Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

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

Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.

Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.

Gut microbiome insights from 16S rRNA analysis of 17-year periodical cicadas (Hemiptera: Magicicada spp.) Broods II, VI, and X

Periodical cicadas (Hemiptera: Magicicada) have coevolved with obligate bacteriome-inhabiting microbial symbionts, yet little is known about gut microbial symbiont composition or differences in composition among allochronic Magicicada broods (year classes) which emerge parapatrically or allopatrically in the eastern United States. Here, 16S rRNA amplicon sequencing was performed to determine gut bacterial community profiles of three periodical broods, including II (Connecticut and Virginia, 2013), VI (North Carolina, 2017), and X (Maryland, 2021, and an early emerging nymph collected in Ohio, 2017). Results showed similarities among all nymphal gut microbiomes and between morphologically distinct 17-year Magicicada, namely Magicicada septendecim (Broods II and VI) and 17-year Magicicada cassini (Brood X) providing evidence of a core microbiome, distinct from the microbiome of burrow soil inhabited by the nymphs. Generally, phyla Bacteroidetes [Bacteroidota] (> 50% relative abundance), Actinobacteria [Actinomycetota], or Proteobacteria [Pseudomonadota] represented the core. Acidobacteria and genera Cupriavidus, Mesorhizobium, and Delftia were prevalent in nymphs but less frequent in adults. The primary obligate endosymbiont, Sulcia (Bacteroidetes), was dominant amongst core genera detected. Chryseobacterium were common in Broods VI and X. Chitinophaga, Arthrobacter, and Renibacterium were common in Brood X, and Pedobacter were common to nymphs of Broods II and VI. Further taxonomic assignment of unclassified Alphaproteobacteria sequencing reads allowed for detection of multiple copies of the Hodgkinia 16S rRNA gene, distinguishable as separate operational taxonomic units present simultaneously. As major emergences of the broods examined here occur at 17-year intervals, this study will provide a valuable comparative baseline in this era of a changing climate.

Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice

Simple Summary

New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales.

Abstract

Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.

High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.

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

Rhinonyssidae (Mesostigmata) is a family of nasal mites only found in birds. All species are hematophagous endoparasites, which may damage the nasal cavities of birds, and also could be potential reservoirs or vectors of other infections. However, the role of members of Rhinonyssidae as disease vectors in wild bird populations remains uninvestigated, with studies of the microbiomes of Rhinonyssidae being almost non-existent. In the nasal mite (Tinaminyssus melloi) from rock doves (Columba livia), a previous study found evidence of a highly abundant putatively endosymbiotic bacteria from Class Alphaproteobacteria. Here, we expanded the sample size of this species (two different hosts- ten nasal mites from two independent samples per host), incorporated contamination controls, and increased sequencing depth in shotgun sequencing and genome-resolved metagenomic analyses. Our goal was to increase the information regarding this mite species and its putative endosymbiont. We obtained a metagenome assembled genome (MAG) that was estimated to be 98.1% complete and containing only 0.9% possible contamination. Moreover, the MAG has characteristics typical of endosymbionts (namely, small genome size an AT bias). Overall, our results support the presence of a potential endosymbiont, which is the first described for avian nasal mites to date, and improve the overall understanding of the microbiota inhabiting these mites.