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Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds


In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.

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Data availability

All data generated or analyzed during this study are included in this published article (and its supplementary information files).


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We acknowledge the Environmental Service of the Municipality of Ferrara for their support during field investigation. We are also grateful to the UNIBO student Alessia De Matteis for the precious contribution in the experimental work.


This study was funded by the University of Bologna (RFO grant). AF is financed by the ELECTRA project that has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 826244.

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Conceptualization: Stefano Fedi, Daniele Ghezzi, Maria Filippini, Martina Cappelletti; methodology: Stefano Fedi, Daniele Ghezzi, Martina Cappelletti; formal analysis and investigation: Stefano Fedi, Daniele Ghezzi, Maria Filippini, Andrea Firrincieli; writing—original draft preparation: Stefano Fedi, Daniele Ghezzi, Maria Filippini; Andrea Firrincieli; writing—review and editing: Stefano Fedi, Daniele Ghezzi, Maria Filippini, Davide Zannoni; funding acquisition: Davide Zannoni, Alessandro Gargini; supervision: Stefano Fedi, Alessandro Gargini, Davide Zannoni

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Correspondence to Stefano Fedi.

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figure 10

Fig. S1. Rarefaction analysis of the Illumina sequencing data from Caretti and Manzi sites. (PNG 4063 kb)

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Ghezzi, D., Filippini, M., Cappelletti, M. et al. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. Environ Sci Pollut Res 28, 23017–23035 (2021).

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  • Bioremediation
  • Reductive dechlorination
  • Chloroethylene
  • 16S rRNA
  • Microbial community