An extended colloid filtration theory for modeling Escherichia coli transport in 3-D fracture networks.

Microbial transport in fractured carbonate rock using enhanced solutions is a significant and neglected research topic in the literature. We propose an extended colloid filtration theory (CFT) combined with a particle-tracking following streamlines (PTFS) model for the rapid prediction of breakthrough curves (BTCs) and plumes of pathogens in three-dimensional (3-D) discrete fracture networks (DFNs). We adapted CFT in porous media to pathogen transport in fractures containing Terra Rossa (soil) deposits. As an example of the model capability, a simulation was used to predict the 3-D motion field and Escherichia coli count in groundwater originating from the Forcatella managed aquifer recharge (MAR) Facility (Brindisi, Italy) using a DFN composed of 3,900 fractures. In arid regions, MAR facilities are significant for sustaining basic human needs, such as freshwater supply for drinking and crop production. The Markov chain Monte Carlo (MCMC) technique was applied to E. coli counts in the collected water samples to increase data representativeness. The pathogen transport coefficients were further supported by batch filtration tests carried out in the CNR/IRSA Laboratory (Bari, Italy). The mean E. coli attachment rate coefficient of 0.15 × 10-8 m2 d-1 (sticking efficiency = 1.1 × 10-8 m) resulted in a 2.1 log10 removal in 600 m of reclaimed water filtration. The simulation output visualized the E. coli 3-D pathways in groundwater and the positions of contaminated groundwater spring outflows on Forcatella Beach. The simulation results agreed with the mean MCMC output of E. coli concentrations in bathing water under unperturbed geochemical and environmental flow and transport conditions. However, results indicate that concentrations of pathogenic strains, parasites, and enteric viruses may enter the marine environment of MAR sites during flood periods.

Geological activity shapes the microbiome in deep-subsurface aquifers by advection.

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

Tracing groundwater circulation in a valuable mineral water basin with geochemical and isotopic tools: the case of FERRARELLE, Riardo basin, Southern Italy.

The Riardo basin hosts groundwater exploited for the production of high quality, naturally sparkling, bottled water (e.g., Ferrarelle water), and circulating in a system constituted by highly fractured Mesozoic carbonates, overlain by more impervious volcanic rocks of the Roccamonfina complex. The two formations are locally in hydraulic connection and dislocated by deep-rooted faults. The study aimed at elucidating groundwater origin and circulation, using isotopic tracers (δ18O, δ2H, δ11B and 87Sr/86Sr) coupled to groundwater dating (Tritium, CFCs and SF6). Besides recharge by local precipitation over the Riardo hydrogeological basin, stable isotope ratios in water indicated an extra-basin recharge, likely from the elevated surrounding carbonate reliefs (e.g., Maggiore and Matese Mts.). The mineralization process, promoted by the deep CO2 flux, controls the B and Sr contents. However, their isotopic ratios did not allow discriminating between circulation in the volcanic and in the carbonate aquifers, as in the latter the isotopic composition differed from the original marine signature. Groundwater model ages ranged from ~ 30 years for the volcanic endmember to > 70 years for the deep, mineralized end-member, with longer circuits recharged at higher elevations. Overall, the results of this study were particularly relevant for mineral water exploitation. A recharge from outside the hydrogeological basin could be evidenced, especially for the more mineralized and valuable groundwater, and an active recent recharge was detected for the whole Riardo system. Both findings will contribute to the refinement of the hydrogeological model and water budget, and to a sustainable development of the resource.

Autotrophic denitrification supported by biotite dissolution in crystalline aquifers (1): New insights from short-term batch experiments.

We investigate denitrification mechanisms through batch experiments using crushed rock and groundwater from a granitic aquifer subject to long term pumping (Ploemeur, France). Except for sterilized experiments, extensive denitrification reaction induces NO3 decreases ranging from 0.3 to 0.6mmol/L. Carbon concentrations, either organic or inorganic, remain relatively stable and do not document potential heterotrophic denitrification. Batch experiments show a clear effect of mineral dissolution which is documented through cation (K, Na, Ca) and Fluoride production. These productions are tightly related to denitrification progress during the experiment. Conversely, limited amounts of SO4, systematically lower than autotrophic denitrification coupled to sulfur oxidation stoichiometry, are produced during the experiments which indicates that sulfur oxidation is not likely even when pyrite is added to the experiments. Analysis of cation ratios, both in isolated minerals of the granite and within water of the batch, allow the mineral dissolution during the experiments to be quantified. Using cation ratios, we show that batch experiments are characterized mainly by biotite dissolution. As biotite contains 21 to 30% of Fe and 0.3 to 1.7% of F, it constitutes a potential source for these two elements. Denitrification could be attributed to the oxidation of Fe(II) contained in biotite. We computed the amount of K and F produced through biotite dissolution when entirely attributing denitrification to biotite dissolution. Computed amounts show that this process may account for the observed K and F produced. We interpret these results as the development of microbial activity which induces mineral dissolution in order to uptake Fe(II) which is used for denitrification. Although pyrite is probably available, SO4 and cation measurements favor a large biotite dissolution reaction which could account for all the observed Fe production. Chemical composition of groundwater produced from the Ploemeur site indicates similar denitrification processes although original composition shows mainly plagioclase dissolution.

Autotrophic denitrification supported by biotite dissolution in crystalline aquifers: (2) transient mixing and denitrification dynamic during long-term pumping.

We investigated the mixing and dynamic of denitrification processes induced by long-term pumping in the crystalline aquifer of Ploemeur (Brittany, France). Hydrological and geochemical parameters have been continuously recorded over 15 boreholes in 5km2 on a 25-year period. This extensive spatial and temporal monitoring of conservative as well as reactive compounds is a key opportunity to identify aquifer-scale transport and reactive processes in crystalline aquifers. Time series analysis of the conservative elements recorded at the pumped well were used to determine mixing fractions from different compartments of the aquifer on the basis of a Principal Component Analysis approach coupled with an end-member mixing analysis. We could reveal that pumping thus induces a thorough reorganization of fluxes known as capture, favoring infiltration and vertical fluxes in the recharge zone, and upwelling of deep and distant water at long-term time scales. These mixing fractions were then used to quantify the extent of denitrification linked to pumping. Based on the results from batch experiments described in a companion paper, our computations revealed that i) autotrophic denitrification processes are dominant in this context where carbon sources are limited, that ii) nitrate reduction does not only come from the oxidation of pyrite as classically described in previous studies analyzing denitrification processes in similar contexts, and that iii) biotite plays a critical role in sustaining the nitrate reduction process. Both nitrate reduction, sulfate production as well as fluor release ratios support the hypothesis that biotite plays a key role of electron donor in this context. The batch-to-site similarities support biotite availability and the role by bacterial communities as key controls of nitrate removal in such crystalline aquifers. However, the long term data monitoring also indicates that mixing and reactive processes evolve extremely slowly at the scale of the decade.