Defensive Symbiont Genotype Distributions Are Linked to Parasitoid Attack Networks

Facultative symbionts are widespread in arthropods and can provide important services such as protection from natural enemies. Yet what shapes associations with defensive symbionts in nature remains unclear. Two hypotheses suggest that interactions with either antagonists or host plants explain the prevalence of symbionts through shared selective pressures or vectors of symbiont transmission. Here we investigate the factors determining similarities in the Hamiltonella defensa symbiosis shared amongst field-collected aphid species. After accounting for host species relatedness, we find that Hamiltonella's genotype distribution aligns with sharing the same parasitoids, rather than host plants, highlighting parasitoids and hosts as key selective agents shaping the symbiosis across aphid species. Our data indicates parasitoid host specificity drives the prevalence of specific aphid-Hamiltonella associations, suggesting defensive symbioses are maintained by the selective pressure imposed by dominant parasitoids and their aphid hosts. These findings underscore the importance of interactions with natural enemies in explaining patterns of defensive symbiosis in nature.

Aphid populations are frequently infected with facultative endosymbionts

The occurrence of facultative endosymbionts has been studied in many commercially important crop pest aphids, but their occurrence and effects in non-commercial aphid species in natural populations have received less attention. We screened 437 aphid samples belonging to 106 aphid species for the eight most common facultative aphid endosymbionts. We found one or more facultative endosymbionts in 53% (56 of 106) of the species investigated. This likely underestimates the situation in the field because facultative endosymbionts are often present in only some colonies of an aphid species. Oligophagous aphid species carried facultative endosymbionts significantly more often than monophagous species. We did not find a significant correlation between ant tending and facultative endosymbiont presence. In conclusion, we found that facultative endosymbionts are common among aphid populations. This study is, to our knowledge, the first of its kind in the Netherlands and provides a basis for future research in this field. For instance, it is still unknown in what way many of these endosymbionts affect their hosts, which is important for determining the importance of facultative endosymbionts to community dynamics.

High specificity of symbiont-conferred resistance in an aphid-parasitoid field community

Host-parasite coevolution is mediated by genetic interactions between the antagonists and may lead to reciprocal adaptation. In the black bean aphid, Aphis fabae fabae, resistance to parasitoids can be conferred by the heritable bacterial endosymbiont Hamiltonella defensa. H. defensa has been shown to be variably protective against different parasitoid species, and different genotypes of the black bean aphid's main parasitoid Lysiphlebus fabarum. However, these results were obtained using haphazard combinations of laboratory-reared insect lines with different origins, making it unclear how representative they are of natural, locally (co)adapted communities. We therefore comprehensively sampled the parasitoids of a natural A. f. fabae population and measured the ability of the five most abundant species to parasitize aphids carrying the locally prevalent H. defensa haplotypes. H. defensa provided resistance only against the dominant parasitoid L. fabarum (70% of all parasitoids), but not against less abundant parasitoids, and resistance to L. fabarum acted in a genotype-specific manner (G × G interactions between H. defensa and L. fabarum). These results confirm that strong species- and genotype-specificity of symbiont-conferred resistance is indeed a hallmark of wild A. f. fabae populations, and they are consistent with symbiont-mediated adaptation of aphids to the parasitoids posing the highest risk.

Mobile elements create strain-level variation in the services conferred by an aphid symbiont

Heritable, facultative symbionts are common in arthropods, often functioning in host defence. Despite moderately reduced genomes, facultative symbionts retain evolutionary potential through mobile genetic elements (MGEs). MGEs form the primary basis of strain-level variation in genome content and architecture, and often correlate with variability in symbiont-mediated phenotypes. In pea aphids (Acyrthosiphon pisum), strain-level variation in the type of toxin-encoding bacteriophages (APSEs) carried by the bacterium Hamiltonella defensa correlates with strength of defence against parasitoids. However, co-inheritance creates difficulties for partitioning their relative contributions to aphid defence. Here we identified isolates of H. defensa that were nearly identical except for APSE type. When holding H. defensa genotype constant, protection levels corresponded to APSE virulence module type. Results further indicated that APSEs move repeatedly within some H. defensa clades providing a mechanism for rapid evolution in anti-parasitoid defences. Strain variation in H. defensa also correlates with the presence of a second symbiont Fukatsuia symbiotica. Predictions that nutritional interactions structured this coinfection were not supported by comparative genomics, but bacteriocin-containing plasmids unique to co-infecting strains may contribute to their common pairing. In conclusion, strain diversity, and joint capacities for horizontal transfer of MGEs and symbionts, are emergent players in the rapid evolution of arthropods.

Defensive symbiosis in the wild: Seasonal dynamics of parasitism risk and symbiont-conferred resistance

Parasite-mediated selection can rapidly drive up resistance levels in host populations, but fixation of resistance traits may be prevented by costs of resistance. Black bean aphids (Aphis fabae) benefit from increased resistance to parasitoids when carrying the defensive bacterial endosymbiont Hamiltonella defensa. However, due to fitness costs that come with symbiont infection, symbiont-conferred resistance may result in either a net benefit or a net cost to the aphid host, depending on parasitoid presence as well as on the general ecological context. Balancing selection may therefore explain why in natural aphid populations, H. defensa is often found at intermediate frequencies. Here we present a 2-year field study where we set out to look for signatures of balancing selection in natural aphid populations. We collected temporally well-resolved data on the prevalence of H. defensa in A. f. fabae and estimated the risk imposed by parasitoids using sentinel hosts. Despite a marked and consistent early-summer peak in parasitism risk, and significant changes in symbiont prevalence over time, we found just a weak correlation between parasitism risk and H. defensa frequency dynamics. H. defensa prevalence in the populations under study was, in fact, better explained by the number of heat days that previous aphid generations were exposed to. Our study grants an unprecedentedly well-resolved insight into the dynamics of endosymbiont and parasitoid communities of A. f. fabae populations, and it adds to a growing body of empirical evidence suggesting that not only parasitism risk, but rather multifarious selection is shaping H. defensa prevalence in the wild.

Evidence of phylosymbiosis in Formica ants

Introduction

Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes.

Methods

To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing.

Results

We reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences.

Discussion

Our results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.

Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species

Facultative symbionts are common in insects and can provide their hosts with significant adaptations. Yet we still have a limited understanding of what shapes their distributions, such as why particular symbiont strains are common in some host species yet absent in others. To address this question, we genotyped the defensive symbiont Hamiltonella defensa in 26 aphid species that commonly carry this microbe. We found that Hamiltonella strains were strongly associated with specific aphid species and that strains found in one host species rarely occurred in others. To explain these associations, we reciprocally transferred the Hamiltonella strains of three aphid species, Acyrthosiphon pisum, Macrosiphoniella artemisiae and Macrosiphum euphorbiae, and assessed the impact of Hamiltonella strain on: the stability of the symbiosis, aphid fecundity and parasitoid resistance. We demonstrate that the Hamiltonella strains found in nature are locally adapted to specific aphid hosts, and their ecology: aphids tend to carry Hamiltonella strains that are efficiently transmitted to their offspring, non-lethal, and that provide strong protection against their dominant parasitoid species. Our results suggest that facultative symbiont distributions are shaped by selection from natural enemies, and the host itself, resulting in locally adapted symbioses that provide significant benefits against prevailing natural enemies.