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Elucidating the influence of resident seed and soil microbiota on the developing creeping bentgrass microbiome

Doherty Joseph R., Jo Anne Crouch, Joseph A. Roberts
Agrosystems, geosciences & environment 2020 v.3 no.1 pp. e20038
Agrostis stolonifera, Eurotiomycetes, Proteobacteria, autoclaving, environmental DNA, high-throughput nucleotide sequencing, leaves, metagenomics, peat, phytobiome, rhizosphere, seedling emergence, seeds, sequence diversity, soil bacteria, soil fungi, soil sterilization, sowing
Characterization of the plant microbiome may allow for the development of diagnostic tools or improvements in plant health. To that end, this project sought to determine the influence that resident seed and soil microbiota exert on the developing creeping bentgrass (Agrostis stolonifera L. cv. 007) microbiome. A sterile growth environment was created in a laminar flow hood. Sterile 50 ml conical tubes were filled with autoclaved or non‐autoclaved soil (85% sand and 15% peat) and seeded with 007 creeping bentgrass. Foliage and rhizosphere samples were taken at emergence, 2, 4, and 6 wk post‐emergence, and soil samples were taken at the conclusion of the experiment. Amplicon sequencing libraries were generated from extracted environmental DNA, sequenced using an Illumina MiSeq, and analyzed in R. After quality control 3.32 × 10⁷ sequences were grouped into 2,273 bacterial and 303 fungal amplicon sequence variants (ASVs). Bacterial and fungal ASVs were predominantly members of the Proteobacteria and Eurotiomycetes, respectively. Over the 6‐wk sampling period the microbial communities were stable, with taxonomic shifts occurring mainly in low relative abundant taxa. Ordination of Bray‐Curtis distance matrices revealed significant differences in community centroids between grass planted in autoclaved and non‐autoclaved soil. However, taxonomic profiling showed these differences were due to shifts in taxa present at low relative abundances <.5%). Data show that the microbiota originating from the seed exerts only a minimal influence over the microbiome of developing creeping bentgrass compared to the soil microbiome.