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Solarization effects on the soil microbiome at an organic vegetable farm in the Pacific Northwest (USA)

Jennifer Parke: Oregon State University

<div>Soil solarization is effective for managing certain soilborne plant pathogens and weeds without using chemical pesticides. Little is known about non-target effects on soil microbial communities. We compared the soil microbiomes from solarized and non-solarized treatments at an organic vegetable farm in western Oregon. DNA was extracted from soil samples collected at the beginning and end of the four-week trial, and the 16S (bacteria and archaea) and ITS1 (fungi and oomycete) amplicons were sequenced using the Illumina MiSeq platform. Sequences were quality filtered and queried against Greengenes (for 16S), UNITE (for fungal ITS) and an in-house oomycete ITS1 reference database for identification at 97% sequence similarity with known species, followed by diversity analysis using QIIME. Relative OTU abundance was adjusted to account for total DNA in each sample. Soil solarization had a large effect on beta-diversity for fungal and bacterial communities. A decline in total OTU abundance was observed in solarized relative to non-solarized soil. For bacteria, the phyla Bacteriodetes, Acidobacteria, Actinobacteria, and Proteobacteria were most impacted. Fungal and oomycete genera most affected included <em>Monographella, Cercophora, Fusarium, Alternaria, Mortierella, Cryptococcus </em>and<em> Pythium.</em> Understanding solarization effects on the soil microbiome is important for predicting impacts on pathogens and beneficial microbes, and optimizing soil health.</div>