Soil DNA evidence for altered microbial diversity after long-term application of municipal wastewater

Abstract

Water resources constitute a social, agricultural and economic problem in most countries of the southern Mediterranean Basin. Alternative strategies have been developed such as the reuse of municipal wastewater for irrigation in agriculture. Despite numerous advantages for soil fertility and crop productivity, recycling wastewater in soils also has several ecotoxicological and sanitary problems. Few investigations have assessed the risk by evaluating the impact of wastewater irrigation on soil microbes. Here, we report for the first time the short- and long-term effects of treated municipal wastewater irrigation on the density and genetic structure of bacterial and fungal soil communities. Soils from agricultural sites in Tunisia that had been irrigated with wastewater for 4, 8, 16 and 26 years were characterised. Soil physicochemical and microbial characteristics were assessed by sampling at 0–20 and 20–40 cm depth at each site. Quantitative changes in bacterial and fungal communities were measured by indirect counts on synthetic culture media and qualitative modifications were evaluated by using molecular ecology methods: B- and F-ARISA for Bacterial and Fungal Automated Ribosomal Intergenic Spacer Analysis, respectively. These methods allowed genotyping the structure of bacterial and fungal communities from soil DNA extracts. Our results revealed a significant increase in microbial densities related to the duration of irrigation with wastewater. In addition, wastewater irrigation led to changes in the genetic structure of bacterial and fungal communities, the magnitude and specificity of these changes being significantly correlated with the duration of such irrigation. These results show that wastewater management schemes have a major effect on indigenous microbial abundance and composition in soils that could be related to the recurrent inputs of organic compounds and mineral/metallic elements. In an agro-ecological context, irrigation with municipal wastewater represents an impacting practice that now needs to be evaluated more fully in terms of ecosystem services for sustainable agriculture.