Range-expanding pests and pathogens in a warming world

Recent advances in the population biology and management of maize foliar fungal pathogens Exserohilum turcicum, Cercospora zeina and Bipolaris maydis in Africa

Maize is the most widely cultivated and major security crop in sub-Saharan Africa. Three foliar diseases threaten maize production on the continent, namely northern leaf blight, gray leaf spot, and southern corn leaf blight. These are caused by the fungi Exserohilum turcicum, Cercospora zeina, and Bipolaris maydis, respectively. Yield losses of more than 10% can occur if these pathogens are diagnosed inaccurately or managed ineffectively. Here, we review recent advances in understanding the population biology and management of the three pathogens, which are present in Africa and thrive under similar environmental conditions during a single growing season. To effectively manage these pathogens, there is an increasing adoption of breeding for resistance at the small-scale level combined with cultural practices. Fungicide usage in African cropping systems is limited due to high costs and avoidance of chemical control. Currently, there is limited knowledge available on the population biology and genetics of these pathogens in Africa. The evolutionary potential of these pathogens to overcome host resistance has not been fully established. There is a need to conduct large-scale sampling of isolates to study their diversity and trace their migration patterns across the continent.

It's a Trap! Part I: Exploring the Applications of Rotating-Arm Impaction Samplers in Plant Pathology

Although improved knowledge on the movement of airborne plant pathogens is likely to benefit plant health management, generating this knowledge is often far more complicated than anticipated. This complexity is driven by the dynamic nature of environmental variables, diversity among pathosystems that are targeted, and the unique needs of each research group. When using a rotating-arm impaction sampler, particle collection is dependent on the pathogen, environment, research objectives, and limitations (monetary, environmental, or labor). Consequently, no design will result in 100% collection efficiency. Fortunately, it is likely that multiple approaches can succeed despite these constraints. Choices made during design and implementation of samplers can influence the results, and recognizing this influence is crucial for researchers. This article is for beginners in the art and science of using rotating-arm impaction samplers; it provides a foundation for designing a project, from planning the experiment to processing samples. We present a relatively nontechnical discussion of the factors influencing pathogen dispersal and how placement of the rotating-arm air samplers alters propagule capture. We include a discussion of applications of rotating-arm air samplers to demonstrate their versatility and potential in plant pathology research as well as their limitations.

Advancing crop disease resistance through genome editing: a promising approach for enhancing agricultural production

Modern agriculture has encountered several challenges in achieving constant yield stability especially due to disease outbreaks and lack of long-term disease-resistant crop cultivars. In the past, disease outbreaks in economically important crops had a major impact on food security and the economy. On the other hand climate-driven emergence of new pathovars or changes in their host specificity further poses a serious threat to sustainable agriculture. At present, chemical-based control strategies are frequently used to control microbial pathogens and pests, but they have detrimental impact on the environment and also resulted in the development of resistant phyto-pathogens. As a replacement, cultivating engineered disease-resistant crops can help to minimize the negative impact of regular pesticides on agriculture and the environment. Although traditional breeding and genetic engineering have been instrumental in crop disease improvement but they have certain limitations such as labour intensity, time consumption, and low efficiency. In this regard, genome editing has emerged as one of the potential tools for improving disease resistance in crops by targeting multiple traits with more accuracy and efficiency. For instance, genome editing techniques, such as CRISPR/Cas9, CRISPR/Cas13, base editing, TALENs, ZFNs, and meganucleases, have proved successful in improving disease resistance in crops through targeted mutagenesis, gene knockouts, knockdowns, modifications, and activation of target genes. CRISPR/Cas9 is unique among these techniques because of its remarkable efficacy, low risk of off-target repercussions, and ease of use. Some primary targets for developing CRISPR-mediated disease-resistant crops are host-susceptibility genes (the S gene method), resistance genes (R genes) and pathogen genetic material that prevents their development, broad-spectrum disease resistance. The use of genome editing methods has the potential to notably ameliorate crop disease resistance and transform agricultural practices in the future. This review highlights the impact of phyto-pathogens on agricultural productivity. Next, we discussed the tools for improving disease resistance while focusing on genome editing. We provided an update on the accomplishments of genome editing, and its potential to improve crop disease resistance against bacterial, fungal and viral pathogens in different crop systems. Finally, we highlighted the future challenges of genome editing in different crop systems for enhancing disease resistance.

Complementary roles of EPS, T3SS and Expansin for virulence of Erwinia tracheiphila, the causative agent of cucurbit wilt

Erwinia tracheiphila (Smith) is a recently emerged plant pathogen that causes severe economic losses in cucurbit crops in temperate Eastern North America. E. tracheiphila is xylem restricted, and virulence is thought to be related to Exopolysaccharides (EPS) and biofilm formation, which occlude the passage of sap in xylem vessels and causes systemic wilt. However, the role of EPS and biofilm formation, and their contribution to disease in relation to other virulence loci are unknown. Here, we use deletion mutants to explore the roles of EPS, Hrp Type III secretion system (Hrp T3SS) and Expansin in plant colonization and virulence. Then, we quantify the expression of the genes encoding these factors during infection. Our results show that Exopolysaccharides are essential for E. tracheiphila survival in host plants, while Hrp T3SS and Expansin are dispensable for survival but needed for systemic wilt symptom development. EPS and Hrp T3SS display contrasting expression patterns in the plant, reflecting their relevance in different stages of the infection. Finally, we show that expression of the eps and hrpT3SS operons is downregulated in mildly increased temperatures, suggesting a link between expression of these virulence factors and geographic restriction of E. tracheiphila to temperate regions. Our work highlights how E. tracheiphila virulence is a complex trait where several loci are coordinated during infection. These results further shed light into the relationship between virulence factors and the ecology of this pathosystem, which will be essential for developing sustainable management strategies for this emerging pathogen.

Monitoring the phenology of plant pathogenic fungi: why and how?

Phenology is a key adaptive trait of organisms, shaping biotic interactions in response to the environment. It has emerged as a critical topic with implications for societal and economic concerns due to the effects of climate change on species' phenological patterns. Fungi play essential roles in ecosystems, and plant pathogenic fungi have significant impacts on global food security. However, the phenology of plant pathogenic fungi, which form a huge and diverse clade of organisms, has received limited attention in the literature. This diversity may have limited the use of a common language for comparisons and the integration of phenological data for these taxonomic groups. Here, we delve into the concept of 'phenology' as applied to plant pathogenic fungi and explore the potential drivers of their phenology, including environmental factors and the host plant. We present the PhenoFun scale, a phenological scoring system suitable for use with all fungi and fungus-like plant pathogens. It offers a standardised and common tool for scientists studying the presence, absence, or predominance of a particular phase, the speed of phenological phase succession, and the synchronism shift between pathogenic fungi and their host plants, across a wide range of environments and ecosystems. The application of the concept of 'phenology' to plant pathogenic fungi and the use of a phenological scoring system involves focusing on the interacting processes between the pathogenic fungi, their hosts, and their biological, physical, and chemical environment, occurring during the life cycle of the pathogen. The goal is to deconstruct the processes involved according to a pattern orchestrated by the fungus's phenology. Such an approach will improve our understanding of the ecology and evolution of such organisms, help to understand and anticipate plant disease epidemics and their future evolution, and make it possible to optimise management models, and to encourage the adoption of cropping practices designed from this phenological perspective.

Assessing the potential phytosanitary threat of the house cricket Acheta domesticus

Phytosanitary threats can pose substantial risks to global agriculture and ecological systems, affecting biodiversity, human well-being, and food security. Meanwhile, global warming is projected to exacerbate these threats in the future. One in Europe already widely distributed potential phytosanitary threat that may benefit from global warming is the house cricket Acheta domesticus. This study explored the potential of A. domesticus as a relevant non-native phytosanitary threat under changing climatic conditions by conducting a series of functional response experiments across a temperature gradient (20, 25, and 30 °C). Acheta domesticus exhibited comparable patterns of seed consumption and functional responses. Seed type (millet seeds, wheat grains) and temperature increase influenced the damage inflicted on seeds, with softer and smaller seeds being more susceptible to damage, further amplified by warmer temperatures. The study's outcomes underline the phytosanitary threat that A. domesticus may pose. Considering the species' established presence and adaptable nature in urban environments exacerbates the potential for A. domesticus to transition to rural and agricultural areas. Its increasing production as a food item, paired with the here-identified potential to damage seeds, emphasizes the need for proactive and science-based strategies to address emerging phytosanitary threats driven by non-native species under changing climatic conditions. As global temperatures continue to rise, the assessment and management of potential pest species like A. domesticus will be crucial for safeguarding agriculture productivity and ecological balance.

Early warning and management of invasive crop pests under global warming: estimating the global geographical distribution patterns and ecological niche overlap of three Diabrotica beetles

Invasive alien pests (IAPs) pose a major threat to global agriculture and food production. When multiple IAPs coexist in the same habitat and use the same resources, the economic loss to local agricultural production increases. Many species of the Diabrotica genus, such as Diabrotica barberi, Diabrotica undecimpunctata, and Diabrotica virgifera, originating from the USA and Mexico, seriously damaged maize production in North America and Europe. However, the potential geographic distributions (PGDs) and degree of ecological niche overlap among the three Diabrotica beetles remain unclear; thus, the potential coexistence zone is unknown. Based on environmental and species occurrence data, we used an ensemble model (EM) to predict the PGDs and overlapping PGD of the three Diabrotica beetles. The n-dimensional hypervolumes concept was used to explore the degree of niche overlap among the three species. The EM showed better reliability than the individual models. According to the EM results, the PGDs and overlapping PGD of the three Diabrotica beetles were mainly distributed in North America, Europe, and Asia. Under the current scenario, D. virgifera has the largest PGD ranges (1615 × 104 km2). In the future, the PGD of this species will expand further and reach a maximum under the SSP5-8.5 scenario in the 2050s (2499 × 104 km2). Diabrotica virgifera showed the highest potential for invasion under the current and future global warming scenarios. Among the three studied species, the degree of ecological niche overlap was the highest for D. undecimpunctata and D. virgifera, with the highest similarity in the PGD patterns and maximum coexistence range. Under global warming, the PGDs of the three Diabrotica beetles are expected to expand to high latitudes. Identifying the PGDs of the three Diabrotica beetles provides an important reference for quarantine authorities in countries at risk of invasion worldwide to develop specific preventive measures against pests.

Impacts of abiotic factors on the growth of three commercial biological control agents, on the growth and mycotoxinogenesis of Fusarium graminearum and on their interaction

BACKGROUND

Evolving climatic conditions impact the behavior of microorganisms. The lack of efficiency of beneficial microorganisms against pathogens can be due to these evolving abiotic factors more favorable to the development and adaptation of pathogens. It is therefore of great interest to understand their impact (especially temperature increase and relative humidity (RH) variation) on pathogenic and non-pathogenic microorganisms. This work aimed to examine the possible effects of increasing temperature (20, 25, 30 and 33 °C) and RH (40%, 50%, 60% and 80%) on the growth and mycotoxin production (deoxynivalenol (DON) and zearalenone (ZEN)) of Fusarium graminearum, on the growth of three commercial biocontrol agents (BCAs; Mycostop®, Xedavir® and Polyversum®) and on the pathogen-BCA interaction.

RESULTS

Results demonstrated that BCAs have contrasting impacts on the growth and mycotoxinogenesis of F. graminearum depending on abiotic factors. At 25 °C and regardless of RH, commercial BCAs limit DON production by F. graminearum, but at 30 °C and intermediate RH, Xedavir® is no longer effective. The ability of Xedavir® to control the production of ZEN production by F. graminearum is also affected by abiotic factors. However, increasing temperature has an opposite effect on its ability to control the accumulation of ZEN. Polyversum® oomycete is the BCA with the most resilient efficacy against F. graminearum toxinogenesis under the different abiotic factors.

CONCLUSION

This work provides new knowledge of the effect of these abiotic parameters on the interaction between BCA and F. graminearum, especially on the production of mycotoxins. It paves the way for the development of efficient and resilient mycotoxin biocontrol strategies using beneficial microorganisms against F. graminearum, thus contributing to global food security. © 2023 Society of Chemical Industry.

Redesigning crop varieties to win the race between climate change and food security

Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.

Available cloned genes and markers for genetic improvement of biotic stress resistance in rice

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

Climate change, host plant availability, and irrigation shape future region-specific distributions of the Sitobion grain aphid complex

BACKGROUND

Understanding where species occur using species distribution models has become fundamental to ecology. Although much attention has been paid to invasive species, questions about climate change related range shifts of widespread insect pests remain unanswered. Here, we incorporated bioclimatic factors and host plant availability into CLIMEX models to predict distributions under future climate scenarios of major cereal pests of the Sitobion grain aphid complex (Sitobion avenae, S. miscanthi, and S. akebiae). Additionally, we incorporated the application of irrigation in our models to explore the relevance of a frequently used management practice that may interact with effects of climate change of the pest distributions.

RESULTS

Our models predicted that the area potentially at high risk of outbreaks of the Sitobion grain aphid complex would increase from 41.3% to 53.3% of the global land mass. This expansion was underlined by regional shifts in both directions: expansion of risk areas in North America, Europe, most of Asia, and Oceania, and contraction of risk areas in South America, Africa, and Australia. In addition, we found that host plant availability limited the potential distribution of pests, while the application of irrigation expanded it.

CONCLUSION

Our study provides insights into potential risk areas of insect pests and how climate, host plant availability, and irrigation affect the occurrence of the Sitobion grain aphid complex. Our results thereby support agricultural policy makers, farmers, and other stakeholders in their development and application of management practices aimed at maximizing crop yields and minimizing economic losses. © 2023 Society of Chemical Industry.

Modeling plant diseases under climate change: evolutionary perspectives

Infectious plant diseases are a major threat to global agricultural productivity, economic development, and ecological integrity. There is widespread concern that these social and natural disasters caused by infectious plant diseases may escalate with climate change and computer modeling offers a unique opportunity to address this concern. Here, we analyze the intrinsic problems associated with current modeling strategies and highlight the need to integrate evolutionary principles into polytrophic, eco-evolutionary frameworks to improve predictions. We particularly discuss how evolutionary shifts in functional trade-offs, relative adaptability between plants and pathogens, ecosystems, and climate preferences induced by climate change may feedback to future plant disease epidemics and how technological advances can facilitate the generation and integration of this relevant knowledge for better modeling predictions.

Whether curse or blessing: A counterintuitive perspective on global pest thrips infestation under climatic change with implications to agricultural economics

The improvement and application of pest models to predict yield losses is still a challenge for the scientific community. However, pest models were targeted chiefly towards scheduling scouting or pesticide applications to deal with pest infestation. Thysanoptera (thrips) significantly impact the productivity of many economically important crops worldwide. Until now, no comprehensive study is available on the global distribution of pest thrips, as well as on the extent of cropland vulnerability worldwide. Further, nothing is known about the climate change impacts on these insects. Thus the present study was designed to map the global distribution and quantify the extent of cropland vulnerability in the present and future climate scenarios using data of identified pest thrips within the genus, i.e., Thrips, Frankliniella, and Scirtothrips. Our found significant niche contraction under the climate change scenarios and thrips may reside primarily in their thermal tolerance thresholds. About 3,98,160 km² of cropland globally was found to be affected in the present scenario. However, it may significantly reduce to 5530 Km² by 2050 and 1990 km² by 2070. Further, the thrips distribution mostly getting restricted to Eastern North America, the North-western of the Indian sub-continent, and the north of Europe. Among all realms, thrips may lose ground in the Indo-Malayan realm at the most and get restricted to only 27 out of 825 terrestrial ecoregions. The agrarian communities of the infested regions may get benefit if these pests get wiped out, but on the contrary, we may lose species diversity. Moreover, the vacated niche may attract other invasive species, which may seriously impact the species composition and agricultural productivity. The present study findings can be used in making informed decisions about prioritizing future economic and research investments on the thrips in light of anticipated climate change impacts.

In the wind: Invasive species travel along predictable atmospheric pathways

Invasive species such as insects, pathogens, and weeds reaching new environments by traveling with the wind, represent unquantified and difficult-to-manage biosecurity threats to human, animal, and plant health in managed and natural ecosystems. Despite the importance of these invasion events, their complexity is reflected by the lack of tools to predict them. Here, we provide the first known evidence showing that the long-distance aerial dispersal of invasive insects and wildfire smoke, a potential carrier of invasive species, is driven by atmospheric pathways known as Lagrangian coherent structures (LCS). An aerobiological modeling system combining LCS modeling with species biology and atmospheric survival has the potential to transform the understanding and prediction of atmospheric invasions. The proposed modeling system run in forecast or hindcast modes can inform high-risk invasion events and invasion source locations, making it possible to locate them early, improving the chances of eradication success.

Genome-wide association studies in plant pathosystems: success or failure?

Harnessing natural genetic variation is an established alternative to artificial genetic variation for investigating the molecular dialog between partners in plant pathosystems. Herein, we review the successes of genome-wide association studies (GWAS) in both plants and pathogens. While GWAS in plants confirmed that the genetic architecture of disease resistance is polygenic, dynamic during the infection kinetics, and dependent on the environment, GWAS shortened the time of identification of quantitative trait loci (QTLs) and revealed both complex epistatic networks and a genetic architecture dependent upon the geographical scale. A similar picture emerges from the few GWAS in pathogens. In addition, the ever-increasing number of functionally validated QTLs has revealed new molecular plant defense mechanisms and pathogenicity determinants. Finally, we propose recommendations to better decode the disease triangle.

Aggregation pheromones have a non-linear effect on oviposition behavior in Drosophila melanogaster

Female fruit flies (Drosophila melanogaster) oviposit at communal sites where the larvae may cooperate or compete for resources depending on group size. This offers a model system to determine how females assess quantitative social information. We show that the concentration of pheromones found on a substrate increases linearly with the number of adult flies that have visited that site. Females prefer oviposition sites with pheromone concentrations corresponding to an intermediate number of previous visitors, whereas sites with low or high concentrations are unattractive. This dose-dependent decision is based on a blend of 11-cis-Vaccenyl Acetate (cVA) indicating the number of previous visitors and heptanal (a novel pheromone deriving from the oxidation of 7-Tricosene), which acts as a dose-independent co-factor. This response is mediated by detection of cVA by odorant receptor neurons Or67d and Or65a, and at least five different odorant receptor neurons for heptanal. Our results identify a mechanism allowing individuals to transform a linear increase of pheromones into a non-linear behavioral response.

Himalayan mountains imposing a barrier on gene flow of wheat yellow rust pathogen in the bordering regions of Pakistan and China

The wheat yellow rust pathogen has been shown to be diverse and potentially originated in the Himalayan region. Although Himalayan populations of Pakistan, Nepal and Bhutan have been previously compared, little is known about the relative divergence and diversity in Puccinia striiformis populations in the bordering regions of Pakistan and China. To assess the relative diversity and divergence in these regions of Pakistan (Gilgit-Baltistan, Hazara and Azad Jammu Kashmir) and China (Xinjiang, Qinghai, Tibet, Sichuan, Guizhou and Yunnan), a total of 1245 samples were genotyped using 17 microsatellite SSR markers. A clear divergence was observed between the bordering regions of Pakistan and China (F_ST = 0.28) without any resampling of genetic groups and multilocus genotypes across two sides of the Himalayan mountains. The closest subpopulations across the two countries were Xinjiang and Gilgit-Baltistan (Nei's distance = 0.147), which were close geographically. A very high diversity and recombinant population structure was observed in both populations, though slightly higher in China (Genotypic diversity = 0.970; r¯d = 0.000) than in Pakistan (Genotypic diversity = 0.902; r¯d = 0.065). The distribution of genetic groups and resampling of MLGs revealed more gene flow across Yunnan, Guizhou and Sichuan regions in China, while between Hazara and Azad-Jammu Kashmir in Pakistan. The lack of gene flow between Pakistan and China populations is due to geographical barriers and a large patch of land without wheat. The information on the relative diversity and divergence in different geographical zones of the pathogen center of diversity and neighboring region should be considered in resistant wheat deployment while considering the invasion potential of the pathogen at regional and global contexts.

Temperature increase modifies susceptibility to Verticillium wilt in Medicago spp and may contribute to the emergence of more aggressive pathogenic strains

Global warming is expected to have a direct impact on plant disease patterns in agro-eco-systems. However, few analyses report the effect of moderate temperature increase on disease severity due to soil-borne pathogens. For legumes, modifications of root plant-microbe interactions either mutualistic or pathogenic due to climate change may have dramatic effects. We investigated the effect of increasing temperature on the quantitative disease resistance to Verticillium spp., a major soil-borne fungal pathogen, in the model legume Medicago truncatula and the crop M. sativa. First, twelve pathogenic strains isolated from various geographical origin were characterized with regard to their in vitro growth and pathogenicity at 20°C, 25°C and 28°C. Most of them exhibited 25°C as the optimum temperature for in vitro parameters, and between 20°C and 25°C for pathogenicity. Second, a V. alfalfae strain was adapted to the higher temperature by experimental evolution, i.e. three rounds of UV mutagenesis and selection for pathogenicity at 28°C on a susceptible M. truncatula genotype. Inoculation of monospore isolates of these mutants on resistant and susceptible M. truncatula accessions revealed that at 28°C they were all more aggressive than the wild type strain, and that some had acquired the ability to cause disease on resistant genotype. Third, one mutant strain was selected for further studies of the effect of temperature increase on the response of M. truncatula and M. sativa (cultivated alfalfa). The response of seven contrasted M. truncatula genotypes and three alfalfa varieties to root inoculation was followed using disease severity and plant colonization, at 20°C, 25°C and 28°C. With increasing temperature, some lines switched from resistant (no symptoms, no fungus in the tissues) to tolerant (no symptoms but fungal growth into the tissues) phenotypes, or from partially resistant to susceptible. Further studies in greenhouse evidence the reduction in plant fitness due to disease in susceptible lines. We thus report that root pathogenic interactions are affected by anticipated global warming, with trends towards increased plant susceptibility and larger virulence for hot-adapted strains. New threats due to hot-adapted strains of soil-borne pathogens, with possibly wider host range and increased aggressiveness, might occur.

Climate change and plant pathogens

Global food security is threatened by climate change, both directly through responses of crop physiology and productivity, and indirectly through responses of plant-associated microbiota, including plant pathogens. While the interactions between host plants, pathogens and environmental drivers can be complex, recent research is beginning to indicate certain overall patterns in how plant diseases will affect crop production in future. Here, we review the results of three methodological approaches: large-scale observational studies, process-based disease models and experimental comparisons of pathosystems under current and future conditions. We find that observational studies have tended to identify rising temperatures as the primary driver of disease impact. Process-based models suggest that rising temperatures will lead to latitudinal shifts in disease pressure, but drying conditions could mitigate disease risk. Experimental studies suggest that rising atmospheric CO₂ will exacerbate disease impacts. Plant diseases may therefore counteract any crop yield increases due to climate change.

Plant defense under Arctic light conditions: Can plants withstand invading pests?

Global warming is predicted to change the growth conditions for plants and crops in regions at high latitudes (>60° N), including the Arctic. This will be accompanied by alterations in the composition of natural plant and pest communities, as herbivorous arthropods will invade these regions as well. Interactions between previously non-overlapping species may occur and cause new challenges to herbivore attack. However, plants growing at high latitudes experience less herbivory compared to plants grown at lower latitudes. We hypothesize that this finding is due to a gradient of constitutive chemical defense towards the Northern regions. We further hypothesize that higher level of defensive compounds is mediated by higher level of the defense-related phytohormone jasmonate. Because its biosynthesis is light dependent, Arctic summer day light conditions can promote jasmonate accumulation and, hence, downstream physiological responses. A pilot study with bilberry (Vaccinium myrtillus) plants grown under different light regimes supports the hypothesis.

Long-term sex-dependent inflammatory response of adult frogs to ammonium exposure during the larval stage

Among others, the global change involves a worldwide increase in cropland area, with the concomitant rise in nitrogenous fertilizer supplementation and species range alterations, including parasites and pathogens. As most animals rely on their immune systems against these infectious agents, studying the potential effects of nitrogenous compounds on animal immune response is vital to understand their susceptibility to infections under these altered circumstances. Being subjected to an alarming process of global declines, amphibians are the object of particular attention, given their sensitivity to these compounds, especially to ammonium. Moreover, whereas adults can actively avoid polluted patches, larvae are confined within their waterbodies, thus exposed to contaminants in it. In this work, we test whether chronic exposure to a sublethal dose of ammonium during the larval stage of Pelophylax perezi frogs, released from all contamination after metamorphosis, leads to impaired inflammatory response to phytohemagglutinin in adults. We also test whether such a response differs between agrosystem individuals as compared with conspecifics from natural habitats. We found negative carryover effects of chronic exposure of larvae to ammonium on adult inflammatory response, which could imply a greater susceptibility to pathogens and parasites. However, this damage is only true for males, which, according to the immunocompetence handicap hypothesis, could be a consequence of a testosterone-triggered impairment of male immune function. In disagreement with our prediction, however, we detected no differences in the inflammatory response of agrosystem frogs to phytohemagglutinin as compared with natural habitat conspecifics.

Introduction to the Collection: Climate Change, Insect Pests, and Beneficial Arthropods in Production Systems

Climate change is expected to alter pressure from insect pests and the abundance and effectiveness of insect pollinators across diverse agriculture and forestry systems. In response to warming, insects are undergoing or are projected to undergo shifts in their geographic ranges, voltinism, abundance, and phenology. Drivers include direct effects on the focal insects and indirect effects mediated by their interactions with species at higher or lower trophic levels. These climate-driven effects are complex and variable, sometimes increasing pest pressure or reducing pollination and sometimes with opposite effects depending on climatic baseline conditions and the interplay of these drivers. This special collection includes several papers illustrative of these biological effects on pests and pollinators. In addition, in response to or anticipating climate change, producers are modifying production systems by introducing more or different crops into rotations or as cover crops or intercrops or changing crop varieties, with potentially substantial effects on associated insect communities, an aspect of climate change that is relatively understudied. This collection includes several papers illustrating these indirect production system-level effects. Together, biological and management-related effects on insects comprise the necessary scope for anticipating and responding to the effects of climate change on insects in agriculture and forest systems.

Strategies for the production of dsRNA biocontrols as alternatives to chemical pesticides

Current crop pest control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes and agricultural practices. However, many insects, plant viruses, and fungi have no current means of control or have developed resistance against traditional pesticides. dsRNA is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. The successful commercialisation of dsRNA based biocontrols for effective pest management strategies requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. A number of methods exist for the production and delivery of dsRNA based biocontrols and here we review alternative methods currently employed and emerging new approaches for their production. Additionally, we highlight potential challenges that will need to be addressed prior to widespread adoption of dsRNA biocontrols as novel sustainable alternatives to traditional chemical pesticides.

Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus

Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.

Climate Change Effects on Pathogen Emergence: Artificial Intelligence to Translate Big Data for Mitigation

Plant pathology has developed a wide range of concepts and tools for improving plant disease management, including models for understanding and responding to new risks from climate change. Most of these tools can be improved using new advances in artificial intelligence (AI), such as machine learning to integrate massive data sets in predictive models. There is the potential to develop automated analyses of risk that alert decision-makers, from farm managers to national plant protection organizations, to the likely need for action and provide decision support for targeting responses. We review machine-learning applications in plant pathology and synthesize ideas for the next steps to make the most of these tools in digital agriculture. Global projects, such as the proposed global surveillance system for plant disease, will be strengthened by the integration of the wide range of new data, including data from tools like remote sensors, that are used to evaluate the risk ofplant disease. There is exciting potential for the use of AI to strengthen global capacity building as well, from image analysis for disease diagnostics and associated management recommendations on farmers' phones to future training methodologies for plant pathologists that are customized in real-time for management needs in response to the current risks. International cooperation in integrating data and models will help develop the most effective responses to new challenges from climate change.

Field and Landscape Risk Factors Impacting Flavescence Dorée Infection: Insights from Spatial Bayesian Modeling in the Bordeaux Vineyards

Flavescence dorée (FD) is a quarantine disease threatening European vineyards. Its management is based on mandatory insecticide treatments and the uprooting of infected plants identified during annual surveys. Field surveys are currently not optimized because the drivers affecting FD spread in vineyard landscapes remain poorly understood. We collated a georeferenced dataset of FD detection, collected from 34,581 vineyard plots over 5 years in the South West France wine region. Spatial models fitted with integrated nested Laplace approximation were used to identify local and landscape factors affecting FD detection and infection. Our analysis highlights the importance of sampling period on FD detection and of local practices and landscape context on FD infection. At field scale, altitude and cultivar choice were the main factors affecting FD infection. In particular, the odds ratio of FD infection in fields planted with the susceptible Cabernet Sauvignon, Cabernet Franc, or Muscadelle varieties were approximately twice those in fields planted with the less susceptible Merlot. Field infection was also affected by the field's immediate surroundings (within a circle with a radius of 150 to 200 m), corresponding to landscapes of 7 to 12 ha. In particular, the probability of FD infection increased with the proportions of forest and urban land and with the proportion of susceptible cultivars, demonstrating that the cultivar composition impacts FD epidemiology at landscape scale. The satisfactory predictive performance of the model for identifying districts with a prevalence of FD detection >10% of the fields suggests that it could be used to target areas in which future surveys would be most valuable.

Multidecadal, continent-level analysis indicates agricultural practices impact wheat aphid loads more than climate change

Temperature has a large influence on insect abundances, thus under climate change, identifying major drivers affecting pest insect populations is critical to world food security and agricultural ecosystem health. Here, we conducted a meta-analysis with data obtained from 120 studies across China and Europe from 1970 to 2017 to reveal how climate and agricultural practices affect populations of wheat aphids. Here we showed that aphid loads on wheat had distinct patterns between these two regions, with a significant increase in China but a decrease in Europe over this time period. Although temperature increased over this period in both regions, we found no evidence showing climate warming affected aphid loads. Rather, differences in pesticide use, fertilization, land use, and natural enemies between China and Europe may be key factors accounting for differences in aphid pest populations. These long-term data suggest that agricultural practices impact wheat aphid loads more than climate warming.

Occurrence of Macrophomina phaseolina on Chickpea in Italy: Pathogen Identification and Characterization

Climate change has led to the spread of plant pathogens in novel environments, causing dramatic crop losses and economic damage. Botryosphaeriaceae represents a massive fungal family, containing a huge number of plant pathogens, which are able to infect several hosts. Among them, Macrophomina phaseolina is a necrotrophic fungus, responsible for several plant diseases, including the soft stem rot of common bean, crown rot on strawberry and charcoal rot of several legumes. Here, Macrophomina, causing crown charcoal rot in chickpeas, was isolated from symptomatic plants in Cicerale (SA), Campania, South Italy. Morphological and molecular characterization was carried out and pathogenicity tests were performed. Phylogenetic analyses were performed comparing Macrophomina strains coming from different geographic areas and hosts. The experiments confirmed the pathogenicity of the isolate CREA OF 189.2 on chickpea, while host range highlighted the polyphagous nature of this strain; thus, symptoms were reported on lentils, common bean and cantaloupe. The multidisciplinary approach allows us to increase the knowledge about this emerging pathogen. To the best of our knowledge, this is the first report on Macrophomina phaseolina from chickpeas in Italy.

The Impacts of Climate Change on the Potential Distribution of Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae) in China

Simple Summary

Plodia interpunctella (Hübner) is an important grain storage pest in China that is distributed in almost every province and that has caused huge economic losses. In this study, we adjusted the biological parameters of the Indian grain borer and then used the CLIMEX model to predict the detailed potential distribution of P. interpunctella in China under current and future conditions. Under historical climatic conditions, the central, northeastern, and southern regions of China are highly suitable habitats for it. Because of temperature change in the future climate, suitable habitats will increase in the eastern part of Qinghai and will decrease in the mid-eastern, northeastern, and southeastern parts of China. This study provides important information for controlling the further spread of the Indian corn borer in China.

Abstract

The Indian meal moth Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae) is a notorious stored-grain pest that can be found in most parts of China. The corpses, excretions, and other secretions of P. interpunctella larvae cause serious grain pollution, seriously affecting the nutritional and economic value of stored grain in China. To elucidate the potential distribution of P. interpunctella in China, we used the CLIMEX 4.0 model to project the potential distribution of the pest using historical climate data (1960–1990) and estimated future climate data (2030, 2050, and 2070). Under the historical climate situation, P. interpunctella was distributed in most areas of China, and its highly favorable habitats account for 48.14% of its total potential distribution. Because of temperature change in the future climate, suitable habitats will increase in the eastern part of Qinghai and will decrease in the mid-eastern, northeastern, and southeastern parts of China. Under these scenarios, the area of this pest’s highly favorable habitat will be reduced by 1.24 million km², and its proportion will decrease to about 28.48%. These predicted outcomes will help to distinguish the impact of climate change on the potential distribution of P. interpunctella, thereby providing important information to design early forecasting and strategies to prevent pest harm to stored grain.

Uncovering the Research Gaps to Alleviate the Negative Impacts of Climate Change on Food Security: A Review

Climatic variability has been acquiring an extensive consideration due to its widespread ability to impact food production and livelihoods. Climate change has the potential to intersperse global approaches in alleviating hunger and undernutrition. It is hypothesized that climate shifts bring substantial negative impacts on food production systems, thereby intimidating food security. Vast developments have been made addressing the global climate change, undernourishment, and hunger for the last few decades, partly due to the increase in food productivity through augmented agricultural managements. However, the growing population has increased the demand for food, putting pressure on food systems. Moreover, the potential climate change impacts are still unclear more obviously at the regional scales. Climate change is expected to boost food insecurity challenges in areas already vulnerable to climate change. Human-induced climate change is expected to impact food quality, quantity, and potentiality to dispense it equitably. Global capabilities to ascertain the food security and nutritional reasonableness facing expeditious shifts in biophysical conditions are likely to be the main factors determining the level of global disease incidence. It can be apprehended that all food security components (mainly food access and utilization) likely be under indirect effect via pledged impacts on ménage, incomes, and damages to health. The corroboration supports the dire need for huge focused investments in mitigation and adaptation measures to have sustainable, climate-smart, eco-friendly, and climate stress resilient food production systems. In this paper, we discussed the foremost pathways of how climate change impacts our food production systems as well as the social, and economic factors that in the mastery of unbiased food distribution. Likewise, we analyze the research gaps and biases about climate change and food security. Climate change is often responsible for food insecurity issues, not focusing on the fact that food production systems have magnified the climate change process. Provided the critical threats to food security, the focus needs to be shifted to an implementation oriented-agenda to potentially cope with current challenges. Therefore, this review seeks to have a more unprejudiced view and thus interpret the fusion association between climate change and food security by imperatively scrutinizing all factors.

Chemically-modified dsRNA induces RNAi effects in insects in vitro and in vivo: A potential new tool for improving RNA-based plant protection

Global agriculture loses over $100 billion of produce annually to crop pests such as insects. Many of these crop pests either are not currently controlled by artificial means or have developed resistance against chemical pesticides. Long dsRNAs are capable of inducing RNAi in insects and are emerging as novel, highly selective alternatives for sustainable insect management strategies. However, there are significant challenges associated with RNAi efficacy in insects. In this study, we synthesized a range of chemically modified long dsRNAs in an approach to improve nuclease resistance and RNAi efficacy in insects. Our results showed that dsRNAs containing phosphorothioate modifications demonstrated increased resistance to southern green stink bug saliva nucleases. Phosphorothioate-modified and 2′-fluoro-modified dsRNA also demonstrated increased resistance to degradation by soil nucleases and increased RNAi efficacy in Drosophila melanogaster cell cultures. In live insects, we found chemically modified long dsRNAs successfully resulted in mortality in both stink bug and corn rootworm. These results provide further mechanistic insight into the dependence of RNAi efficacy on nucleotide modifications in the sense or antisense strand of the dsRNA in insects and demonstrate for the first time that RNAi can successfully be triggered by chemically modified long dsRNAs in insect cells or live insects.

Contrasting National Plant Protection Needs, Perceptions and Techno-Scientific Capabilities in the Asia-Pacific Region

Pests and pathogens inflict considerable losses in global agri-food production and regularly trigger the (indiscriminate) use of synthetic pesticides. In the Asia-Pacific, endemic and invasive organisms compromise crop yields, degrade farm profitability and cause undesirable social-environmental impacts. In this study, we systematically assess the thematic foci, coherence and inclusiveness of plant protection programs of 11 Asia-Pacific countries. Among 23 economically important diseases and 55 pests, survey respondents identified rice blast, rice brown planthopper, citrus greening disease, Tephritid fruit flies and fall armyworm as threats of regional allure. These organisms are thought to lower crop yields by 20–35% and cause management expenditures up to US$2,250 per hectare and year. Though decision-makers are familiar with integrated pest management (IPM), national programs are invariably skewed toward curative pesticide-intensive control. Pesticide reductions up to 50–100% are felt to be feasible and potentially can be attained through full-fledged IPM campaigns and amended policies. To rationalize farmers' pesticide use, decision criteria (e.g., economic thresholds) wait to be defined for multiple crop x pest systems and (participatory) training needs to be conducted e.g., on (pest, disease) symptom recognition or field-level scouting. Efforts are equally needed to amend stakeholder perceptions on ecologically based measures e.g., biological control. Given that several Asia–Pacific countries possess robust techno-scientific capacities in various IPM domains (e.g., taxonomy, molecular diagnostics, socioeconomics), they can take on an active role in regionally coordinated campaigns. As such, one can reinvigorate IPM and ensure that preventative, non-chemical pest management ultimately becomes the norm instead of the exception throughout the Asia–Pacific.

Climate Adaptation, Drought Susceptibility, and Genomic-Informed Predictions of Future Climate Refugia for the Australian Forest Tree Eucalyptus globulus

Understanding the capacity of forest tree species to adapt to climate change is of increasing importance for managing forest genetic resources. Through a genomics approach, we modelled spatial variation in climate adaptation within the Australian temperate forest tree Eucalyptus globulus, identified putative climate drivers of this genomic variation, and predicted locations of future climate refugia and populations at-risk of future maladaptation. Using 812,158 SNPs across 130 individuals from 30 populations (i.e., localities) spanning the species’ natural range, a gradientForest algorithm found 1177 SNPs associated with locality variation in home-site climate (climate-SNPs), putatively linking them to climate adaptation. Very few climate-SNPs were associated with population-level variation in drought susceptibility, signalling the multi-faceted nature and complexity of climate adaptation. Redundancy analysis (RDA) showed 24% of the climate-SNP variation could be explained by annual precipitation, isothermality, and maximum temperature of the warmest month. Spatial predictions of the RDA climate vectors associated with climate-SNPs allowed mapping of genomically informed climate selective surfaces across the species’ range under contemporary and projected future climates. These surfaces suggest over 50% of the current distribution of E. globulus will be outside the modelled adaptive range by 2070 and at risk of climate maladaptation. Such surfaces present a new integrated approach for natural resource managers to capture adaptive genetic variation and plan translocations in the face of climate change.

Weather fluctuation can override the effects of integrated nutrient management on fungal disease incidence in the rice fields in Taiwan

Both weather fluctuation and farming system influence the epidemiology of crop diseases. However, short-term experiments are difficult to mechanistically extrapolate into long-term ecological responses. Using a mechanistic model with Bayesian inference, long-term data spanning 10 years were used to construct relationships among weather fluctuation (temperature, relative humidity, wind, and rainfall), farming system (conventional and low-external-input farming), and crop disease in experimental rice fields in Taiwan. Conventional and low-external-input farming had similar influences on the disease incidence of rice blast. Temperature had a positive influence on the disease incidence only under high relative humidity. Rainfall positively affected the disease incidence until an optimum level of rainfall. Low-external-input farming, with a lower application of fertilizers and other sustainable nutrient management, achieved similar effects on the disease incidence to those achieved by conventional farming. This suggests that weather fluctuation may override the effect of the farming systems on fungal disease incidence in rice fields.

Evolution of thermal physiology alters the projected range of threespine stickleback under climate change

Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of its range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback (Gasterosteus aculeatus). Using these data, we created geographical range projections using a mechanistic niche area approach under two climate change scenarios. Under both scenarios, trait data were either static ("no evolution" models), allowed to evolve at observed evolutionary rates ("evolution" models) or allowed to evolve at a rate of evolution scaled by the trait variance that is explained by quantitative trait loci (QTL; "scaled evolution" models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.

Comparing, evaluating and combining statistical species distribution models and CLIMEX to forecast the distributions of emerging crop pests

BACKGROUND

Forecasting the spread of emerging pests is widely requested by pest management agencies in order to prioritise and target efforts. Two widely used approaches are statistical Species Distribution Models (SDMs) and CLIMEX, which uses ecophysiological parameters. Each have strengths and weaknesses. SDMs can incorporate almost any environmental condition and their accuracy can be formally evaluated to inform managers. However, accuracy is affected by data availability and can be limited for emerging pests, and SDMs usually predict year-round distributions, not seasonal outbreaks. CLIMEX can formally incorporate expert ecophysiological knowledge and predicts seasonal outbreaks. However, the methods for formal evaluation are limited and rarely applied. We argue that both approaches can be informative and complementary, but we need tools to integrate and evaluate their accuracy. Here we develop such an approach, and test it by forecasting the potential global range of the tomato pest Tuta absoluta.

RESULTS

The accuracy of previously developed CLIMEX and new statistical SDMs were comparable on average, but the best statistical SDM techniques and environmental data substantially outperformed CLIMEX. The ensembled approach changes expectations of T. absoluta's spread. The pest's environmental tolerances and potential range in Africa, the Arabian Peninsula, Central Asia and Australia will be larger than previous estimates.

CONCLUSION

We recommend that CLIMEX be considered one of a suite of SDM techniques and thus evaluated formally. CLIMEX and statistical SDMs should be compared and ensembled if possible. We provide code that can be used to do so when employing the biomod suite of SDM techniques. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Changes in the genetic composition of Myzus persicae nicotianae populations in Chile and frequency of insecticide resistance mutations

Myzus persicae is a cosmopolitan aphid that is highly polyphagous and an important agricultural pest. The subspecies M. persicae nicotianae has been described for highly specialized phenotypes adapted to tobacco (Nicotiana tabacum). In Chile, the population of M. persicae nicotianae was originally composed of a single red genotype that did not possess insecticide resistance mutations. However, in the last decade, variation in the colour of tobacco aphids has been observed in the field. To determine whether this variation stems from the presence of new genotypes, sampling was carried out across the entire distribution of tobacco cultivation regions in Chile. The aphids collected were genotyped, and the frequency of kdr (L1014F), super-kdr (M918T), modification of acetylcholinesterase (MACE) and nicotinic acetylcholine receptor β subunit (nAChRβ) mutations associated with insecticide resistance was determined. A total of 16 new genotypes of M. persicae nicotianae were detected in Chile: four of them possessed the MACE mutation, and none of them possessed the kdr, super-kdr or nAChRβ mutation. The previously described red genotype was not detected in any of the sampled fields over two seasons. These results raise questions about the mechanisms underlying changes in the genetic structure of M. persicae nicotianae populations in Chile. Future research aimed at addressing these questions could provide new insight into aphid evolution and agricultural practices.

Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future

Simple Summary

Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today.

Abstract

Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.

Application of Gene Editing for Climate Change in Agriculture

Climate change imposes a severe threat to agricultural systems, food security, and human nutrition. Meanwhile, efforts in crop and livestock gene editing have been undertaken to improve performance across a range of traits. Many of the targeted phenotypes include attributes that could be beneficial for climate change adaptation. Here, we present examples of emerging gene editing applications and research initiatives that are aimed at the improvement of crops and livestock in response to climate change, and discuss technical limitations and opportunities therein. While only few applications of gene editing have been translated to agricultural production thus far, numerous studies in research settings have demonstrated the potential for potent applications to address climate change in the near future.

Nonlinear shifts in infectious rust disease due to climate change

Range shifts of infectious plant disease are expected under climate change. As plant diseases move, emergent abiotic-biotic interactions are predicted to modify their distributions, leading to unexpected changes in disease risk. Evidence of these complex range shifts due to climate change, however, remains largely speculative. Here, we combine a long-term study of the infectious tree disease, white pine blister rust, with a six-year field assessment of drought-disease interactions in the southern Sierra Nevada. We find that climate change between 1996 and 2016 moved the climate optimum of the disease into higher elevations. The nonlinear climate change-disease relationship contributed to an estimated 5.5 (4.4-6.6) percentage points (p.p.) decline in disease prevalence in arid regions and an estimated 6.8 (5.8-7.9) p.p. increase in colder regions. Though climate change likely expanded the suitable area for blister rust by 777.9 (1.0-1392.9) km² into previously inhospitable regions, the combination of host-pathogen and drought-disease interactions contributed to a substantial decrease (32.79%) in mean disease prevalence between surveys. Specifically, declining alternate host abundance suppressed infection probabilities at high elevations, even as climatic conditions became more suitable. Further, drought-disease interactions varied in strength and direction across an aridity gradient-likely decreasing infection risk at low elevations while simultaneously increasing infection risk at high elevations. These results highlight the critical role of aridity in modifying host-pathogen-drought interactions. Variation in aridity across topographic gradients can strongly mediate plant disease range shifts in response to climate change.

Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems

Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.

The persistent threat of emerging plant disease pandemics to global food security

Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world. Now a global human pandemic is threatening the health of millions on our planet. A stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages. In order to tackle these grand challenges, a new set of tools that include disease surveillance and improved detection technologies including pathogen sensors and predictive modeling and data analytics are needed to prevent future outbreaks. Herein, we describe an integrated research agenda that could help mitigate future plant disease pandemics.

How Do Pathogens Evolve Novel Virulence Activities?

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plant pest surveillance: from satellites to molecules

Plant pests and diseases impact both food security and natural ecosystems, and the impact has been accelerated in recent years due to several confounding factors. The globalisation of trade has moved pests out of natural ranges, creating damaging epidemics in new regions. Climate change has extended the range of pests and the pathogens they vector. Resistance to agrochemicals has made pathogens, pests, and weeds more difficult to control. Early detection is critical to achieve effective control, both from a biosecurity as well as an endemic pest perspective. Molecular diagnostics has revolutionised our ability to identify pests and diseases over the past two decades, but more recent technological innovations are enabling us to achieve better pest surveillance. In this review, we will explore the different technologies that are enabling this advancing capability and discuss the drivers that will shape its future deployment.

Differential gene responses in different varieties of pomegranate during the pathogenesis of Xanthomonas axonopodis pv. punicae

Bacterial blight (BB) caused by Xanthomonas axonopodis pv. punicae (Xap) is the major scourge in pomegranate cultivation leading to an extensive yield loss up to 60-80%. Hence, identifying a novel resistance source for BB is very necessary for developing a suitable management strategy. Host range analysis and cross-inoculation studies revealed that Xap is specific to pomegranate and there are no alternative hosts to the pathogen. Screening of 149 accessions recorded the varied disease resistance levels with mean disease severity of 30.67%. Accession lines IC318735, IC318724, and IC318762 exhibited maximum disease tolerance by exhibiting the lowest disease severity of 4.91, 5.66, and 6.82%, respectively. Comparative expression analysis of defence genes in IC318724 and IC318735 recorded significant upregulation of phenylalanine ammonia-lyase (PAL), callose synthase-3 (CS3), chitinase, pathogenesis-related protein-1 (PR1), and pathogenesis-related protein-10 (PR10), indicating these genes might be actively involved in conferring disease tolerance. Abiotic elicitors were tested to induce systemic resistance in agronomically superior and widely adapted variety Bhagwa for managing BB of pomegranate. Among the various elicitors tested; proline (600 ppm), gamma-aminobutyric acid (600 ppm), chitosan (600 ppm), β-aminobutyric acid (200 ppm), laminarin (600 ppm), and eugenol (200 ppm) recorded maximum disease protection in prophylactic treatment with disease protection of 89.59, 88.59, 87.15, 86.08, 81.05, and 78.72%, respectively. Similar observations were recorded when these were applied as curative treatment. The present study will broaden our understanding of host-pathogen interactions during BB infection in pomegranate, also aid in developing ideal approach for developing effective disease management.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02721-y.

Trends in Varietal Diversity of Main Staple Crops in Asia and Africa and Implications for Sustainable Food Systems

Crop species and varietal diversity on farm have the potential to trigger multiple regulating and provisioning ecosystem services. The latter is commonly assessed through targeted studies covering a select number of geographies and crop species, precluding comparisons across crops and at scale. This study draws on a large dataset on the varietal release dynamics for 11 major food crops in 44 countries of Asia and Africa to assess trends in diversity across crops and regions with a 50-year perspective. Our results show an increasing reduction of crop varietal diversity linked to the spatial displacement of traditional landraces. This trend occurs at a faster rate in Asia than in Africa. So-called mega varieties tend to increasingly dominate agricultural landscapes, adding to spatial homogeneity. We further found a negative association between varietal richness and its relative abundance, challenging the relationship between crop improvement and varietal diversity. Our results show that among cereal, pulse, and root and tuber crops, varietal diversity is lowest for cereals in Asia and highest for root and tubers in Africa. The analysis contributes new information useful to prioritize crops for which increasing varietal diversity may lead to more sustainable food systems.

Fight hard or die trying: when plants face pathogens under heat stress

In their natural environment, plants are exposed to biotic or abiotic stresses that occur sequentially or simultaneously. Plant responses to these stresses have been studied widely and have been well characterised in simplified systems involving single plant species facing individual stress. Temperature elevation is a major abiotic driver of climate change and scenarios have predicted an increase in the number and severity of epidemics. In this context, here we review the available data on the effect of heat stress on plant-pathogen interactions. Considering 45 studies performed on model or crop species, we discuss the possible implications of the optimum growth temperature of plant hosts and pathogens, mode of stress application and temperature variation on resistance modulations. Alarmingly, most identified resistances are altered under temperature elevation, regardless of the plant and pathogen species. Therefore, we have listed current knowledge on heat-dependent plant immune mechanisms and pathogen thermosensory processes, mainly studied in animals and human pathogens, that could help to understand the outcome of plant-pathogen interactions under elevated temperatures. Based on a general overview of the mechanisms involved in plant responses to pathogens, and integrating multiple interactions with the biotic environment, we provide recommendations to optimise plant disease resistance under heat stress and to identify thermotolerant resistance mechanisms.