![]() In total, we sequenced 373 phyllosphere epiphyte (leaf surface) and soil samples across the two growing seasons in 20. ![]() Additionally, several lines of evidence suggest that the soil is a key reservoir of leaf microbiota, but also that the leaf habitat selects for particular taxa that generally are not prominent in the soil. Leveraging the Great Lakes Bioenergy Research Center’s Biofuel Cropping System Experiment (BCSE a randomized block design established at Michigan State’s Kellogg Biological Station in 2008), we ask two questions of the bacterial and archaeal communities (henceforth: microbiomes) inhabiting the leaf surfaces and the associated soils of switchgrass and miscanthus: (1) Are there seasonal patterns of phyllosphere microbiome assembly? If so, are these patterns consistent across fields of the same crop, different crops, and years? (2) To what extent might soil serve as a reservoir of phyllosphere diversity? We find strong seasonal patterns of assembly that is consistent across crops and years, and prioritize a core set of leaf-associated microbiota that are persistent over the season but fluctuate in their relative contributions to the community. Improved understanding of the phyllosphere microbiome is expected to advance goals to predict or manage changes in biomass quality in response to abiotic stress like drought 27, 28, 29, 30, 31 or biotic stress like foliar pathogens 32, 33, 34. Upon senescence, the aboveground biomass is harvested for conversion to biofuels and related bioproducts. In the field, these grasses provide extensive leaf habitat, with a seasonal maximum leaf area index (LAI) of 6.2 for switchgrass, and 10 m 2 leaf surface per m 2 land for miscanthus 22, as compared to a maximum LAI of 3.2 for corn 26. To leverage plant microbiomes to support productivity and resilience to environmental stress both above and below ground 19, 20, 21, there is a need to advance foundational knowledge of phyllosphere microbiome diversity and dynamics.īiofuel crops like miscanthus and switchgrass are selected to have extended growing seasons, to produce ample phyllosphere biomass, and to maintain high productivity when grown on marginal lands that are not optimal for food agriculture 22, 23, 24, 25. Despite this importance, knowledge of phyllosphere microbiomes remains relatively modest, especially for agricultural crops 3, 16, 17, 18. ![]() Phyllosphere microorganisms are also thought to play important roles in Earth’s biogeochemical cycles by moderating methanol emissions from plants 13, 14 and contributing to global nitrogen fixation 15. ![]() Phyllosphere microorganisms may provide numerous benefits to plants, including increased stress tolerance 5, 6, 7, promotion of growth and reproduction 8, 9, 10, protection from foliar pathogens 11, and, with soil microbes, control of flowering phenology 12. The phyllosphere (aerial parts of plants) represents the largest environmental surface area of microbial habitation on the planet 1, 2, 3, and much of that surface area is cultivated agriculture, including an estimated 1.5 × 10 7 km 2 of cropland 4. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. Virtually all leaf taxa are also detected in soil source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is an important reservoir of phyllosphere diversity. We sample leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identify core leaf taxa based on occupancy. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass ( Panicum virgatum L.) and miscanthus ( Miscanthus x giganteus). Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress.
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