Clay beads as artificial trapping matrices for monitoring bacterial distribution among urban stormwater infiltration systems and their connected aquifers

  • Florian Mermillod-BlondinEmail author
  • J. Voisin
  • L. Marjolet
  • P. Marmonier
  • B. Cournoyer


Stormwater infiltration systems (SIS) have been developed to limit surface runoff and flooding in urban areas. The impacts of such practices on the ecological and biological quality of groundwater ecosystems remain poorly studied due to the lack of efficient methodologies to assess microbiological quality of aquifers. In the present study, a monitoring method based on the incubation of artificial matrices (clay beads) is presented to evaluate microbial biomass, microbial activities, and bacterial community structure. Four microbial variables (biomass, dehydrogenase and hydrolytic activities, bacterial community structures) were measured on clay beads incubated in three urban water types (stormwater surface runoffs, SIS-impacted and non-impacted groundwaters) for six SIS. Analyses based on next-generation sequencing (NGS) of partial rrs (16S rRNA) PCR products (V5-V6) were used to compare bacterial community structures of biofilms on clay beads after 10 days of incubation with those of waters collected from the same sampling points at three occasions. Biofilm biomass and activities on clay beads were indicative of nutrient transfers from surface to SIS-impacted groundwaters. Biofilms allowed impacts of SIS on groundwater bacterial community structures to be determined. Although bacterial communities on clay beads did not perfectly match those of waters, clay beads captured the most abundant bacterial taxa. They also captured bacterial taxa that were not detected in waters collected at three occasions during the incubation, demonstrating the integrative character of this approach. Monitoring biofilms on clay beads also allowed the tracking of bacterial genera containing species representing health concerns.


Infiltration basins Environmental monitoring Microbial biomass and activity Next generation sequencing (NGS) Metabarcoding 16S rRNA 



This work was supported by l’Agence Nationale de la Recherche [ANR-16-CE32-0006 FROG], Lyon Metropole within the framework of the experimental observatory for urban hydrology (OTHU,, and the French national research program for environmental and occupational health of Anses under the terms of project “Iouqmer” EST 2016/1/120. We thank Félix Vallier, Antonin Vienney, and Laurent Simon for support and advices during field and laboratory work.

Supplementary material

10661_2019_7190_MOESM1_ESM.xlsx (8.6 mb)
Supplementary Table 1 (XLSX 8775 kb)


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNAVilleurbanneFrance
  2. 2.UMR Ecologie Microbienne, Research Team “Bacterial Opportunistic Pathogens and Environment”, Université Lyon 1 & VetAgro Sup, CNRS 5557, INRA 1418Univ LyonMarcy L’EtoileFrance

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