Context-dependent parasite infection affects trophic niche in populations of sympatric stickleback species

Host habitat rather than evolutionary history explains gut microbiome diversity in sympatric stickleback species

Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.

Narrower isotopic niche size in fish infected by the intestinal parasite Pomphorhynchus sp. compared to uninfected ones

Examples of parasite-related effects on intermediate crustacean hosts are numerous but their ecological consequences on their vertebrate hosts are scarce. Here, we address the role of macroparasite infections on the trophic niche structure of definitive hosts and its potential physiological consequences using wild fish populations infected with an acantochephalan parasite Pomphorhynchus sp., a trophically transmitted intestinal worm. Infected and uninfected fish were sampled from six populations on the Marne River, France and the prevalence of intestinal parasites in the host populations ranged from 50% to 90%. Although the isotopic ratios (δ¹³ C and δ¹⁵ N) did not differ between infected and uninfected fish, we found a consistent pattern of isotopic niche size being considerably smaller in infected hosts when compared with noninfected ones. This was not explained by interindividual differences in intrinsic factors such as length/age or body condition between infected and uninfected fish. These results suggest a potential niche specialization of infected fish, which did not impair their energetic status.