Supplementary Tables.pdf

Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial Bombus impatiens queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated communities before, during, and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees.