Variable microbiomes between mosquito lines are maintained across different environments

The composition of the microbiome is shaped by both environment and host in most organisms, but in the mosquito Aedes aegypti the role of the host in shaping the microbiome is poorly understood. Previously, we had shown that four lines of Ae. aegypti harbored different microbiomes when reared in the same insectary under identical conditions. To determine whether these lines differed from each other across time and in different environments, we characterized the microbiome of the same four lines of Ae. aegypti reared in the original insectary and at another institution. While it was clear that the environment influenced the microbiomes of these lines, we did still observe distinct differences in the microbiome between lines within each insectary. Clear differences were observed in alpha diversity, beta diversity, and abundance of specific bacterial taxa. To determine if the line specific differences in the microbiome were maintained across environments, pair-wise differential abundances of taxa was compared between insectaries. Lines were most similar to other lines from the same insectary than to the same line reared in a different insectary. Additionally, relatively few differentially abundant taxa identified between pairs of lines were shared across insectaries, indicating that line specific properties of the microbiome are not conserved across environments, or that there were distinct microbiota within each insectary. Overall, these results demonstrate that mosquito lines under the same environmental conditions have different microbiomes across microbially- diverse environments and host by microbe interactions affecting microbiome composition and abundance is dependent on environmentally available bacteria.Author summary: The mosquito microbiome plays a critical role in shaping interactions with human pathogens. The factors that contribute to shaping the composition of the mosquito microbiome are of high importance due to its role in pathogen interactions and the successful development of control strategies. In other organisms, both host and environment shape the microbiome composition, but the role of the host in shaping the mosquito microbiome is less clear. Previously, we have shown that different lines of Aedes aegypti harbor different microbiomes when reared in the same environment. We were curious to see if these differences could still be detected after further generations in the same insectary and across environments in a different insectary. We found that the microbiome differed between these lines in each insectary indicating both host and environment play a role in establishing the microbiome. Our results indicate that different lines of Ae. aegypti will interact with their environment differently to shape their microbiome, which could potentially influence interactions with human pathogens and/or the effectiveness of control strategies. More broadly, our results are of interest for the ecology of host-microbe interactions.