Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2016
Publication Date: 1/1/2017
Citation: Bakker, M.G., Moorman, T.B., Kaspar, T.C., Manter, D.K. 2017. Isolation of cultivation-resistant oomycetes, first detected as amplicon sequences, from roots of herbicide-terminated winter rye. Phytobiomes Journal. 1(1):24-35. doi: 10.1094/PBIOMES-10-16-0011-R.
Interpretive Summary: We used DNA sequencing to identify the kinds of fungi and oomcyetes that were present in the roots of a cereal rye cover crop, and how the types and abundances of these organisms changed as the rye cover crop died after herbicide was applied. This information is useful in judging the extent to which cereal rye cover crops may increase disease pressure for corn seedlings planted into cover crop residue. We discovered some unexpected species of oomycetes, which did not grow readily using traditional approaches in the laboratory. One of these oomycetes, Pythium sp_F86, appears to be an undescribed species of Pythium. We validated the presence of these organisms, originally detected simply by DNA sequence, by successfully culturing P. volutum and Pythium sp_F86 on a modified growth medium. We also showed that the roots of corn seedlings grown following a cereal rye cover crop were more heavily infected by Pythium volutum than corn seedlings that were not planted into a cover crop. We also observed changes over time in the fungi growing in cereal rye roots, and detected several potential pathogens of corn among the fungi associated with dead cereal rye roots. In summary, this study suggests that several oomycetes that have not been considered important corn pathogens should be given more attention, and that management to reduce disease risk may be necessary when cover cropping with cereal rye before corn.
Technical Abstract: 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. High throughput amplicon sequencing enables a broad survey of organisms present in an environment, while avoiding the biases associated with cultivation-based assessments of microbial community composition. We used high throughput amplicon sequencing to characterize the composition and structure of oomycete and fungal communities associated with a cereal rye cover crop, and to track their community dynamics in the first several weeks after cover crop termination via herbicide application. Pythium volutum and Pythium sp_F86, an unknown species within Pythium Clade B, were the dominant oomycetes associated with cereal rye roots and exhibited contrasting spatial patterns of abundance across the field site. Lagena radicicola was another abundant oomycete associated with rye roots. 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 that we revealed dominant oomycete taxa which would likely have been missed entirely under a traditional cultivation-based approach. With modified semi-selective media, we were able to isolate P. volutum and Pythium sp_F86 from the field site. We also demonstrate elevated densities of P. volutum in corn seedlings grown following a cereal rye cover crop, compared to corn seedlings grown following a winter fallow. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with cereal rye a cover crop were more diverse and more dynamic over time. Several potential pathogens of corn seedlings were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, and highlights the need for deliberate management to reduce seedling disease risk in corn following cereal rye cover crops.