Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Abstract

26Perennial grasses are promising feedstocks for biofuel production, and there is potential to 27 leverage their native microbiomes to increase their productivity and resilience to 28 environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal 29 assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, 30 switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We sampled 31 leaves and soil every three weeks from pre-emergence through senescence for two 32 consecutive switchgrass growing seasons and one miscanthus season, and identified core leaf 33 taxa based on abundance and occupancy. Virtually all leaf taxa are also detected in soil; 34 source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil 35 is important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late 36 season groups that were consistent across years and crops. This consistency in leaf 37 microbiome dynamics and core members is promising for microbiome manipulation or 38 management to support biofuel crop production. 39The phyllosphere (aerial parts of plants) represents the largest environmental surface 40 area of microbial habitation on the planet 1-3 , and much of that surface area is cultivated 41 agriculture, including an estimated 1.5 x 10 7 km 2 of cropland 4 . Phyllosphere microorganisms 42 may provide numerous benefits to plants, including increased stress tolerance 5-7 , promotion of 43 growth and reproduction 8-10 , protection from foliar pathogens 11 , and, with soil microbes, 44 control of flowering phenology 12 . Phyllosphere microorganisms are also thought to play 45 important roles in Earth's biogeochemical cycles by moderating methanol emissions from 46 plants 13,14 and contributing to global nitrogen fixation 15 . Despite this importance, knowledge 47 Leveraging the Great Lakes Bioenergy Research Center's Biofuel Cropping System 61 Experiment (BCSE; a randomized block design established at Michigan State's Kellogg Biological 62 Station in 2008), we asked two questions of the bacterial and archaeal communities 63 (henceforth: "microbiomes") inhabiting the leaf surfaces and the associated soils of switchgrass 64 and miscanthus: 1) Are there seasonal patterns of phyllosphere microbiome assembly? If so, 65 are these patterns consistent across fields of the same crop, different crops, and years? 2) To 66 what extent might soil serve as a reservoir of phyllosphere diversity? 67 68 Results and Discussion 69 5 Sequencing summary and alpha diversity 70In total, we sequenced 373 phyllosphere epiphyte (leaf surface) and soil samples across 71 the two growing seasons in 2016 and 2017. The number of sequences per sample after our 97% 72 OTU (operational taxonomic unit) clustering pipeline ranged from 20,647 to 359,553. The 73 percentage of sequences belonging to chloroplasts and mitochondria per sample range 74 between 0.2-99.8%, but 235 of the samples (63%) had fewer than 10% chloroplasts and 75 mitochondria...

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