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Remnant areas hosting natural vegetation in agricultural landscapes can impact the disease epidemiology and evolutionary dynamics of crop pathogens. However, the potential consequences for crop diseases of the composition, the spatial configuration and the persistence time of the agro-ecological interface – the area where crops and remnant vegetation are in contact – have been poorly studied. Here, we develop a demographic-genetic simulation model to study how the spatial and temporal distribution of remnant wild vegetation patches embedded in an agricultural landscape can drive the emergence of a crop pathogen and its subsequent specialisation on the crop host. We found that landscape structures that promoted larger pathogen populations on the wild host facilitated the emergence of a crop pathogen but such landscape structures also reduced the potential for the pathogen population to adapt to the crop. In addition, the evolutionary trajectory of the pathogen population was determined by interactions between the factors describing the landscape structure and those describing the pathogen life-histories. Our study contribute to a better understanding of how the shift of land-use patterns in agricultural landscapes might influence crop diseases to provide predictive tools to evaluate management practices.

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.

Plant viruses infecting crop species are causing long-lasting economic losses and are endangering food security worldwide. Ongoing events, such as climate change, changes in agricultural practices, globalization of markets or changes in plant virus vector populations, are affecting plant virus life cycles. Because farmer’s fields are part of the larger environment, the role of wild plant species in plant virus life cycles can provide information about underlying processes during virus transmission and spread. This review focuses on the Solanaceae family, which contains thousands of species growing all around the world, including crop species, wild flora and model plants for genetic research. In a first part, we analyze various viruses infecting Solanaceae plants across the agro-ecological interface, emphasizing the important role of virus interactions between the cultivated and wild zones as global changes affect these environments on both local and global scales. To cope with these changes, it is necessary to adjust prophylactic protection measures and diagnostic methods. As illustrated in the second part, a complex virus research at the landscape level is necessary to obtain relevant data, which could be overwhelming. Based on evidence from previous studies we conclude that Solanaceae plant communities can be targeted to address complete life cycles of viruses with different life strategies within the agro-ecological interface. Data obtained from such research could then be used to improve plant protection methods by taking into consideration environmental factors that are impacting the life cycles of plant viruses.

Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.

Ponds in agricultural areas are ubiquitous water retention systems acting as reactive biogeochemical hotspots controlling pesticide dissipation and transfer at the catchment scale. Several issues need to be addressed in order to understand, follow-up and predict the role of ponds in limiting pesticide transfer at the catchment scale. In this review, we present a critical overview of functional processes underpinning pesticide dissipation in ponds. We highlight the need to distinguish degradative and non-degradative processes and to understand the role of the sediment-water interface in pesticide dissipation. Yet it is not well-established how pesticide dissipation in ponds governs the pesticide transfer at the catchment scale under varying hydro-climatic conditions and agricultural operation practices. To illustrate the multi-scale and dynamic aspects of this issue, we sketch a modelling framework integrating the role of ponds at the catchment scale. Such an integrated framework can improve the spatial prediction of pesticide transfer and risk assessment across the catchment-ponds-river continuum to facilitate management rules and operations.

The use of global and regional climate models has been increasing in the past few decades, in order to analyze the future of natural resources and the socio-economic aspects of climate change. However, these climate model outputs can be quite biased, which makes it challenging to use them directly for analysis purpose. Therefore, a tool named Climate Data Bias Corrector was developed to correct the bias in climatic projections of historical and future periods for three primary climatic variables—rainfall, temperature (maximum and minimum), and solar radiation. It uses the quantile mapping approach, known for its efficiency and low computational cost for bias correction. Its Graphical User Interface (GUI) was made to be feasible to take input and give output in commonly used file formats—comma and tab delimited file formats. It also generates month-wise cumulative density function (CDF) plot of a random station/grid to allow the user to investigate the effectiveness of correction statistically. The tool was verified with a case study on several agro-ecological zones of India and found to be efficient.