Changes in microbial communities in an apple orchard and its adjacent bush soil in response to season, land-use, and violet root rot infestation

Soil microbial communities in an apple orchard and its adjacent boundary bush with or without infestation by violet root rot were investigated for 2 years. Effects of season (spring, summer, and fall), land-use (apple orchard and boundary bush), and violet root rot (infested and healthy) on soil microbial populations, microbial activity, and microbial community structures were determined using physiological, cytochemical, and molecular (PCR-DGGE) approaches. Seasonal fluctuations were significant (P<0.05) in viable bacteria and fungal populations, bacterial FAME, fluorescein diacetate (FDA) hydrolysis, and diversity (H′) and evenness (J′) of community-level physiological profile (CLPP) in both years. However, seasonal differences of soil microbial guilds that utilize carbon substrate groups observed in the first year were not reproduced in the second year. The land-use factor differentiated the apple orchard from the boundary bush where viable bacterial population, bacterial FAME and FDA hydrolysis were significantly greater in both years. Infestation status of violet root rot, on the other hand, significantly increased bacterial FAME and FDA hydrolysis in both years. In addition, neither the land-use nor the disease infestation factor significantly influenced the utilization patterns of individual substrate guilds for the 2 years. In both years, saturated fatty acids were significantly more abundant in the orchard than in the bush soil, and monosaturated fatty acids vice versa. Principal component analyses for CLPP, FAME, and denaturing gradient gel electrophoresis (DGGE) consistently exhibited that, although the violet root rot influenced the soil microbial community structures both in the apple orchard and the boundary bush, overall magnitude of the difference in communities between the violet root rot infested and non-infested sites in the bush were greater than in the orchard, irrespective of the season. These results suggested that the seasonal and the land-use factors affected soil microbial community both quantitatively and qualitatively, whereas the impact of the violet root rot on the soil microbial community was mainly qualitative and more pronounced in the adjacent bush than in the orchard.