Making sense of Integrated Pest Management (IPM) in the light of evolution

Host Plant Effects on Sexual Selection Dynamics in Phytophagous Insects

Natural selection is notoriously dynamic in nature, and so, too, is sexual selection. The interactions between phytophagous insects and their host plants have provided valuable insights into the many ways in which ecological factors can influence sexual selection. In this review, we highlight recent discoveries and provide guidance for future work in this area. Importantly, host plants can affect both the agents of sexual selection (e.g., mate choice and male-male competition) and the traits under selection (e.g., ornaments and weapons). Furthermore, in our rapidly changing world, insects now routinely encounter new potential host plants. The process of adaptation to a new host may be hindered or accelerated by sexual selection, and the unexplored evolutionary trajectories that emerge from these dynamics are relevant to pest management and insect conservation strategies. Examining the effects of host plants on sexual selection has the potential to advance our fundamental understanding of sexual conflict, host range evolution, and speciation, with relevance across taxa.

Pesticides vs. Biopesticides: From Pest Management to Toxicity and Impacts on the Environment and Human Health

The environmental pollution that occurs in direct response to the widespread use of man-made/conventional pesticides results from many chemicals that require a long period of time, often decades, to degrade. The synthetic nature of pesticides also harms animals, beneficial insects, microorganisms, and plants, as well as humans. Fortunately, however, there are many natural pesticides, the so-called biopesticides, that are also effective against pests and more importantly, do not interfere with the well-being of ecosystems. Consequently, most biopesticides are safer for use around people and pets than man-made pesticides because, for example, they can be easily washed away from fruits and vegetables. The natural habitat is a rich resource with a wide selection of plants, many of which are also used to treat diseases in humans, animals, and plants. Out of concern for public health, environmental safety, and the stringent regulation of pesticide residues in agricultural commodities, the use of biopesticides is becoming increasingly important, but questions regarding potential pest resistance to these products may arise, just as is the case with conventional pesticides. Therefore, the performance and potential role of biopesticides in the management of plant pests should be prioritized due to their sustainability and importance to human and environmental welfare. In this review, we propose to highlight a scenario in which we discuss in detail the main constraints posed by the use of pesticides compared to biopesticides, starting with issues regarding their definition and continuing on to issues related to their toxicity and their impact on the environment and human health.

resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes

The evolution of pesticide resistance is a widespread problem with potentially severe consequences for global food security. We introduce the resevol R package, which simulates individual-based models of pests with evolving genomes that produce complex, polygenic, and covarying traits affecting pest life history and pesticide resistance. Simulations are modelled on a spatially-explicit and highly customisable landscape in which crop and pesticide application and rotation can vary, making the package a highly flexible tool for both general and tactical models of pest management and resistance evolution. We present the key features of the resevol package and demonstrate its use for a simple example simulating pests with two covarying traits. The resevol R package is open source under GNU Public License. All source code and documentation are available on GitHub.

Occurrence Regionalization of Kiwifruit Brown Spot in Sichuan

Kiwifruit brown spot caused by Corynespora cassiicola is the most significant fungal disease in Sichuan, resulting in premature defoliation, which had a significant impact on yield and fruit quality. The objective of the study was to determine the occurrence regularity and suitability of kiwifruit brown spot in Sichuan. The occurrence of the disease in the main producing region was continuously monitored, the maximum entropy (MaxEnt) model was used to predict its potential distribution, and the key environmental variables were identified using the jackknife method. The results indicated that kiwifruit brown spot was widely distributed across the entire producing region in Sichuan, predominantly affecting the variety "Hongyang". The incidence (p < 0.01) and disease index (p < 0.05) showed a significant positive correlation with the cultivar, and decreased with the altitude increasing. The average area under the ROC curve (AUC) of 10 replicates was 0.933 ± 0.012, with an accuracy of 84.44% in a field test, confirming the reliability of the predicted results. The highly suitable distribution areas of kiwifruit brown spot were mainly located in the Chengdu and Ya'an regions. The entire Panzhihua region was an unsuitable distribution area, and the entire Pujiang County and Mingshan District were highly suitable distribution areas. The key environmental variables affecting the potential distribution of kiwifruit brown spot included isothermality (24.3-33.7%), minimum temperature in August (16.3-23.6 °C), maximum temperature in July (25.5-31.2 °C), minimum temperature in June (15.6-20.9 °C), precipitation in August (158-430 mm), and average temperature in October (15.6-18.8 °C). This study provides a theoretical basis for the reasonable layout of the cultivar and the precise prevention and control of the disease.

The Epichloë festucae Antifungal Protein Efe-AfpA Has Activity against Numerous Plant Pathogens

Fungal plant pathogens can present major problems for most crop species. Currently, control of fungal diseases relies heavily on the use of fungicides. However, there are problems associated with fungicide use, including potential toxicity to non-target organisms and the development of resistance in the target fungus. New strategies are being sought to reduce fungicide use. One area of active research is the potential use of antifungal proteins from various fungal species as alternatives or complements to traditional fungicides. An antifungal protein, Efe-AfpA, from the fungal endophyte Epichloë festucae was previously found to protect plants from the pathogen Clarireedia jacksonii, the causal agent of dollar spot disease. Here we report that Efe-AfpA also has inhibitory activity against other important plant pathogens. These results suggest that it may be possible to develop Efe-AfpA as a biofungicide to target a broad range of destructive plant pathogens.

The power of the smallest: The inhibitory activity of microbial volatile organic compounds against phytopathogens

Plant diseases caused by phytopathogens result in huge economic losses in agriculture. In addition, the use of chemical products to control such diseases causes many problems to the environment and to human health. However, some bacteria and fungi have a mutualistic relationship with plants in nature, mainly exchanging nutrients and protection. Thus, exploring those beneficial microorganisms has been an interesting and promising alternative for mitigating the use of agrochemicals and, consequently, achieving a more sustainable agriculture. Microorganisms are able to produce and excrete several metabolites, but volatile organic compounds (VOCs) have huge biotechnology potential. Microbial VOCs are small molecules from different chemical classes, such as alkenes, alcohols, ketones, organic acids, terpenes, benzenoids and pyrazines. Interestingly, volatilomes are species-specific and also change according to microbial growth conditions. The interaction of VOCs with other organisms, such as plants, insects, and other bacteria and fungi, can cause a wide range of effects. In this review, we show that a large variety of plant pathogens are inhibited by microbial VOCs with a focus on the in vitro and in vivo inhibition of phytopathogens of greater scientific and economic importance in agriculture, such as Ralstonia solanacearum, Botrytis cinerea, Xanthomonas and Fusarium species. In this scenario, some genera of VOC-producing microorganisms stand out as antagonists, including Bacillus, Pseudomonas, Serratia and Streptomyces. We also highlight the known molecular and physiological mechanisms by which VOCs inhibit the growth of phytopathogens. Microbial VOCs can provoke many changes in these microorganisms, such as vacuolization, fungal hyphal rupture, loss of intracellular components, regulation of metabolism and pathogenicity genes, plus the expression of proteins important in the host response. Furthermore, we demonstrate that there are aspects to investigate by discussing questions that are still not very clear in this research area, especially those that are essential for the future use of such beneficial microorganisms as biocontrol products in field crops. Therefore, we bring to light the great biotechnological potential of VOCs to help make agriculture more sustainable.

Incorporating Microbial Species Interaction in Management of Freshwater Toxic Cyanobacteria: A Systems Science Challenge

Water resources are critically important, but also pose risks of exposure to toxic and pathogenic microbes. Increasingly, a concern is toxic cyanobacteria, which have been linked to the death and disease of humans, domesticated animals, and wildlife in freshwater systems worldwide. Management approaches successful at reducing cyanobacterial abundance and toxin production have tended to be short-term solutions applied on small scales (e.g., algaecide application) or solutions that entail difficult multifaceted investments (e.g., modification of landscape and land use to reduce nutrient inputs). However, implementation of these approaches can be undermined by microbial species interactions that (a) provide toxic cyanobacteria with protection against the method of control or (b) permit toxic cyanobacteria to be replaced by other significant microbial threats. Understanding these interactions is necessary to avoid such scenarios and can provide a framework for novel strategies to enhance freshwater resource management via systems science (e.g., pairing existing physical and chemical approaches against cyanobacteria with ecological strategies such as manipulation of natural enemies, targeting of facilitators, and reduction of benthic occupancy and recruitment). Here, we review pertinent examples of the interactions and highlight potential applications of what is known.

Pathogen Adaptation to American (Rpv3-1) and Eurasian (Rpv29) Grapevine Loci Conferring Resistance to Downy Mildew

Durable resistance is a key objective in genetic improvement for disease resistance in grapevines, which must survive for years in the field in the presence of adaptable pathogen populations. In this study, the adaptation of 72 Northern Italian isolates of Plasmopara viticola, the downy mildew agent, has been investigated into Bianca, possessing Rpv3-1, the most frequently exploited resistance locus for genetic improvement, and Mgaloblishvili, a Vitis vinifera variety possessing the newly discovered Rpv29 locus. Infection parameters (latency period, infection frequency, and disease severity) and oospore production and viability were evaluated and compared to those of Pinot noir, the susceptible reference. The expected levels of disease control were achieved by both resistant cultivars (>90% on Bianca; >25% on Mgaloblishvili), despite the high frequency of isolates able to grow on one (28%) or both (46%) accessions. The disease incidence and severity were limited by both resistant cultivars and the strains able to grow on resistant accessions showed signatures of fitness penalties (reduced virulence, infection frequency, and oospore density). Together, these results indicate an adequate pathogen control but suitable practices must be adopted in the field to prevent the diffusion of the partially adapted P. viticola strains to protect resistance genes from erosion.

Pesticide resistance in arthropods: Ecology matters too

Pesticide resistance development is an example of rapid contemporary evolution that poses immense challenges for agriculture. It typically evolves due to the strong directional selection that pesticide treatments exert on herbivorous arthropods. However, recent research suggests that some species are more prone to evolve pesticide resistance than others due to their evolutionary history and standing genetic variation. Generalist species might develop pesticide resistance especially rapidly due to pre‐adaptation to handle a wide array of plant allelochemicals. Moreover, research has shown that adaptation to novel host plants could lead to increased pesticide resistance. Exploring such cross‐resistance between host plant range evolution and pesticide resistance development from an ecological perspective is needed to understand its causes and consequences better. Much research has, however, been devoted to the molecular mechanisms underlying pesticide resistance while both the ecological contexts that could facilitate resistance evolution and the ecological consequences of cross‐resistance have been under‐studied. Here, we take an eco‐evolutionary approach and discuss circumstances that may facilitate cross‐resistance in arthropods and the consequences cross‐resistance may have for plant–arthropod interactions in both target and non‐target species and species interactions. Furthermore, we suggest future research avenues and practical implications of an increased ecological understanding of pesticide resistance evolution.

Evolutionary Ecology of Plant-Arthropod Interactions in Light of the "Omics" Sciences: A Broad Guide

Aboveground plant-arthropod interactions are typically complex, involving herbivores, predators, pollinators, and various other guilds that can strongly affect plant fitness, directly or indirectly, and individually, synergistically, or antagonistically. However, little is known about how ongoing natural selection by these interacting guilds shapes the evolution of plants, i.e., how they affect the differential survival and reproduction of genotypes due to differences in phenotypes in an environment. Recent technological advances, including next-generation sequencing, metabolomics, and gene-editing technologies along with traditional experimental approaches (e.g., quantitative genetics experiments), have enabled far more comprehensive exploration of the genes and traits involved in complex ecological interactions. Connecting different levels of biological organization (genes to communities) will enhance the understanding of evolutionary interactions in complex communities, but this requires a multidisciplinary approach. Here, we review traditional and modern methods and concepts, then highlight future avenues for studying the evolution of plant-arthropod interactions (e.g., plant-herbivore-pollinator interactions). Besides promoting a fundamental understanding of plant-associated arthropod communities' genetic background and evolution, such knowledge can also help address many current global environmental challenges.

Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments

Understanding pest evolution in agricultural systems is crucial for developing effective and innovative pest control strategies. Types of cultivation, such as crop monocultures versus polycultures or crop rotation, may act as a selective pressure on pests’ capability to exploit the host’s resources. In this study, we examined the herbivorous mite Aceria tosichella (commonly known as wheat curl mite), a widespread wheat pest, to understand how fluctuating versus stable environments influence its niche breadth and ability to utilize different host plant species. We subjected a wheat‐bred mite population to replicated experimental evolution in a single‐host environment (either wheat or barley), or in an alternation between these two plant species every three mite generations. Next, we tested the fitness of these evolving populations on wheat, barley, and on two other plant species not encountered during experimental evolution, namely rye and smooth brome. Our results revealed that the niche breadth of A. tosichella evolved in response to the level of environmental variability. The fluctuating environment expanded the niche breadth by increasing the mite’s ability to utilize different plant species, including novel ones. Such an environment may thus promote flexible host‐use generalist phenotypes. However, the niche expansion resulted in some costs expressed as reduced performances on both wheat and barley as compared to specialists. Stable host environments led to specialized phenotypes. The population that evolved in a constant environment consisting of barley increased its fitness on barley without the cost of utilizing wheat. However, the population evolving on wheat did not significantly increase its fitness on wheat, but decreased its performance on barley. Altogether, our results indicated that, depending on the degree of environmental heterogeneity, agricultural systems create different conditions that influence pests’ niche breadth evolution, which may in turn affect the ability of pests to persist in such systems.

Whole genome sequencing elucidates the species‐wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI‐resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, shortly after the introduction of SDHIs. Two primary mutations in the SDH complex (SdhB‐H278Y and SdhC‐H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. For this project, we performed whole‐genome sequencing for 48 A. solani isolates from potato fields across Europe to better characterize the pathogen's genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. The isolates can be grouped into seven genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. We found clear evidence for recombination on the genome, and the observed admixtures might indicate a higher adaptive potential of the fungus than previously thought. Yet, we cannot link the observed recombination events to different Sdh mutations. The same Sdh mutations appear in different, non‐admixed genetic backgrounds; therefore, we conclude they arose independently. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes, apparent admixture in the populations, and evidence for recombination indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

Varroa destructor from the Laboratory to the Field: Control, Biocontrol and IPM Perspectives-A Review

Varroa destructor is a real challenger for beekeepers and scientists: fragile out of the hive, tenacious inside a bee colony. From all the research done on the topic, we have learned that a better understanding of this organism in its relationship with the bee but also for itself is necessary. Its biology relies mostly on semiochemicals for reproduction, nutrition, or orientation. Many treatments have been developed over the years based on hard or soft acaricides or even on biocontrol techniques. To date, no real sustainable solution exists to reduce the pressure of the mite without creating resistances or harming honeybees. Consequently, the development of alternative disruptive tools against the parasitic life cycle remains open. It requires the combination of both laboratory and field results through a holistic approach based on health biomarkers. Here, we advocate for a more integrative vision of V. destructor research, where in vitro and field studies are more systematically compared and compiled. Therefore, after a brief state-of-the-art about the mite's life cycle, we discuss what has been done and what can be done from the laboratory to the field against V. destructor through an integrative approach.

The effects of host plant species and larval density on immune function in the polyphagous moth Spodoptera littoralis

Immune functions are costly, and immune investment is usually dependent on the individual's condition and resource availability. For phytophagous insects, host plant quality has large effects on performance, for example growth and survival, and may also affect their immune function. Polyphagous insects often experience a large variation in quality among different host plant species, and their immune investment may thus vary depending on which host plant species they develop on. Larvae of the polyphagous moth Spodoptera littoralis have previously been found to exhibit density-dependent prophylaxis as they invest more in certain immune responses in high population densities. In addition, the immune response of S. littoralis has been shown to depend on nutrient quality in experiments with artificial diet. Here, I studied the effects of natural host plant diet and larval density on a number of immune responses to understand how host plant species affects immune investment in generalist insects, and whether the density-dependent prophylaxis could be mediated by host plant species. While host plant species in general did not mediate the density-dependent immune expression, particular host plant species was found to increase larval investment in certain functions of the immune system. Interestingly, these results indicate that different host plants may provide a polyphagous species with protection against different kinds of antagonisms. This insight may contribute to our understanding of the relationship between preference and performance in generalists, as well as having applied consequences for sustainable pest management.

Focused Identification of Germplasm Strategy (FIGS): polishing a rough diamond

Focused Identification of Germplasm Strategy (FIGS) has been advocated as an efficient approach to predict and harness variation in adaptive traits in genebanks or wild populations of plants. However, a weakness of the current FIGS approach is that it only utilizes a priori knowledge of one evolutionary factor: natural selection. Further optimization is needed to capture elusive traits, and this review shows that nonadaptive evolutionary processes (gene flow and genetic drift) should be incorporated to increase precision. Focusing on plant resistance to insect herbivores, we also note that historic selection pressures can be difficult to disentangle, and provide suggestions for successful mining based on eco-evolutionary theory. We conclude that with such refinement FIGS has high potential for enhancing breeding efforts and hence sustainable plant production.

The use of pesticides in Polish agriculture after integrated pest management (IPM) implementation

The aim of the conducted study was to characterize the attitudes and practices of Polish farmers in the area of performing chemical plant protection treatments. A particular attention was paid to identifying the relationship between the direction of changes in the volume of chemical plant protection product consumption and selected attributes of farms. The main time range of the analyses covered the period of 2013-2017. Statistical data and results of representative surveys carried out on a sample of 1101 farms in Poland were used in the research process. Due to the large number of variants of the analysed variables, a multiple correspondence analysis was used, which made it possible to determine the correlation between the examined features (direction of changes in pesticide use relative to the farm area, economic size of the farm and location of the farm). Statistical analysis showed the existence of strong relationships between the physical (1) and economic (2) size of farms and the direction of changes in pesticide consumption ((1) φ2 = 0.0907; (2) φ2 = 0.1141)). According to empirical studies, the reduction of pesticide consumption took place mainly on the smallest farms. The implementation of the integrated plant protection directive has not resulted in significant changes in the form of reduced pesticide use in large-scale field crops. This raises the need to modify the strategy and model of crop protection in large-scale field crops in Poland.

The impact of female mating strategies on the success of insect control technologies

Attempts to control insect pests and disease vectors have a long history. Recently, new technology has opened a whole new range of possible methods to suppress or transform natural populations. But it has also become clear that a better understanding of the ecology of targeted populations is needed. One key parameter is mating behaviour. Often modified males are released which need to successfully reproduce with females while competing with wild males. Insect control techniques can be affected by target species' mating ecology, and conversely mating ecology is likely to evolve in response to manipulation attempts. A better understanding of (female) mating behaviour will help anticipate and overcome potential challenges, and thus make desirable outcomes more likely.

Effector Avr4 in Phytophthora infestans Escapes Host Immunity Mainly Through Early Termination

Effector genes play critical roles in the antagonistic interactions between plants and pathogens. However, knowledge of mutation mechanisms and evolutionary processes in effector genes and the contribution of climatic factors to the evolution of effector genes are fragmented but important in sustainable management of plant diseases and securing food supply under changing climates. Here, we used a population genetic approach to explore the evolution of the Avr4 gene in Phytophthora infestans, the causal agent of potato blight. We found that the Avr4 gene exhibited a high genetic diversity generated by point mutation and sequence deletion. Frameshifts caused by a single base-pair deletion at the 194th nucleotide position generate two stop codons, truncating almost the entire C-terminal, which is important for effector function and R4 recognition in all sequences. The effector is under natural selection for adaptation supported by comparative analyses of population differentiation (FST ) and isolation-by-distance between Avr4 sequences and simple sequence repeat marker loci. Furthermore, we found that local air temperature was positively associated with pairwise FST in the Avr4 sequences. These results suggest that the evolution of the effector gene is influenced by local air temperature, and the C-terminal truncation is one of the main mutation mechanisms in the P. infestans effector gene to circumvent the immune response of potato plants. The implication of these results to agricultural and natural sustainability in future climate conditions is discussed.

Biotic Yield Losses in the Southern Amazon, Brazil: Making Use of Smartphone-Assisted Plant Disease Diagnosis Data

Pathogens and animal pests (P&A) are a major threat to global food security as they directly affect the quantity and quality of food. The Southern Amazon, Brazil's largest domestic region for soybean, maize and cotton production, is particularly vulnerable to the outbreak of P&A due to its (sub)tropical climate and intensive farming systems. However, little is known about the spatial distribution of P&A and the related yield losses. Machine learning approaches for the automated recognition of plant diseases can help to overcome this research gap. The main objectives of this study are to (1) evaluate the performance of Convolutional Neural Networks (ConvNets) in classifying P&A, (2) map the spatial distribution of P&A in the Southern Amazon, and (3) quantify perceived yield and economic losses for the main soybean and maize P&A. The objectives were addressed by making use of data collected with the smartphone application Plantix. The core of the app's functioning is the automated recognition of plant diseases via ConvNets. Data on expected yield losses were gathered through a short survey included in an "expert" version of the application, which was distributed among agronomists. Between 2016 and 2020, Plantix users collected approximately 78,000 georeferenced P&A images in the Southern Amazon. The study results indicate a high performance of the trained ConvNets in classifying 420 different crop-disease combinations. Spatial distribution maps and expert-based yield loss estimates indicate that maize rust, bacterial stalk rot and the fall armyworm are among the most severe maize P&A, whereas soybean is mainly affected by P&A like anthracnose, downy mildew, frogeye leaf spot, stink bugs and brown spot. Perceived soybean and maize yield losses amount to 12 and 16%, respectively, resulting in annual yield losses of approximately 3.75 million tonnes for each crop and economic losses of US$2 billion for both crops together. The high level of accuracy of the trained ConvNets, when paired with widespread use from following a citizen-science approach, results in a data source that will shed new light on yield loss estimates, e.g., for the analysis of yield gaps and the development of measures to minimise them.