Heritable endosymbionts of Drosophila

The role of animal hosts in shaping gut microbiome variation

Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Characterization of bacteria expectorated during forced salivation of the Phlebotomus papatasi: A neglected component of sand fly infectious inoculums

The infectious inoculum of a sand fly, apart from its metacyclic promastigotes, is composed of factors derived from both the parasite and the vector. Vector-derived factors, including salivary proteins and the gut microbiota, are essential for the establishment and enhancement of infection. However, the type and the number of bacteria egested during salivation is unclear. In the present study, sand flies of Phlebotomus papatasi were gathered from three locations in hyperendemic focus of zoonotic cutaneous leishmaniasis (ZCL) in Isfahan Province, Iran. By using the forced salivation assay and targeting the 16S rRNA barcode gene, egested bacteria were characterized in 99 (44%) out of 224 sand flies. Culture-dependent and culture-independent methods identified the members of Enterobacter cloacae and Spiroplasma species as dominant taxa, respectively. Ten top genera of Spiroplasma, Ralstonia, Acinetobacter, Reyranella, Undibacterium, Bryobacter, Corynebacterium, Cutibacterium, Psychrobacter, and Wolbachia constituted >80% of the saliva microbiome. Phylogenetic analysis displayed the presence of only one bacterial species for the Spiroplasma, Ralstonia, Reyranella, Bryobacter and Wolbachia, two distinct species for Cutibacterium, three for Undibacterium and Psychrobacter, 16 for Acinetobacter, and 27 for Corynebacterium, in the saliva. The abundance of microbes in P. papatasi saliva was determined by incorporating the data on the read counts and the copy number of 16S rRNA gene, about 9,000 bacterial cells, per sand fly. Both microbiological and metagenomic data indicate that bacteria are constant companions of Leishmania, from the intestine of the vector to the vertebrate host. This is the first forced salivation experiment in a sand fly, addressing key questions on infectious bite and competent vectors.

Wolbachia symbionts control sex in a parasitoid wasp using a horizontally acquired gene

Host reproduction can be manipulated by bacterial symbionts in various ways. Parthenogenesis induction is the most effective type of reproduction manipulation by symbionts for their transmission. Insect sex is determined by regulation of doublesex (dsx) splicing through transformer2 (tra2) and transformer (tra) interaction. Although parthenogenesis induction by symbionts has been studied since the 1970s, its underlying molecular mechanism is unknown. Here we identify a Wolbachia parthenogenesis-induction feminization factor gene (piff) that targets sex-determining genes and causes female-producing parthenogenesis in the haplodiploid parasitoid Encarsia formosa. We found that Wolbachia elimination repressed expression of female-specific dsx and enhanced expression of male-specific dsx, which led to the production of wasp haploid male offspring. Furthermore, we found that E. formosa tra is truncated and non-functional, and Wolbachia has a functional tra homolog, termed piff, with an insect origin. Wolbachia PIFF can colocalize and interact with wasp TRA2. Moreover, Wolbachia piff has coordinated expression with tra2 and dsx of E. formosa. Our results demonstrate the bacterial symbiont Wolbachia has acquired an insect gene to manipulate the host sex determination cascade and induce parthenogenesis in wasps. This study reveals insect-to-bacteria horizontal gene transfer drives the evolution of animal sex determination systems, elucidating a striking mechanism of insect-microbe symbiosis.

Wolbachia infection at least partially rescues the fertility and ovary defects of several new Drosophila melanogaster bag of marbles protein-coding mutants

The D. melanogaster protein coding gene bag of marbles ( bam ) plays a key role in early male and female reproduction by forming complexes with partner proteins to promote differentiation in gametogenesis. Like another germline gene, Sex lethal , bam genetically interacts with the endosymbiont Wolbachia , as Wolbachia rescues the reduced fertility of a bam hypomorphic mutant. Here, we explored the specificity of the bam-Wolbachia interaction by generating 22 new bam mutants, with ten mutants displaying fertility defects. Nine of these mutants trend towards rescue by the w Mel Wolbachia variant, with eight statistically significant at the fertility and/or cytological level. In some cases, fertility was increased a striking 20-fold. There is no specificity between the rescue and the known binding regions of bam , suggesting w Mel does not interact with one singular bam partner to rescue the reproductive phenotype. We further tested if w Mel interacts with bam in a non-specific way, by increasing bam transcript levels or acting upstream in germline stem cells. A fertility assessment of a bam RNAi knockdown mutant reveals that w Mel rescue is specific to functionally mutant bam alleles and we find no obvious evidence of w Mel interaction with germline stem cells in bam mutants.

Author Summary

Reproduction in the Drosophila melanogaster fruit fly is dependent on the bag of marbles ( bam ) gene, which acts early in the process of generating eggs and sperm. Mutations to this gene negatively impact the fertility of the fly, causing it to be sterile or have fewer progeny. Interestingly, we find that the bacteria Wolbachia , which resides within reproductive cells across a wide range of insects, partially restores the fertility and ovary phenotype of several bam mutants of which the resultant Bam protein is altered from wildtype. The protein function of Bam is further suggested to be important by the lack of rescue for a fly that has a fertility defect due to low expression of a non-mutated bam gene. Previous work makes similar conclusions about Wolbachia with another reproductive gene, Sex lethal ( Sxl ), highlighting the potential for rescue of fertility mutants to occur in a similar way across different genes. An understanding of the ways in which Wolbachia can affect host reproduction provides us with context with which to frame Wolbachia 's impact on host genes, such as bam and Sxl, and consider the evolutionary implications of Wolbachia 's infection in D. melanogaster fruit flies.

The toxins of vertically transmitted Spiroplasma

Vertically transmitted (VT) microbial symbionts play a vital role in the evolution of their insect hosts. A longstanding question in symbiont research is what genes help promote long-term stability of vertically transmitted lifestyles. Symbiont success in insect hosts is due in part to expression of beneficial or manipulative phenotypes that favor symbiont persistence in host populations. In Spiroplasma, these phenotypes have been linked to toxin and virulence domains among a few related strains. However, these domains also appear frequently in phylogenetically distant Spiroplasma, and little is known about their distribution across the Spiroplasma genus. In this study, we present the complete genome sequence of the Spiroplasma symbiont of Drosophila atripex, a non-manipulating member of the Ixodetis clade of Spiroplasma, for which genomic data are still limited. We perform a genus-wide comparative analysis of toxin domains implicated in defensive and reproductive phenotypes. From 12 VT and 31 non-VT Spiroplasma genomes, ribosome-inactivating proteins (RIPs), OTU-like cysteine proteases (OTUs), ankyrins, and ETX/MTX2 domains show high propensity for VT Spiroplasma compared to non-VT Spiroplasma. Specifically, OTU and ankyrin domains can be found only in VT-Spiroplasma, and RIP domains are found in all VT Spiroplasma and three non-VT Spiroplasma. These domains are frequently associated with Spiroplasma plasmids, suggesting a possible mechanism for dispersal and maintenance among heritable strains. Searching insect genome assemblies available on public databases uncovered uncharacterized Spiroplasma genomes from which we identified several spaid-like genes encoding RIP, OTU, and ankyrin domains, suggesting functional interactions among those domain types. Our results suggest a conserved core of symbiont domains play an important role in the evolution and persistence of VT Spiroplasma in insects.

A male-killing Wolbachia endosymbiont is concealed by another endosymbiont and a nuclear suppressor

Bacteria that live inside the cells of insect hosts (endosymbionts) can alter the reproduction of their hosts, including the killing of male offspring (male killing, MK). MK has only been described in a few insects, but this may reflect challenges in detecting MK rather than its rarity. Here, we identify MK Wolbachia at a low frequency (around 4%) in natural populations of Drosophila pseudotakahashii. MK Wolbachia had a stable density and maternal transmission during laboratory culture, but the MK phenotype which manifested mainly at the larval stage was lost rapidly. MK Wolbachia occurred alongside a second Wolbachia strain expressing a different reproductive manipulation, cytoplasmic incompatibility (CI). A genomic analysis highlighted Wolbachia regions diverged between the 2 strains involving 17 genes, and homologs of the wmk and cif genes implicated in MK and CI were identified in the Wolbachia assembly. Doubly infected males induced CI with uninfected females but not females singly infected with CI-causing Wolbachia. A rapidly spreading dominant nuclear suppressor genetic element affecting MK was identified through backcrossing and subsequent analysis with ddRAD SNPs of the D. pseudotakahashii genome. These findings highlight the complexity of nuclear and microbial components affecting MK endosymbiont detection and dynamics in populations and the challenges of making connections between endosymbionts and the host phenotypes affected by them.

Unraveling the Role of Antimicrobial Peptides in Insects

Antimicrobial peptides (AMPs) are short, mainly positively charged, amphipathic molecules. AMPs are important effectors of the immune response in insects with a broad spectrum of antibacterial, antifungal, and antiparasitic activity. In addition to these well-known roles, AMPs exhibit many other, often unobvious, functions in the host. They support insects in the elimination of viral infections. AMPs participate in the regulation of brain-controlled processes, e.g., sleep and non-associative learning. By influencing neuronal health, communication, and activity, they can affect the functioning of the insect nervous system. Expansion of the AMP repertoire and loss of their specificity is connected with the aging process and lifespan of insects. Moreover, AMPs take part in maintaining gut homeostasis, regulating the number of endosymbionts as well as reducing the number of foreign microbiota. In turn, the presence of AMPs in insect venom prevents the spread of infection in social insects, where the prey may be a source of pathogens.

Low Endosymbiont Incidence in Drosophila Species Across Peninsula Thailand

Arthropods are known to harbor several endosymbionts, such as Cardinium, Rickettsia, Spiroplasma, and Wolbachia. Wolbachia, for example, are the most widespread known endosymbionts in the world, which are found in about half of all arthropod species. To increase their transmission, these endosymbionts must manipulate their hosts in several ways such as cytoplasmic incompatibility and male killing. In tropical regions, endosymbiont diversity has not been studied exhaustively. Here, we checked four endosymbionts, including Cardinium, Rickettsia, Spiroplasma, and Wolbachia, in eleven Drosophila species found in Thai Peninsula. The Wolbachia strain wRi-like was found in all populations of Drosophila ananassae and Drosophila simulans. Furthermore, we found two new strains, wMalA and wMalB, in two populations of Drosophila malerkotliana. Besides Wolbachia, we did not find any of the above endosymbionts in all fly species. This work reveals the hidden diversity of endosymbionts in Drosophila and is the first exhaustive study on Drosophila in the region.

Rapid divergence in independent aspects of the compatibility phenotype in a Spiroplasma-Drosophila interaction

Heritable symbionts represent important components of the biology, ecology and evolution of their arthropod hosts. Particular microbial taxa have become common across arthropods as a consequence of their ability to establish in new host species. For a host shift to occur, the symbiont must be exposed to a novel host and then be compatible: it must not cause excess pathology, must have good vertical transmission and must possess a drive phenotype that enables spread. Here we investigate the lability of compatibility to symbiosis with Spiroplasma. We used transinfection to establish the protective Spiroplasma symbiont from Drosophila hydei in two closely related novel hosts, Drosophila simulans and Drosophila melanogaster. The Spiroplasma had contrasting compatibility in the two species, exhibiting pathology and low vertical transmission but delivering protection from wasp attack in D. melanogaster but being asymptomatic and transmitted with high efficiency but with lower protection in D. simulans. Further work indicated that pathological interactions occurred in two other members of the melanogaster species group, such that D. simulans was unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasizes the rapidity with which host-symbiont compatibility evolves, despite compatibility itself not being subject to direct selection. Further, the requirement to fit three independent components of compatibility (pathology, transmission, protection) is probably to be a major feature limiting the rate of host shifts that will likely impact on the utility of Spiroplasma in pest and vector control. Moving forward, the variation between sibling species pairs provides an opportunity to identify the mechanisms behind variable compatibility, which will drive hypotheses as to the evolutionary drivers of compatibility variation.

Preliminary Characterization of Phage-Like Particles from the Male-Killing Mollicute Spiroplasma poulsonii (an Endosymbiont of Drosophila)

Bacteriophages are vastly abundant, diverse, and influential, but with few exceptions (e.g. the Proteobacteria genera Wolbachia and Hamiltonella), the role of phages in heritable bacteria-arthropod interactions, which are ubiquitous and diverse, remains largely unexplored. Despite prior studies documenting phage-like particles in the mollicute Spiroplasma associated with Drosophila flies, genomic sequences of such phage are lacking, and their effects on the Spiroplasma-Drosophila interaction have not been comprehensively characterized. We used a density step gradient to isolate phage-like particles from the male-killing bacterium Spiroplasma poulsonii (strains NSRO and MSRO-Br) harbored by Drosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Several lines of evidence suggest that we recovered phage-like particles of similar features (shape, size, DNA content) to those previously reported in Drosophila-associated Spiroplasma strains. We recovered three ~ 19 kb phage-like contigs (two in NSRO and one in MSRO-Br) containing 21-24 open reading frames, a read-alignment pattern consistent with circular permutation, and terminal redundancy (at least in NSRO). Although our results do not allow us to distinguish whether these phage-like contigs represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We also recovered two smaller non-phage-like contigs encoding a known Spiroplasma toxin (Ribosome Inactivating Protein; RIP), and an insertion element, suggesting that they are packaged into particles. Substantial homology of our particle-derived contigs was found in the genome assemblies of members of the Spiroplasma poulsonii clade.

Characterization of the first Wolbachia from the genus Scaptodrosophila, a male-killer from the rainforest species S. claytoni

The Scaptodrosophila genus represents a large group of drosophilids with a worldwide distribution and a predominance of species in Australia, but there is little information on the presence and impacts of Wolbachia endosymbionts in this group. Here we describe the first Wolbachia infection from this group, wClay isolated from Scaptodrosophila claytoni (van Klinken), a species from the east coast of Australia. The infection is polymorphic in natural populations, occurring at a frequency of around 6%-10%. wClay causes male killing, producing female-biased lines; most lines showed 100% male killing, though in 1 line it was <80%. The lines need to be maintained through the introduction of males unless the infection is removed by tetracycline treatment. wClay is transmitted at a high fidelity (98.6%) through the maternal lineage and has been stable in 2 laboratory lines across 24 generations, suggesting it is likely to persist in populations. The infection has not been previously described but is closely related to the male-killing Wolbachia recently described from Drosophila pandora based on multilocus sequence typing and the wsp gene. Male-killing Wolbachia are likely to be common in drosophilids but remain difficult to detect because the infections can often be at a low frequency.

Disproportionate investment in Spiralin B production limits in-host growth and favors the vertical transmission of Spiroplasma insect endosymbionts

Insects frequently harbor endosymbionts, which are bacteria housed within host tissues. These associations are stably maintained over evolutionary timescales through vertical transmission of endosymbionts from host mothers to their offspring. Some endosymbionts manipulate host reproduction to facilitate spread within natural populations. Consequently, such infections have major impacts on insect physiology and evolution. However, technical hurdles have limited our understanding of the molecular mechanisms underlying such insect-endosymbiont interactions. Here, we investigate the nutritional interactions between endosymbiotic partners using the tractable insect Drosophila melanogaster and its natural endosymbiont Spiroplasma poulsonii. Using a combination of functional assays, metabolomics, and proteomics, we show that the abundance and amino acid composition of a single Spiroplasma membrane lectin, Spiralin B (SpiB), dictates the amino acid requirements of the endosymbiont and determines its proliferation within host tissues. Ectopically increasing SpiB levels in host tissues disrupts localization of endosymbionts in the fly egg chambers and decreases vertical transmission. We find that SpiB is likely to be required by the endosymbiont to enter host oocytes, which may explain the massive investment of S. poulsonii in SpiB synthesis. SpiB both permits vertical transmission of the symbiont and limits its growth in nutrient-limiting conditions for the host; therefore, a single protein plays a pivotal role in ensuring durability of the interaction in a variable environment.

Temperature effects on cellular host-microbe interactions explain continent-wide endosymbiont prevalence

Endosymbioses influence host physiology, reproduction, and fitness, but these relationships require efficient microbe transmission between host generations to persist. Maternally transmitted Wolbachia are the most common known endosymbionts,¹ but their frequencies vary widely within and among host populations for unknown reasons.^2,3 Here, we integrate genomic, cellular, and phenotypic analyses with mathematical models to provide an unexpectedly simple explanation for global wMel Wolbachia prevalence in Drosophila melanogaster. Cooling temperatures decrease wMel cellular abundance at a key stage of host oogenesis, producing temperature-dependent variation in maternal transmission that plausibly explains latitudinal clines of wMel frequencies on multiple continents. wMel sampled from a temperate climate targets the germline more efficiently in the cold than a recently differentiated tropical variant (∼2,200 years ago), indicative of rapid wMel adaptation to climate. Genomic analyses identify a very narrow list of wMel alleles-most notably, a derived stop codon in the major Wolbachia surface protein WspB-that underlie thermal sensitivity of cellular Wolbachia abundance and covary with temperature globally. Decoupling temperate wMel and host genomes further reduces transmission in the cold, a pattern that is characteristic of host-microbe co-adaptation to a temperate climate. Complex interactions among Wolbachia, hosts, and the environment (GxGxE) mediate wMel cellular abundance and maternal transmission, implicating temperature as a key determinant of Wolbachia spread and equilibrium frequencies, in conjunction with Wolbachia effects on host fitness and reproduction.^4,5 Our results motivate the strategic use of locally selected wMel variants for Wolbachia-based biocontrol efforts, which protect millions of individuals from arboviruses that cause human disease.⁶.

The wall-less bacterium Spiroplasma poulsonii builds a polymeric cytoskeleton composed of interacting MreB isoforms

A rigid cell wall defines the morphology of most bacteria. MreB, a bacterial homologue of actin, plays a major role in coordinating cell wall biogenesis and defining cell shape. Spiroplasma are wall-less bacteria that robustly grow with a characteristic helical shape. Paradoxal to their lack of cell wall, the Spiroplasma genome contains five homologs of MreB (SpMreBs). Here, we investigate the function of SpMreBs in forming a polymeric cytoskeleton. We found that, in vivo, Spiroplasma maintain a high concentration of all MreB isoforms. By leveraging a heterologous expression system that bypasses the poor genetic tractability of Spiroplasma, we found that SpMreBs produced polymeric filaments of various morphologies. We characterized an interaction network between isoforms that regulate filament formation and patterning. Therefore, our results support the hypothesis where combined SpMreB isoforms would form an inner polymeric cytoskeleton in vivo that shapes the cell in a wall-independent manner.

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The five Spiroplasma MreB isoforms are extremely abundant proteins in vivo

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Each isoform produces filaments when expressed in a heterologous system

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SpMreBs form an interaction network that regulates filament length and shape

Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism

Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host–microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota–brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect–microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect–microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.

Rapid Divergence of Key Spermatogenesis Genes in nasuta-Subgroup of Drosophila

The crosses between closely related Drosophila species usually produce sterile hybrid males with spermatogenesis disrupted at post-meiotic phase, especially in sperm individualization stage than the pre-meiotic stage. This is possibly due to the rapid interspecies divergence of male sex and reproduction-related genes. Here we annotated 11 key spermatogenesis genes in 35 strains of species belonging to nasuta-subgroup of Drosophila, where many interspecies crosses produce sterile males. We characterized the divergence and polymorphism in the protein coding regions by employing gene-wide, codon-wide, and lineage-specific selection analysis to test the mode and strength of selection acting on these genes. Our analysis showed signature of positive selection at bag of marbles (bam) and benign gonial cell neoplasma (bgcn) despite the selection constrains and the absence of endosymbiont infection which could potentially drive rapid divergence due to an arms race while roughex (rux) showed lineage-specific rapid divergence in frontal sheen complex of nasuta-subgroup. cookie monster (comr) showed rapid divergence consistent with the possibility of meiotic arrest observed in sterile hybrids of Drosophila species. Rapid divergence observed at don juan (dj) and Mst98Ca-like was consistent with fused sperm-tail abnormality observed in the hybrids of Drosophila nasuta and Drosophila albomicans. These findings highlight the potential role of rapid nucleotide divergence in bringing about hybrid incompatibility in the form of male sterility; however, additional genetic manipulation studies can widen our understanding of hybrid incompatibilities. Furthermore, our study emphasizes the importance of young species belonging to nasuta-subgroup of Drosophila in studying post-zygotic reproductive isolation mechanisms.

Efficiencies of stationary sampling tools for the tsetse fly Glossina fuscipes fuscipes in western Kenya

Monitoring the effectiveness of tsetse fly control interventions that aim to reduce transmission of African trypanosomiasis requires highly efficient sampling tools that can catch flies at low densities. The sticky small target (StS-target) has previously been shown to be more effective in sampling Glossina fuscipes fuscipes compared to the biconical trap. However, its efficiency in terms of the proportion of flies it catches out of those that visit it has not been reported. Furthermore, there are no reports on whether tsetse samples caught using the StS-target can be used for subsequent processes such as molecular tests. In this study, we evaluated the efficiency of the biconical trap and targets for sampling G. f. fuscipes. All targets were tiny (0.25 × 0.50 m) but varied in their capture system. We used targets with sticky surface (StS-targets) and those with an electrified surface (ES-targets). We also assessed the suitability of flies caught on the StS-target for molecular tests by amplifying DNA of bacterial communities. Randomized block design experiments were undertaken in Mbita area and Manga Island on Lake Victoria of western Kenya. Fly catches of each sampling tool were compared to those of the sampling tool flanked by electric (E) nets and analyzed using a negative binomial regression. The total catch for each sampling tool alone was divided by the total catch of the sampling tool flanked by two E-nets to obtain its efficiency expressed as a percentage. A proportion of flies caught on the StS-target was preserved for molecular tests. Overall, the efficiencies of the biconical trap, ES-target and StS-target were 7.7%, 13.3% and 27.0%, respectively. A higher proportion of females (69 to 79%) than males approached all the sampling tools, but the trap efficiency was greater for male G. f. fuscipes than females. Furthermore, sequencing the 16S rRNA gene from fly samples caught on the StS-target revealed the presence of Spiroplasma. Our results indicate that the SS-target is the most efficient trap to monitor G. f. fuscipes population during interventions, with the biconical trap being the least efficient, and samples collected from StS-targets are suitable for molecular studies.

Frequent Drivers, Occasional Passengers: Signals of Symbiont-Driven Seasonal Adaptation and Hitchhiking in the Pea Aphid, Acyrthosiphon pisum

Insects harbor a variety of maternally inherited bacterial symbionts. As such, variation in symbiont presence/absence, in the combinations of harbored symbionts, and in the genotypes of harbored symbiont species provide heritable genetic variation of potential use in the insects' adaptive repertoires. Understanding the natural importance of symbionts is challenging but studying their dynamics over time can help to elucidate the potential for such symbiont-driven insect adaptation. Toward this end, we studied the seasonal dynamics of six maternally transferred bacterial symbiont species in the multivoltine pea aphid (Acyrthosiphon pisum). Our sampling focused on six alfalfa fields in southeastern Pennsylvania, and spanned 14 timepoints within the 2012 growing season, in addition to two overwintering periods. To test and generate hypotheses on the natural relevance of these non-essential symbionts, we examined whether symbiont dynamics correlated with any of ten measured environmental variables from the 2012 growing season, including some of known importance in the lab. We found that five symbionts changed prevalence across one or both overwintering periods, and that the same five species underwent such frequency shifts across the 2012 growing season. Intriguingly, the frequencies of these dynamic symbionts showed robust correlations with a subset of our measured environmental variables. Several of these trends supported the natural relevance of lab-discovered symbiont roles, including anti-pathogen defense. For a seventh symbiont-Hamiltonella defensa-studied previously across the same study periods, we tested whether a reported correlation between prevalence and temperature stemmed not from thermally varying host-level fitness effects, but from selection on co-infecting symbionts or on aphid-encoded alleles associated with this bacterium. In general, such "hitchhiking" effects were not evident during times with strongly correlated Hamiltonella and temperature shifts. However, we did identify at least one time period in which Hamiltonella spread was likely driven by selection on a co-infecting symbiont-Rickettsiella viridis. Recognizing the broader potential for such hitchhiking, we explored selection on co-infecting symbionts as a possible driver behind the dynamics of the remaining six species. Out of twelve examined instances of symbiont dynamics unfolding across 2-week periods or overwintering spans, we found eight in which the focal symbiont underwent parallel frequency shifts under single infection and one or more co-infection contexts. This supported the idea that phenotypic variation created by the presence/absence of individual symbionts is a direct target for selection, and that symbiont effects can be robust under co-habitation with other symbionts. Contrastingly, in two cases, we found that selection may target phenotypes emerging from symbiont co-infections, with specific species combinations driving overall trends for the focal dynamic symbionts, without correlated change under single infection. Finally, in three cases-including the one described above for Hamiltonella-our data suggested that incidental co-infection with a (dis)favored symbiont could lead to large frequency shifts for "passenger" symbionts, conferring no apparent cost or benefit. Such hitchhiking has rarely been studied in heritable symbiont systems. We propose that it is more common than appreciated, given the widespread nature of maternally inherited bacteria, and the frequency of multi-species symbiotic communities across insects.

Molecular population genetics of Sex-lethal (Sxl) in the Drosophila melanogaster species group: a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster

Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in D. melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and W. pipientis’ ability to manipulate reproduction in Drosophila, we carried out a careful study of both the population genetics (within four Drosophila species) and molecular evolutionary analysis (across 20 Drosophila species) of Sxl. Consistent with earlier studies, we find that selective constraint has played a prominent role in Sxl’s molecular evolution within Drosophila, but we also observe patterns that suggest both episodic bursts of protein evolution and recent positive selection at Sxl. The episodic nature of Sxl’s protein evolution is discussed in light of its genetic interaction with W. pipientis.

The First Report for the Presence of Spiroplasma and Rickettsia in Red Palm Weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) in Egypt

PURPOSE

The study of the Red Palm Weevil (RPW), Rhynchophorus ferrugineus (Olivier), as an invasive pest of palm trees.

METHODS

In this study, 36 RPW individuals were collected from 6 different locations in Egypt. The presences of endosymbionts in the RPW individuals were assayed. The phylogenetic analysis of the RPW inhabiting Egypt was conducted using Cytochrome c oxidase sub-unit 1 (CO1) gene.

RESULTS

Spiroplasma was found, for the first time, in all individuals, while Rickettsia was found, for the first time, in individuals collected from only 3 of the 6 locations. Endosymbionts harbouring Egyptian RPW were closely related to those harbouring Diptera and\or Trombidiformes associated with palm trees. This may be due to horizontal transmission through palm sap or through ectoparasites living on the RPW. Finally, the phylogenetic analysis of the RPW inhabiting Egypt was conducted. The collected individuals were closely related to Saudi Arabia specimens collected from the eastern region. Thus, Saudi Arabia may be the origin of the RPW which invaded Egypt. Individuals from populations inhabiting the same geographical locations were closely related. This may be due to secondary invasion incidents that may have taken place through transportation of infested date palm trees and offshoots from infected to uninfected locations.

CONCLUSION

This study reports the first incidence for the presence and coexistence of Spiroplasma and Rickettsia in RPW collected from Egypt. In addition, it was found that the collected individuals of RPW were closely related to a Saudi haplotype. Thus, Saudi Arabia may be the origin of infection which invaded Egypt.

Dual proteomics of Drosophila melanogaster hemolymph infected with the heritable endosymbiont Spiroplasma poulsonii

Insects are frequently infected with heritable bacterial endosymbionts. Endosymbionts have a dramatic impact on their host physiology and evolution. Their tissue distribution is variable with some species being housed intracellularly, some extracellularly and some having a mixed lifestyle. The impact of extracellular endosymbionts on the biofluids they colonize (e.g. insect hemolymph) is however difficult to appreciate because biofluid composition can depend on the contribution of numerous tissues. Here we investigate Drosophila hemolymph proteome changes in response to the infection with the endosymbiont Spiroplasma poulsonii. S. poulsonii inhabits the fly hemolymph and gets vertically transmitted over generations by hijacking the oogenesis in females. Using dual proteomics on infected hemolymph, we uncovered a weak, chronic activation of the Toll immune pathway by S. poulsonii that was previously undetected by transcriptomics-based approaches. Using Drosophila genetics, we also identified candidate proteins putatively involved in controlling S. poulsonii growth. Last, we also provide a deep proteome of S. poulsonii, which, in combination with previously published transcriptomics data, improves our understanding of the post-transcriptional regulations operating in this bacterium.

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.

The Antiviral Effects of the Symbiont Bacteria Wolbachia in Insects

Wolbachia is a maternally transmitted bacterium that lives inside arthropod cells. Historically, it was viewed primarily as a parasite that manipulates host reproduction, but more recently it was discovered that Wolbachia can also protect Drosophila species against infection by RNA viruses. Combined with Wolbachia's ability to invade insect populations due to reproductive manipulations, this provides a way to modify mosquito populations to prevent them transmitting viruses like dengue. In this review, we discuss the main advances in the field since Wolbachia's antiviral effect was discovered 12 years ago, identifying current research gaps and potential future developments. We discuss that the antiviral effect works against a broad range of RNA viruses and depends on the Wolbachia lineage. We describe what is known about the mechanisms behind viral protection, and that recent studies suggest two possible mechanisms: activation of host immunity or competition with virus for cellular resources. We also discuss how association with Wolbachia may influence the evolution of virus defense on the insect host genome. Finally, we investigate whether the antiviral effect occurs in wild insect populations and its ecological relevance as a major antiviral component in insects.

Thermal sensitivity of the Spiroplasma-Drosophila hydei protective symbiosis: The best of climes, the worst of climes

The outcome of natural enemy attack in insects is commonly influenced by the presence of protective symbionts in the host. The degree to which protection functions in natural populations, however, will depend on the robustness of the phenotype and symbiosis to variation in the abiotic environment. We studied the impact of a key environmental parameter-temperature-on the efficacy of the protective effect of the symbiont Spiroplasma on its host Drosophila hydei, against attack by the parasitoid wasp Leptopilina heterotoma. In addition, we investigated the thermal sensitivity of the symbiont's vertical transmission, which may be a key determinant of the ability of the symbiont to persist. We found that vertical transmission was more robust than previously considered, with Spiroplasma being maintained at 25°C, at 18°C and with 18/15°C diurnal cycles, with rates of segregational loss only increasing at 15°C. Protection against wasp attack was ablated before symbiont transmission was lost, with the symbiont failing to rescue the fly host at 18°C. We conclude that the presence of a protective symbiosis in natural populations cannot be simply inferred from the presence of a symbiont whose protective capacity has been tested under narrow controlled conditions. More broadly, we argue that the thermal environment is likely to represent an important determinant of the evolutionary ecology of defensive symbioses in natural environments, potentially driving seasonal, latitudinal and altitudinal variation in symbiont frequency.

Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility

Cytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.

Food Resource Sharing of Alder Leaf Beetle Specialists (Coleoptera: Chrysomelidae) as Potential Insect-Plant Interface for Horizontal Transmission of Endosymbionts

Recent studies suggest that endosymbionts of herbivore insects can be horizontally transferred to other herbivores feeding on the same host plants, whereby the plant acts as an intermediate stage in the chain of transmission. If this mechanism operates, it is also expected that insect communities sharing the same host plant will have higher chances to share their endosymbionts. In this study, we use a high-throughput 16S rRNA metabarcoding approach to investigate the presence, diversity, and potential sharing of endosymbionts in several species of leaf beetles (Coleoptera: Chrysomelidae) of a local community specialized on an alder diet in North America. Rickettsia and Wolbachia were predominant in the sample, with strong evidence for each species having their own dominant infection, of either or both types of bacteria. However, all species shared a much lower proportion of a particular Wolbachia type, compatible with the same strain dominant in one of the species of leaf beetles. Crucially, the same 16S rRNA haplotype of Wolbachia was found on alder leaf extracts. The combined evidence and the absence of this strain in a syntopic species of leaf beetle feeding on a different host plant support the hypothesis that at least the initial stages of the mechanism that would allow horizontal transmission of endosymbionts across species feeding on the same plant is possible. The accessibility and characteristics of endosymbiont associations of this system make it suitable for deeper analyses of their diversity and transmission in natural conditions.

Environmental and Genetic Contributions to Imperfect wMel-Like Wolbachia Transmission and Frequency Variation

Maternally transmitted Wolbachia bacteria infect about half of all insect species. They usually show imperfect maternal transmission and often produce cytoplasmic incompatibility (CI). Irrespective of CI, Wolbachia frequencies tend to increase when rare only if they benefit host fitness. Several Wolbachia, including wMel that infects Drosophila melanogaster, cause weak or no CI and persist at intermediate frequencies. On the island of São Tomé off West Africa, the frequencies of wMel-like Wolbachia infecting Drosophila yakuba (wYak) and Drosophila santomea (wSan) fluctuate, and the contributions of imperfect maternal transmission, fitness effects, and CI to these fluctuations are unknown. We demonstrate spatial variation in wYak frequency and transmission on São Tomé. Concurrent field estimates of imperfect maternal transmission do not predict spatial variation in wYak frequencies, which are highest at high altitudes where maternal transmission is the most imperfect. Genomic and genetic analyses provide little support for D. yakuba effects on wYak transmission. Instead, rearing at cool temperatures reduces wYak titer and increases imperfect transmission to levels observed on São Tomé. Using mathematical models of Wolbachia frequency dynamics and equilibria, we infer that temporally variable imperfect transmission or spatially variable effects on host fitness and reproduction are required to explain wYak frequencies. In contrast, spatially stable wSan frequencies are plausibly explained by imperfect transmission, modest fitness effects, and weak CI. Our results provide insight into causes of wMel-like frequency variation in divergent hosts. Understanding this variation is crucial to explain Wolbachia spread and to improve wMel biocontrol of human disease in transinfected mosquito systems.

Transformation of the Drosophila Sex-Manipulative Endosymbiont Spiroplasma poulsonii and Persisting Hurdles for Functional Genetic Studies

Insects are frequently infected by bacterial symbionts that greatly affect their physiology and ecology. Most of these endosymbionts are, however, barely tractable outside their native host, rendering functional genetics studies difficult or impossible. Spiroplasma poulsonii is a facultative bacterial endosymbiont of Drosophila melanogaster that manipulates the reproduction of its host by killing its male progeny at the embryonic stage. S. poulsonii, although a very fastidious bacterium, is closely related to pathogenic Spiroplasma species that are cultivable and genetically modifiable. In this work, we present the transformation of S. poulsonii with a plasmid bearing a fluorescence cassette, leveraging techniques adapted from those used to modify the pathogenic species Spiroplasma citri We demonstrate the feasibility of S. poulsonii transformation and discuss approaches for mutant selection and fly colonization, which are persisting hurdles that must be overcome to allow functional bacterial genetics studies of this endosymbiont in vivo IMPORTANCE Dozens of bacterial endosymbiont species have been described and estimated to infect about half of all insect species. However, only a few them are tractable in vitro, which hampers our understanding of the bacterial determinants of the host-symbiont interaction. Developing a transformation method for S. poulsonii is a major step toward genomic engineering of this symbiont, which will foster basic research on endosymbiosis. This could also open the way to practical uses of endosymbiont engineering through paratransgenesis of vector or pest insects.

Corn Stunt Disease: An Ideal Insect-Microbial-Plant Pathosystem for Comprehensive Studies of Vector-Borne Plant Diseases of Corn

Over 700 plant diseases identified as vector-borne negatively impact plant health and food security globally. The pest control of vector-borne diseases in agricultural settings is in urgent need of more effective tools. Ongoing research in genetics, molecular biology, physiology, and vector behavior has begun to unravel new insights into the transmission of phytopathogens by their insect vectors. However, the intricate mechanisms involved in phytopathogen transmission for certain pathosystems warrant further investigation. In this review, we propose the corn stunt pathosystem (Zea mays-Spiroplasma kunkelii-Dalbulus maidis) as an ideal model for dissecting the molecular determinants and mechanisms underpinning the persistent transmission of a mollicute by its specialist insect vector to an economically important monocotyledonous crop. Corn stunt is the most important disease of corn in the Americas and the Caribbean, where it causes the severe stunting of corn plants and can result in up to 100% yield loss. A comprehensive study of the corn stunt disease system will pave the way for the discovery of novel molecular targets for genetic pest control targeting either the insect vector or the phytopathogen.

Wolbachia pipientis Associated With Tephritid Fruit Fly Pests: From Basic Research to Applications

Members of the true fruit flies (family Tephritidae) are among the most serious agricultural pests worldwide, whose control and management demands large and costly international efforts. The need for cost-effective and environmentally friendly integrated pest management (IPM) has led to the development and implementation of autocidal control strategies. These approaches include the widely used sterile insect technique and the incompatible insect technique (IIT). IIT relies on maternally transmitted bacteria (namely Wolbachia) to cause a conditional sterility in crosses between released mass-reared Wolbachia-infected males and wild females, which are either uninfected or infected with a different Wolbachia strain (i.e., cytoplasmic incompatibility; CI). Herein, we review the current state of knowledge on Wolbachia-tephritid interactions including infection prevalence in wild populations, phenotypic consequences, and their impact on life history traits. Numerous pest tephritid species are reported to harbor Wolbachia infections, with a subset exhibiting high prevalence. The phenotypic effects of Wolbachia have been assessed in very few tephritid species, due in part to the difficulty of manipulating Wolbachia infection (removal or transinfection). Based on recent methodological advances (high-throughput DNA sequencing) and breakthroughs concerning the mechanistic basis of CI, we suggest research avenues that could accelerate generation of necessary knowledge for the potential use of Wolbachia-based IIT in area-wide integrated pest management (AW-IPM) strategies for the population control of tephritid pests.

Detection of Wolbachia Infections in Natural and Laboratory Populations of the Moroccan Hessian Fly, Mayetiola destructor (Say)

Mayetiola destructor (Hessian fly) is a destructive pest of wheat in several parts of the world. Here, we investigated the presence of reproductive symbionts and the effect of the geographical location on the bacterial community associated to adult Hessian flies derived from four major wheat producing areas in Morocco. Using specific 16S rDNA PCR assay, Wolbachia infection was observed in 3% of the natural populations and 10% of the laboratory population. High throughput sequencing of V3-V4 region of the bacterial 16S rRNA gene revealed that the microbiota of adult Hessian flies was significantly influenced by their native regions. A total of 6 phyla, 10 classes and 79 genera were obtained from all the samples. Confirming the screening results, Wolbachia was identified as well in the natural Hessian flies. Phylogenetic analysis using the sequences obtained in this study indicated that there is one Wolbachia strain belonging to supergroup A. To our knowledge, this is the first report of Wolbachia in Hessian fly populations. The observed low abundance of Wolbachia most likely does not indicate induction of reproductive incompatibility. Yet, this infection may give a new insight into the use of Wolbachia for the fight against Hessian fly populations.

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.

Long-Term Dynamics Among Wolbachia Strains During Thermal Adaptation of Their Drosophila melanogaster Hosts

Climate change is a major evolutionary force triggering thermal adaptation in a broad range of species. While the consequences of global warming are being studied for an increasing number of species, limited attention has been given to the evolutionary dynamics of endosymbionts in response to climate change. Here, we address this question by studying the dynamics of Wolbachia, a well-studied endosymbiont of Drosophila melanogaster. D. melanogaster populations infected with 13 different Wolbachia strains were exposed to novel hot and cold laboratory environments for up to 180 generations. The short-term dynamics suggested a temperature-related fitness difference resulting in the increase of clade V strains in the cold environment only. Our long-term analysis now uncovers that clade V dominates in all replicates after generation 60 irrespective of temperature treatment. We propose that adaptation of the Drosophila host to either temperature or Drosophila C virus (DCV) infection are the cause of the replicated, temporally non-concordant Wolbachia dynamics. Our study provides an interesting case demonstrating that even simple, well-controlled experiments can result in complex, but repeatable evolutionary dynamics, thus providing a cautionary note on too simple interpretations on the impact of climate change.

Metacommunity theory for transmission of heritable symbionts within insect communities

Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined "communities of communities" linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host-associated microbial systems. Successfully incorporating microbiota into community-level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.

Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

Spiroplasma poulsonii is a vertically transmitted endosymbiont of Drosophila melanogaster that causes male-killing, that is the death of infected male embryos during embryogenesis. Here, we report a natural variant of S. poulsonii that is efficiently vertically transmitted yet does not selectively kill males, but kills rather a subset of all embryos regardless of their sex, a phenotype we call 'blind-killing'. We show that the natural plasmid of S. poulsonii has an altered structure: Spaid, the gene coding for the male-killing toxin, is deleted in the blind-killing strain, confirming its function as a male-killing factor. Then we further investigate several hypotheses that could explain the sex-independent toxicity of this new strain on host embryos. As the second non-male-killing variant isolated from a male-killing original population, this new strain raises questions on how male-killing is maintained or lost in fly populations. As a natural knock-out of Spaid, which is unachievable yet by genetic engineering approaches, this variant also represents a valuable tool for further investigations on the male-killing mechanism.

A large self-transmissible resistance plasmid from Nigeria contains genes that ameliorate a carrying cost

Antimicrobial resistance is rapidly expanding, in a large part due to mobile genetic elements. We screened 94 fecal fluoroquinolone-resistant Escherichia coli isolates from Nigeria for six plasmid-mediated quinolone resistance (PMQR) genes. Sixteen isolates harbored at least one of the PMQR genes and four were positive for aac-6-Ib-cr. In one strain, aac-6-Ib-cr was mapped to a 125 Kb self-transmissible IncFII plasmid, pMB2, which also bears bla_CTX-M-15, seven other functional resistance genes and multiple resistance pseudogenes. Laboratory strains carrying pMB2 grew faster than isogenic strains lacking the plasmid in both rich and minimal media. We excised a 32 Kb fragment containing transporter genes and several open-reading frames of unknown function. The resulting 93 Kb mini-plasmid conferred slower growth rates and lower fitness than wildtype pMB2. Trans-complementing the deletion with the cloned sitABCD genes confirmed that they accounted for the growth advantage conferred by pMB2 in iron-depleted media. pMB2 is a large plasmid with a flexible resistance region that contains loci that can account for evolutionary success in the absence of antimicrobials. Ancillary functions conferred by resistance plasmids can mediate their retention and transmissibility, worsening the trajectory for antimicrobial resistance and potentially circumventing efforts to contain resistance through restricted use.

Species-specific transcriptional profiles of the gut and gut microbiome of Ceratitis quilicii and Ceratitis rosa sensu stricto

The fruit fly species, Ceratitis rosa sensu stricto and Ceratitis quilicii, are sibling species restricted to the lowland and highland regions, respectively. Until recently, these sibling species were considered as allopatric populations of C. rosa with distinct bionomics. We used deep Next Generation Sequencing (NGS) technology on intact guts of individuals from the two sibling species to compare their transcriptional profiles and simultaneously understand gut microbiome and host molecular processes and identify distinguishing genetic differences between the two species. Since the genomes of both species had not been published previously, the transcriptomes were assembled de novo into transcripts. Microbe-specific transcript orthologs were separated from the assembly by filtering searches of the transcripts against microbe databases using OrthoMCL. We then used differential expression analysis of host-specific transcripts (i.e. those remaining after the microbe-specific transcripts had been removed) and microbe-specific transcripts from the two-sibling species to identify defining species-specific transcripts that were present in only one fruit fly species or the other, but not in both. In C. quilicii females, bacterial transcripts of Pectobacterium spp., Enterobacterium buttiauxella, Enterobacter cloacae and Klebsiella variicola were upregulated compared to the C. rosa s.s. females. Comparison of expression levels of the host transcripts revealed a heavier investment by C. quilicii (compared with C. rosa s.s.) in: immunity; energy production; cell proliferation; insecticide resistance; reproduction and proliferation; and redox reactions that are usually associated with responses to stress and degradation of fruit metabolites.

Links between metamorphosis and symbiosis in holometabolous insects

Many animals depend on microbial symbionts to provide nutrition, defence or other services. Holometabolous insects, as well as other animals that undergo metamorphosis, face unique constraints on symbiont maintenance. Microbes present in larvae encounter a radical transformation of their habitat and may also need to withstand chemical and immunological challenges. Metamorphosis also provides an opportunity, in that symbiotic associations can be decoupled over development. For example, some holometabolous insects maintain the same symbiont as larvae and adults, but house it in different tissues; in other species, larvae and adults may harbour entirely different types or numbers of microbes, in accordance with shifts in host diet or habitat. Such flexibility may provide an advantage over hemimetabolous insects, in which selection on adult-stage microbial associations may be constrained by its negative effects on immature stages, and vice versa. Additionally, metamorphosis itself can be directly influenced by symbionts. Across disparate insect taxa, microbes protect hosts from pathogen infection, supply nutrients essential for rebuilding the adult body and provide cues regulating pupation. However, microbial associations remain completely unstudied for many families and even orders of Holometabola, and future research will undoubtedly reveal more links between metamorphosis and microbiota, two widespread features of animal life. This article is part of the theme issue 'The evolution of complete metamorphosis'.

Effect of heritable symbionts on maternally-derived embryo transcripts

Maternally-transmitted endosymbiotic bacteria are ubiquitous in insects. Among other influential phenotypes, many heritable symbionts of arthropods are notorious for manipulating host reproduction through one of four reproductive syndromes, which are generally exerted during early developmental stages of the host: male feminization; parthenogenesis induction; male killing; and cytoplasmic incompatibility (CI). Major advances have been achieved in understanding mechanisms and identifying symbiont factors involved in reproductive manipulation, particularly male killing and cytoplasmic incompatibility. Nonetheless, whether cytoplasmically-transmitted bacteria influence the maternally-loaded components of the egg or early embryo has not been examined. In the present study, we investigated whether heritable endosymbionts that cause different reproductive phenotypes in Drosophila melanogaster influence the mRNA transcriptome of early embryos. We used mRNA-seq to evaluate differential expression in Drosophila embryos lacking endosymbionts (control) to those harbouring the male-killing Spiroplasma poulsonii strain MSRO-Br, the CI-inducing Wolbachia strain wMel, or Spiroplasma poulsonii strain Hyd1; a strain that lacks a reproductive phenotype and is naturally associated with Drosophila hydei. We found no consistent evidence of influence of symbiont on mRNA composition of early embryos, suggesting that the reproductive manipulation mechanism does not involve alteration of maternally-loaded transcripts. In addition, we capitalized on several available mRNA-seq datasets derived from Spiroplasma-infected Drosophila melanogaster embryos, to search for signals of depurination of rRNA, consistent with the activity of Ribosome Inactivating Proteins (RIPs) encoded by Spiroplasma poulsonii. We found small but statistically significant signals of depurination of Drosophila rRNA in the Spiroplasma treatments (both strains), but not in the symbiont-free control or Wolbachia treatment, consistent with the action of RIPs. The depurination signal was slightly stronger in the treatment with the male-killing strain. This result supports a recent report that RIP-induced damage contributes to male embryo death.

Correlation and causation between the microbiome, Wolbachia and host functional traits in natural populations of drosophilid flies

Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, Drosophila neotestacea and Drosophila putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA-Seq of individual flies. Among-fly variation in microbiota composition did not partition strongly by sex or species, and included multiple modules, that is, sets of bacterial taxa whose abundance varied in concert across different flies. The abundance of bacteria in several modules varied significantly with multiple host transcripts, especially in females, but the identity of the correlated host transcriptional functions differed with host species, including epithelial barrier function in D. falleni, muscle function in D. putrida, and insect growth and development in D. neotestacea. In D. neotestacea, which harbours the endosymbionts Wolbachia and Spiroplasma, Wolbachia promotes the abundance of Spiroplasma, and is positively correlated with abundance of Lactobacillales and Bacteroidales. Furthermore, most correlations between host gene expression and relative abundance of bacterial modules were co-correlated with abundance of Wolbachia (but not Spiroplasma), indicative of an interdependence between host functional traits, microbiota composition and Wolbachia abundance in this species. These data suggest that, in these natural populations of drosophilid flies, different host species interact with microbial communities in functionally different ways that can vary with the abundance of endosymbionts.

A Wolbachia infection from Drosophila that causes cytoplasmic incompatibility despite low prevalence and densities in males

Wolbachia bacteria are common insect endosymbionts transmitted maternally and capable of spreading through insect populations by cytoplasmic incompatibility (CI) when infected males cause embryo death after mating with uninfected females. Selection in the Wolbachia endosymbiont occurs on female hosts and is expected to favour strong maternal transmission to female offspring, even at the cost of reduced CI. With maternal leakage, nuclear genes are expected to be selected to suppress cytoplasmic incompatibility caused by males while also reducing any deleterious effects associated with the infection. Here we describe a new type of Wolbachia strain from Drosophila pseudotakahashii likely to have arisen from evolutionary processes on host and/or Wolbachia genomes. This strain is often absent from adult male offspring, but always transmitted to females. It leads to males with low or non-detectable Wolbachia that nevertheless show CI. When detected in adult males, the infection has a low density relative to that in females, a phenomenon not previously seen in Wolbachia infections of Drosophila. This Wolbachia strain is common in natural populations, and shows reduced CI when older (infected) males are crossed. These patterns highlight that endosymbionts can have strong sex-specific effects and that high frequency Wolbachia strains persist through effects on female reproduction. Female-limited Wolbachia infections may be of applied interest if the low level of Wolbachia in males reduces deleterious fitness effects on the host.

Functional analysis of RIP toxins from the Drosophila endosymbiont Spiroplasma poulsonii

Background

Insects frequently live in close relationship with symbiotic bacteria that carry out beneficial functions for their host, like protection against parasites and viruses. However, in some cases, the mutualistic nature of such associations is put into question because of detrimental phenotypes caused by the symbiont. One example is the association between the vertically transmitted facultative endosymbiont Spiroplasma poulsonii and its natural host Drosophila melanogaster. Whereas S. poulsonii protects its host against parasitoid wasps and nematodes by the action of toxins from the family of Ribosome Inactivating Proteins (RIPs), the presence of S. poulsonii has been reported to reduce host’s life span and to kill male embryos by a toxin called Spaid. In this work, we investigate the harmful effects of Spiroplasma RIPs on Drosophila in the absence of parasite infection.

Results

We show that only two Spiroplasma RIPs (SpRIP1 and SpRIP2) among the five RIP genes encoded in the S. poulsonii genome are significantly expressed during the whole Drosophila life cycle. Heterologous expression of SpRIP1 and 2 in uninfected flies confirms their toxicity, as indicated by a reduction of Drosophila lifespan and hemocyte number. We also show that RIPs can cause the death of some embryos, including females.

Conclusion

Our results indicate that RIPs released by S. poulsonii contribute to the reduction of host lifespan and embryo mortality. This suggests that SpRIPs may impact the insect-symbiont homeostasis beyond their protective function against parasites.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1410-1) contains supplementary material, which is available to authorized users.

Drosophila female fertility and juvenile hormone metabolism depends on the type of Wolbachia infection

Maternally inherited intracellular bacteria Wolbachia cause both parasitic and mutualistic effects on their numerous insect hosts that include manipulating the host reproductive system in order to increase the bacteria spreading in a host population, and increasing the host fitness. Here we demonstrate that the type of Wolbachia infection determines the effect on Drosophila melanogaster egg production as a proxy for fecundity and metabolism of juvenile hormone (JH), which acts as gonadotropin in adult insects. For this study we used six D. melanogaster lineages carrying the nuclear background of interbred Bi90 lineage and cytoplasmic backgrounds with Wolbachia of different genotype variants or without it. wMelCS genotype of Wolbachia decreases the egg production in the infected D. melanogaster females in the beginning of oviposion and increases it later (since the sixth day after eclosion), wMelPop Wolbachia strain causes the opposite effect, while wMel, wMel2 and wMel4 genotypes of Wolbachia do not show any effect on these traits compared to uninfected Bi90 D. melanogaster females. The intensity of JH catabolism negatively correlates with the fecundity level in the flies carrying both wMelCS and wMelPop Wolbachia. The JH catabolism in females infected with genotypes of wMel group does not differ from that in uninfected females. The effects of wMelCS and wMelPop infection on egg production can be leveled by the modulation of JH titre (via precocene/JH treatment of the flies). Thus, at least one of the mechanisms, promoting the effect of Wolbachia on D. melanogaster female fecundity, is mediated by JH.

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.

A bioinformatics approach to identifying Wolbachia infections in arthropods

Wolbachia is the most widespread endosymbiont, infecting >20% of arthropod species, and capable of drastically manipulating the host's reproductive mechanisms. Conventionally, diagnosis has relied on PCR amplification; however, PCR is not always a reliable diagnostic technique due to primer specificity, strain diversity, degree of infection and/or tissue sampled. Here, we look for evidence of Wolbachia infection across a wide array of arthropod species using a bioinformatic approach to detect the Wolbachia genes ftsZ, wsp, and the groE operon in next-generation sequencing samples available through the NCBI Sequence Read Archive. For samples showing signs of infection, we attempted to assemble entire Wolbachia genomes, and in order to better understand the relationships between hosts and symbionts, phylogenies were constructed using the assembled gene sequences. Out of the 34 species with positively identified infections, eight species of arthropod had not previously been recorded to harbor Wolbachia infection. All putative infections cluster with known representative strains belonging to supergroup A or B, which are known to only infect arthropods. This study presents an efficient bioinformatic approach for post-sequencing diagnosis and analysis of Wolbachia infection in arthropods.

Persistent postmating, prezygotic reproductive isolation between populations

Studying reproductive barriers between populations of the same species is critical to understand how speciation may proceed. Growing evidence suggests postmating, prezygotic (PMPZ) reproductive barriers play an important role in the evolution of early taxonomic divergence. However, the contribution of PMPZ isolation to speciation is typically studied between species in which barriers that maintain isolation may not be those that contributed to reduced gene flow between populations. Moreover, in internally fertilizing animals, PMPZ isolation is related to male ejaculate-female reproductive tract incompatibilities but few studies have examined how mating history of the sexes can affect the strength of PMPZ isolation and the extent to which PMPZ isolation is repeatable or restricted to particular interacting genotypes. We addressed these outstanding questions using multiple populations of Drosophila montana. We show a recurrent pattern of PMPZ isolation, with flies from one population exhibiting reproductive incompatibility in crosses with all three other populations, while those three populations were fully fertile with each other. Reproductive incompatibility is due to lack of fertilization and is asymmetrical, affecting female fitness more than males. There was no effect of male or female mating history on reproductive incompatibility, indicating that PMPZ isolation persists between populations. We found no evidence of variability in fertilization outcomes attributable to different female × male genotype interactions, and in combination with our other results, suggests that PMPZ isolation is not driven by idiosyncratic genotype × genotype interactions. Our results show PMPZ isolation as a strong, consistent barrier to gene flow early during speciation and suggest several targets of selection known to affect ejaculate-female reproductive tract interactions within species that may cause this PMPZ isolation.

In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction

Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongly affects its host’s physiology, for example by causing male killing or by protecting it against various parasites. Despite intense work on this model since the 1950s, attempts to cultivate endosymbiotic Spiroplasma in vitro have failed so far. Here, we developed a method to sustain the in vitro culture of S. poulsonii by optimizing a commercially accessible medium. We also provide a complete genome assembly, including the first sequence of a natural plasmid of an endosymbiotic Spiroplasma species. Last, by comparing the transcriptome of the in vitro culture to the transcriptome of bacteria extracted from the host, we identified genes putatively involved in host-symbiont interactions. This work provides new opportunities to study the physiology of endosymbiotic Spiroplasma and paves the way to dissect insect-endosymbiont interactions with two genetically tractable partners.

The discovery of insect bacterial endosymbionts (maternally transmitted bacteria) has revolutionized the study of insects, suggesting novel strategies for their control. Most endosymbionts are strongly dependent on their host to survive, making them uncultivable in artificial systems and genetically intractable. Spiroplasma poulsonii is an endosymbiont of Drosophila that affects host metabolism, reproduction, and defense against parasites. By providing the first reliable culture medium that allows a long-lasting in vitro culture of Spiroplasma and by elucidating its complete genome, this work lays the foundation for the development of genetic engineering tools to dissect endosymbiosis with two partners amenable to molecular study. Furthermore, the optimization method that we describe can be used on other yet uncultivable symbionts, opening new technical opportunities in the field of host-microbes interactions.

Symbiont interactions with non-native hosts limit the formation of new symbioses

Background

Facultative symbionts are common in eukaryotes and can provide their hosts with significant fitness benefits. Despite the advantage of carrying these microbes, they are typically only found in a fraction of the individuals within a population and are often non-randomly distributed among host populations. It is currently unclear why facultative symbionts are only found in certain host individuals and populations. Here we provide evidence for a mechanism to help explain this phenomenon: that when symbionts interact with non-native host genotypes it can limit the horizontal transfer of symbionts to particular host lineages and populations of related hosts.

Results

Using reciprocal transfections of the facultative symbiont Hamiltonella defensa into different pea aphid clones, we demonstrate that particular symbiont strains can cause high host mortality and inhibit offspring production when injected into aphid clones other than their native host lineage. However, once established, the symbiont’s ability to protect against parasitoids was not influenced by its origin. We then demonstrate that H. defensa is also more likely to establish a symbiotic relationship with aphid clones from a plant-adapted population (biotype) that typically carry H. defensa in nature, compared to clones from a biotype that does not normally carry this symbiont.

Conclusions

These results provide evidence that certain aphid lineages and populations of related hosts are predisposed to establishing a symbiotic relationship with H. defensa. Our results demonstrate that host-symbiont genotype interactions represent a potential barrier to horizontal transmission that can limit the spread of symbionts, and adaptive traits they carry, to certain host lineages.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1143-z) contains supplementary material, which is available to authorized users.

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral

Determining the extent to which Symbiodinium communities in corals are inherited versus environmentally acquired is fundamental to understanding coral resilience and to predicting coral responses to stressors like warming oceans that disrupt this critical endosymbiosis. We examined the fidelity with which Symbiodinium communities in the brooding coral Seriatopora hystrix are vertically transmitted and the extent to which communities are genetically regulated, by genotyping the symbiont communities within 60 larvae and their parents (9 maternal and 45 paternal colonies) using high-throughput sequencing of the ITS2 locus. Unexpectedly, Symbiodinium communities associated with brooded larvae were distinct from those within parent colonies, including the presence of types not detected in adults. Bayesian heritability (h²) analysis revealed that 33% of variability in larval Symbiodinium communities was genetically controlled. Results highlight flexibility in the establishment of larval symbiont communities and demonstrate that symbiont transmission is not exclusively vertical in brooding corals. Instead, we show that Symbiodinium transmission in S. hystrix involves a mixed-mode strategy, similar to many terrestrial invertebrate symbioses. Also, variation in the abundances of common Symbiodinium types among adult corals suggests that microhabitat differences influence the structure of in hospite Symbiodinium communities. Partial genetic regulation coupled with flexibility in the environmentally acquired component of Symbiodinium communities implies that corals with vertical transmission, like S. hystrix, may be more resilient to environmental change than previously thought.