Microbial community responses to disease management soil treatments used in flower bulb cultivation

Abstract

A number of management practices, such as soil fumigation and flooding, have been employed in efforts to control diseases and weeds in the cultivation of ornamental flower bulbs. However, such treatments may affect the suppression of Pythium root rot, a serious problem in ornamental bulb culture. To gain insight into the nature of Pythium suppression in such soils, we sought to describe the changes that these soil treatments induce in the microbial community in order to determine if particular microbial components of the system could be associated with suppression. Four polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) strategies, two targeting bacteria and two targeting fungi, were used to compare the soil-borne microbial communities of untreated, fumigated, flooded and sterilized, compost-amended soils; the dominant community members were tentatively identified by sequencing of DGGE bands. For all profiling strategies, the compost treatment of sterilized soil appeared to have the most profound effect on the dominant microbial populations in the soil. In general, different primer sets that targeted the same microbial groups, bacteria or fungi, appeared to detect the same microbial taxa, although certain sequence types were detected in only a single profiling strategy. DNA-based microbial community profiles alone were poor predictors of Pythium suppression, as the dominant microbial populations remained mostly intact, even after rigorous soil treatments such as fumigation and flooding. The restoration of suppressive activity against Pythium in compost-amended soil was associated with a different microbial community than observed in untreated, suppressive soils. Thus, although previous studies have shown the suppression of Pythium to be mediated by biological agents, effects of different microbial communities can lead to this suppression.