Soil microbial ecology associated with disease control of Fusarium oxysporum f. Sp. Cucumerinum in Cucumis sativus cultivation following soil fumigation with anhydrous ammonia in China

Fusarium oxysporum f. sp. Cucumerinum is a pathogen affecting cucumber (Cucumis sativus) production in China. Soil fumigation and rotation of cucumber with other crops are two methods which increase yield and reduce disease incidence in cucumber monoculture that has low yield and high disease incidence. The soil microbial communities of soil fumigated with anhydrous ammonia and rotation of cucumber with tomato and celery were investigated to control disease in cucumber monoculture. In 2013, a time series from two treatments was sampled in tripicate 1) soil fumigated with anhydrous ammonia and 2) soil not fumigated in cucumber monoculture near Jinhua, Zhejiang, China. In 2014, eight composite soil samples were collected from each of three treatments 1) soil fumigated with anhydrous ammonia in 2013, 2) soil in tomato-celery-cucumber crop rotation and 3) soil not fumigated in the same cucumber monoculture fields as the year prior. Soil microbial communities were identified using bioinformatics software tools to analyze sequenced amplicons of 16s and ITS1 rDNA from soil sample extracted DNA. In 2013, Comparing fumigated to not fumigated soil immediately following fumigation 116 unique fungal species and 28 unique bacterial genera were significantly affected (P < 0.10). Following fumigation, 55 fungal species were significantly enriched (P < 0.10) in an initial ecological succession that led to the later domination by a smaller community of late successional species. In 2014, the fungal taxon associated with the pathogen, Fusarium oxysporum, was significantly reduced in both fumigated and rotation treatment soil (P < 0.1). Both fumigated and rotation treatments had microbial communities significantly different than the not fumigated treatment, but fumigated treatment microbial communities were lacking important taxon, some genera which are implicated in plant growth promotion. Fumigated and rotation treatment expressed disease control based on significantly different microbial communities suggesting consequences for resilience and broader soil function.