Functional Profiles of Phyllosphere and Rhizosphere Metagenomes Differ Across Milkweed Species

Monarchs and their milkweed hosts are well studied for mechanisms of plant defence and insect counter‐defence, but little is known about their associated microbiomes in this iconic system. It is unclear how herbivore‐induced changes in milkweed microbiomes are linked to chemical defensive responses (i.e., plant secondary metabolites). Metagenomics was used to characterise functional gene profiles of bacterial communities associated with plant tissues and monarch caterpillars feeding in milkweed spp. ( Asclepias curassavica L., 1753, Asclepias syriaca L., 1762, and Asclepias tuberosa subsp. tuberosa ). We compared the influence of monarch feeding and milkweed spp. on phyllosphere and rhizosphere communities. Shotgun metagenomic sequencing was used to profile microbial diversity, predict annotative functions, assess microbial plant secondary metabolite (PSM) degradation potential, and look for enrichment of PSM degradation pathways. Findings show phyllosphere and rhizosphere microbiomes have distinct functional gene profiles and the presence of potential PSM metabolism genes that varied across milkweed spp. Rhizosphere metagenomes had more genes and metabolic pathways involved in degradation/detoxification of known classes of PSMs. In relation to milkweed defensive chemical profiles, we saw an inverse pattern of PSM metabolism pathways and enzymes. Overall, results suggested greater potential for PSM metabolism in rhizosphere compared to phyllosphere communities.