American ginseng is an important herbal medicinal crop in China. In recent years, there has been an increasing market demand for ginseng, but the production area has been shrinking due to problems associated with continuous monocropping. We analyzed the microbiome in bulk soils to assess whether and, if so, what changes in the bulk soil microbiome are associated with continuous American ginseng cropping. The alpha diversity of fungi and bacteria was significantly lower in the soils planted with American ginseng than the virgin (non-planted) land. The relative abundance of Fusarium spp. and Ilyonectria spp., known plant root pathogens, was much higher in the soils cropped with American ginseng than the non-planted. On the other hand, a number of bacteria with biodegradation function, such as Methylibium spp., Sphingomonas spp., Variovorax spp., and Rubrivivax spp., had lower abundance in the soils cropped with American ginseng than the non-cropped. In addition, soil pH was lower in the field planted with American ginseng than the non-planted. Accumulation of fungal root pathogens and reduction of soil pH may, therefore, have contributed to the problems associated with continuous monocropping of American ginseng.

Verticillium dahliae is a widely distributed soilborne pathogen that causes vascular wilt in more than 200 plant species. Defoliating and nondefoliating symptoms caused by the disease that result in either the loss or retention of leaves in infected plants, respectively, in hosts such as cotton, olive, and okra, divide the causal agent into defoliating and nondefoliating pathotypes. Our goal in this current work was to generate genome resources for the defoliating strain XJ592 and the nondefoliating strain XJ511 of V. dahliae isolated from cotton in China.

Understanding the origins and migration routes of phytopathogen inoculum is essential in predicting disease development and formulating control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen threatening wheat production by long-distance migration. Due to large variation in geographic features, climatic conditions, and wheat production systems, inter-regional Pst dispersal routes in China remain largely unknown. In the present research, we sequenced 154 Pst isolates sampled from all the major wheat-growing regions in China to study the Pst population structure. Western Qinling Mountains, Himalayan region, and Guizhou Plateau were found to be centers of Pst origin in China. Combined with trajectory tracking and field disease surveys, long-distance Pst migration routes from individual origins were proposed. The present findings will improve current understanding of Pst origin and migration in China and emphasize the need for managing stripe rust at the national scale.