Gut microbiota instead of host genotype drive the specificity in the interaction of a natural host-parasite system

Specific interactions between parasite genotypes and host genotypes (G_p × G_h) are commonly found in invertebrate systems, but are largely lacking a mechanistic explanation. The genotype of invertebrate hosts can be complemented by the genomes of microorganisms living on or within the host (‘microbiota’). We investigated whether the bacterial gut microbiota of bumble bees (Bombus terrestris) can account for the specificity of interactions between individuals from different colonies (previously taken as host genotype proxy) and genotypes of the parasite Crithidia bombi. For this, we transplanted the microbiota between individuals of six colonies. Both the general infection load and the specific success of different C. bombi genotypes were mostly driven by the microbiota, rather than by worker genotype. Variation in gut microbiota can therefore be responsible for specific immune phenotypes and the evolution of gut parasites may be driven by interactions with ‘microbiota types’ as well as with host genotypes.     

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.     

Aphid and host‐plant genotype × genotype interactions under elevated CO2

1. Elevated CO₂ can alter plant physiology and morphology, and these changes are expected to impact diet quality for insect herbivores. While the plastic responses of insect herbivores have been well studied, less is known about the propensity of insects to adapt to such changes. Genetic variation in insect responses to elevated CO₂ and genetic interactions between insects and their host plants may exist and provide the necessary raw material for adaptation. 2. We used clonal lines of Rhopalosiphum padi (L.) aphids to examine genotype‐specific responses to elevated CO₂. We used the host plant Schedonorus arundinaceus (tall fescue; Schreb), which is capable of asexual reproduction, to investigate host plant genotype‐specific effects and possible host plant‐by‐insect genotype interactions. The abundance and density of three R. padi genotypes on three tall fescue genotypes under three concentrations of CO₂ (ambient, 700, and 1000 ppm) in a controlled greenhouse environment were examined. 3. Aphid abundance decreased in the 700 ppm CO₂ concentration, but increased in the 1000 ppm concentration relative to ambient. The effect of CO₂ on aphid density was dependent on host plant genotype; the density of aphids in high CO₂ decreased for two plant genotypes but was unchanged in one. No interaction between aphid genotype and elevated CO₂ was found, nor did we find significant genotype‐by‐genotype interactions. 4. This study suggests that the density of R. padi aphids feeding on tall fescue may decrease under elevated CO₂ for some plant genotypes. The likely impact of genotype‐specific responses on future changes in the genetic structure of plant and insect populations is discussed.     

Diversity and evolutionary patterns of bacterial gut associates of corbiculate bees

The animal gut is a habitat for diverse communities of microorganisms (microbiota). Honeybees and bumblebees have recently been shown to harbour a distinct and species poor microbiota, which may confer protection against parasites. Here, we investigate diversity, host specificity and transmission mode of two of the most common, yet poorly known, gut bacteria of honeybees and bumblebees: Snodgrassella alvi (Betaproteobacteria) and Gilliamella apicola (Gammaproteobacteria). We analysed 16S rRNA gene sequences of these bacteria from diverse bee host species across most of the honeybee and bumblebee phylogenetic diversity from North America, Europe and Asia. These focal bacteria were present in 92% of bumblebee species and all honeybee species but were found to be absent in the two related corbiculate bee tribes, the stingless bees (Meliponini) and orchid bees (Euglossini). Both Snodgrassella alvi and Gilliamella apicola phylogenies show significant topological congruence with the phylogeny of their bee hosts, albeit with a considerable degree of putative host switches. Furthermore, we found that phylogenetic distances between Gilliamella apicola samples correlated with the geographical distance between sampling locations. This tentatively suggests that the environmental transmission rate, as set by geographical distance, affects the distribution of G. apicola infections. We show experimentally that both bacterial taxa can be vertically transmitted from the mother colony to daughter queens, and social contact with nest mates after emergence from the pupa greatly facilitates this transmission. Therefore, sociality may play an important role in vertical transmission and opens up the potential for co‐evolution or at least a close association of gut bacteria with their hosts.     

Ample genetic variation but no evidence for genotype specificity in an all‐parthenogenetic host–parasitoid interaction

Antagonistic coevolution between hosts and parasites can result in negative frequency‐dependent selection and may thus be an important mechanism maintaining genetic variation in populations. Negative frequency‐dependence emerges readily if interactions between hosts and parasites are genotype‐specific such that no host genotype is most resistant to all parasite genotypes, and no parasite genotype is most infective on all hosts. Although there is increasing evidence for genotype specificity in interactions between hosts and pathogens or microparasites, the picture is less clear for insect host–parasitoid interactions. Here, we addressed this question in the black bean aphid (Aphis fabae) and its most important parasitoid Lysiphlebus fabarum. Because both antagonists are capable of parthenogenetic reproduction, this system allows for powerful tests of genotype × genotype interactions. Our test consisted of exposing multiple host clones to different parthenogenetic lines of parasitoids in all combinations, and this experiment was repeated with animals from four different sites. All aphids were free of endosymbiotic bacteria known to increase resistance to parasitoids. We observed ample genetic variation for host resistance and parasitoid infectivity, but there was no significant host clone × parasitoid line interaction, and this result was consistent across the four sites. Thus, there is no evidence for genotype specificity in the interaction between A. fabae and L. fabarum, suggesting that the observed variation is based on rather general mechanisms of defence and attack.     

The bumble bee microbiome increases survival of bees exposed to selenate toxicity

Bumble bees are important and widespread insect pollinators who face many environmental challenges. For example, bees are exposed to the metalloid selenate when foraging on pollen and nectar from plants growing in contaminated soils. As it has been shown that the microbiome of animals reduces metalloid toxicity, we assayed the ability of the bee microbiome to increase survivorship against selenate challenge. We exposed uninoculated or microbiota-inoculated Bombus impatiens workers to a field-realistic dose of 0.75 mg l⁻¹ selenate and found that microbiota-inoculated bees survive slightly but significantly longer than uninoculated bees. Using 16S rRNA gene sequencing, we found that selenate exposure altered gut microbial community composition and relative abundance of specific core bacteria. We also grew two core bumble bee microbes – Snodgrassella alvi and Lactobacillus bombicola – in selenate-spiked media and found that these bacteria grew in the tested concentrations of 0.001–10 mg l⁻¹ selenate. Furthermore, the genomes of these microbes harbour genes involved in selenate detoxification. The bumble bee microbiome slightly increases survivorship when the host is exposed to selenate, but the specific mechanisms and colony-level benefits under natural settings require further study.     

BUZZING BEES: COMMUNICATION BETWEEN BUMBLE BEE SOCIAL PARASITES (HYMENOPTERA: APIDAE) AND THEIR HOSTS

ABSTRACT

Although sounds are produced by highly eusocial bees in a variety of contexts, their meaning and evolution are poorly understood. In this study we examined the communicative function of sound during dominance disputes in primitively eusocial bumble bees (Hymenoptera: Apidae). The interaction between sound production and dominance behaviour was studied in the context of parasitism by obligate bumble bee social parasites (Psythyrus spp.). Females of Psithyrus bohemicus and P. vestalis produced sound during dominance interactions in bumble bee host colonies. Parasites mauled and pushed host bees, after which they buzzed with their wings folded. The sounds were broad band, with a mean frequency of 820 Hz for the loudest harmonic produced by a P. bohemicus female. The frequency range of recorded sounds matched that of the vibratory stimuli to which isolated bumble bee workers responded. Buzzing by some bumble bee social parasites may assist them in advertising a position of dominance in egg-laying hierarchies established in the absence of pheromonal inhibition of ovarian development.     

Specificity between Lactobacilli and Hymenopteran Hosts Is the Exception Rather than the Rule

Lactobacilli (Lactobacillales: Lactobacillaceae) are well known for their roles in food fermentation, as probiotics, and in human health, but they can also be dominant members of the microbiota of some species of Hymenoptera (ants, bees, and wasps). Honey bees and bumble bees associate with host-specific lactobacilli, and some evidence suggests that these lactobacilli are important for bee health. Social transmission helps maintain associations between these bees and their respective microbiota. To determine whether lactobacilli associated with social hymenopteran hosts are generally host specific, we gathered publicly available Lactobacillus 16S rRNA gene sequences, along with Lactobacillus sequences from 454 pyrosequencing surveys of six other hymenopteran species (three sweat bees and three ants). We determined the comparative secondary structural models of 16S rRNA, which allowed us to accurately align the entire 16S rRNA gene, including fast-evolving regions. BLAST searches and maximum-likelihood phylogenetic reconstructions confirmed that honey and bumble bees have host-specific Lactobacillus associates. Regardless of colony size or within-colony oral sharing of food (trophallaxis), sweat bees and ants associate with lactobacilli that are closely related to those found in vertebrate hosts or in diverse environments. Why honey and bumble bees associate with host-specific lactobacilli while other social Hymenoptera do not remains an open question. Lactobacilli are known to inhibit the growth of other microbes and can be beneficial whether they are coevolved with their host or are recruited by the host from environmental sources through mechanisms of partner choice.     

Complex genotype interactions influence social fitness during the developmental phase of the social amoeba Dictyostelium discoideum

When individuals interact, phenotypic variation can be partitioned into direct genetic effects (DGEs) of the individuals’ own genotypes, indirect genetic effects (IGEs) of their social partners’ genotypes and epistatic interactions between the genotypes of interacting individuals (‘genotype‐by‐genotype (G×G) epistasis’). These components can all play important roles in evolutionary processes, but few empirical studies have examined their importance. The social amoeba Dictyostelium discoideum provides an ideal system to measure these effects during social interactions and development. When starved, free‐living amoebae aggregate and differentiate into a multicellular fruiting body with a dead stalk that holds aloft viable spores. By measuring interactions among a set of natural strains, we quantify DGEs, IGEs and G×G epistasis affecting spore formation. We find that DGEs explain most of the phenotypic variance (57.6%) whereas IGEs explain a smaller (13.3%) but highly significant component. Interestingly, G×G epistasis explains nearly a quarter of the variance (23.0%), highlighting the complex nature of genotype interactions. These results demonstrate the large impact that social interactions can have on development and suggest that social effects should play an important role in developmental evolution in this system.     

Genotype matching in a parasitoid–host genotypic food web: an approach for measuring effects of environmental change

Food webs typically quantify interactions between species, whereas evolution operates through the success of alleles within populations of a single species. To bridge this gap, we quantify genotypic interaction networks among individuals of a single specialized parasitoid species and its obligate to cyclically parthenogenetic aphid host along a climatic gradient. As a case study for the kinds of questions genotype food webs could be used to answer, we show that genetically similar parasitoids became more likely to attack genetically similar hosts in warmer sites (i.e. there was network‐wide congruence between the within‐species shared allelic distance of the parasitoid and that of its host). Narrowing of host‐genotype‐niche breadth by parasitoids could reduce resilience of the network to changes in host genetic structure or invasion by novel host genotypes and inhibit biological control. Thus, our approach can be easily used to detect changes to sub‐species‐level food webs, which may have important ecological and evolutionary implications, such as promoting host‐race specialization or the accelerated loss of functional diversity following extinctions of closely related genotypes.     

Defining the colour pattern phenotype in bumble bees (Bombus): a new model for evo devo

Few insects exhibit the striking colour pattern radiation found in bumble bees (Bombus), which have diversified globally into a wide range of colours and patterns. Their potent sting is often advertised by conspicuous bands of contrasting colour commonly mimicked by scores of harmless (Batesian mimics) and noxious species (Müllerian co‐mimics). Despite extensive documentation of colour pattern diversification, next to nothing is known about the genetic regulation of pattern formation in bumble bees, hindering progress toward a more general model of the evolution of colour pattern mimicry. A critical first step in understanding the colour pattern genotype is an unambiguous understanding of the phenotype under selection, which has not been objectively defined in bumble bees. Here, we quantitatively define the principal colour pattern elements that comprise the phenotype array across all species. Matrix analysis of meticulously scored colour patterns of ～95% of described species indicates there are 12 discrete primary ‘ground plan’ elements in common among all species, many of which correspond to segmentation patterning. Additional secondary elements characterize individual species and geographical variants. The boundaries of these elements appear to correspond to expression patterns of Hox genes in Drosophila and Apis but also suggest novel post‐Hox specialization of abdominal patterning. Our findings provide the first foundation for exploring candidate genes regulating adaptive pattern variation in bumble bees and broaden the framework for understanding common genetic mechanisms of pattern evolution in insects. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 384–404.     

Within‐host interactions shape virulence‐related traits of trematode genotypes

Within‐host interactions between co‐infecting parasites can significantly influence the evolution of key parasite traits, such as virulence (pathogenicity of infection). The type of interaction is expected to predict the direction of selection, with antagonistic interactions favouring more virulent genotypes and synergistic interactions less virulent genotypes. Recently, it has been suggested that virulence can further be affected by the genetic identity of co‐infecting partners (G × G interactions), complicating predictions on disease dynamics. Here, we used a natural host–parasite system including a fish host and a trematode parasite to study the effects of G × G interactions on infection virulence. We exposed rainbow trout (Oncorhynchus mykiss) either to single genotypes or to mixtures of two genotypes of the eye fluke Diplostomum pseudospathaceum and estimated parasite infectivity (linearly related to pathogenicity of infection, measured as coverage of eye cataracts) and relative cataract coverage (controlled for infectivity). We found that both traits were associated with complex G × G interactions, including both increases and decreases from single infection to co‐infection, depending on the genotype combination. In particular, combinations where both genotypes had low average infectivity and relative cataract coverage in single infections benefited from co‐infection, while the pattern was opposite for genotypes with higher performance. Together, our results show that infection outcomes vary considerably between single and co‐infections and with the genetic identity of the co‐infecting parasites. This can result in variation in parasite fitness and consequently impact evolutionary dynamics of host–parasite interactions.     

Beneficial microbes going underground of root immunity

Plant roots interact with an enormous diversity of commensal, mutualistic, and pathogenic microbes, which poses a big challenge to roots to distinguish beneficial microbes from harmful ones. Plants can effectively ward off pathogens following immune recognition of conserved microbe‐associated molecular patterns (MAMPs). However, such immune elicitors are essentially not different from those of neutral and beneficial microbes that are abundantly present in the root microbiome. Recent studies indicate that the plant immune system plays an active role in influencing rhizosphere microbiome composition. Moreover, it has become increasingly clear that root‐invading beneficial microbes, including rhizobia and arbuscular mycorrhiza, evade or suppress host immunity to establish a mutualistic relationship with their host. Evidence is accumulating that many free‐living rhizosphere microbiota members can suppress root immune responses, highlighting root immune suppression as an important function of the root microbiome. Thus, the gate keeping functions of the plant immune system are not restricted to warding off root‐invading pathogens but also extend to rhizosphere microbiota, likely to promote colonization by beneficial microbes and prevent growth‐defense tradeoffs triggered by the MAMP‐rich rhizosphere environment.     

Uncovering the drivers of host‐associated microbiota with joint species distribution modelling

In addition to the processes structuring free‐living communities, host‐associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host‐specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model‐based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host‐specific factors are in structuring the microbiota; and (c) co‐occurrence networks to visualize microbe‐to‐microbe associations.     

Transgenerational developmental effects of species‐specific,maternally transmitted microbiota in Onthophagus dung beetles

1. The significance of host–microbe interactions is increasingly appreciated across biological disciplines, yet to what extent these interactions influence developmental outcomes within and across generations remains poorly understood. 2. This study investigated the putative role of host–microbe interactions in the adaptive diversification of Onthophagus dung beetles, one of the most species‐rich and ecologically successful genera of insects. Onthophagus mothers vertically transmit growth‐ and fitness‐enhancing gut symbionts to their offspring through a faecal secretion known as the pedestal. 3. Pedestals were reciprocally exchanged between two ecologically similar congeneric Onthophagus species to assess the degree to which pedestal microbiota from one species can substitute for those of another. 4. It was found that the presence of a heterospecific pedestal delays development and increases mortality, and that the fitness costs of non‐host‐specific microbiota are maintained transgenerationally. 5. Collectively, these results support the hypothesis that Onthophagus beetles maintain, interact with, and are dependent upon host species‐specific microbial communities to support normal growth and development. The implications of these results are discussed in the context of host microbiota coevolution.     

Different responses of pollinating bees to size variation and sexual phases in flowers ofCampanula

To examine the response of pollinating bees to size and sexual phases of flowers, we constructed an artificial population ofCampanula having large flower variation and presented it to potentially pollinating bees in nurseries. The pollinating bee groups (halictid, megachilid and bumble bees) responded differentially to both the flower size and to the sexual phases of the flowers. Whereas visitation rate of megachilid bees increased with the flower size, those of halictid bees and bumble bees did not show particular trends; for example, bumble bees visited almost all of the flowers consistently. Visitation frequencies to male-and female-phased flowers were significantly different between megachilids at Tokyo and halictids. This study indicates that pollinator attraction could not solely explain the evolution of the flower size inCampanula, and that other factors such as pollen transfer efficiency, should be considered.     

Genotypes and their interaction effects on reproduction and mating‐induced immune activation in Drosophila melanogaster

Mating causes considerable alterations in female physiology and behaviour, and immune gene expression, partly due to proteins transferred from males to females during copulation. The magnitude of these phenotypic changes could be driven by the genotypes of males and females, as well as their interaction. To test this, we carried out a series of genotype‐by‐genotype (G × G) experiments using Drosophila melanogaster populations from two distant geographical locations. We expected lines to have diverged in male reproductive traits and females to differ in their responses to these traits. We examined female physiological and behavioural post‐mating responses to male mating traits, that is behaviour and ejaculate composition, in the short to mid‐term (48 hr) following mating. We then explored whether a sexually transferred molecule, sex peptide (SP), is the mechanism behind our observed female post‐mating responses. Our results show that the genotypes of both sexes as well as the interaction between male and female genotypes affect mating and post‐mating reproductive traits. Immune gene expression of three candidate genes increased in response to mating and was genotype‐dependent but did not show a G × G signature. Males showed genotype‐dependent SP expression in the 7 days following eclosion, but female genotypes showed no differential sensitivity to the receipt of SP. The two genotypes demonstrated clear divergence in physiological traits in short‐ to mid‐term responses to mating, but the longer‐term consequences of these initial dynamics remain to be uncovered.