Full-length 16S ribosomal RNA gene sequencing reveals dynamics of tick-adapted and environmentally derived bacteria in the microbiome of the black-legged tick, Ixodes scapularis in Nova Scotia, Canada

Lyme disease is a tick-borne illness caused by the spirochaete bacterium Borrelia (Borreliella) burgdorferi. The black-legged tick Ixodes scapularis, which transmits B. burgdorferi and several other human pathogens, is endemic to the eastern United States and, due to climate change, is rapidly expanding into central and eastern Canada. Amplification and sequencing of bacterial DNA from I. scapularis is increasingly used to monitor the presence and abundance of B. burgdorferi and associated bacteria. However, variation in the nature of molecular data collected across studies presents challenges for analysis and interpretation. Here we use full-length Oxford Nanopore 16S ribosomal RNA gene amplicon sequencing to characterize the microbiome of I. scapularis, with an explicit focus on distinguishing between tick-adapted bacteria (endosymbionts and pathogens) and environmentally acquired bacteria (external sources, including soil, vegetation or vertebrate hosts). We show that environmental dominance strength differs between these two ecological classes of bacteria, and that environmental dominance does not appear to represent stochastic background alone; environmentally derived bacterial taxa detected in tick microbiomes are not mere contaminants. Paired soil microbiome profiling from tick collection sites will be required to test whether environmental dominance and associated co-occurrence structure track with seasonal changes in exposure and environmental microbial populations.