Long-term tillage and crop rotation regimes reshape soil-borne oomycete communities in soybean, corn, and wheat production systems

The Oomycetes are eukaryotic microorganisms that include devastating plant pathogens causing substantial losses in the agricultural sector. However, to better manage soil-borne oomycetes, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. We employed an ampliconbased high-throughput sequencing of the Internal Transcribed Spacer 1 (ITS1) region to characterize the soil oomycetes communities over three consecutive years (2016-2018). The field experiment utilized a two-way factorial design with tillage (conventional tillage vs. no till, 2 levels) and rotation (monoculture of soybean, corn, or wheat, and corn-soybean-wheat rotation, 4 levels) regimes. 294 Amplicon Sequence Variants (ASV) were assigned to oomycetes. Grain yield for corn responded significantly to tillage, wheat responded only to crop rotation, and soybean yield was unaffected. No-till (NT) resulted in a reduced community diversity and compositional structure heterogeneity. Crop rotation reshaped oomycete community compositional structure under conventional tillage (CT) only. The most genera recovered were Globisporangium (80.0% in abundance, 174 ASV) and Pythium (19.2%, 80 ASV). Eight species differed in abundance between CT and NT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing this important group of pathogens. Soybean seedling vitality was lowest in soybean monoculture and rotation under CT and in corn monoculture under CT.