Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Abstract

Perennial grasses are promising feedstocks for biofuel production. The phyllosphere (aerial surfaces) of these cellulosic crops provide a sizable surface area of microbial habitation. Leaf microbial communities may benefit the host plant, have consequence for biomass deconstruction, and interact with foliar pathogens. Here, we characterized the origins, diversity, and assembly of bacterial and archaeal communities of two perennial cellulosic feedstocks: switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We used 16S rRNA gene sequencing to assess microbiome structure on leaves and soils, following crop phenology every three weeks from pre-emergence through senescence for one miscanthus growing season and two consecutive switchgrass seasons. We found abundant and persistent core leaf taxa that originated in soil but were adapted for life on the leaf, rather than vagabonds that randomly disperse from air or soil. Seasonal and host-specific assembly suggested a functional relationship between the phyllosphere microbiomes and plants. This foundational knowledge advances goals to leverage native microbiomes to promote crop wellness and productivity in the field, and specifically in support of biofuels agriculture.