Fluorescence In Situ Hybridization in soil and water ecosystems: an useful method for studying the effect of xenobiotics on bacterial community structure

The ability of soil and groundwater ecosystems to recover from chemical contamination is primarily dependent on the presence of a microbial community which has the ability to remove it. Nevertheless, there has been a little research into these communities because it is strictly dependent on methods capable of identifying and characterizing their community structure and functioning. The use of molecular methods makes it possible to overcome this kind of identification limitation. In this work, we applied the fluorescence in situ hybridization (FISH) method to different samples, such as soil and groundwater contaminated with s-triazine herbicides (simazine or terbuthylazine) and surface water treated with the pharmaceutical oseltamivir carboxylate (Tamiflu). We compared the bacterial community structure in the presence/absence of these xenobiotics. The use of 16S rRNA-targeted oligonucleotide probes, designed specifically for the main phylogenetic levels (Archaea, Bacteria, -, -, -, "-subdivision of Proteobacteria, Planctomycetes, Gram-positive bacteria with a high or low DNA GþC content, Cytophaga-Flavobacter-Bacteroides phylum, and sulfate-reducing bacteria), and a DAPI stain made it possible to assess the structure of the bacterial community and its changes in the presence of these xenobiotics in all the ecosystems studied.