Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition

Genomic investigations of successful invasions: the picture emerging from recent studies

Invasion biology aims to identify traits and mechanisms that contribute to successful invasions, while also providing general insights into the mechanisms underlying population expansion and adaptation to rapid climate and habitat changes. Certain phenotypic attributes have been linked to successful invasions, and the role of genetics has been critical in understanding adaptation of invasive species. Nevertheless, a comprehensive summary evaluating the most common evolutionary mechanisms associated with successful invasions across species and environments is still lacking. Here we present a systematic review of studies since 2015 that have applied genomic tools to investigate mechanisms of successful invasions across different organisms. We examine demographic patterns such as changes in genomic diversity at the population level, the presence of genetic bottlenecks and gene flow in the invasive range. We review mechanisms of adaptation such as selection from standing genetic variation and de novo mutations, hybridisation and introgression, all of which can have an impact on invasion success. This comprehensive review of recent articles on the genomic diversity of invasive species led to the creation of a searchable database to provide researchers with an accessible resource. Analysis of this database allowed quantitative assessment of demographic and adaptive mechanisms acting in invasive species. A predominant role of admixture in increasing levels of genetic diversity enabling molecular adaptation in novel habitats is the most important finding of our study. The "genetic paradox" of invasive species was not validated in genomic data across species and ecosystems. Even though the presence of genetic drift and bottlenecks is commonly reported upon invasion, a large reduction in genomic diversity is rarely observed. Any decrease in genetic diversity is often relatively mild and almost always restored via gene flow between different invasive populations. The fact that loci under selection are frequently detected suggests that adaptation to novel habitats on a molecular level is not hindered. The above findings are confirmed herein for the first time in a semi-quantitative manner by molecular data. We also point to gaps and potential improvements in the design of studies of mechanisms driving rapid molecular adaptation in invasive populations. These include the scarcity of comprehensive studies that include sampling from multiple native and invasive populations, identification of invasion sources, longitudinal population sampling, and the integration of fitness measures into genomic analyses. We also note that the potential of whole genome studies is often not exploited fully in predicting invasive potential. Comparative genomic studies identifying genome features promoting invasions are underrepresented despite their potential for use as a tool in invasive species control.

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing

Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE

Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

Characterization of the microbial communities in Tunisian wild populations of the Mediterranean fruit fly (Ceratitis capitata) and their implications for the future implementation of the sterile insect technique

Insects and their associated microbiota have developed a sustained and mutually beneficial relationship, characterized by the influence of the symbiotic microorganisms on the host's physiological processes and fitness parameters. The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), is one of the world's most ubiquitous, invasive, and harmful agricultural pests. In Tunisia, the medfly is widely distributed across all bioclimatic zones. However, in the absence of surveillance, infestations can escalate drastically, causing damage levels as high as 100%. Our study aimed to characterize the microbiome profile of Tunisian medfly populations from Zaghouan, Tozeur, Siliana, and Bizerte to understand the microbial dynamics implicated in the invasiveness and adaptability potential if SIT is applied. We conducted amplicon sequencing using MiSeq Illumina and a culture-dependent approach. Our findings revealed notable differences in symbiotic communities across regions. For instance, Serratia was prevalent in Tozeur populations, while Klebsiella showed high abundance in Bizerte. The composition of the bacterial communities within the medfly populations was influenced by several factors including the environmental conditions, geographical location, developmental stage, and the sex of the insects. Investigating the intricate relationship between insects and their microbiota is pivotal for understanding their biology and developing effective pest management strategies. Additionally, the isolation of bacteria from adult and larval medflies collected in the Bizerte region revealed the presence of bacterial species that could be utilized as attractants or supplements in larval artificial diets in the case of application of the SIT aiming at producing competitive sterile males.

Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata)

The Mediterranean fruit fly (Ceratitis capitata) is a globally invasive species and an economically significant pest of fruit crops. Understanding the evolutionary history and local climatic adaptation of this species is crucial for developing effective pest management strategies. We conducted a comprehensive investigation using whole genome sequencing to explore (i) the invasion history of C. capitata with an emphasis on historical admixture and (ii) local climatic adaptation across African, European, Central, and South American populations of C. capitata. Our results suggest a stepwise colonization of C. capitata in Europe and Latin America in which Mediterranean and Central American populations share an ancestral lineage. Conversely, South American invasion history is more complex, and our results partly suggest an old secondary invasion into South America from Europe or a colonization of South America directly from Africa, followed by admixture with an European lineage. Throughout its invasive range, C. capitata is challenged with diverse climatic regimes. A genome wide association study identified a relationship between allele frequency changes and specific bioclimatic variables. Notably, we observed a significant allele frequency shift related to adaptation to cold stress (BIO6), highlighting the species' ability to rapidly adapt to seasonal variations in colder climates.

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai'i

Sterile insect technique (SIT) is a useful strategy for preventing and mitigative establishment of invasive insect species. SIT of the pest tephritid Mediterranean fruit fly, Ceratitis capitata (Wiedemann, 1824)WiedemannWiedemann, has been effective in preventing population establishment in vulnerable agricultural areas of the United States. However, irradiation-induced sterilization can have detrimental impacts resulting in reduced performance metrics. Mediterranean fruit fly males reared for SIT have been shown to have differences in their microbiomes relative to other population sources, which has been postulated to be a factor in how well flies compete with wild conspecifics. To identify baseline performance metrics on the effects of irradiation on the gut microbiome of mass-reared flies in Hawai'i, a study was performed to assess performance metrics and microbiome (bacterial 16S rRNA) variation across multiple timepoints. Mediterranean fruit fly pupae were selected from mass-reared trays intended for release, and paired samples were either irradiated or remained as controls and transported to the laboratory for evaluation. Irradiated flies exhibited fewer successful fliers, more rapid mortality rates, and were less active relative to control nonirradiated flies. Contrary to initial expectations, irradiation did not exert substantial impacts on the composition or diversity of bacterial reads. Samples were primarily comprised of sequences classified as Klebsiella and there were low levels of both read and taxonomic diversity relative to other 16S surveys of medfly. Although this study does not demonstrate a strong effect of irradiation alone on the Mediterranean fruit fly microbiome, there are several explanations for this discrepancy.

Probiotic consortium modulating the gut microbiota composition and function of sterile Mediterranean fruit flies

The sterile insect technique (SIT) remains a successful approach in managing pest insects. However, the long-term mass rearing and sterilizing radiation associated with SIT have been observed to induce physiological and ecological fitness decline in target insects. This decline may be attributed to various factors, including commensal microbiota dysbiosis, selection procedures, loss of heterozygosity, and other complex interactions.. There is evidence that the bacterial symbiont of insects may play critical roles in digestion, development, reproduction, and behavior. Probiotics are an increasingly common approach for restoring the intestinal microbiota structure and fitness parameters of sterile insects, particularly in the Vienna 8 genetic sexing strain (V8-GSS) of the Mediterranean fruit fly (medfly), Ceratitis capitata. Here, we explore the influence of the previously isolated bacterial strain, Lactococcus lactis, Enterobacter sp., and Klebsiella oxytoca, administration as probiotic consortia (LEK-PC) to the larvae and/or adult diet over the course of 20 rearing generations on fitness parameters. The experiment was carried out in four colonies: a control colony (C), one to which probiotics were not added, one to which probiotics were added to the larval medium (L+), one to which probiotics were added to the adult medium (A+), and one to which probiotics were added to both the larval and adult mediums (AL+). Emergence, flight ability, survival under stress conditions, and mating competitiveness, were all significantly improved by the LEK-PC treatment independently of the administration stage. The intestinal microbiota structure of various medfly V8-GSS colonies also underwent a significant shift, despite the fact that the core microbial community was unaffected by the LEK-PC administration stage, according to 16S metagenomics sequencing. Comparison of the metabolic function prediction and associated carbohydrate enzymes among colonies treated with "LEK-PC" showed an enrichment of metabolic functions related to carbohydrates, amino acids, cofactors, and vitamins metabolism, as well as, glycoside hydrolase enzymes in the AL+ colony compared to the control. This study enriches the knowledge regarding the benefits of probiotic treatment to modulate and restore the intestinal microbiota of C. capitata sterile males for a better effectiveness of the SIT.

Macaronesian Plants as Promising Biopesticides against the Crop Pest Ceratitis capitata

Ceratitis capitata is responsible for significant economic losses in the fruit production industry, and the market lacks biopesticides that are effective but also cheaper and less contaminating, with fewer negative impacts on the environment. In this regard, the present study suggests as potential options ethanolic extracts from several Macaronesian plants, which inhibit the oviposition and are toxic to C. capitata, and whose preparation involve a non-toxic solvent (i.e., ethanol), low energy expenditure and cheap apparatus (i.e., maceration at room temperature). Among the evaluated species, the extracts of Hedychium gardnerianum, Cistus symphytifolius and Salvia canariensis are the most active (50 mg/mL), revealing an increase in C. capitata adults' mortality from 21.15% to 27.41% after 72 h, a value statistically identical to azadirachtin (25.93%) at the recommended concentration (0.88 mg/mL). Considering the quantity and biomass available to prepare a biopesticide in the future, and the level of activity, the ethanolic extract of H. gardnerianum was fractionated and each fraction tested. The water fraction at 50 mg/mL proved to be more effective than the original extract, both in terms of mortality (57.69%), with LT50 = 72.5 h, and oviposition deterrence (83.43%), values statistically higher than those obtained by azadirachtin at 0.88 mg/mL. Analysis of this fraction by HPLC-MS/MS showed that it is mainly composed of glycosylated derivatives of quercetin and myricetin in addition to some triterpenes. These findings highlight some Macaronesian species, and in particular, the more polar fraction of H. gardnerianum ethanolic extract, as promising and ecological alternatives to conventional insecticides, for use in the integrated management of the C. capitata pest.

Biosecurity and Management Strategies for Economically Important Exotic Tephritid Fruit Fly Species in Australia

Exotic tephritid incursions are of high concern to Australia's biosecurity and its horticultural industries. It is vital that Australia remains ready to respond to incursions as they arise, as an incursion of tephritid fruit fly species will result in significant economic losses. In this review, we compared Australian incursion management strategies for fruit flies with global management strategies and identified possible areas where improvements could be made in an Australian context. Overall, Australia has a good understanding of the main tephritid threats, of which Bactrocera species from across the Torres Strait (northern Australia) are of most concern. Effective tools for tephritid detection and early warning surveillance at points of entry are in place at ports and in horticultural areas Australia-wide and provide the basis for initiating biosecurity responses in the event of an incursion. Area-wide control measures used in successful eradication attempts globally are available for use in Australia. However, a specific tephritid emergency response plan identifying suitable response measures and control options for species of concern is not yet available. We have identified that Australia has the policies and management tools available to respond to an exotic tephritid incursion, but the speed at which this could be accomplished would be greatly improved by the development of species-specific emergency response plans.

Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies

Gut microbiota are important contributors to insect success. Host-microbe interactions are dynamic and can change as hosts age and/or encounter different environments. A turning point in these relationships the transition from immature to adult life stages, particularly for holometabolous insects where there is radical restructuring of the gut. Improved knowledge of population and community dynamics of gut microbiomes upon adult emergence inform drivers of community assembly and physiological aspects of host-microbe interactions. Here, we evaluated the bacterial communities of the pest tephritid species melon fly (Zeugodacus cucurbitae) and Medditeranean fruit fly (medfly, Ceratitis capitata) associated with the pupae life stage and timepoints immediately following adult eclosion. We used a combination of culturing to determine cultivatable bacterial titers, qPCR to determine 16S-rRNA SSU copy numbers, and 16S V4 sequencing to determine changes in communities. Both culturing and qPCR revealed that fly bacterial populations declined upon adult emergence by 10 to 100-fold followed by recovery within 24 h following eclosion. Titers reached ~ 107 CFUs (~ 108 16S rRNA copies) within a week post-emergence. We also observed concurrent changes in amplicon sequence variance (ASVs), where the ASV composition differed overtime for both melon fly and medfly adults at different timepoints. Medfly, in particular, had different microbiome compositions at each timepoint, indicating greater levels of variation before stabilization. These results demonstrate that tephritid microbiomes experience a period of flux following adult emergence, where both biomass and the makeup of the community undergoes dramatic shifts. The host-microbe dynamics we document suggest plasticity in the community and that there may be specific periods where the tephritid gut microbiome may be pliable to introduce and establish new microbial strains in the host.