Quantitative PCR Monitoring of Antibiotic Resistance Genes and Bacterial Pathogens in Three European Artificial Groundwater Recharge Systems

Aquifer recharge presents advantages for integrated water management in the anthropic cycle, namely, advanced treatment of reclaimed water and additional dilution of pollutants due to mixing with natural groundwater. Nevertheless, this practice represents a health and environmental hazard because of the presence of pathogenic microorganisms and chemical contaminants. To assess the quality of water extracted from recharged aquifers, the groundwater recharge systems in Torreele, Belgium, Sabadell, Spain, and Nardò, Italy, were investigated for fecal-contamination indicators, bacterial pathogens, and antibiotic resistance genes over the period of 1 year. Real-time quantitative PCR assays for Helicobacter pylori, Yersinia enterocolitica, and Mycobacterium avium subsp. paratuberculosis, human pathogens with long-time survival capacity in water, and for the resistance genes ermB, mecA, blaSHV-5, ampC, tetO, and vanA were adapted or developed for water samples differing in pollutant content. The resistance genes and pathogen concentrations were determined at five or six sampling points for each recharge system. In drinking and irrigation water, none of the pathogens were detected. tetO and ermB were found frequently in reclaimed water from Sabadell and Nardò. mecA was detected only once in reclaimed water from Sabadell. The three aquifer recharge systems demonstrated different capacities for removal of fecal contaminators and antibiotic resistance genes. Ultrafiltration and reverse osmosis in the Torreele plant proved to be very efficient barriers for the elimination of both contaminant types, whereas aquifer passage followed by UV treatment and chlorination at Sabadell and the fractured and permeable aquifer at Nardò posed only partial barriers for bacterial contaminants.     

Microbial biomass in a shallow, urban aquifer contaminated with aromatic hydrocarbons: analysis by phospholipid fatty acid content and composition

The city of Perth contains a number of sites that have been contaminated with hydrocarbons due to leakage from petroleum underground storage tanks. Microbial biomass in groundwater and sediment cores from above and below the water table, and from within and outside a plume of hydrocarbon contamination, was examined using phospholipid fatty acid methyl ester analysis. Microbial numbers, calculated from the phospholipid content, ranged from 0·9 × 10⁶ to 7·8 × 10⁶' Escherichia coli equivalent cells' g⁻¹ dry wt of sediment. Over 96% of the microbial biomass was attached to the sediment and the proportion of attached cells did not decrease within the plume of contaminants. The amount of biomass within aquifer samples seemed to be related more to the proximity of the rhizosphere to the shallow aquifer, and other unknown urban inputs, rather than to the effects of the plume of contaminants. Fatty acids common to many bacterial groups dominated within the plume, and as such the analyses gave limited insight into microbial community structure. For site assessment of intrinsic remediation of shallow aquifers in urban areas, estimates of microbial biomass may not provide information that is readily applicable to plume management.     

Survey of human virus occurrence in wastewater-recharged groundwater on Long Island.

Treated wastewater effluents and groundwater observation wells from three sewage recharge installations located on Long Island were assayed on a monthly basis for indigenous human enteroviruses and coliform bacteria for a period of 1 year. Viruses were detected in groundwater at sites where recharge basins were located less than 35 feet (ca. 10.6 m) above the aquifer. Results from one of the sites indicated the horizontal transfer of viable viruses through the groundwater aquifer.     

Survey of human virus occurrence in wastewater-recharged groundwater on Long Island.

Treated wastewater effluents and groundwater observation wells from three sewage recharge installations located on Long Island were assayed on a monthly basis for indigenous human enteroviruses and coliform bacteria for a period of 1 year. Viruses were detected in groundwater at sites where recharge basins were located less than 35 feet (ca. 10.6 m) above the aquifer. Results from one of the sites indicated the horizontal transfer of viable viruses through the groundwater aquifer.     

Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contamination.     

Intrinsic potential for immediate biodegradation of toluene in a pristine,energy-limited aquifer

Pristine and energy-limited aquifers are considered to have a low resistance and resilience towards organic pollution. An experiment in an indoor aquifer system revealed an unexpected high intrinsic potential for the attenuation of a short-term toluene contamination. A 30 h pulse of 486 mg of toluene, used as a model contaminant, and deuterated water (D₂O) through an initially pristine, oxic, and organic carbon poor sandy aquifer revealed an immediate aerobic toluene degradation potential. Based on contaminant and tracer break-through curves, as well as mass balance analyses and reactive transport modelling, a contaminant removal of 40 % over a transport distance of only 4.2 m in less than one week of travel time was obtained. The mean first-order degradation rate constant was λ = 0.178 day^?1, corresponding to a half-life time constant T_1/2 of 3.87 days. Toluene-specific stable carbon isotope analysis independently proved that the contaminant mass removal can be attributed to microbial biodegradation. Since average doubling times of indigenous bacterial communities were in the range of months to years, the aerobic biodegradation potential observed is assumed to be present and active in the pristine, energy-limited groundwater ecosystems at any time. Follow-up experiments and field studies will help to quantify the immediate natural attenuation potential of aquifers for selected priority contaminants and will try to identify the key-degraders within the autochthonous microbial communities.     

Antibiotic-resistant Escherichia coli in karstic systems: a biological indicator of the origin of fecal contamination?

Occurrences of antibiotic-resistant Escherichia coli in two springs of a karstic system (NW France) providing drinking water were determined to study the role of aquifers in the dissemination of the resistance genes. Water samples were collected during wet and dry periods and after a heavy rainfall event to investigate E. coli density, antibiotic resistance patterns, and occurrences of class 1, 2, and 3 integrons. By observing patterns of the resistant isolates (i.e. number and type of resistances) and their occurrences, we were able to define two resistant subpopulations, introduced in the aquifer via surface water: (1) R1-2, characterized by one or two resistance(s), essentially to chloramphenicol and/or tetracycline (96.5%), was always found during the heavy rainfall event; (2) R3-10, characterized by three or more resistances, mostly resistant to tetracycline (94.1%) and beta-lactams (86%), was found transiently. Class 1 and 2 integrons were detected, mostly in the R3-10 subpopulation for class 1 integrons. The characteristics of these two subpopulations strongly suggest that the contamination originates from pasture runoff for the R1-2 subpopulation and from wastewater treatment plant effluents for the R3-10 subpopulation. These two subpopulations of E. coli could be used as biological indicators to determine the origin of groundwater contamination.     

Modeling of a Field Experiment on Bioremediation of Chlorobenzenes in Groundwater

The aquifer below an abandoned chemical plant in Hamburg, Germany, is heavily contaminated with chlorinated aromatic compounds, mainly chlorobenzenes. Preliminary evaluations made evident that pump-and-treat remediation of the site would be inefficient due to adsorption of the contaminants and the possible presence of dense nonaqueous phase liquid (DNAPL) in the aquifer. Other preliminary studies indicated that benzenes with a low degree of chlorination, which account for the bulk of the contamination in the aquifer, were aerobically degradable. Thus, in situ bioremediation using dissolved oxygen as an oxidant was proposed as an alternative to pump-and-treat remediation.

To assess the feasibility of bioremediation at this site, a pilot study was conducted on a 55 m x 30 m test plot that was equipped with two injection wells, six extraction wells, and 18 observation wells. Water saturated with oxygen using pure oxygen gas was injected for a period of 433 days.

Application of the three-dimensional reactive transport model, Transport, Biochemistry, and Chemistry (TBC), allowed the distinction between transport and reactive processes and the evaluation of oxygen consuming processes. Preliminary mass balance considerations had indicated that a significant portion of the injected oxygen was used for oxidation of inorganic compounds instead of the contaminants. The model calculations allowed quantification of these effects. Simulation results suggested that in situ bioremediation occurred at the site, but with an unacceptably low efficiency. Only 2% of the injected oxygen was used for contaminant degradation, while 63% was consumed by inorganic reductants, presumably mainly pyrite. Approximately 32% of the injected oxygen was extracted by the extraction wells and approximately 3% remained in the aquifer after the pilot study was completed.     

Maintenance and stability of introduced genotypes in groundwater aquifer material

Three indigenous groundwater bacterial strains and Pseudomonas putida harboring plasmids TOL (pWWO) and RK2 were introduced into experimentally contaminated groundwater aquifer microcosms. Maintenance of the introduced genotypes was measured over time by colony hybridization with gene probes of various specificity. On the basis of the results of colony hybridization quantitation of the introduced organisms and genes, all introduced genotypes were stably maintained at approximately 10(5) positive hybrid colonies g-1 of aquifer microcosm material throughout an 8-week incubation period. Concomitant removal of the environmental contaminants, viz., toluene, chlorobenzene, and styrene, in both natural (uninoculated) and inoculated aquifer microcosms was also demonstrated. The results indicate that introduced catabolic plasmids, as well as indigenous organisms, can be stably maintained in groundwater aquifer material without specific selective pressure for the introduced genotypes. These results have positive implications for in situ treatment and biodegradation in contaminated aerobic groundwater aquifers.     

Maintenance and stability of introduced genotypes in groundwater aquifer material.

Three indigenous groundwater bacterial strains and Pseudomonas putida harboring plasmids TOL (pWWO) and RK2 were introduced into experimentally contaminated groundwater aquifer microcosms. Maintenance of the introduced genotypes was measured over time by colony hybridization with gene probes of various specificity. On the basis of the results of colony hybridization quantitation of the introduced organisms and genes, all introduced genotypes were stably maintained at approximately 10(5) positive hybrid colonies g-1 of aquifer microcosm material throughout an 8-week incubation period. Concomitant removal of the environmental contaminants, viz., toluene, chlorobenzene, and styrene, in both natural (uninoculated) and inoculated aquifer microcosms was also demonstrated. The results indicate that introduced catabolic plasmids, as well as indigenous organisms, can be stably maintained in groundwater aquifer material without specific selective pressure for the introduced genotypes. These results have positive implications for in situ treatment and biodegradation in contaminated aerobic groundwater aquifers.     

Dynamics of an Oligotrophic Bacterial Aquifer Community during Contact with a Groundwater Plume Contaminated with Benzene, Toluene, Ethylbenzene, and Xylenes: an In Situ Mesocosm Study

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contamination.     

Spatial and temporal changes in microbial community structure associated with recharge-influenced chemical gradients in a contaminated aquifer

In a contaminated water-table aquifer, we related microbial community structure on aquifer sediments to gradients in 24 geochemical and contaminant variables at five depths, under three recharge conditions. Community amplified ribsosomal DNA restriction analysis (ARDRA) using universal 16S rDNA primers and denaturing gradient gel electrophoresis (DGGE) using bacterial 16S rDNA primers indicated: (i). communities in the anoxic, contaminated central zone were similar regardless of recharge; (ii). after recharge, communities at greatest depth were similar to those in uncontaminated zones; and (iii). after extended lack of recharge, communities at upper and lower aquifer margins differed from communities at the same depths on other dates. General aquifer geochemistry was as important as contaminant or terminal electron accepting process (TEAP) chemistry in discriminant analysis of community groups. The Shannon index of diversity (H) and the evenness index (E), based on DGGE operational taxonomic units (OTUs), were statistically different across community groups and aquifer depths. Archaea or sulphate-reducing bacteria 16S rRNA abundance was not clearly correlated with TEAP chemistry indicative of methanogenesis or sulphate reduction. Eukarya rRNA abundance varied by depth and date from 0 to 13% of the microbial community. This contaminated aquifer is a dynamic ecosystem, with complex interactions between physical, chemical and biotic components, which should be considered in the interpretation of aquifer geochemistry and in the development of conceptual or predictive models for natural attenuation or remediation.     

The water relations of two evergreen tree species in a karst savanna

The ecohydrology of karst has not received much attention, despite the disproportionally large contribution of karst aquifers to freshwater supplies. Karst savannas, like many savannas elsewhere, are encroached by woody plants, with possibly negative consequences on aquifer recharge. However, the role of savanna tree species in hydrological processes remains unclear, not least because the location and water absorption zones of tree roots in the spatially complex subsurface strata are unknown. This study examined the water sources and water relations of two savanna trees, Quercus fusiformis (Small) and Juniperus ashei (Buchholz) in the karst region of the eastern Edwards Plateau, Texas (USA). Stable isotope analysis of stem water revealed that both species took up evaporatively enriched water during the warm season, suggesting a relatively shallow water source in the epikarst, the transition zone between soil and bedrock. Q. fusiformis had consistently higher predawn water potentials than J. ashei during drought, and thus was probably deeper-rooted and less capable of maintaining gas exchange at low water potentials. Although the water potential of both species recovered after drought-breaking spring and summer rain events, associated shifts in stem water isotope ratios did not indicate significant uptake of rainwater from the shallow soil. A hypothesis is developed to explain this phenomenon invoking a piston-flow mechanism that pushes water stored in macropores into the active root zones of the trees. Epikarst structure varied greatly with parent material and topography, and had strong effects on seasonal fluctuations in plant water status. The study suggests that tree species of the Edwards Plateau do not commonly reduce aquifer recharge by tapping directly into perched water tables, but more likely by reducing water storage in the epikarst. A more general conclusion is that models of savanna water relations based on Walter's two-layer model may not apply unequivocally to karst savannas.     

Influence of precipitation and soil on transport of fecal enterococci in fractured limestone aquifers

Limestone aquifers provide the main drinking water resources of southern Italy. The groundwater is often contaminated by fecal bacteria because of the interaction between rocks having high permeability and microbial pollutants introduced into the environment by grazing and/or manure spreading. The microbial contamination of springwater in picnic areas located in high mountains can cause gastrointestinal illness. This study was carried out in order to analyze the interaction between Enterococcus faecalis and the soil of a limestone aquifer and to verify the influence of this interaction on the time dependence of groundwater contamination. E. faecalis was chosen because, in the study area involved, it represents a better indicator than Escherichia coli. The research was carried out through field (springwater monitoring) and laboratory experiments (column tests with intact soil blocks). The transport of bacterial cells through soil samples was analyzed by simulating an infiltration event that was monitored in the study area. Comparison of laboratory results with data acquired in the field showed that discontinuous precipitation caused an intermittent migration of microorganisms through the soil and produced, together with dispersion in the fractured medium (unsaturated and saturated zones), an articulated breakthrough at the spring. The short distances of bacterial transport in the study area produced a significant daily variability of bacterial contamination at the field scale.     

Distribution of Methanotrophs in Trichloroethylene-Contaminated Aquifers in a Natural Gas Field

The distribution of methanotrophs was examined in shallow aquifers contaminated with trichloroethylene in the southern Kanto gas field, Chiba, Japan. The total populations of methanotrophs and the numbers of methanotrophs producing soluble methane monooxygenase (sMMO) were determined separately. Hydrostratigraphic units of a Pleistocene to Holocene stratum consisted of three aquifers separated by nontransmissive silt layers. Dissolved methane concentrations increased with depth and were highest in the third aquifer. The number of methanotrophs was higher in the second aquifer than in the first aquifer. A clear relationship was observed between microbial populations and lithofacies. The greatest abundance of methanotrophs was observed in the coarse sand layers of the second aquifer, with the lowest abundance observed in silt layers. The high abundance of methanotrophs in the coarse sand in the second aquifer implied that this part of the stratum plays an important role in in situ bioremediation.     

Relationship between aquifer biofilms and unattached microbial indicators of urban groundwater contamination

Aquifers, springs and other groundwater‐dependent ecosystems are threatened by urban land use, which causes water quality deterioration through nutrient loading, sewage infiltration, groundwater extraction and, along coasts, seawater intrusion. The presence of certain microbes in groundwater can indicate that an aquifer is anthropogenically contaminated. Interpretations made from observations of indicator microbes in groundwater are limited because the relationship between the presumably allochthonous indicator microbes and relevant autochthonous microbial communities has not been characterized. This study addressed whether autochthonous aquifer biofilms can influence the presence of presumed microbial indicators in groundwater, and simultaneously used microbial indicators to trace sources of urban contamination at a karst spring of conservation concern. These questions were approached using a 17‐month time series analysis of attached biofilm and adjacent unattached bacteria in the submerged karst aquifer conduit associated with this spring. Environmental 16S rRNA gene sequencing was performed to characterize these communities, and community structure data were contextualized with groundwater geochemical and hydrogeological measurements. Linear regression models were developed to explain the relative abundance patterns of indicator microbes and other unattached microbes at this site. The results of this study suggest that dominant aquifer biofilms do not influence the presence of unattached microbial taxa that are presumed to be indicators of groundwater contamination, and generated new information about the origin of coliform bacteria at the study site. These results build confidence in the use of microbial indicators in groundwater‐dependent ecosystem conservation strategies and inform future management plans for urban aquifers and springs worldwide.     

Modeling the Impact of Oxygen Reaeration on Natural Attenuation

Based on studies of leaking petroleum storage tank (LPST) sites in Texas and California, the average plume of benzene, toluene, ethylene, and xylenes (BTEX) is between 61 and 132 m (200 and 400 ft) long. Standard modeling of BTEX plumes produces plumes well in excess of observed plume lengths. The amount of oxygen carried into the plume zone with clean upgradient water often is insufficient to account for the levels of biodegradation observed in these studies. Traditional recharge of oxygen-containing water into an aquifer adds insufficient oxygen to the system and cannot account for the observed plume lengths. Research has shown that anaerobic processes can contribute to biodegradation in certain cases; however, anaerobic pathways are not included in this work. Reaeration of oxygen-depleted aquifers by diffusive transport of oxygen through the vadose zone has generally been neglected as a way to introduce oxygen into surficial aquifers. The observed plume lengths and preliminary laboratory results indicate that this source of oxygen should be accounted for in any natural attenuation model of BTEX contamination. This approach to modeling reaeration has been incorporated into the finite-element groundwater flow and contaminant transport code, FLOTRAN. Adding diffusion-driven reaeration to the modeling process produces BTEX plumes consistent with observed plume lengths.     

Influence of Precipitation and Soil on Transport of Fecal Enterococci in Fractured Limestone Aquifers

Limestone aquifers provide the main drinking water resources of southern Italy. The groundwater is often contaminated by fecal bacteria because of the interaction between rocks having high permeability and microbial pollutants introduced into the environment by grazing and/or manure spreading. The microbial contamination of springwater in picnic areas located in high mountains can cause gastrointestinal illness. This study was carried out in order to analyze the interaction between Enterococcus faecalis and the soil of a limestone aquifer and to verify the influence of this interaction on the time dependence of groundwater contamination. E. faecalis was chosen because, in the study area involved, it represents a better indicator than Escherichia coli. The research was carried out through field (springwater monitoring) and laboratory experiments (column tests with intact soil blocks). The transport of bacterial cells through soil samples was analyzed by simulating an infiltration event that was monitored in the study area. Comparison of laboratory results with data acquired in the field showed that discontinuous precipitation caused an intermittent migration of microorganisms through the soil and produced, together with dispersion in the fractured medium (unsaturated and saturated zones), an articulated breakthrough at the spring. The short distances of bacterial transport in the study area produced a significant daily variability of bacterial contamination at the field scale.     

Intrinsic bioremediation in a solvent-contaminated alluvial groundwater

An industrial site contaminated with a mixture of volatile organic compounds in its subsurface differed from previously reported locations in that the contamination consisted of a mixture of chlorinated, brominated, and non-halogenated aromatic and aliphatic solvents in an alluvial aquifer. The source area was adjacent to a river. Of the contaminants present in the aquifer, benzene, toluene, and chlorobenzene (BTC) were of primary concern. Studies of the physical, chemical, and microbiological characteristics of site groundwater were conducted. The studies concentrated on BTC, but also addressed the fate of the other aquifer VOCs. Gas chromatographic analyses performed on laboratory microcosms demonstrated that subsurface microorganisms were capable of BTC degradation. Mineralization of BTC was demonstrated by the release of ¹⁴CO₂ from radiolabelled BTC. In the field, distribution patterns of nutrients and electron acceptors were consistent with expression of in situ microbial metabolic activity: methane, conductivity, salinity and o-phosphate concentrations were all positively correlated with contaminant concentration; while oxidation-reduction potential, nitrate, dissolved oxygen and sulfate concentrations were negatively correlated. Total aerobes, aerotolerant anaerobes, BTC-specific degraders, and acridine orange direct microscopic microorganism counts were strongly and positively correlated with field contaminant concentrations. The relative concentrations of benzene and toluene were lower away from the core of the plume compared to the less readily metabolized compound, chlorobenzene. Hydrodynamic modeling of electron-acceptor depletion conservatively estimated that 450 kg of contaminant have been removed from the subsurface yearly. Models lacking a biodegradation term predicted that 360 kg of contaminant would reach the river annually, which would result in measurable contaminant concentrations. River surveillance, however, has only rarely detected these compounds in the sediment and then only at trace concentrations. Thus, the combination of field modeling, laboratory studies, and site surveillance data confirm that significant in situ biodegradation of the contaminants has occurred. These studies establish the presence of intrinsic bioremediation of groundwater contaminants in this unusual industrial site subsurface habitat. Received 01 December 1995/ Accepted in revised form 27 July 1996