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Because of the use of agricultural land for wine production and the frequent use of copper (Cu)-based fungicides, Cu concentration has been increasing in soils in many parts of the world. In vineyards with acid parent materials, low soil pH may also encourage Cu toxicity, but it is common to use lime in order to increase the soil pH and improve crop yields. Thus, vineyard soils may have large variations in pH, which will affect the microbial communities, making it difficult to isolate possible toxic effects of Cu on soil microbes. Here, analyses of phospholipid fatty acid (PLFA) patterns and pollution-induced community tolerance (PICT, using leucine incorporation) were used to study the effect of Cu accumulation at small to medium concentrations in acid soils (pH 4.0–5.8) in vineyards with different land-use history (young, old and abandoned vineyards). The results suggested that soil pH played a dominant role in determining the composition of the microbial community of the soils. Only a small effect of soil Cu could be detected and the effect on microbial community composition was much less than the pH effect. PICT analysis suggested that bacterial communities in old vineyards were more tolerant of Cu than those in the abandoned vineyards. However, increased PICT (Cu tolerance of the bacterial community) was not directly correlated with Cu concentration in the soils. Instead, the estimated Cu tolerance was significantly correlated with soil pH.