Spatial and temporal dynamics of microbial communities in an aquifer contaminated by chlorinated solvents

Chlorinated solvents are widely spread, recalcitrant environmental pollutants. In contaminated aquifers, they are generally biodegraded by OrganoHalide Respiring Bacteria (OHRB) that reduce them in the anaerobic dehalorespiration process. However, aerobic direct and cometabolic oxidative processes can also co-exist. In order to define the microbial composition of an aquifer chronically and heavily contaminated by chlorinated solvents, never microbiologically characterized before, here we studied the groundwater autochthonous microbial communities and monitored their changes over time. The main chlorinated contaminant detected in the aquifer is 1,2-dichloroethane (1,2-DCA), whose concentrations undergo high fluctuations over time and have exceeded one gram per liter. Groundwater samples were collected from eight piezometers placed in the study area and were analyzed for microbial diversity by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and for taxonomic profiling by 16S rRNA gene metagenomic sequencing. Autochthonous microbial communities were unexpectedly characterized by very high alpha and beta diversity. Among the identified taxa, chemolithotrophic, methylotrophic, sulphate-reducing and sulfur-oxidizing bacteria were revealed, while the relative abundance of known dechlorinating anaerobic and aerobic bacteria was very low. However, a large part of most groundwater communities was made up of unclassified taxa. Groundwater from the most 1,2-DCA contaminated area was sampled in three moments over two years and 16S rRNA gene Illumina sequencing was applied on metagenomic DNA from each sampling event. The microbial characterization revealed a reduction in bacterial diversity and an enrichment in Helicobacteraceae and Desulfuromonadaceae families over time. The presence of the dehalorespiring genera Dehalococcoides, Dehalogenimonas and Desulfuromonas was also PCR detected using phylogenetic biomarkers. In conclusion, the low relative abundance of known anaerobic or aerobic dechlorinating taxa suggests a poor intrinsic biodegradation potential, consistent with the deep and chronic contamination at the site. However, this limited dechlorinating potential of groundwater could be exploited in bioremediation interventions, if properly biostimulated.