Structural and functional changes in nitrifying microbial communities during the degradation of fungicides in vineyard litter

Plant residues left on vineyards ground surface, collectively termed litter, are microenvironments characterized by high microbial activity involved in many important ecological processes such as the degradation of organic xenobiotics and the release in soil of nutrients. Nitrification is one of the main processes occurring in litter, and it is the resultant of ammonia oxidation carried out mainly by Bacteria and Crenarchaeota. Nitrification activity is an established soil health indicator reflecting the microbial community status in various environmental conditions. Little is known about the degradation of fungicides in litter environments and the related effects on nitrifiers. We constructed vineyard litter microcosms in order to assess the degradation of two widely used fungicides with different persistence (cyprodynil and penconazole) and to concomitantly assess changes in nitrification activity as well as in the structure of the nitrifiying bacterial and crenarcheota community for a period of 100 days. Fungicide degradation patterns correlated well with potential nitrification demonstrating the consistency of this indicator among various environments. PCR-DGGE analysis of nitrifying Bacteria and Crenarchaeota using DNA and transcripts of the amoA (ammonia monooxygenase subunit A) gene showed several changes especially at transcriptional level as a result of both time and fungicide application.