Bacterial Community Diversity Harboured by Interacting Species

Abstract

All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing). Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

Fig 1. Distribution of OTUs (97% similarity) among the four host species.

Fig 2. Relationship between bacterial communities via UniFrac distances.

(A): Hierarchical clustering of weighted pairwise UniFrac distances between microbial communities of the different samples based on their distribution of bacterial 16S rDNA gene sequences (v4-v5 region). (B): Principal coordinates plot (PCoA) generated using weighted UniFrac distances between the bacterial communities for each sample analysed. Different shapes represent species: inverted triangle = D. radicum, upright triangle = T. rapae, square = A. bipustulata, circle = A. bilineata. Colours represent sampling zones: white = western, grey = eastern, black = central (for A. bilineata only). Two technical replicates are used, but with the exception of eastern D. radicum they are so similar as to appear superposed on the graph.

Fig 3. Maximum likelihood tree of Wolbachia spp. obtained from the 16S V4-V5 fragment.

Information is presented in the following order: bacteria name; host name in brackets (when available); OTU number for Delia radicum, Aleochara bilineata, Aleochara bipustulata and Trybliographa rapae. Bootstrap values (≥60; black) are given for each branch. Scaling is expressed in the proportion of substituted bases per site. Capital letters A to M refer to Wolbachia ‘supergroups’.

Fig 4. Maximum likelihood tree of Rickettsia spp. obtained from the 16S V4-V5 fragment.

Information is presented in the following order: bacteria name; host name in brackets (when available); OTU number for Aleochara bilineata and Trybliographa rapae. Bootstrap values (≥60; black) are given for each branch. Scaling is expressed in the proportion of substituted bases per site.

Fig 5. Maximum likelihood tree of Spiroplasma spp. obtained from the 16S V4-V5 fragment.

Information is presented in the following order: bacteria name; host name in brackets (when available); OTU number for Delia radicum, Aleochara bilineata, Aleochara bipustulata and Trybliographa rapae. Bootstrap values (≥60; black) are given for each branch. Scaling is expressed in the proportion of substituted bases per site. Roman letters indicate serological groups.

Fig 6. Maximum likelihood tree of Wolbachia spp. obtained from 16S V4-V5, 16S wspec and fbpA fragments.

The Wolbachia hosts and the supergroup of the Wolbachia (when available) are indicated. Bootstrap values are given for each branch. Scaling is expressed in the proportion of substituted bases per site.