Abstract
The holobiont theory captures the concept that an organism is not only itself, but also all of its associated microbes together forming one integrated 'evolutionary unit'. The hologenome theory posits that the whole genome of an organism includes its genes as well as the genes of its associated microorganisms. The microbiome is thus regarded as necessary for an organism's development and health. Microbes may provide functional benefits to the organism they occupy and form symbiotic relationships with. This is true for parasites as well, which often rely on their microbiome for survival and success at exploiting their host. Parasites such as nematomorphs, with complex life cycles, go through multiple distinct life stages, multiple hosts, and both parasitic and free-living environments. Each of these life factors introduces its own selective pressures that can shape an organism's microbiome. I characterised the entire microbiome of parasite and host antagonists, using the New Zealand native hairworms Gordius paranensis and Euchordodes nigromaculatus (phylum Nematomorpha) and their cave wētā hosts (Orthoptera: Rhaphidophoridae) to investigate host and parasite microbiomes overlap. Current microbiome research focuses mainly on bacteria, and more recently, viruses. This thesis aims to expand on this by utilising RNA and metatranscriptomic techniques to consider additional microbial domains. RNA was extracted from the tissue of hairworms and the haemolymph of cave wētā and sequenced using Illumina sequencing. Two bioinformatic pipelines were utilised, one to identify viral contigs and the other targeting all species of viruses, bacteria, fungi, archaea, and protists in all groups. With this, I also aimed to challenge previous findings suggesting that nematomorphs were microbe-free. I found that parasites harbour their own unique microbial taxa, in addition to microbes shared with infected wētā, many of which are not found in uninfected wētā. This suggests i hairworms do not rely on their host to develop a microbiome, though they may interact with their host's microbiome. As hairworms progress through their life stages, they exhibit a core microbiome; however, microbial community composition varies significantly across life stages, i.e. from the parasitic juvenile stage to the adult free-living stage, suggesting the life stage and environment have a significant effect on the parasite's microbiome. Therefore, hairworm microbiomes are dynamic across the life cycle and modulated by the host, the parasite's development, and the environment. The hairworm's diverse microbiome and its shifting composition at the juvenile-to-adult transition raise the intriguing possibility that its symbiotic microbes contribute to the iconic host manipulation (suicidal water-jumping) associated with hairworms.