Bioremediation of a Polluted Groundwater: Microbial Community Comparison of Treated and Untreated Aquifer through Next Generation Sequencing

Bioremediation is an active process for the detoxification of polluted ambient media employing the metabolism of microbes, while natural attenuation relies on physical, chemical and biological processes occurring without human intervention. A shallow aquifer (A0) was treated using a bioremediation approach through the amendment of whey to detoxify the most abundant contaminants: 1,1,2,2- tetrachloroethane (1,1,2,2-TeCA), perchloroethene (PCE) and trichloroethene (TCE). A deeper aquifer (A1), showing lower concentration of the contaminants, was left untreated. In A0, a concomitant decrease of more chlorinated molecules 1,1,2,2-TeCA, PCE and TCE and an increase of less halogenated molecules such as trichloroethane (1,1,2-TCA), cis-dichloroethene (cis-DCE) and vinyl chloride (VC) were observed, suggesting that a reductive dechlorination took place. In contrast, the aquifer A1 did not show a significant decrease of contaminants during this period. A metagenomic approach (shot gun and 16S rRNA gene) was then used to investigate the microbial population of the two aquifers. A massive presence of the dehalogenator Dehalococcoides mccartyi (D. mccartyi) and a spectrum of different Geobacter species were detected in A0, after the treatment. The metagenome assembly of shotgun (SG) data further indicated a significant presence of methanogenic archaea, most likely from class Methanomassiliicoccales, at a level comparable to that of D. mccartyi. Instead, A1 was characterized by the species Burkholderia, Curvibacter and Flavobacterium. These results indicate that the autochthonous microbial consortia reflected the geochemistry of the two aquifers, with a dominant population thriving in an anoxic and nutrient rich environment implicated in reductive dehalogenation in A0 and a more diverse population, not able to decompose the pollutants, in A1.