Insertion sequence polymorphism and genomic rearrangements uncover hidden Wolbachia diversity in Drosophila suzukii and D. subpulchrella

Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America

Wolbachia, a group of Gram-negative symbiotic bacteria, infects nematodes and a wide range of arthropods. Diaphorina citri Kuwayama, the vector of Candidatus Liberibacter asiaticus (CLas) that causes citrus greening disease, is naturally infected with Wolbachia (wDi). However, the interaction between wDi and D. citri remains poorly understood. In this study, we performed a pan-genome analysis using 65 wDi genomes to gain a comprehensive understanding of wDi. Based on average nucleotide identity (ANI) analysis, we classified the wDi strains into Asia and North America strains. The ANI analysis, principal coordinates analysis (PCoA), and phylogenetic tree analysis supported that the D. citri in Florida did not originate from China. Furthermore, we found that a significant number of core genes were associated with metabolic pathways. Pathways such as thiamine metabolism, type I secretion system, biotin transport, and phospholipid transport were highly conserved across all analyzed wDi genomes. The variation analysis between Asia and North America wDi showed that there were 39,625 single-nucleotide polymorphisms (SNPs), 2153 indels, 10 inversions, 29 translocations, 65 duplications, 10 SV-based insertions, and 4 SV-based deletions. The SV-based insertions and deletions involved genes encoding transposase, phage tail tube protein, ankyrin repeat (ANK) protein, and group II intron-encoded protein. Pan-genome analysis of wDi contributes to our understanding of the geographical population of wDi, the origin of hosts of D. citri, and the interaction between wDi and its host, thus facilitating the development of strategies to control the insects and huanglongbing (HLB).

Wolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms

Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.

Drosophila suzukii (Diptera: Drosophilidae): A Decade of Research Towards a Sustainable Integrated Pest Management Program

Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) also known as spotted-wing drosophila (SWD), is a pest native to Southeast Asia. In the last few decades, the pest has expanded its range to affect all major European and American fruit production regions. SWD is a highly adaptive insect that is able to disperse, survive, and flourish under a range of environmental conditions. Infestation by SWD generates both direct and indirect economic impacts through yield losses, shorter shelf life of infested fruit, and increased production costs. Fresh markets, frozen berries, and fruit export programs have been impacted by the pest due to zero tolerance for fruit infestation. As SWD control programs rely heavily on insecticides, exceedance of maximum residue levels (MRLs) has also resulted in crop rejections. The economic impact of SWD has been particularly severe for organic operations, mainly due to the limited availability of effective insecticides. Integrated pest management (IPM) of SWD could significantly reduce chemical inputs but would require substantial changes to horticultural management practices. This review evaluates the most promising methods studied as part of an IPM strategy against SWD across the world. For each of the considered techniques, the effectiveness, impact, sustainability, and stage of development are discussed.

Living in the endosymbiotic world of Wolbachia: A centennial review

The most widespread intracellular bacteria in the animal kingdom are maternally inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia's host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark reproductive phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, the interdisciplinary science of this symbiosis stands as a model for consolidating and teaching the integrative rules of endosymbiotic life.

Living in the endosymbiotic world of Wolbachia: A centennial review

The most widespread intracellular bacteria in the animal kingdom are maternally inherited endosymbionts of the genus Wolbachia. Their prevalence in arthropods and nematodes worldwide and stunning arsenal of parasitic and mutualistic adaptations make these bacteria a biological archetype for basic studies of symbiosis and applied outcomes for curbing human and agricultural diseases. Here, we conduct a summative, centennial analysis of living in the Wolbachia world. We synthesize literature on Wolbachia's host range, phylogenetic diversity, genomics, cell biology, and applications to filarial, arboviral, and agricultural diseases. We also review the mobilome of Wolbachia including phage WO and its essentiality to hallmark reproductive phenotypes in arthropods. Finally, the Wolbachia system is an exemplar for discovery-based science education using biodiversity, biotechnology, and bioinformatics lessons. As we approach a century of Wolbachia research, the interdisciplinary science of this symbiosis stands as a model for consolidating and teaching the integrative rules of endosymbiotic life.

Infection effects of the new microsporidian species Tubulinosema suzukii on its host Drosophila suzukii

Microsporidian infections of insects are important natural constraints of population growth, often reducing lifespan, fecundity and fertility of the infected host. The recently discovered Tubulinosema suzukii infects Drosophila suzukii (spotted wing drosophila, SWD), an invasive pest of many fruit crops in North America and Europe. In laboratory tests, fitness effects on larval and adult stages were explored. High level infection after larval treatment caused up to 70% pupal mortality, a decreased lifespan and a 70% reduced oviposition of emerging adults in biparental infection clusters. A shift to higher proportion of female offspring compared to controls suggested a potential parthenogenetic effect after microsporidian infection. A clear sex-linkage of effects was noted; females were specifically impaired, as concluded from fecundity tests with only infected female parents. Additive effects were noted when both parental sexes were infected, whereas least effects were found with only infected male parents, though survival of males was most negatively affected if they were fed with T. suzukii spores in the adult stage. Although most negative effects on fitness parameters were revealed after larval treatment, infection of offspring was never higher than 4%, suggesting limited vertical transmission. For that reason, a self-reliant spread in natural SWD populations would probably only occur by spore release from cadavers or frass.

Large scale genome reconstructions illuminate Wolbachia evolution

Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence.

By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.

Ongoing Coevolution of Wolbachia and a Widespread Invasive Ant, Anoplolepis gracilipes

While Wolbachia are commonly found among arthropods, intraspecific infection rates can vary substantially across the geographic populations. Here we report nearly 100% prevalence of Wolbachia in the global populations of the yellow crazy ant, Anoplolepis gracilipes. To understand coevolutionary history between Wolbachia and A. gracilipes, we identified single nucleotide polymorphisms (SNPs) in Wolbachia from the ant across 12 geographical regions and compared the phylogeny of SNP-based Wolbachia to patterns of the ant's mitochondrial DNA (mtDNA) variation. Our results revealed a strong concordance between phylogenies of Wolbachia and host mtDNA, providing immediate evidence of co-divergence. Among eight identified SNP loci separating the genetic clusters of Wolbachia, seven loci are located in potential protein-coding genes, three of which being non-synonymous SNPs that may influence gene functions. We found a Wolbachia hypothetical protein gene with signature of positive selection. These findings jointly allow us to characterize Wolbachia-ant coevolution and also raise a question about mechanism(s) underlying maintenance of high prevalence of Wolbachia during the colonization of this invasive ant.

Age, tissue, genotype and virus infection regulate Wolbachia levels in Drosophila

The bacterial symbiont Wolbachia can protect insects against viral pathogens, and the varying levels of antiviral protection are correlated with the endosymbiont load within the insects. To understand why Wolbachia strains differ in their antiviral effects, we investigated the factors controlling Wolbachia density in five closely related strains in their natural Drosophila hosts. We found that Wolbachia density varied greatly across different tissues and between flies of different ages, and these effects depended on the host-symbiont association. Some endosymbionts maintained largely stable densities as flies aged while others increased, and these effects in turn depended on the tissue being examined. Measuring Wolbachia rRNA levels in response to viral infection, we found that viral infection itself also altered Wolbachia levels, with Flock House virus causing substantial reductions in symbiont loads late in the infection. This effect, however, was virus-specific as Drosophila C virus had little impact on Wolbachia in all of the five host systems. Because viruses have strong tissue tropisms and antiviral protection is thought to be cell-autonomous, these effects are likely to affect the virus-blocking phenomenon. However, we were unable to find any evidence of a correlation between Wolbachia and viral titres within the same tissues. We conclude that Wolbachia levels within flies are regulated in a complex host-symbiont-virus-dependent manner and this trinity is likely to influence the antiviral effects of Wolbachia.

Endosymbiont diversity in natural populations of Tetranychus mites is rapidly lost under laboratory conditions

Although the diversity of bacterial endosymbionts in arthropods is well documented, whether and how such diversity is maintained remains an open question. We investigated the temporal changes occurring in the prevalence and composition of endosymbionts after transferring natural populations of Tetranychus spider mites from the field to the laboratory. These populations, belonging to three different Tetranychus species (T. urticae, T. ludeni and T. evansi) carried variable infection frequencies of Wolbachia, Cardinium, and Rickettsia. We report a rapid change of the infection status of these populations after only 6 months of laboratory rearing, with an apparent loss of Rickettsia and Cardinium, while Wolbachia apparently either reached fixation or was lost. We show that Wolbachia had variable effects on host longevity and fecundity, and induced variable levels of cytoplasmic incompatibility (CI) in each fully infected population, despite no sequence divergence in the markers used and full CI rescue between all populations. This suggests that such effects are largely dependent upon the host genotype. Subsequently, we used these data to parameterize a theoretical model for the invasion of CI-inducing symbionts in haplodiploids, which shows that symbiont effects are sufficient to explain their dynamics in the laboratory. This further suggests that symbiont diversity and prevalence in the field are likely maintained by environmental heterogeneity, which is reduced in the laboratory. Overall, this study highlights the lability of endosymbiont infections and draws attention to the limitations of laboratory studies to understand host-symbiont interactions in natural populations.

Symbiosis: Wolbachia Host Shifts in the Fast Lane

The inherited bacterium Wolbachia is an important component of the biology of many arthropods. What makes it so common? An analysis of drosophilids revealed one strain host shifts at a surprisingly high rate, infecting eight species in under 30,000 years.

Optimization of native biocontrol agents, with parasitoids of the invasive pest Drosophila suzukii as an example

The development of biological control methods for exotic invasive pest species has become more challenging during the last decade. Compared to indigenous natural enemies, species from the pest area of origin are often more efficient due to their long coevolutionary history with the pest. The import of these well-adapted exotic species, however, has become restricted under the Nagoya Protocol on Access and Benefit Sharing, reducing the number of available biocontrol candidates. Finding new agents and ways to improve important traits for control agents ("biocontrol traits") is therefore of crucial importance. Here, we demonstrate the potential of a surprisingly under-rated method for improvement of biocontrol: the exploitation of intraspecific variation in biocontrol traits, for example, by selective breeding. We propose a four-step approach to investigate the potential of this method: investigation of the amount of (a) inter- and (b) intraspecific variation for biocontrol traits, (c) determination of the environmental and genetic factors shaping this variation, and (d) exploitation of this variation in breeding programs. We illustrate this approach with a case study on parasitoids of Drosophila suzukii, a highly invasive pest species in Europe and North America. We review all known parasitoids of D. suzukii and find large variation among and within species in their ability to kill this fly. We then consider which genetic and environmental factors shape the interaction between D. suzukii and its parasitoids to explain this variation. Insight into the causes of variation informs us on how and to what extent candidate agents can be improved. Moreover, it aids in predicting the effectiveness of the agent upon release and provides insight into the selective forces that are limiting the adaptation of indigenous species to the new pest. We use this knowledge to give future research directions for the development of selective breeding methods for biocontrol agents.

Diversity and distribution of Wolbachia in relation to geography, host plant affiliation and life cycle of a heterogonic gall wasp

BACKGROUND

The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we survey Wolbachia in Belonocnema treatae, a widely distributed North American cynipid gall forming wasp that exhibits regional host specialization on three species of oaks and alternation of sexually and asexually reproducing generations. We investigated whether patterns of Wolbachia infection and diversity in B. treatae are associated with the insect's geographic distribution, host plant association, life cycle, and mitochondrial evolutionary history.

RESULTS

Screening of 463 individuals from 23 populations including sexual and asexual generations from all three host plants across the southern U.S. showed an average infection rate of 56% with three common Wolbachia strains: wTre1-3 and an additional rare variant wTre4. Phylogenetic analysis based on wsp showed that these strains are unrelated and likely independently inherited. We found no difference in Wolbachia infection frequency among host plant associated populations or between the asexual and sexual generations, or between males and females of the sexual generation. Partially incomplete Wolbachia transmission rates might explain the occurrence of uninfected individuals. A parallel analysis of the mitochondrial cytochrome oxidase I gene in B. treatae showed high mtDNA haplotype diversity in both infected and uninfected populations suggesting an ancestral infection by Wolbachia as well as a clear split between eastern and western B. treatae mtDNA clades with a sequence divergence of > 6%. The strain wTre1 was present almost exclusively in the western clade while wTre2 and wTre3 occur almost exclusively in eastern populations. In contrast, the same strains co-occur as double-infections in Georgia and triple-infections in two populations in central Florida.

CONCLUSIONS

The diversity of Wolbachia across geographically and genetically distinct populations of B. treatae and the co-occurrence of the same strains within three populations highlights the complex infection dynamics in this system. Moreover, the association of distinct Wolbachia strains with mitochondrial haplotypes of its host in populations infected by different Wolbachia strains suggests a potential role of the endosymbiont in reproductive isolation in B. treatae.