Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

Abstract

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata)

“…Also, the MAG has characteristics typical of endosymbionts with an AT bias (GC content = 0.31) and a small genome size (1,269,226 bp). In particular, compared to the MAGs from Doña et al 2021 [ 53 ], the MAG has lower GC content, and a smaller genome size than any of the MAGs from that study. The metaWRAP Classify_bins module classified the MAG as belonging to the family Bartonellaceae.…”

“…This MAG was detected in mite samples but not in the mucus samples, thus supporting its exclusive association with the mites. The comparative analyses indicate that this genome was AT-biased, and the genome size was small (see Results), e.g., compared to a previous study on endosymbionts of lice [ 53 ]. Altogether, these characteristics have been reported as typical of arthropod endosymbionts [ 52 , 55 ].…”

“…Accordingly, we explored the relative position of the putative endosymbiont MAG in a “Genome size ∼ GC content” correlation plot. Specifically, we compared our results to those from Doña et al 2021 [ 53 ], who used this approach to identify potential endosymbionts in lice. Finally, we aligned the MAG to the partial one previously assembled in Osuna-Mascaró et al, 2020 [ 32 ], using Mauve (MCM algorithm and default parameters) [ 54 ], and we estimated the pairwise genetic distances between both MAGs.…”

Does ecological drift explain variation in microbiome composition among groups in a social host species?

“…Although variation among host genotypes may influence host specificity through differential selection on members of the microbiome (Ahern et al, 2021; Early et al, 2017), many host species have a set of microbes prevalent across the host distribution range (Kwong et al, 2014; Mallott & Amato, 2021; Neu et al, 2021). Nevertheless, within a given species and population, considerable inter‐individual, spatial, and temporal variation in the composition of the microbiome and other symbionts exists (Blekhman et al, 2015; Dona et al, 2021; Suzuki, 2017). A substantial proportion of this variation in microbiome composition among hosts result from extrinsic factors involved in deterministic and stochastic processes.…”

“…Nevertheless, within a given species and population, considerable inter-individual, spatial, and temporal variation in the composition of the microbiome and other symbionts exists (Blekhman et al, 2015;Dona et al, 2021;Suzuki, 2017). A substantial proportion of this variation in microbiome composition among hosts result from extrinsic factors involved in deterministic and stochastic processes.…”