Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress. 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). 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. 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. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production.

Press disturbances are stressors that are extended or ongoing relative to the generation times of community members, and, due to their longevity, have the potential to alter communities beyond the possibility of recovery. They also provide key opportunities to investigate ecological resilience and to probe biological limits in the face of prolonged stressors. The underground coal mine fire in Centralia, Pennsylvania has been burning since 1962 and severely alters the overlying surface soils by elevating temperatures and depositing coal combustion pollutants. As the fire burns along the coal seams to disturb new soils, previously disturbed soils return to ambient temperatures, resulting in a chronosequence of fire impact. We used 16S rRNA gene sequencing to examine bacterial and archaeal soil community responses along two active fire fronts in Centralia, and investigated the influences of assembly processes (selection, dispersal and drift) on community outcomes. The hottest soils harbored the most variable and divergent communities, despite their reduced diversity. Recovered soils converged toward similar community structures, demonstrating resilience within 10–20 years and exhibiting near-complete return to reference communities. Measured soil properties (selection), local dispersal, and neutral community assembly models could not explain the divergences of communities observed at temperature extremes, yet beta-null modeling suggested that communities at temperature extremes follow niche-based processes rather than null. We hypothesize that priority effects from responsive seed bank transitions may be key in explaining the multiple equilibria observed among communities at extreme temperatures. These results suggest that soils generally have an intrinsic capacity for robustness to varied disturbances, even to press disturbances considered to be ‘extreme', compounded, or incongruent with natural conditions.

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...

Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.