Characterizing cultivable soil microbial communities from copper fungicide-amended olive orchard and vineyard soils

Abstract

Use of copper-based fungicides has led to an increase in the total Cu content in agriculture soils. The focus of this study was to determine fractionation of Cu and to investigate the structure and the diversity of cultivable bacterial communities in two vineyards (one 25 years old and one 2 years old), one olive orchard and two forest soils. All soils developed on an Oligocene sandstone. The concentration of total Cu in the old vineyard (176.6 mg kg−1) and olive orchard (145.5–296.7 mg kg−1) was from 5 to 10 times higher than in forest soils. The major amount of Cu was found bound to the humic substances in cultivated soils, whereas in forest soils Cu was found in the residual mineral fraction. A relationship was found between the number of cultivable Cu-tolerant bacteria and total Cu content in soil. In the cultivated soils, Cu had a toxicological effect on bacterial community, and thereby Cu-levels > to 145 mg kg−1 could be a risk to soil biota. Microbial communities were analysed by community level physiological profiling (CLPP), using the Biolog system, and by the amplified ribosomal DNA restriction analysis (ARDRA) approach. Only when cell suspensions containing 104 colony-forming units (c.f.u.) were inoculated in each well of Biolog EcoPlates it was possible to discriminate microbial communities from different soil samples. As expected, 16S ARDRA showed that cultivated soils had a lower microbial diversity in respect to forest soils.