, and infB gene targets were carried out using primers and protocols previously described (Rosenblueth et al. 2004). One sequence for each isolate’s gene target (eight total) was deposited in NCBI GenBank (accessions MK217521 to MK217522; MK235993 to MK235998). In BLAST searches, sequence fragments of 16S rDNA, rpoB, phoE, and infB from isolates G18-1365 and G18-1376 resulted in 99% identity with Klebsiella variicola strains. Multilocus sequence analysis (MEGA X, Kumar et al. 2018) of those sequences yielded a concatenated phylogenetic tree that placed both isolates within the K. variicola clade. Isolates G18-1365 and G18-1376 have been deposited at the BCCM, Ghent University (accessions LMG 31122 and LMG 31123, respectively). K. variicola has been reported to cause similar bacterial rots in banana and carrot (Chandrashekar et al. 2018; Fan et al. 2016). Before management can be prescribed, further studies are necessary to determine disease incidence and if this species is the sole cause of toppling or is part of a larger disease complex, and to understand the mode of transmission within and among plantain farms. Additionally, similarity to human pathogenic strains should be studied to determine if there is a human health risk posed by K. variicola isolates causing soft rot in plantain.

This article addresses the modelling of crop health and its impact on crop losses, with a special emphasis on plant diseases. Plant disease epidemiological models have many different shapes. We propose a summary of modelling structures for plant disease epidemics, which stem from the concepts of infection rate, of site, of basic infection rate corrected for removals (Rc), and of basic reproductive number (R0). Crop losses, the quantitative and qualitative impacts of diseases and pests on crop performances, can be expressed along many different dimensions. We focus on yield loss, defined as the difference between the attainable yield and the actual yield, in a production situation. The modelling of yield loss stems from the concept of damage mechanism, which can be applied to the wide range of organisms (including pathogens, weeds, arthropods, or nematodes) that may negatively affect crop growth and performances. Damage mechanisms are incorporated in crop growth models to simulate yield losses. In both fields, epidemiology and crop loss, we discuss the process of model development, including model simplification. We emphasize model simplification as a main avenue towards model genericity. This is especially relevant to enable addressing the diversity of crop pathogens and pests. We also discuss the usefulness of considering differing evaluation criteria depending on the stage of model development, and thus, depending on modelling objectives. We illustrate progress made on two global key crops where model simplification has been critical; rice and wheat. Modelling pests and diseases, and of the yield losses they cause on these two crops, lead us to propose the concept of crop health syndrome as a set of injury functions, each representing the dynamics of an injury (such as, for example, the time-course of an epidemic). Crop health in a given context can be represented by the set of such injury functions, which in turn can be used as drivers for crop loss models.

Wheat is at peak quality soon after harvest. Subsequently, diverse biota use wheat as a resource in storage, including insects and mycotoxin-producing fungi. Transportation networks for stored grain are crucial to food security and provide a model system for an analysis of the population structure, evolution, and dispersal of biota in networks. We evaluated the structure of rail networks for grain transport in the United States and Eastern Australia to identify the shortest paths for the anthropogenic dispersal of pests and mycotoxins, as well as the major sources, sinks, and bridges for movement. We found important differences in the risk profile in these two countries and identified priority control points for sampling, detection, and management. An understanding of these key locations and roles within the network is a new type of basic research result in postharvest science and will provide insights for the integrated pest management of high-risk subpopulations, such as pesticide-resistant insect pests.

Maize lethal necrosis (MLN) has emerged as a serious threat to food security in sub-Saharan Africa. MLN is caused by coinfection with two viruses, Maize chlorotic mottle virus and a potyvirus, often Sugarcane mosaic virus. To better understand the dynamics of MLN and to provide insight into disease management, we modeled the spread of the viruses causing MLN within and between growing seasons. The model allows for transmission via vectors, soil, and seed, as well as exogenous sources of infection. Following model parameterization, we predict how management affects disease prevalence and crop performance over multiple seasons. Resource-rich farmers with large holdings can achieve good control by combining clean seed and insect control. However, crop rotation is often required to effect full control. Resource-poor farmers with smaller holdings must rely on rotation and roguing, and achieve more limited control. For both types of farmer, unless management is synchronized over large areas, exogenous sources of infection can thwart control. As well as providing practical guidance, our modeling framework is potentially informative for other cropping systems in which coinfection has devastating effects. Our work also emphasizes how mathematical modeling can inform management of an emerging disease even when epidemiological information remains scanty. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Pathogen buildup in vegetative planting material, termed seed degeneration, is a major problem in many low-income countries. When smallholder farmers use seed produced on-farm or acquired outside certified programs, it is often infected. We introduce a risk assessment framework for seed degeneration, evaluating the relative performance of individual and combined components of an integrated seed health strategy. The frequency distribution of management performance outcomes was evaluated for models incorporating biological and environmental heterogeneity, with the following results. (1) On-farm seed selection can perform as well as certified seed, if the rate of success in selecting healthy plants for seed production is high; (2) when choosing among within-season management strategies, external inoculum can determine the relative usefulness of ‘incidence-altering management’ (affecting the proportion of diseased plants/seeds) and ‘rate-altering management’ (affecting the rate of disease transmission in the field); (3) under severe disease scenarios, where it is difficult to implement management components at high levels of effectiveness, combining management components can be synergistic and keep seed degeneration below a threshold; (4) combining management components can also close the yield gap between average and worst-case scenarios. We also illustrate the potential for expert elicitation to provide parameter estimates when empirical data are unavailable. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The structure of seed systems has important implications for how likely they are to effectively supply high quality seed to communities of farmers. We evaluated seed system networks defined by a regional potato farmer consortium (CONPAPA) in Tungurahua, Ecuador. Networks were structured around farmer seed and potato transactions and their sources of information about pest and disease management. We performed a scenario analysis of disease spread that takes into account interacting biophysical, socioeconomic and informational elements. CONPAPA provides training, seed improvement and potato processing and marketing for its members. The high centrality of CONPAPA in the network means that disease management interventions, such as training, monitoring and variety dissemination should target CONPAPA staff and processing facilities. The market in Ambato, the largest nearby town, was the next most useful place to monitor. Farmers reported receiving advice about disease and pest management through trusted CONPAPA technical staff. Local agricultural stores were also reported as providing advice to many farmers, but were viewed by farmers as significantly less reliable. Training of store owners could provide one way to improve outcomes in this seed system. Farmer access to information (number and quality of sources) was equal for both genders. Female farmers had a smaller than expected amount of the market share, however. In CONPAPA there is 47% adoption of improved seed, much higher than the 2% rate reported for Ecuador in general. This is probably improving yields significantly for small farmers in the consortium. Agricultural seed systems and network analyses provide one window into a variety of global change phenomena encompassing environmental and societal concerns.

Seed systems are critical for deployment of improved varieties, and serve as major conduits for the spread of seed-borne pathogens. Vegetatively propagated crops in low-income countries are particularly vulnerable to seed degeneration, where yield is lowered through successive cycles of propagation because of pathogen accumulation. We evaluated the structure of an informal sweetpotato seed system for its vulnerability to the spread of epidemics, and its utility for disseminating improved varieties. During the 2014 growing season (April-Oct), vine sellers were surveyed weekly in the Gulu Region of Northern Uganda. Our analysis draws on tools from network theory to evaluate the potential for epidemic spread in this region. Utilizing empirical 2014 seed transaction data and estimated spatial spread, we constructed a seed transaction network, which was used to simulate the introduction of a pathogen, and evaluated the influence of both epidemic starting point and quarantine treatments on epidemic progress. Results indicate that the starting position in the network is critical for epidemic progress and final epidemic outcomes. Quarantine of 30 villages lowered epidemic progress up to 65.7%, when compared to the control (no quarantine), over 20 timesteps in 500 realizations. The percent control conferred by quarantine treatments was also influenced by the epidemic starting point. Considering equal likelihood of any node being an introduction point for a new epidemic, villages of particular utility for disease monitoring were also identified. Sensitivity analysis identified important parameters and priorities for future data collection. We compared the utility of node degree, betweenness, closeness, and eigenvector centrality for selecting quarantine locations, finding that betweenness had more limited utility. This analysis pipeline can be applied to provide recommendations for a wide variety of seed systems.

Pathogen build-up in vegetative planting material, termed seed degeneration, is a major problem in many low-income countries. When smallholder farmers use seed produced on-farm or acquired outside certified programs, it is often infected. We introduce a risk assessment framework for seed degeneration, evaluating the relative performance of individual and combined components of an integrated seed health strategy. The frequency distribution of management performance outcomes was evaluated for models incorporating biological and environmental heterogeneity, with the following results. (1) On-farm seed selection can perform as well as certified seed, if the rate of success in selecting healthy plants for seed production is high; (2) When choosing among within-season management strategies, external inoculum can determine the relative usefulness of ‘incidence-altering management’ (affecting the proportion of diseased plants/seeds) and rate-altering management (affecting the rate of disease transmission in the field); (3) Under severe disease scenarios, where it is difficult to implement management components at high levels of effectiveness, combining management components can produce synergistic benefits and keep seed degeneration below a threshold; (4) Combining management components can also close the yield gap between average and worst-case scenarios. We also illustrate the potential for expert elicitation to provide parameter estimates when data are unavailable.

The literature on the importance of plant pathogens sometimes emphasizes their possible role in historical foodshortages and even in famines. Aside from such major crises, plant pathogens should also be seen as important reducers of crop performances, with impacts on system sustainability, from the ecological, agronomical, social, and economic standpoints – all contributing ultimately to affecting food security. These views need reconciliation in order to produce a clearer picture of the multidimensional effects of plant disease epidemics. Such a picture is needed for disease management today, but would also be useful for future policies. This article attempts to develop a framework that would enable assessment of the impacts of plant diseases, referred collectively to as crop health, on food security via its components. We have combined three different existing definitions of food security in order to develop a framework consisting of the following six components: (1) Availability. Primary production; (2) Availability. Import - Stockpiles; (3) Access. Physical and supply chain; (4) Access. Economic; (5) Stability of food availability; (6) Utility-Safety-Quality- Nutritive value. In this framework, components of food security are combined with three attributes of production situations: the nature of the considered crop (i.e. food- or non- food), the structure of farms (i.e. subsistence or commercial), and the structure of markets (i.e. weakly organized and local, to strongly organized and globalized). The resulting matrix: [Food security components] × [Attributes of production situations] provides a framework where the impacts of chronic, acute, and emerging plant disease epidemics on food security can be examined. We propose that, given the number of components and interactions at play, a systems modelling approach is required to address the functioning of food systems exposed to plant disease risks. This approach would have application in both the management of the current attrition of crop performances by plant diseases, and also of possible disease-induced shocks. Such an approach would also enable quantifying shifts in disease vulnerability of production situations, and therefore, of food systems, as a result of climate change, globalization, and evolving crop health.

As a result of human activities, an ever-increasing portion of Earth’s natural landscapes now lie adjacent to agricultural lands. This border between wild and agricultural communities represents an agro-ecological interface, which may be populated with crop plants, weeds of crop systems, and non-crop plants that vary from exotic to native in origin. Plant viruses are important components of the agro-ecological interface because of their ubiquity, dispersal by arthropod vectors, and ability to colonize both crop and wild species. Here we provide an overview of research on plant-virus dynamics across this interface and suggest three research priorities: (1) an increased effort to identify and describe plant virus diversity and distribution in its entirety across agricultural and ecological boundaries; (2) multi-scale studies of virus transmission to develop predictive power in estimating virus propagation across landscapes; and (3) quantitative evaluation of the influence of viruses on plant fitness and populations in environmental contexts beyond crop fields. We close by emphasizing that agro-ecological interfaces are dynamic, influenced by the human-mediated redistribution of plants, vectors, and viruses around the world, climate change, and the development of new crops. Consideration of virus interactions within these environmentally complex systems promises new insight into virus, plant, and vector dynamics from molecular mechanisms to ecological consequences.

This study evaluated the reactions of seven common C4 grasses of the tallgrass prairie of the USA Great Plains to the economically important wheat pathogens Pyrenophora tritici-repentis and Gaeumannomyces graminis var. tritici (Ggt) isolated from wheat. The P. tritici-repentis isolates (race 1) were pathogenic on all grasses tested, but symptom severity was markedly low. Three of the grass species inoculated with Ggt were highly susceptible, while four species exhibited no symptoms. Because measures of connectedness can provide a proxy for population processes, connectedness was evaluated within and among the seven grass species in representative tallgrass prairie environments for all potential pathogen-sharing patterns. Andropogon gerardii was ubiquitous, so all plant species were well connected to it. Andropogon scoparius (= Schizachyrium scoparium), Sorghastrum nutans and Panicum virgatum were fairly common but specialized to particular environments. Bouteloua curtipendula was uncommon but occurred in all environments, while Buchlo€e dactyloides and Bouteloua gracilis were uncommon and only occurred in upland sites. Co-occurrence of plant species was generally not reciprocal in that, for many species pairs, species A rarely occurred without potential exposure to inoculum from species B, while species B commonly occurred without species A. The three grass species susceptible to Ggt may act as sources of inoculum for each other within tallgrass prairie, with the potential to influence fitness, and tallgrass prairie and commercial wheat ecosystems in the Great Plains also have the potential to share both pathogens.

The response of plant disease to weather variables such as temperature and precipitation is well known, and has been the basis for disease forecasting models used in decision-making by farmers and policy makers. Thus, plant disease risk can readily shift under climate change. Predicting changes in risk under climate change is complicated by the many biological interactions that result in disease. For example, some plant diseases occur when the phenology of plant and pathogen are aligned, in the case of Fusarium head blight so that spores are ready to infect during wheat flowering. There are numerous examples of experiments involving simulated climate change that have shown changes in disease risk. Finding indicators of climate change effects on disease in real agricultural or natural systems is more challenging because of the correlative nature of the observations and the potential for many other factors to influence disease, such as changes in host abundance. Assessments of global disease databases suggest some pathogen range shifts consistent with predicted outcomes for climate change. There are also several cases of emerging tree diseases in which climate change has likely played a role.

Seed potato degeneration, the reduction in yield or quality caused by an accumulation of pathogens and pests in planting material due to successive cycles of vegetative propagation, has been a long-standing production challenge for potato growers around the world. In developed countries this problem has been overcome by general access to and frequent use of seed, produced by specialized growers, that has been certified to have pathogen and pest incidence below established thresholds, often referred to as certified seed. The success of certified seed in developed countries has concentrated the research and development agenda on the establishment of similar systems in developing countries. Despite these efforts, certified seed has had little penetration into the informal seed systems currently in place in most developing countries. Small-scale farmers in these countries continue to plant seed tubers acquired through the informal seed system, i.e. produced on-farm or acquired from neighbours or local markets. Informal seed tubers frequently have poor health status, leading to significant reductions in yield and/or market value. This review emphasizes the need to refocus management efforts in developing countries on improving the health status of seed tubers in the informal system by integrating disease resistance and on-farm management tools with strategic seed replacement. This ‘integrated seed health strategy’ can also prolong the good health status of plants derived from certified seed, which would otherwise be diminished due to potential rapid infection from neighbouring fields. Knowledge gaps, development challenges and impacts of this integrated seed health strategy are discussed.

Network models of human epidemics can often be improved by including the effects of behaviour modification in response to information about the approach of epidemics. Similarly, there are opportunities to incorporate the flow of information and its effects in plant disease epidemics in network models at multiple scales. (1) In the case of human management networks for plant disease, each node of a network has four main components: plant communities, microbial communities, human information (among researchers, extension agents, farmers, and other stakeholders), and environmental conditions, along with their interactions. The links between nodes, representing the rate of movement between them, have three parts: the rates for plant materials, the rates for microbes, and the rates for information. Network resilience for information flow is an important goal for such systems. Game theory can provide insights into how human agents decide how to invest their efforts in strengthening information networks, and how policies can support more resilient networks. (2) For the case of within-plant signalling networks, each node has a comparable set of four main components: plant signals (often in the form of phytohormones) and development status, microbial communities and plant disease status, microbial signals (often in the form of quorum sensing molecules), and micro-environmental conditions, along with their interactions. In effect, human information is replaced by plant signals and microbial signals in this second model. The links between nodes have three parts: the rates for microbes, the rates for microbial signals (which may move separately from the microbes, themselves), and the rates for plant signals. Understanding how to enhance adaptive plant signalling networks and microbial signalling networks that support plant productivity, and disrupt microbial signalling networks that contribute to pathogenicity, will be an important step for improved disease management.

The impacts of climate change on ecosystem services are complex in the sense that effective prediction requires consideration of a wide range of factors. Useful analysis of climate-change impacts on crops and native plant systems will often require consideration of the wide array of other biota that interact with plants, including plant diseases, animal herbivores, and weeds. We present a framework for analysis of complexity in climate-change effects mediated by plant disease. This framework can support evaluation of the level of model complexity likely to be required for analysing climate-change impacts mediated by disease. Our analysis incorporates consideration of the following set of questions for a particular host, pathogen, host–pathogen combination, or geographic region. 1. Are multiple biological interactions important? 2. Are there environmental thresholds for population responses? 3. Are there indirect effects of global change factors on disease development? 4. Are spatial components of epidemic processes affected by climate? 5. Are there feedback loops for management? 6. Are networks for intervention technologies slower than epidemic networks? 7. Are there effects of plant disease on multiple ecosystem services? 8. Are there feedback loops from plant disease to climate change? Evaluation of these questions will help in gauging system complexity, as illustrated for fusarium head blight and potato late blight. In practice, it may be necessary to expand models to include more components, identify those components that are the most important, and synthesize such models to include the optimal level of complexity for planning and research prioritization.

Pyrosequencing was used to study the effect of rotation and tillage on total bacterial communities. We designed primers to the bacterial 16s rDNA and amplified DNA from soil samples from a long-term tillage/rotation trial in Kansas for two seasons. The 2 × 2 factorial trial had two rotation treatments (wheat–wheat and wheat–soybean) and two tillage treatments (conventional and no-till). A total of 20,180 16s rDNA sequences were generated and 2337 operational taxonomic units (OTUs) were assembled using a 97% similarity cut-off. The phylum Proteobacteria represented 38% of 299 identified taxa. The second most abundant phylum was Acidobacteria, making up 20% of the sequences, the majority of which were Acidobacteria Group 1. The phyla Actinobacteria and Gemmatimonadetes comprised 12% and 3.5% of the sequences. Other groups detected included TM7, Nitrospira, Verrucomicrobia, and Bacteroidetes. Some clusters of Acidobacteria Group 1 were more frequent in continuous wheat versus wheat–soybean rotation, some Acidobacteria Group 2 were more frequent in no-till, and some Acidobacteria Group 4 were more frequent in wheat–soybean rotation. These results were validated by quantitative real-time PCR. Pyrosequencing provided taxonomic information about the overall bacterial community, and detected community shifts resulting from different cropping practices.

Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina, a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58% among isolates in the tallgrass prairie, 71% in the maize fields, 75% in the sorghum fields and 80% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate 'hybrids' with novel genetic profiles and pathogenic capabilities.

Cheatham, M. R., Rouse, M. N., Esker, P. D., Ignacio, S., Pradel, W., Raymundo, R., Sparks, A. H., Forbes, G. A., Gordon, T. R., and Garrett, K. A. 2009. Beyond yield: Plant disease in the context of ecosystem services. Phytopathology 99:1228-1236. The ecosystem services concept provides a means to define successful disease management more broadly, beyond short-term crop yield evaluations. Plant disease can affect ecosystem services directly, such as through removal of plants providing services, or indirectly through the effects of disease management activities, including pesticide applications, tillage, and other methods of plant removal. Increased plant biodiversity may reduce disease risk if susceptible host tissue becomes less common, or may increase risk if additional plant species are important in completing pathogen life cycles. Arthropod and microbial biodiversity may play similar roles. Distant ecosystems may provide a disservice as the setting for the evolution of pathogens that later invade a focal ecosystem, where plants have not evolved defenses. Conversely, distant ecosystems may provide a service as sources of genetic resources of great value to agriculture, including disease resistance genes. Good policies are needed to support conservation and optimal use of genetic resources, protect ecosystems from exotic pathogens, and limit the homogeneity of agricultural systems. Research is needed to provide policy makers, farmers, and consumers with the information required for evaluating trade-offs in the pursuit of the full range of ecosystem services desired from managed and native ecosystems.

More than two-thirds of cropland in the United States is devoted to the production of just four crop species—maize, wheat, soybeans, and cotton— raising concerns that homogenization of the American agricultural landscape could facilitate widespread disease and pest outbreaks, compromising the national food supply. As a new component in national agricultural risk assessment, we employed a graph-theoretic approach to examine the connectivity of these crops across the United States. We used county crop acreage to evaluate the landscape resistance to transmission—the degree to which host availability limits spread in any given region—for pests or pathogens dependent on each crop. For organisms that can disperse under conditions of lower host availability, maize and soybean are highly connected at a national scale, compared with the more discrete regions of wheat and cotton production. Determining the scales at which connectivity becomes disrupted for organisms with different dispersal abilities may help target rapid-response regions and the development of strategic policies to enhance agricultural landscape heterogeneity.

We surveyed the prevalence and amount of leaf damage related to herbivory and pathogens on 12 pairs of exotic (invasive and noninvasive) and ecologically similar native plant species in tallgrass prairie to examine whether patterns of damage match predictions from the enemy release hypothesis. We also assessed whether natural enemy impacts differed in response to key environmental factors in tallgrass prairie by surveying the prevalence of rust on the dominant C4 grass, Andropogon gerardii, and its congeneric invasive exotic C4 grass, A. bladhii, in response to fire and nitrogen fertilization treatments. Overall, we found that the native species sustain 56.4% more overall leaf damage and 83.6% more herbivore-related leaf damage when compared to the exotic species. Moreover, we found that the invasive exotic species sustained less damage from enemies relative to their corresponding native species than the noninvasive exotic species. Finally, we found that burning and nitrogen fertilization both significantly increased the prevalence of rust fungi in the native grass, while rust fungi rarely occurred on the exotic grass. These results indicate that reduced damage from enemies may in part explain the successful naturalization of exotic species and the spread of invasive exotic species in tallgrass prairie.

Bockus, W. W., Su, Z., Garrett, K. A., Gill, B. S., Stack, J. P., Fritz, A. K., Roozeboom, K. L., and Martin, T. J. 2007. Number of experiments needed to determine wheat disease phenotypes for four wheat diseases. Plant Dis. 91:103-108. Disease phenotypes for winter wheat cultivars were determined in numerous inoculated greenhouse and field experiments over many years. For four diseases, Fusarium head blight, tan spot, Septoria leaf blotch, and Stagonospora leaf blotch, at least 20 cultivars each had been evaluated in a minimum of five experiments. Reference cultivars of known disease reaction were included in each experiment, which allowed transformation of the percent disease severity data to a 1-to-9 scale for comparisons between experiments. Variations in scale values obtained for individual cultivars among the different experiments were used to calculate standard deviations for disease phenotype data. Standard deviations were used to calculate the number of experiment repetitions needed within each disease to achieve different levels of accuracy (margins of error). A margin of error of ±1.5 for the 1-to-9 scale was chosen as the best level of accuracy. Rounding values within this range would put the estimated disease phenotype within ±1 unit of the actual phenotype. To achieve a margin of error of ±1.5 for Fusarium head blight, tan spot, Septoria leaf blotch, and Stagonospora leaf blotch would require a mean that was calculated from a minimum of five, five, seven, and eight experiments, respectively. Personnel who report disease phenotype data to wheat producers or breeders should be aware of the number of experiments upon which they are basing their reports and adjust any disclaimers accordingly. Similarly, wheat breeders should be aware of the inherent variability in phenotyping these four wheat diseases and make appropriate adjustments to their selection protocols. With a minimum of five experimental repetitions, disease phenotype values obtained from inoculated greenhouse and field experiments had very high correlations (r = 0.81 to 0.92, P < 0.0001) with published Kansas State University Research and Extension ratings obtained from commercial fields. Additional keywords: Fusarium graminearum, Septoria tritici

Jiang, W., Garrett, K. A., Peterson, D. E., Harvey, T. L., Bowden, R. L., and Fang, L. 2005. The window of risk for emigration of Wheat streak mosaic virus varies with host eradication method. Plant Dis. 89:853-858. The wheat curl mite (WCM), Aceria tosichella, the vector of Wheat streak mosaic virus (WSMV), often survives the summer on volunteer wheat (Triticum aestivum) and may disperse from this “green bridge” in fall to newly planted winter wheat. Because some methods for managing volunteer wheat do not directly kill WCM, there is a window of risk for WCM and WSMV emigration after management has been applied. WCM survival in response to treatment of wheat by glyphosate, paraquat, stem cutting, and withholding water was measured in greenhouse experiments to determine how this window of risk for emigration varies with management. WCM populations on plants treated with paraquat or stem cutting decreased from the beginning of the sampling period. WCM populations on plants treated with glyphosate or that received no water increased up to 3 days after application and then decreased by 10 days after application. If glyphosate is used to manage volunteer wheat infested with WCM, it should be applied well before wheat is planted in fall. WCM in declining populations tended to be in an upright posture that could facilitate emigration via wind. The total green leaf area was strongly correlated with the number of WCM for treated plants and could be used in the field to predict the posttreatment survival of mites that pose a risk of emigration.

Perennial grain production will likely present unique challenges for managing diseases that affect the productivity and longevity of crops being considered. Typical cultural practices effective at reducing soil- and residue-borne pathogens, such as annual crop rotations, delayed fall planting, and tillage, are not feasible in perennial systems. Consequently, soil- and residue-borne pathogens, and pathogens such as root colonizers and viruses that survive in live tissue, may increase in importance in a perennial grain crop. Resistance genes will undeniably be important defenses against disease. However, it is seldom, if ever, possible to incorporate within a single cultivar resistance to all existing and future important diseases. Furthermore, genes vulnerable to ‘boom and bust’ cycles are generally short-lived when deployed in monocultures. For these reasons, the use of mixtures of crop cultivars or species that vary in resistance functions will likely be an important strategy for managing diseases and pests of perennial grains. Burning of plant residue, a natural phenomenon in native perennial grass systems, may also be an effective disease management strategy. The successful implementation of these management tools may reduce or eliminate the risk that perennial grain crops will become pathogen refugia that affect neighboring annual plantings and the productivity of perennial plants.

Pests and diseases reduce agricultural yields and are an important wildcard in the evaluation of future climate impacts. A unique global record of pests and diseases provides evidence for poleward expansions of their distributions.

Cox, C. M., Garrett, K. A., Bowden, R. L., Fritz, A. K., Dendy, S. P., and Heer, W. F. 2004. Cultivar mixtures for the simultaneous management of multiple diseases: Tan spot and leaf rust of wheat. Phytopathology 94:961-969. Because of differences in life histories between Puccinia triticina, a highly specialized, polycyclic, windborne pathogen with a shallow dispersal gradient, and Pyrenophora tritici-repentis, a residue-borne pathogen with a steep dispersal gradient, wheat mixtures are expected to be more effective at controlling leaf rust than tan spot. The objectives of this research were to determine the effect of two-cultivar mixtures with varying proportions and different pathogen resistance profiles on the severity of tan spot and leaf rust, to evaluate yield of the mixtures in the presence or absence of disease, and to directly compare the relative effectiveness of cultivar mixing for tan spot versus leaf rust. In a field experiment at two sites in Kansas over two growing seasons, winter wheat cvs. Jagger and 2145, which have differential resistance reactions to leaf rust and tan spot, each were planted in proportions of 0.25, 0.50, 0.75, and 1.00. Plots were inoculated with each pathogen alone, both pathogens, treated with a fungicide, or exposed to ambient conditions. For both diseases for all siteyears, severity decreased substantially on the susceptible cultivar as the proportion of that cultivar decreased in mixture. Mixtures were significantly more effective at reducing leaf rust than tan spot in three of four site-years. Mixtures generally yielded the same as the weighted mean of components in monoculture although, in two of three site-years, at least one fungicide-treated and one diseased mixture each yielded higher than expected values. Although this particular mixture produced only modest yield benefits, the potential for simultaneous reductions in tan spot and leaf rust was demonstrated. Additional keywords: blends, frequency-dependent effects, host diversity, plant diversity, polyculture, variety mixture.

For pathogens with highly localized inoculum, controlled positioning of susceptible plants can be used to delay exposure to the pathogen. For example, when wheat is direct-drilled in fields where wheat was infected by Gaeumannomyces graminis var. tritici (Ggt) in the previous season, the remaining rows of wheat crowns serve as an inoculum source for the new wheat planting. In order to determine how different seeding patterns of wheat might affect yield loss to Ggt, we constructed a mathematical model in three stages. First, we calculated the probability density function for the distance between a new seed and the nearest old row of crowns for two main planting scenarios: parallel to the previous year's rows or at an angle to them. Second, we used estimates from Kabbage and Bockus (Kabbage, M. and Bockus, W. W. 2002. Plant Disease 86, 298-303) of the yield loss to Ggt as a function of the distance between wheat seed and inoculum source. Third, we combined these two models to estimate the average yield loss for different planting patterns. We estimated that planting parallel to and between the previous year's rows would cut yield loss almost in half for a typical row spacing compared to angled planting, provided there was not an important offset, or bias, in the position of the parallel planting. Planter wobble was relatively unim- portant if there was no systematic bias in position.

Summary Three aspects of integrated disease management are considered. The first is the epidemiological synergism that can be derived through combining management tactics, and through disease management at regional scales. Field studies with potato late blight are used to demonstrate epidemiological impacts of integrating host resistance, fungicides, host density, and host genetic diversity. The importance of considering spatial scale and regional disease management are demonstrated with examples of cultivar mixtures in three different pathosystems. The second aspect is the potential for integrated management to increase the durability of resistance, e.g., through reduction of pathogen population size and imposition of disruptive selection. At this point in time, most information on this topic is limited to arguments of logic and to the results of mathematical models; empirical data are largely lacking. We suggest that current theoretical approaches need to be supplemented with inclusion of more complex processes, such as the effect of fitness modifiers in pathogen populations and the influence of quantitative adaptation of pathogens to their hosts. The third aspect is integration of resistance into overall crop management, including factors such as the balance between yield potential and disease resistance and the management of genotype x environment interaction. Such integration will increase the likelihood that farmers will utilize durable resistance, and will be demonstrated with examples from wheat production in the Pacific Northwest region of the USA.

Plant disease causes regular substantial losses to agricultural production, causing famine in some cases, and also damage to natural plant systems. Fungi, oomycetes, bacteria, viruses, nematodes, and other groups can cause plant disease. The interaction between pathogens and plants is often strongly determined by weather. For example, leaf surface moisture is critical to infection for many foliar pathogens. Temperature influences infection processes for pathogens as well as determining rates of reproduction of arthropods that vector pathogens. As weather patterns change, disease risk also changes, requiring that strategies for management be updated to new conditions.

Garrett, K. A., and Mundt, C. C. 2000. Host diversity can reduce potato late blight severity for focal and general patterns of primary inoculum. Phytopathology 90:1307-1312. The use of host diversity as a tool for management of potato late blight has not been viewed as promising in the past. But the increasing importance of late blight internationally has brought new consideration to all potential management tools. We studied the effect of host diversity on epidemics of potato late blight in Oregon, where there was little outside inoculum. The experimental system consisted of susceptible potato cv. Red LaSoda and a highly resistant breeding selection, inoculated with local isolates of US-8 Phytophthora infestans. Potatoes were grown in singlegenotype plots and also in a mixture of 10 susceptible and 26 resistant potato plants. Half of the plots received inoculation evenly thr oughout the plot (general inoculation) and half received an equal quan tity of inoculum in only one corner of the plot (focal inoculation). The area under the disease progress curve (AUDPC) was greater in single genotype stands of susceptible cv. Red LaSoda inoculated throughout the plot than with stands inoculated in one focus. The host-diversity effect on foliar late blight was significant in both years of the investigation; the AUDPC was reduced by an average of 37% in 1997 and 36% in 1998, compared with the mean disease level for the potato genotypes grown separately. Though the evidence for influence of inoculum pattern on host-diversity effects was weak (P = 0.15), in both years there was a trend toward greater hostdiversity effects for general inoculation. Statistical significance of hostdiversity effects on tuber yield and blight were found only in one of the two years. In that year, tuber yield from both the resistant and susceptible cultivar was increased in mixtures compared with single genotype stands and tuber blight was decreased in mixtures for susceptible cv. Red LaSoda. Additional keywords: cultivar mixtures, genetic diversity, spatial pattern of inoculum, variety mixtures.

The response of epiphytic populations of Pseudomonas syringae and other bacteria on dry bean plants to four copper-based bactericides was evaluated. The bactericides showed little difference in efficacy, but epiphytic populations on pinto bean leaflets, flowers, and pods were occasionally reduced when compared to populations on non-treated control plants, especially after repeated bactericide applications. Although there was a trend toward a relationship between epiphytic leaflet and flower populations, there were cases where P. syringae was undetected on one organ but abundant in samples from the other organ. P. syringae pv. syringae strains recovered from epiphytic populations demonstrated much greater copper resistance than did strains of P. syringae pv. phaseolicola, as measured by growth on media amended with cupric hydroxide. This difference between the pathovars may have implications for integrated pest management strategies.

*Continuous planting of crops containing single disease resistance (R) genes imposes a strong selection for virulence in pathogen populations, often rendering the R gene ineffective. Increasing environmental temperatures may complicate R-gene-mediated disease control because high temperatures often promote disease development and reduce R gene effectiveness. Here, performance of one rice bacterial blight disease R gene was assessed in field and growth chamber studies to determine the influence of temperature on R gene effectiveness and durability. *Disease severity and virulence of Xanthomonas oryzae pv. oryzae (Xoo) populations were monitored in field plots planted to rice with and without the bacterial blight R gene Xa7 over 11 yr. The performance of Xa7 was determined in high- and low-temperature regimes in growth chambers. *Rice with Xa7 exhibited less disease than lines without Xa7 over 11 yr, even though virulence of Xoo field populations increased. Xa7 restricted disease more effectively at high than at low temperatures. Other R genes were less effective at high temperatures. *We propose that Xa7 restricts disease and Xoo population size more efficiently in high temperature cropping seasons compared with cool seasons creating fluctuating selection, thereby positively impacting durability of Xa7.

Potential responses of plant disease phenology to climate change have been addressed primarily in agricultural systems. As a first step toward understanding the phenology of Uropyxis petalostemonis, a rust fungus commonly infecting the legume Dalea candida in U.S.A. tallgrass prairie, we evaluated the effects of temperature on urediniospore germination. While urediniospore germination for many rust fungi has been reported to decline only when temperatures are well above 25 degrees C, in vitro germination of U. petalostemonis dropped sharply at this temperature. Responses observed on water agar, potato dextrose agar and lima bean agar were similar, although lima bean agar supported a higher percentage germination overall. The low limiting temperatures suggest that most epidemically important new infections by U. petalostemonis occur in spring. High summer temperatures in tallgrass prairie might push infection by this rust fungus species to earlier in the year and select for stronger systemic growth characteristics.

Publisher Summary Plant disease risk is strongly influenced by environmental conditions. While some animal hosts may provide their pathogens with a consistent range of body temperatures, plant pathogens are generally much more exposed to the elements. Plant diseases will tend to respond to climate change, though a number of interactions taking place among host, pathogen, and potential vectors. In some cases, the actions of land managers may also complicate interpretation of climate change effects. This chapter presents a brief introduction to plant diseases and a synthesis of research in plant pathology related to climate change. It discusses the types of evidence for climate change impacts that might be observed in plant disease systems and evaluates what evidence of climate change fingerprints currently exists. The battle against plant disease is not a new one, and plant disease management is essential to feed a growing human population. Plant pathogen groups include fungi, prokaryotes, oomycetes, viruses and viroids, nematodes, parasitic plants, and protozoa. The very different life histories of this diverse group of organisms and their different interactions with host plants produce a wide range of responses to environmental and climatic drivers. Pathogen species may quickly develop resistance to pesticides or adapt to overcome plant disease resistance, and may also adapt to environmental changes, where the rate of adaptation depends on the type of pathogen. Pathogen populations may explode when weather conditions are favorable for disease development. The potentially rapid onset of disease makes it difficult to anticipate the best timing of management measures, especially in areas with high levels of interannual variability in climatic conditions.

Garrett, K. A., and Bowden, R. L. 2002. An Allee effect reduces the invasive potential of Tilletia indica. Phytopathology 92:1152-1159. The Karnal bunt pathogen, Tilletia indica, is heterothallic and depends on encounters on wheat spikes between airborne secondary sporidia of different mating types for successful infection and reproduction. This life history characteristic results in reduced reproductive success for lower population densities. Such destabilizing density dependence at low population levels has been described for a range of animals and plants and is often termed an Allee effect. Our objective was to characterize how the Allee effect might reduce the invasive potential of this economically important pathogen. We developed a simple population model of T. indica that incorporates an Allee effect by calculating the probability of infection for different numbers of secondary sporidia in the infection court. An Allee effect is predicted to be important at the frontier of an invasion, for establishment of new foci by a small population of teliospores, and when the environment is nonconducive for the production of secondary sporidia. Using estimated model parameter values, we demonstrated a theoretical threshold population size below which populations of T. indica were predicted to decline rather than increase. This threshold will vary from season to season as a function of weather variables and their effect on the reproductive potential of T. indica. Deployment of partial resistance or use of fungicides may be more useful if they push population levels below this threshold.

Garrett, K. A., Nelson, R. J., Mundt, C. C., Chacon, G., Jaramillo, R. E., and Forbes, G. A. 2001. The effects of host diversity and other management components on epidemics of potato late blight in the humid highland tropics. Phytopathology 91:993-1000. A field study at three highland sites near Quito, Ecuador, was conducted to determine whether host-diversity effects on potato late blight would be as important as recently found in studies conducted in temperate areas. We compared three potato mixtures and use of mixtures in combination with different planting densities and two fungicide regimes. Treatment comparisons were made by absolute and relative measures of host-diversity effects and incorporating a truncated area under the disease progress curve as a means of standardizing comparisons across sites. Potato-faba intercrops consisting of only 10% potato provided an estimate of the effects of dilution of susceptible host tissue. Host-diversity effects were very different across study sites, with a large host-diversity effect for reduced disease only at the site most distant from commercial potato production. Planting density had little influence on host-diversity effects or on late blight in single-genotype stands. Fungicide use in combination with potato mixtures enhanced a host-diversity effect for reduced late blight. Potato-faba intercrops produced only a small decrease in potato late blight. Effects of host diversity on yield were variable, with the greatest increase in yield for mixtures treated with fungicides at the site most distant from commercial potato production. The effects of host diversity on late blight severity may be less consistent in the tropical highlands than in the temperate zone, but can contribute to integrated disease management.

Garrett, K. A., and Mundt, C. C. 2000. Effects of planting density and the composition of wheat cultivar mixtures on stripe rust: An analysis taking into account limits to the replication of controls. Phytopathology 90: 1313-1321. The effect of plant density on disease is not well understood in populations of a single host plant genotype and has been studied even less in mixtures of host genotypes. We performed an experiment to evaluate the effect of wheat planting density on infection by Puccinia striiformis in experimental plots with a single wheat genotype and in plots with two genotypes making up a range of frequencies. Stripe rust severity in single-genotype plots increased with planting density in 1997 but decreased with planting density in 1998. Disease in host mixtures was compared to the weighted mean of disease levels in the corresponding single-genotype plots. The design of the field experiment included limited replication of these reference treatments (that is, there was not a unique pair of single-genotype plots for each mixture plot); therefore, we devised an analysis based on collapsing the data into independent mean observations. Disease reduction due to host diversity was less when one genotype predominated than when both host genotypes were present at nearly equal frequencies. The greatest mean host-diversity effect for reduced disease was at the intermediate planting density of 250 seeds per m2.

Given the wide range of scales and mechanisms by which pest or disease agents disperse, it is unclear whether there might exist a general relationship between scale of host heterogeneity and spatial spread that could be exploited by available management options. In this model-based study, we investigate the interaction between host distributions and the spread of pests and diseases using an array of models that encompass the dispersal and spread of a diverse range of economically important species: a major insect pest of coniferous forests in western North America, the mountain pine beetle (Dendroctonus ponderosae); the bacterium Pseudomonas syringae, one of the most-widespread and best-studied bacterial plant pathogens; the mosquito Culex erraticus, an important vector for many human and animal pathogens, including West Nile Virus; and the oomycete Phytophthora infestans, the causal agent of potato late blight. Our model results reveal an interesting general phenomenon: a unimodal (‘humpbacked’) relationship in the magnitude of infestation (an index of dispersal or population spread) with increasing grain size (i.e., the finest scale of patchiness) in the host distribution. Pest and disease management strategies targeting different aspects of host pattern (e.g., abundance, aggregation, isolation, quality) modified the shape of this relationship, but not the general unimodal form. This is a previously unreported effect that provides insight into the spatial scale at which management interventions are most likely to be successful, which, notably, do not always match the scale corresponding to maximum infestation. Our findings could provide a new basis for explaining historical outbreak events, and have implications for biosecurity and public health preparedness.

Surveying invasive species can be highly resource intensive, yet near-real-time evaluations of invasion progress are important resources for management planning. In the case of the soybean rust invasion of the United States, a linked monitoring, prediction, and communication network saved U.S. soybean growers approximately $200 M/yr. Modeling of future movement of the pathogen (Phakopsora pachyrhizi) was based on data about current disease locations from an extensive network of sentinel plots. We developed a dynamic network model for U.S. soybean rust epidemics, with counties as nodes and link weights a function of host hectarage and wind speed and direction. We used the network model to compare four strategies for selecting an optimal subset of sentinel plots, listed here in order of increasing performance: random selection, zonal selection (based on more heavily weighting regions nearer the south, where the pathogen overwinters), frequency-based selection (based on how frequently the county had been infected in the past), and frequency-based selection weighted by the node strength of the sentinel plot in the network model. When dynamic network properties such as node strength are characterized for invasive species, this information can be used to reduce the resources necessary to survey and predict invasion progress.