Next-generation biological control: the need for integrating genetics and genomics

Direct parental CRISPR gene editing in the predatory bug Orius strigicollis, a biocontrol agent against small arthropods

BACKGROUND

The predatory flower bug Orius strigicollis serves as a valuable biocontrol agent against small arthropods; however, its effectiveness can vary, especially when population establishment fails due to low prey/pest densities. A promising approach to improve the efficacy of O. strigicollis as a biocontrol agent is through gene editing. However, as females lay their eggs in plant tissue, the conventional embryo injection approach is challenging in this species.

RESULTS

In this study, we aimed to develop an efficient and practical gene editing technique for O. strigicollis using direct parental CRISPR (DIPA-CRISPR). Female bugs at various postemergence stages received Cas9 ribonucleoprotein injections, with subsequent genotyping of their offspring (G0) using PCR and a heteroduplex mobility assay. We targeted the kynurenine 3-monooxygenase gene (cinnabar), pivotal for insect ommochrome pigment biosynthesis. Through experimental optimization, we achieved a peak gene editing efficiency of 52%, i.e., 52% of G0 progeny carried gene-edited alleles when injecting 1 day postemergence. Notably, some gene-edited G0 adults exhibited a red-eye mosaic phenotype, in contrast to the black-eyed wild type. Crossing experiments confirmed the heritability of the introduced mutations in the subsequent generation (G1), enabling the establishment of a cinnabar-knockout line with bright red eyes.

CONCLUSION

We demonstrate that our DIPA-CRISPR gene editing method tailored for O. strigicollis is efficient and practical. Our findings highlight the potency of DIPA-CRISPR as a tool for O. strigicollis genetic engineering and suggest broader applications for enhancing other biocontrol agents. © 2024 Society of Chemical Industry.

High-quality genome of the zoophytophagous stink bug, Nesidiocoris tenuis, informs their food habit adaptation

The zoophytophagous stink bug, Nesidiocoris tenuis, is a promising natural enemy of micro-pests such as whiteflies and thrips. This bug possesses both phytophagous and entomophagous food habits, enabling it to obtain nutrition from both plants and insects. This trait allows us to maintain its population density in agricultural fields by introducing insectary plants, even when the pest prey density is extremely low. However, if the bugs' population becomes too dense, they can sometimes damage crop plants. This dual character seems to arise from the food preferences and chemosensation of this predator. To understand the genomic landscape of N. tenuis, we examined the whole genome sequence of a commercially available Japanese strain. We used long-read sequencing and Hi-C analysis to assemble the genome at the chromosomal level. We then conducted a comparative analysis of the genome with previously reported genomes of phytophagous and hematophagous stink bugs to focus on the genetic factors contributing to this species' herbivorous and carnivorous tendencies. Our findings suggest that the gustatory gene set plays a pivotal role in adapting to food habits, making it a promising target for selective breeding. Furthermore, we identified the whole genomes of microorganisms symbiotic with this species through genomic analysis. We believe that our results shed light on the food habit adaptations of N. tenuis and will accelerate breeding efforts based on new breeding techniques for natural enemy insects, including genomics and genome editing.

Improving the nutritional values of yellow mealworm Tenebrio molitor (Coleoptera: Tenebrionidae) larvae as an animal feed ingredient: a review

Yellow mealworm larvae (YML; Tenebrio molitor) are considered as a valuable insect species for animal feed due to their high nutritional values and ability to grow under different substrates and rearing conditions. Advances in the understanding of entomophagy and animal nutrition over the past decades have propelled research areas toward testing multiple aspects of YML to exploit them better as animal feed sources. This review aims to summarize various approaches that could be exploited to maximize the nutritional values of YML as an animal feed ingredient. In addition, YML has the potential to be used as an antimicrobial or bioactive agent to improve animal health and immune function in production animals. The dynamics of the nutritional profile of YML can be influenced by multiple factors and should be taken into account when attempting to optimize the nutrient contents of YML as an animal feed ingredient. Specifically, the use of novel land-based and aquatic feeding resources, probiotics, and the exploitation of larval gut microbiomes as novel strategies can assist to maximize the nutritional potential of YML. Selection of relevant feed supplies, optimization of ambient conditions, the introduction of novel genetic selection procedures, and implementation of effective post-harvest processing may be required in the future to commercialize mealworm production. Furthermore, the use of appropriate agricultural practices and technological improvements within the mealworm production sector should be aimed at achieving both economic and environmental sustainability. The issues highlighted in this review could pave the way for future approaches to improve the nutritional value of YML.

Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research

Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio-economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.

Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China

The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.

Nuclear and Mitochondrial Genome Assemblies of the Beetle, Zygogramma bicolorata, a Globally Important Biocontrol Agent of Invasive Weed Parthenium hysterophorus

Implementing a genetic-based approach to achieve the full potential of classical biocontrol programs has been advocated for decades. The availability of genome-level information brings the opportunity to scrutinize biocontrol traits for their efficacy and evolvability. However, implementation of this advocacy remains limited to few instances. Biocontrol of a globally noxious weed, Parthenium hysterophorus, by the leaf-feeding beetle, Zygogramma bicolorata, has been in place for more than four decades now, with varying levels of success. As the first step in providing genetic-based improvement to this biocontrol program, we describe the nuclear and mitochondrial assemblies of Z. bicolorata. We assembled the genome from the long-read sequence data, error corrected with high-throughput short reads and checked for contaminants and sequence duplication to produce a 936 Mb nuclear genome. With 96.5% Benchmarking Universal Single-Copy Orthologs completeness and the long terminal repeat assembly index 12.91, we present a reference-quality assembly that appeared to be repeat rich at 62.7% genome-wide and consists of 29,437 protein-coding regions. We detected signature of nuclear insertion of mitochondrial fragments in 80 nuclear positions comprising 13 kb out of 17.9 kb mitochondria genome sequence. This genome, along with its annotations, provides a valuable resource to gain further insights into the biocontrol traits of Z. bicolorata for improving the control of the invasive weed P. hysterophorus.

Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives

Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.

Trait-based approaches to predicting biological control success: challenges and prospects

Identifying traits that are associated with success of introduced natural enemies in establishing and controlling pest insects has occupied researchers and biological control practitioners for decades. Unfortunately, consistent general relationships have been difficult to detect, preventing a priori ranking of candidate biological control agents based on their traits. We summarise previous efforts and propose a series of potential explanations for the lack of clear patterns. We argue that the quality of current datasets is insufficient to detect complex trait-efficacy relationships and suggest several measures by which current limitations may be overcome. We conclude that efforts to address this elusive issue have not yet been exhausted and that further explorations are likely to be worthwhile.

Mycoviral gene-incorporating phytopathogenic fungi: a biocontrol agent

Fungal pathogens cause devastating agroeconomic losses. Chemical fungicides are used to control fungal diseases, although this is not an ecofriendly approach. A recent study by Liu et al. highlighted the use of mycoviral gene-incorporating phytopathogenic fungi as biocontrol agents for disease management.

Variation in sex determination mechanisms may constrain parthenogenesis-induction by endosymbionts in haplodiploid systems

Endosymbionts are maternally transmitted, and therefore benefit from maximizing female offspring numbers. Parthenogenesis-induction (PI) is the most effective type of manipulation for transmission, but has solely been detected in haplodiploid species, whereas cytoplasmic incompatibility (CI) is detected frequently across the arthropod phylum, including haplodiploids. This puzzling observation led us to hypothesize that the molecular sex-determination mechanism of the haplodiploid host may be a constraining factor in the ability of endosymbionts to induce parthenogenesis. Recent insights indicate that PI-endosymbionts may be able to directly manipulate sex-determination genes to induce the necessary steps required for PI in haplodiploids. However, sex-determination cascades vary extensively, so PI-induction would require a specialized and host-dependent tool set. Contrastingly, CI-related genes target conserved cell-cycle mechanisms, are located on mobile elements, and spread easily. Finally, endosymbiont-manipulations may have a strong impact on the effectiveness of haplodiploid biocontrol agents, but can also be used to enhance their efficacy.

Genetic relationships among laboratory lines of the egg parasitoid Trissolcus japonicus from native and adventive populations

Candidate biological control agents of invasive insect pests are increasingly being found in new geographic regions as a result of unintentional introductions. However, testing the degree of genetic differentiation among adventive and native-range populations of these agents is rarely done. We used reduced-representation sequencing of genomic DNA to investigate the relationships among laboratory lines of Trissolcus japonicus (Ashmead) (Hymenoptera, Scelionidae), an egg parasitoid and biological control agent of the brown marmorated stink bug, Halyomorpha halys (Stål) (Hemiptera, Pentatomidae). We compared sequences from multiple adventive populations in North America (Canada, USA) and Europe (Switzerland) with populations sourced from part of its native range in China. We found considerably more genetic variation among lines sourced from adventive populations than among those within native populations. In the Pacific Northwest of North America (British Columbia, Canada and Washington State, USA), we found preliminary evidence of three distinct genetic clusters, two of which were highly dissimilar from all other lines we genotyped. In contrast, we found that other adventive lines with close geographic proximity (two from Ontario, Canada, three from Switzerland) had limited genetic variation. These findings provide a basis for testing biological differences among lines that will inform their use as biological control agents, and provide evidence to support a hypothesis of several independent introductions of T. japonicus in western North America from different source areas.

Finding an egg in a haystack: variation in chemical cue use by egg parasitoids of herbivorous insects

Egg parasitoids of herbivorous insects use an interplay of short- and long-range chemical cues emitted by hosts and host plants to find eggs to parasitize. Volatile compounds that attract egg parasitoids can be identified via behavioral assays and used to manipulate parasitoid behavior in the field for biological control of herbivorous pests. However, how and when a particular cue will be used varies over the life of an individual, as well as at and below species level. Future research should expand taxonomic coverage to explore variation in chemical cue use in more natural, dynamic settings. More nuanced understanding of the variability of egg parasitoid host-finding strategies will aid in disentangling the underlying genetics and further enhancing biological control.

Recent trends in the biotechnology of functional non-digestible oligosaccharides with prebiotic potential

Prebiotics as a part of dietary nutrition can play a crucial role in structuring the composition and metabolic function of intestinal microbiota and can thus help in managing a clinical scenario by preventing diseases and/or improving health. Among the different prebiotics, non-digestible carbohydrates are molecules that selectively enrich a typical class of bacteria with probiotic potential. This review summarizes the current knowledge about the different aspects of prebiotics, such as its production, characterization and purification by various techniques, and its link to novel product development at an industrial scale for wide-scale use in diverse range of health management applications. Furthermore, the path to effective valorization of agricultural residues in prebiotic production has been elucidated. This review also discusses the recent developments in application of genomic tools in the area of prebiotics for providing new insights into the taxonomic characterization of gut microorganisms, and exploring their functional metabolic pathways for enzyme synthesis. However, the information regarding the cumulative effect of prebiotics with beneficial bacteria, their colonization and its direct influence through altered metabolic profile is still getting established. The future of this area lies in the designing of clinical condition specific functional foods taking into consideration the host genotypes, thus facilitating the creation of balanced and required metabolome and enabling to maintain the healthy status of the host.

No neonates without adults: A review of adult black soldier fly biology, Hermetia illucens (Diptera: Stratiomyidae): A review of adult black soldier fly biology, Hermetia illucens (Diptera: Stratiomyidae)

With the potential to process the world's agricultural and food waste, provide sustainable fodder for livestock, aquaculture, and pet animals, as well as act as a source of novel biomolecules, the black soldier fly, Hermetia illucens, has been launched into the leading position within the insects as feed industry. Fulfilment of these goals, however, requires mass-rearing facilities to have a steady supply of neonate larvae, which in-turn requires an efficient mating process to yield fertile eggs; yet, little is known about adult reproductive behavior, nor what physiological factors lead to its emergence. Moreover, fertile egg production tends to be highly variable in colony. Therefore, this review brings together what is currently known of the organismal biology of H. illucens, compiling information on adult morphology, physiology, biogeography, genomics, and behavioral ecology. As a holistic synthesis, it highlights several directions of interest for research to follow.

Breeding toward improved ecological plant-microbiome interactions

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Biological control needs evolutionary perspectives of ecological interactions

While ecological interactions have been identified as determinant for biological control efficiency, the role of evolution remains largely underestimated in biological control programs. With the restrictions on the use of both pesticides and exotic biological control agents (BCAs), the evolutionary optimization of local BCAs becomes central for improving the efficiency and the resilience of biological control. In particular, we need to better account for the natural processes of evolution to fully understand the interactions of pests and BCAs, including in biocontrol strategies integrating human manipulations of evolution (i.e., artificial selection and genetic engineering). In agroecosystems, the evolution of BCAs traits and performance depends on heritable phenotypic variation, trait genetic architecture, selection strength, stochastic processes, and other selective forces. Humans can manipulate these natural processes to increase the likelihood of evolutionary trait improvement, by artificially increasing heritable phenotypic variation, strengthening selection, controlling stochastic processes, or overpassing evolution through genetic engineering. We highlight these facets by reviewing recent studies addressing the importance of natural processes of evolution and human manipulations of these processes in biological control. We then discuss the interactions between the natural processes of evolution occurring in agroecosystems and affecting the artificially improved BCAs after their release. We emphasize that biological control cannot be summarized by interactions between species pairs because pests and biological control agents are entangled in diverse communities and are exposed to a multitude of deterministic and stochastic selective forces that can change rapidly in direction and intensity. We conclude that the combination of different evolutionary approaches can help optimize BCAs to remain efficient under changing environmental conditions and, ultimately, favor agroecosystem sustainability.

Selecting aggressiveness to improve biological control agents efficiency

In agroecosystems, omnivorous predators are recognized as potential biological control agents because of the numerous pest species they prey on. Nonetheless, it could be possible to enhance their efficiency through artificial selection on traits of economical or ecological relevance. Aggressiveness, which defines the readiness of an individual to display agonistic actions toward other individuals, is expected to be related to zoophagy, diet preferences and to a higher attack rate. The study aimed to assess the aggressiveness degree of the damsel bug, Nabis americoferus, and to estimate its heritability. We hypothesized that a high aggressiveness degree can be selected, and that males are more aggressive than females. Using artificial selection, we reared two separate populations, each composed of nine genetically isolated lines characterized by their different aggressiveness degree (aggressive, docile and non-selected). After three generations, we had efficiently selected aggressive behavior. The realized heritability was 0.16 and 0.27 for aggressiveness and docility in the first population. It was 0.25 and 0.23 for the second population. Males were more aggressive than females only for the second population. The potential of these individuals as biological control agents and the ecological consequences of aggressiveness are discussed.

Fungal insecticidal activity elevated by non-risky markerless overexpression of an endogenous cysteine-free protein gene in Beauveria bassiana

BACKGROUND

Fungal insecticides are notorious for slow kill action, an intrinsic trait that can be improved by the genetic engineering of an exogenous or endogenous virulence factor. However, transgenic insecticides expressing exogenous toxin and herbicide-resistant marker genes may cause unexpected ecological risks and are hardly permitted for field release due to strict regulatory hurdles. It is necessary to improve biotechnology that can speed up fungal insect-killing action and exclude ecological risk source.

RESULTS

A markerless transformation system of Beauveria bassiana, a main source of wide-spectrum fungal insecticides, was reconstructed based on the fungal uridine auxotrophy (Δura3). The system was applied for overexpression of the small cysteine-free protein (120 amino acids) gene cfp previously characterized as a regulator of the fungal virulence and gene expression. Three cfp-overexpressed strains showed much faster kill action to Galleria mellonella larvae than the parental wild-type via normal cuticle infection but no change in vegetative growth and aerial condition. The faster kill action was achieved due to not only significant increases in conidial adherence to insect cuticle and total activity of secreted cuticle-degrading Pr1 proteases and of antioxidant enzymes crucial for collapse of insect immune defense but acceleration of hemocoel localization, proliferation in vivo and host death from mummification.

CONCLUSION

The markerless system is free of any foreign DNA fragment as a source of ecologic risk and provides a novel biotechnological approach to enhancing fungal insecticidal activity with non-risky endogenous genes and striding over the regulatory hurdles. © 2022 Society of Chemical Industry.

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions

AIM OF THE STUDY

To characterise the baseline microbial population of the avocado carposphere and understand shifts in community structure from the harvest to ready-to-eat stages.

METHODS AND RESULTS

The changes in surface or stem-end fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer (ITS) region. Avocado fructoplane and stem-end pulp fungal richness differed significantly between postharvest stages with a decline following prochloraz dip treatments. Known postharvest decay-causing genera, Colletotrichum, Fusarium, Alternaria, Epicoccum, Penicillium and Neofusicoccum were detected, with Papiliotrema, Meyerozyma and Aureobasidium confirmed as the most dominant potentially beneficial genera. Postharvest interventions such as prochloraz had a negative non-target effect on the presence of Papiliotrema flavescens on the avocado fructoplane.

CONCLUSION

Our findings reveal a core community of beneficial and pathogenic taxa in the avocado fructoplane, and further highlights the reduction of pathogenic fungi as a consequence of fungicide use.

SIGNIFICANCE AND IMPACT OF THE STUDY

The current study provides important baseline data for further exploration of fungal population shifts in avocado fruit driven by chemical (fungicide) as well as physical (cold storage) interventions.

Penetrance during Wolbachia-mediated parthenogenesis of Trichogramma wasps is reduced by continuous oviposition, associated with exhaustion of Wolbachia titers in ovary and offspring eggs

BACKGROUND

Thelytokous Wolbachia-infected Trichogramma wasps are superior to bisexual uninfected wasps regarding biological control programs. However, continuous oviposition weakens the parthenogenesis-inducing (PI) strength of Wolbachia. Whether this reduced PI strength relates to decreases in the titer of Wolbachia in the ovary and offspring eggs of Trichogramma remains unclear. Here, using fluorescence in situ hybridization (FISH) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) methods, we investigated how the penetrance of Wolbachia-mediated parthenogenesis, Wolbachia density, and distributions of two Wolbachia-infected Trichogramma species, T. pretiosum (TP) and T. dendrolimi (TD), were influenced by different host access treatments [newly-emerged virgin females (NE), 7-day-old females without access to host eggs (NAH), and 7-day-old virgin females with access to host eggs (AH)].

RESULTS

Continuous oviposition decreased Wolbachia PI strength and titers in TP and TD. Continuous oviposition in AH decreased Wolbachia titers in abdomen and offspring eggs of TP and TD females, compared with NAH and NE; NAH had a lower thorax Wolbachia titer than NE. The numbers of parasitized host eggs and offspring wasps, and emergence rates of offspring deposited by AH were lower than those of NE and NAH, for either species.

CONCLUSION

Weakened PI strength, driven by continuous oviposition in Trichogramma wasps, is associated with Wolbachia titer exhaustion in ovary and offspring eggs. Wolbachia density is dependent on PI strength in Trichogramma wasps, highlighting the side effects of continuous oviposition regarding thelytokous Wolbachia-infected Trichogramma in biological control programs. © 2022 Society of Chemical Industry.

Mitochondrial Genomes of Two Asexual Trichogramma (Hymenoptera: Trichogrammatidae) Strains and Comparison with Their Sexual Relatives

Simple Summary

Sexual reproduction is dominant in animals, while asexual lineages are rare and evolutionarily short-lived. However, sexual reproduction has substantial costs, such as male production, inputs to courtship and mating, increased risk of predator exposure, and sexually transmitted diseases. A large body of theories has been proposed to explain the paradox of sex. One favored explanation is that asexuals are more likely to accumulate a greater number of deleterious mutations, known as Muller’s ratchet. Trichogramma is a genus of egg parasitoid wasps and is widely used as a biological control agent for agricultural and forest pests. With asexual lineages in at least 16 species, Trichogramma provides an excellent model to investigate the causes and consequences of asexual reproduction. In this study, we sequenced and assembled two asexual Trichogramma mitogenomes, representing two divergent origins of asexual reproduction. The asexual T. pretiosum is induced by the endosymbiont Wolbachia, while T. cacoeciae presumably originates from interspecific hybridization. To test Muller’s ratchet hypothesis, we compared these two asexual mitogenomes with their sexual relatives and found no association between asexual reproduction and mutation accumulation. This study provides a basis for further investigation into mitochondrial evolution and asexual reproduction in Trichogramma.

Abstract

Despite its substantial costs, sexual reproduction dominates in animals. One popular explanation for the paradox of sex is that asexual reproduction is more likely to accumulate deleterious mutations than sexual reproduction. To test this hypothesis, we compared the mitogenomes of two asexual wasp strains, Trichogramma cacoeciae and T. pretiosum, to their sexual relatives. These two asexual strains represent two different transition mechanisms in Trichogramma from sexual to asexual reproduction. Asexual T. pretiosum is induced by Wolbachia, while T. cacoeciae presumably originated from interspecific hybridization. We sequenced and assembled complete mitochondrial genomes of asexual T. cacoeciae and T. pretiosum. Compared to four sexual relatives, we found no evidence of higher mutation accumulation in asexual Trichogramma mitogenomes than in their sexual relatives. We also did not detect any relaxed selection in asexual Trichogramma mitogenomes. In contrast, the intensified selection was detected in Nad1 and Nad4 of the asexual T. pretiosum mitogenome, suggesting more purifying selection. In summary, no higher mitochondrial mutation accumulation was detected in these two asexual Trichogramma strains. This study provides a basis for further investigating mitochondrial evolution and asexual reproduction in Trichogramma.

Selectivity and molecular stress responses to classical and botanical acaricides in the predatory mite Phytoseiulus persimilis Athias-Henriot (Acari: Phytoseiidae)

BACKGROUND

Acaricide application remains an integral component of integrated pest management (IPM) for the two-spotted spider mite Tetranychus urticae. Species and strains of phytoseiid predatory mites vary significantly in their response to acaricides. For the success of IPM, it is imperative to identify the determinants of selectivity and molecular stress responses of acaricides in predatory mites.

RESULTS

The three classical acaricides bifenazate, cyflumetofen, and fenbutatin oxide did not affect the survival and fecundity of Phytoseiulus persimilis regardless of the route of exposure. Selectivity of the orange oil and terpenoid blend-based botanical acaricides was low via a combination of direct exposure, acaricide-laced diet, and residual exposure but improved when limiting exposure only to diet. To gain insights into the molecular stress responses, the transcriptome of P. persimilis was assembled. Subsequent gene expression analysis of predatory mites orally exposed to fenbutatin oxide and orange oil yielded only a limited xenobiotic stress response. In contrast, P. persimilis exhibited target-site resistance mutations, including I260M in SdhB, I1017M in CHS1, and kdr and super-kdr in VGSC. Extending the screen using available Phytoseiidae sequences uncovered I136T, S141F in cytb, G119S in AChE, and A2083V in ACC, well-known target-sites of acaricides.

CONCLUSION

Selectivity of the tested botanical acaricides to P. persimilis was low but could be enhanced by restricting exposure to a single route. Differential gene expression analysis did not show a robust induced stress response after sublethal exposure. In contrast, this study uncovered target-site mutations that may help to explain the physiological selectivity of several classical acaricides to phytoseiid predators.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.

Improving Natural Enemy Selection in Biological Control through Greater Attention to Chemical Ecology and Host-Associated Differentiation of Target Arthropod Pests

Host-associated differentiation (HAD) refers to cases in which genetically distinct populations of a species (e.g., herbivores or natural enemies) preferentially reproduce or feed on different host species. In agroecosystems, HAD often results in unique strains or biotypes of pest species, each attacking different species of crops. However, HAD is not restricted to pest populations, and may cascade to the third trophic level, affecting host selection by natural enemies, and ultimately leading to HAD within natural enemy species. Natural enemy HAD may affect the outcomes of biological control efforts, whether classical, conservation, or augmentative. Here, we explore the potential effects of pest and natural enemy HAD on biological control in agroecosystems, with emphases on current knowledge gaps and implications of HAD for selection of biological control agents. Additionally, given the importance of semiochemicals in mediating interactions between trophic levels, we emphasize the role of chemical ecology in interactions between pests and natural enemies, and suggest areas of consideration for biological control. Overall, we aim to jump-start a conversation concerning the relevance of HAD in biological control by reviewing currently available information on natural enemy HAD, identifying challenges to incorporating HAD considerations into biological control efforts, and proposing future research directions on natural enemy selection and HAD.

Insect pest management in the age of synthetic biology

Arthropod crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingly sophisticated chemical formulations to control insect pests but, as the scale of agriculture expanded to meet the needs of the global population, concerns about the negative impacts of agricultural practices on biodiversity have grown. While biological solutions, such as biological control agents and pheromones, have previously had relatively minor roles in pest management, biotechnology has opened the door to numerous new approaches for controlling insect pests. In this review, we look at how advances in synthetic biology and biotechnology are providing new options for pest control. We discuss emerging technologies for engineering resistant crops and insect populations and examine advances in biomanufacturing that are enabling the production of new products for pest control.

Hybridization and range expansion in tamarisk beetles (Diorhabda spp.) introduced to North America for classical biological control

With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata × D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.

Long-Read Assembly and Annotation of the Parasitoid Wasp Muscidifurax raptorellus, a Biological Control Agent for Filth Flies

The parasitoid wasp Muscidifurax raptorellus (Hymenoptera: Pteromalidae) is a gregarious species that has received extensive attention for its potential in biological pest control against house fly, stable fly, and other filth flies. It has a high reproductive capacity and can be reared easily. However, genome assembly is not available for M. raptorellus or any other species in this genus. Previously, we assembled a complete circular mitochondrial genome with a length of 24,717 bp. Here, we assembled and annotated a high-quality nuclear genome of M. raptorellus, using a combination of long-read (104× genome coverage) and short-read (326× genome coverage) sequencing technologies. The assembled genome size is 314 Mbp in 226 contigs, with a 97.9% BUSCO completeness score and a contig N50 of 4.67 Mb, suggesting excellent continuity of this assembly. Our assembly builds the foundation for comparative and evolutionary genomic analysis in the genus of Muscidifurax and possible future biocontrol applications.

Consistent variations in personality traits and their potential for genetic improvement of biocontrol agents: Trichogramma evanescens as a case study

Improvements in the biological control of agricultural pests require improvements in the phenotyping methods used by practitioners to select efficient biological control agent (BCA) populations in industrial rearing or field conditions. Consistent inter‐individual variations in behaviour (i.e. animal personality) probably affect BCA efficiency, but have never been taken into account in the development of phenotyping methods, despite having characteristics useful for phenotyping: repeatable (by definition), often heritable, etc. We developed a video‐tracking method targeting animal personality traits and evaluated the feasibility of its use for genetic improvement in the BCA Trichogramma evanescens, by phenotyping 1,049 individuals from 24 isogenic lines. We found consistent individual variations in boldness, activity and exploration. Personality differences between the 24 isogenic lines suggested a genetic origin of the variations in activity and exploration (broad‐sense heritability estimates of 0.06 to 0.11) and revealed a trade‐off between exploration and fecundity.

Food web engineering: ecology and evolution to improve biological pest control

If we are to sustainably provide food to a rapidly growing human population, biological pest control (BPC) should integrate food web theory and evolution. This will account for the impacts of climate warming on the complex community settings of agroecosystems. We review recent studies looking for top-down augmentative pest control being hampered/promoted by biotic (community contexts) and/or abiotic (climate) drivers. Most studies found either positive or neutral effects on BPC. However, most ignored potential evolutionary responses occurring in the environments under study. We propose engineering food webs by engaging in a continuous feedback between ecological and evolutionary data, and individual-based modelling of agroecosystems. This should speed up the procurement of strains of efficient natural enemies better adapted to warming.

Using plant chemistry to improve interactions between plants, herbivores and their natural enemies: challenges and opportunities

Plant secondary (or specialized) metabolites determine multitrophic interaction dynamics. Herbivore natural enemies exploit plant volatiles for host location and are negatively affected by plant defense chemicals that are transferred through herbivores. Recent work shows that herbivore natural enemies can evolve resistance to plant defense chemicals, and that generating plant defense resistance through forward evolution enhances their capacity to prey on herbivores. Here, we discuss how this knowledge can be used to engineer better biocontrol agents. We argue that herbivore natural enemies which are adapted to plant chemistry will likely enhance the efficacy of future pest control efforts. Detailed phenotyping and field experiments will be necessary to quantify costs and benefits of optimizing chemical links between plants and higher trophic levels.

Attraction of Trichogramma Wasps to Butterfly Oviposition-Induced Plant Volatiles Depends on Brassica Species, Wasp Strain and Leaf Necrosis

Within the Brassicaceae, wild as well as crop species are challenged by specialist herbivores including cabbage white butterflies (Pieris spp.). The wild crucifer Brassica nigra responds to oviposition by Pieris butterflies by the synergistic expression of two egg-killing traits. Genotypes that express a hypersensitive response (HR)-like necrosis (direct egg-killing) also emit oviposition-induced plant volatiles (OIPVs) attracting Trichogramma egg parasitoids (indirect egg-killing). This so-called double defense line can result in high butterfly egg mortalities. It remains unknown whether this strategy is unique to B. nigra or more common in Brassica species. To test this, we examined the response of different Trichogramma evanescens lines to OIPVs emitted by B. nigra and three close relatives (Brassica napus, Brassica rapa, and Brassica oleracea). Furthermore, we evaluated whether HR-like necrosis played a role in the attraction toward plant volatiles. Our results show a specificity in wasp attraction to different plant species. Three out of four plant species attracted a specific T. evanescens strain, including the crops B. rapa and B. napus. Parasitoid attraction was positively affected by presence of HR-like necrosis in one plant species. Our findings imply that, despite being a true generalist in terms of host range, T. evanescens shows intraspecific variation during host searching, which should be taken into account when selecting parasitoid lines for biocontrol of certain crops. Finally, we conclude that also crop plants within the Brassicaceae family possess egg-killing traits and can exert the double-defense line which may enable effective selection of egg-killing defense traits by cabbage breeders.

Genome editing for resistance against plant pests and pathogens

The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.

Classical biological control against insect pests in Europe, North Africa, and the Middle East: What influences its success?

Many factors can affect the success and failure of classical biological control. However, these factors have mainly been studied independently of each other, which leaves their relative importance within the complexity of classical biological control (CBC) programmes unknown. Therefore, we set out to take a more holistic view on the factors that may impact the outcome of CBC of insect pests by insect predators and parasitoids. To this end, we filtered the BIOCAT catalogue to extract entries for the Greater Western Palearctic ecozone and added 15 new explanatory variables. These mainly concerned traits of released biological control agents, target pests, and host plants of the target, but also included the number of introductions for specific agent-target combinations as a management aspect. We then analysed the data regarding three levels of success: agent establishment, impact on the target population, and complete control of the target. Between 1890 and 2010 a total of 780 introductions of insects for biological control were undertaken in the analysed area, constituting 416 agent-target combinations. Overall success of agent establishment was 32%, successful impact of single agents on their target was 18%, and success of complete control was 11%. The number of factors significantly influencing the outcome of CBC decreased with increasing level of success. Remarkably few agent-related factors influenced the success: insect predators as agents decreased the probability of establishment and using oligophagous parasitoids significantly decreased the chances of complete control. Other significant factors were related to traits of target pests or their host plants. For example, sap feeders and target pests attacking reproductive plant parts were more likely to be successfully controlled. The rate of success increased with the number of introductions of CBC agents, in particular against univoltine target pests. These findings suggest that a focus on agent-related traits to increase the chances of successful CBC is not fully justified and should be complemented with the consideration of lower trophic levels and other aspects of CBC, such as abiotic factors and management.

Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize

The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.

Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.

Learning can be detrimental for a parasitic wasp

Animals have evolved the capacity to learn, and the conventional view is that learning allows individuals to improve foraging decisions. The parasitoid Telenomus podisi has been shown to parasitize eggs of the exotic stink bug Halyomorpha halys at the same rate as eggs of its coevolved host, Podisus maculiventris, but the parasitoid cannot complete its development in the exotic species. We hypothesized that T. podisi learns to exploit cues from this non-coevolved species, thereby increasing unsuccessful parasitism rates. We conducted bioassays to compare the responses of naïve vs. experienced parasitoids on chemical footprints left by one of the two host species. Both naïve and experienced females showed a higher response to footprints of P. maculiventris than of H. halys. Furthermore, parasitoids that gained an experience on H. halys significantly increased their residence time within the arena and the frequency of re-encounter with the area contaminated by chemical cues. Hence, our study describes detrimental learning where a parasitoid learns to associate chemical cues from an unsuitable host, potentially re-enforcing a reproductive cul-de-sac (evolutionary trap). Maladaptive learning in the T. podisi-H. halys association could have consequences for population dynamics of sympatric native and exotic host species.

Use of zoophytophagous mirid bugs in horticultural crops: Current challenges and future perspectives

In recent years, the use of predatory mirid bugs (Hemiptera: Miridae) in horticultural crops has increased considerably. Mirid bugs are zoophytophagous predators, that is, they display omnivorous behavior and feed on both plants and arthropods. Mirid bugs feed effectively on a wide range of prey, such as whiteflies, lepidopteran eggs and mites. In addition, the phytophagous behavior of mirid bugs can activate defenses in the plants on which they feed. Despite the positive biological attributes, their use still presents some constraints. Their establishment and retention on the crop is not always easy and economic plant damage can be caused by some mirid species. In this review, the current strategies for using zoophytophagous mirid bugs in horticultural crops, mainly Nesidiocoris tenuis, Macrolophus pygmaeus and Dicyphus hesperus, are reviewed. We discuss six different approaches which, in our opinion, can optimize the efficacy of mirids as biocontrol agents and help expand their use into more areas worldwide. In this review we (i) highlight the large number of species and biotypes which are yet to be described and explore their applicability, (ii) present how it is possible to take advantage of the mirid-induced plant defenses to improve pest management, (iii) argue that genetic selection of improved mirid strains is feasible, (iv) explore the use of companion plants and the use of alternative foods to improve the mirid bug management, and finally (vi) discuss strategies for the expansion of mirid bugs as biological control agents to horticultural crops other than just tomatoes. © 2020 Society of Chemical Industry.

Genetic Variation in the Feeding Behavior of Isofemale Lines of Nesidiocoris tenuis

Zoophytophagous predators provide biocontrol services in various major crops of modern horticulture due to the combination of its predatory capacity and the induction of plant defenses derived from its phytophagy. However, under certain conditions of prey scarcity, these natural enemies can inflict plant damage. Exploitation of genetic variation and subsequent selective breeding on foraging traits is a potential alternative to overcome this inconvenience. In this study, we quantified the genetic variation of phytophagy and zoophagy of Nesidiocoristenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator widely used in tomato crops to suppress key pests. We compared nine isofemale lines on their capacity to produce necrotic rings and wilting on tomato plants as a proxy for phytophagy, as well as their efficacy to prey on Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) eggs, as a proxy for zoophagy. Differences between isofemale lines in phytophagy and zoophagy indicated a genetic basis. Variation found in the zoophagy levels was larger than that in phytophagy levels. Our results showed that there is a genetic basis for the variation observed in the feeding behavior of isofemale lines of N.tenuis, highlighting the potential importance of selective breeding for such traits of biocontrol interest.