Isolation of Cultivation-Resistant Oomycetes, First Detected as Amplicon Sequences, from Roots of Herbicide-Terminated Winter Rye

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. We used high throughput amplicon sequencing to characterize the composition and structure of oomycete and fungal communities associated with a rye cover crop, and to track their community dynamics in the first several weeks after herbicide was applied to terminate the cover crop. The dominant oomycetes associated with cereal rye roots were Pythium volutum, Pythium sp. F86 (an unknown species within clade B), and Lagena radicicola. Because P. volutum is sensitive to common additives in isolation media, and L. radicicola is an obligate intracellular parasite, a unique aspect of this work is to reveal the dominance of oomycete taxa that would have been missed entirely under a traditional cultivation-based approach. Based on first detection in an amplicon sequencing survey, we were able to isolate P. volutum and Pythium sp. F86. We demonstrate that both species are pathogenic on corn, and that corn seedlings grown in the field following a rye cover crop show elevated rates of infection by P. volutum, highlighting a potential disease risk associated with cover cropping. P. volutum and Pythium sp. F86 exhibited contrasting spatial patterns of abundance, with nearly complete turnover of the dominant species across the field site. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with a cereal rye cover crop were more diverse and dynamic, with some displacement of basidiomycetes by ascomycetes over time. Several plant pathogens, as well as putative beneficial organisms, were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, highlights the power of culture-independent microbial community assessment to yield new insights, and suggests the need for informed management to reduce seedling disease risk in corn following rye cover crops.