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Zopfi, Jakob

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Zopfi, Jakob
Affiliation principale
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https://libra.unine.ch/handle/123456789/377

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  • Publication
    Accès libre
    Intrinsic biodegradation potential of aromatic hydrocarbons in an alluvial aquifer - Potentials and limits of signature metabolite analysis and two stable isotope-based techniques
    (2011)
    Morasch, Barbara
    ;
    Hunkeler, Daniel 
    ;
    Zopfi, Jakob 
    ;
    Temime, B
    ;
    Höhener, Patrick
    Three independent techniques were used to assess the biodegradation of monoaromatic hydrocarbons and low-molecular weight polyaromatic hydrocarbons in the alluvial aquifer at the site of a former cokery (Flémalle, Belgium).
    Firstly, a stable carbon isotope-based field method allowed quantifying biodegradation of monoaromatic compounds in situ and confirmed the degradation of naphthalene. No evidence could be deduced from stable isotope shifts for the intrinsic biodegradation of larger molecules such as methylnaphthalenes or acenaphthene. Secondly, using signature metabolite analysis, various intermediates of the anaerobic degradation of (poly-) aromatic and heterocyclic compounds were identified. The discovery of a novel metabolite of acenaphthene in groundwater samples permitted deeper insights into the anaerobic biodegradation of almost persistent environmental contaminants. A third method, microcosm incubations with 13C-labeled compounds under in situ-like conditions, complemented techniques one and two by providing quantitative information on contaminant biodegradation independent of molecule size and sorption properties. Thanks to stable isotope labels, the sensitivity of this method was much higher compared to classical microcosm studies. The 13C-microcosm approach allowed the determination of first-order rate constants for 13C-labeled benzene, naphthalene, or acenaphthene even in cases when degradation activities were only small. The plausibility of the third method was checked by comparing 13C-microcosm-derived rates to field-derived rates of the first approach. Further advantage of the use of 13C-labels in microcosms is that novel metabolites can be linked more easily to specific mother compounds even in complex systems. This was achieved using alluvial sediments where 13C-acenaphthyl methylsuccinate was identified as transformation product of the anaerobic degradation of acenaphthene.
  • Publication
    Accès libre
    Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods
    (2009)
    Abe, Yumiko
    ;
    Aravena, Ramon
    ;
    Zopfi, Jakob 
    ;
    Parker, Beth
    ;
    Hunkeler, Daniel 
    The occurrence of chlorinated ethene transformation in a streambed was investigated using concentration and carbon isotope data from water samples taken at different locations and depths within a 15×25 ms tudy area across which a tetrachloroethene (PCE) plume discharges. Furthermore, it was evaluated how the degree of transformation is related to groundwater discharge rates, redox conditions, solid organic matter content (SOM) and microbial factors. Groundwater discharge rates were quantified based on streambed temperatures, and redox conditions using concentrations of dissolved redox-sensitive species. The degree of chlorinated ethene transformation was highly variable in space from no transformation to transformation beyond ethene. Complete reductive dechlorination to ethane and ethene occurred at locations with at least sulfate-reducing conditions and with a residence time in the samples streambed zone (80 cm depth) of at least 10 days. Among these locations, Dehalococcoides was detected using a PCR method where SOM contents were >2% w/w and where transformation proceeded beyond ethene. However, it was not detected at locations with low SOM, which may cause an insufficient H2 supply to sustain a detectably dense Dehalococcoides population. Additionally, it is possible that other organisms are responsible for the biodegradation. A microcosm study with streambed sediments demonstrated the potential of VC oxidation throughout the site even at locations without a pre-exposure to VC, consistent with the detection of the epoxyalkane:coenzyme M transferase (EaCoMT) gene involved in the degradation of chlorinated ethenes via epoxidation. In contrast, no aerobic transformation of cDCE in microcosms over a period of 1.5 years was observed. In summary, the study demonstrated that carbon isotope analysis is a sensitive tool to identify the degree of chlorinated ethene transformation even in hydrologically and geochemically complex streambed systems. In addition, it was observed that the degree of transformation is related to redox conditions, which in turn depend on groundwater discharge rates.
  • Publication
    Métadonnées seulement
    Percolation and Particle Transport in the Unsaturated Zone of a Karst Aquifer
    (2009)
    Pronk, Michiel 
    ;
    Goldscheider, Nico
    ;
    Zopfi, Jakob 
    ;
    Zwahlen, François 
    Recharge and contamination of karst aquifers often occur via the unsaturated zone, but the functioning of this zone has not yet been fully understood. Therefore, irrigation and tracer experiments, along with monitoring of rainfall events, were used to examine water percolation and the transport of solutes, particles, and fecal bacteria between the land surface and a water outlet into a shallow cave. Monitored parameters included discharge, electrical conductivity, temperature, organic carbon, turbidity, particle-size distribution (PSD), fecal indicator bacteria, chloride, bromide, and uranine. Percolation following rainfall or irrigation can be subdivided into a lag phase (no response at the outlet), a piston-flow phase (release of epikarst storage water by pressure transfer), and a mixed-flow phase (increasing contribution of freshly infiltrated water), starting between 20 min and a few hours after the start of recharge event. Concerning particle and bacteria transport, results demonstrate that (1) a first turbidity signal occurs during increasing discharge due to remobilization of particles from fractures (pulse-through turbidity); (2) a second turbidity signal is caused by direct particle transfer from the soil (flow-through turbidity), often accompanied by high levels of fecal indicator bacteria, up to 17,000 Escherichia coli/100 mL; and (3) PSD allows differentiation between the two types of turbidity. A relative increase of fine particles (0.9 to 1.5 mu m) coincides with microbial contamination. These findings help quantify water storage and percolation in the epikarst and better understand contaminant transport and attenuation. The use of PSD as "early-warning parameter" for microbial contamination in karst water is confirmed.
  • Publication
    Accès libre
    Carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride and cis-1,2-dichloroethene
    (2009)
    Abe, Yumiko
    ;
    Aravena, Ramon
    ;
    Zopfi, Jakob 
    ;
    Shouakar-Stash, O
    ;
    Cox, E
    ;
    Roberts, J.D
    ;
    Hunkeler, Daniel 
    The study investigated carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE). The experimental data followed a Rayleigh trend. For aerobic oxidation, the average carbon isotope enrichment factors were -7.2‰ and-8.5‰ for VC and cDCE, respectively, while average chlorine isotope enrichment factors were only -0.3‰ for both compounds. These values are consistent with an initial transformation by epoxidation for which a significant primary carbon isotope effect and only a small secondary chlorine isotope effect is expected. For reductive dechlorination, larger carbon isotope enrichment factors of -25.2‰ for VC and -18.5‰ for cDCE were observed consistent with previous studies. Although the average chlorine isotope enrichment factors were larger than those of aerobic oxidation (-1.8‰ for VC, -1.5‰ for cDCE), they were not as large as typically expected for a primary chlorine isotope effect suggesting that no cleavage of C-Cl bonds takes place during the initial ratelimiting step. The ratio of isotope enrichment factors for chlorine and carbon were substantially different for the two reaction mechanisms suggesting that the reaction mechanisms can be differentiated at the field scale using a dual isotope approach.
  • Publication
    Accès libre
    Microbial communities in karst groundwater and their potential use for biomonitoring
    (2009)
    Pronk, Michiel 
    ;
    Goldscheider, Nicola
    ;
    Zopfi, Jakob 
    The structure, diversity and dynamics of microbial communities from a swallow hole draining agricultural land and two connected karst springs (Switzerland) were studied using molecular microbiological methods and related to hydrological and physicochemical parameters. Storm responses and an annual hydrological cycle were monitored to determine the short- and long-term variability, respectively, of bacterial communities. Statistical analysis of bacterial genetic fingerprints (16S rDNA PCR-DGGE) of spring water samples revealed several clusters that corresponded well with different levels of the allochthonous swallow hole contribution. Microbial communities in spring water samples highly affected by the swallow hole showed low similarities among them, reflecting the high temporal variability of the bacterial communities infiltrating at the swallow hole. Conversely, high similarities among samples with low allochthonous contribution provided evidence for a stable autochthonous endokarst microbial community. Three spring samples, representative for low, medium and high swallow hole contribution, were analysed by cloning/sequencing in order to identify the major bacterial groups in the communities. The autochthonous endokarst microbial community was mainly characterized of δ-Proteobacteria, Acidobacteria and Nitrospira species. A high percentage of unknown sequences suggested further that many karst aquifer bacteria are still undiscovered. Finally, the potential use of groundwater biomonitoring using microbial communities is discussed.
  • Publication
    Accès libre
    Percolation and Particle Transport in the Unsaturated Zone of a Karst Aquifer
    (2008)
    Pronk, Michiel 
    ;
    Goldscheider, Nicola
    ;
    Zopfi, Jakob 
    ;
    Zwahlen, François 
    Recharge and contamination of karst aquifers often occur via the unsaturated zone, but the functioning of this zone has not yet been fully understood. Therefore, irrigation and tracer experiments, along with monitoring of rainfall events, were used to examine water percolation and the transport of solutes, particles, and fecal bacteria between the land surface and a water outlet into a shallow cave. Monitored parameters included discharge, electrical conductivity, temperature, organic carbon, turbidity, particle-size distribution (PSD), fecal indicator bacteria, chloride, bromide, and uranine. Percolation following rainfall or irrigation can be subdivided into a lag phase (no response at the outlet), a piston-flow phase (release of epikarst storage water by pressure transfer), and a mixed-flow phase (increasing contribution of freshly infiltrated water), starting between 20 min and a few hours after the start of recharge event. Concerning particle and bacteria transport, results demonstrate that (1) a first turbidity signal occurs during increasing discharge due to remobilization of particles from fractures (pulse-through turbidity); (2) a second turbidity signal is caused by direct particle transfer from the soil (flow-through turbidity), often accompanied by high levels of fecal indicator bacteria, up to 17,000 Escherichia coli/100 mL; and (3) PSD allows differentiation between the two types of turbidity. A relative increase of fine particles (0.9 to 1.5 μm) coincides with microbial contamination. These findings help quantify water storage and percolation in the epikarst and better understand contaminant transport and attenuation. The use of PSD as "early-warning parameter" for microbial contamination in karst water is confirmed.
  • Publication
    Accès libre
    Particle-Size Distribution As Indicator for Fecal Bacteria Contamination of Drinking Water from Karst Springs
    (2007)
    Pronk, Michiel 
    ;
    Goldscheider, Nico
    ;
    Zopfi, Jakob 
    Continuous monitoring of particle-size distribution (PSD), total organic carbon (TOC), turbidity, discharge and physicochemical parameters, together with analyses of fecal indicator bacteria, particularly Escherichia coli, made it possible to better understand the processes governing pathogen transport in karst groundwater and to establish PSD as indicator for possible microbial contamination of drinking water from karst springs. In the study area near Yverdon-les-Bains, Switzerland, tracer tests proved connection between a sinking stream draining agricultural land and several springs, 4.8–6.3 km away. Tracing and monitoring results demonstrate that (i) suspended particles (turbidity) in the spring water either originate from remobilization of sediments inside the aquifer (autochthonous) or from the sinking stream and land surface (allochthonous); (ii) allochthonous turbidity coincides with increased E. coli and TOC levels; (iii) PSD makes it possible to distinguish the two types of turbidity; (iv) a relative increase of finer particles (0.9–10 µm) indicates allochthonous turbidity and thus possible fecal contamination. The method permits to optimize water treatment and identify periods when the spring water must be rejected. Findings from other test sites confirm the feasibility of this approach.
  • Publication
    Accès libre
    Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system
    (2006)
    Pronk, Michiel 
    ;
    Goldscheider, Nicola
    ;
    Zopfi, Jakob 
    La dynamique du carbone organique, de la turbidité, des bactéries indicatrices de contamination fécale et d’autres paramètres physico-chimiques a été étudiée dans un système karstique proche de la ville d’Yverdon-les-Bains, Suisse. Des mesures en continu ainsi que des échantillonnages ont été effectués à une perte drainant une zone agricole (input), et à deux groupes sourciers (output) qui montrent fréquemment une contamination bactérienne. En période d’étiage, un essai de traçage à l’uranine a été réalisé depuis la perte. Le traceur est apparu aux sources 10–12 jours après l’injection; la masse de restitution totale a été de 29%. Des essais précédents, réalisés en hautes eaux, ont montré des temps de transit plus court. Suite à un événement pluvieux important, un pic de turbidité primaire, synchrone avec l’augmentation du débit, est observé aux sources, indiquant une re-mobilisation des sédiments autochtones de l’aquifère. Un pic de turbidité secondaire apparaît quelques jours plus tard aux sources, suggérant l’arrivée de matériel allochtone de la perte. Cette dernière est accompagnée de pics plus larges de carbone organique et des bactéries indicatrices de contamination fécale. La microbiologie moléculaire (PCR-DGGE) a permis la caractérisation des communautés bactériennes de la perte et des sources. Ces résultats démontrent l’importante influence de la perte sur la qualité de l’eau souterraine, alors que sa contribution au débit du système est négligeable. Le carbone organique semble être un meilleur indicateur de la présence de contamination bactérienne que la turbidité., The dynamics of organic carbon (OC), turbidity, faecal indicator bacteria and physicochemical parameters was studied in a karst system near Yverdon, Switzerland. Online measurements and sampling were done at a swallow hole draining an agricultural surface (the input), and two groups of springs (the outputs) that often show bacterial contamination. A fluorescent tracer that was injected into the swallow hole during low-flow conditions first arrived at the springs 10–12 days after injection; the total recovery rate was 29%. Previous tracer tests during high-flow conditions gave shorter travel times. After a major rainfall event, a primary turbidity peak was observed at the springs. It coincides with the rising limb of the hydrograph, indicating remobilisation of autochthonous particles from the aquifer. A secondary turbidity peak occurs several days later, suggesting the arrival of allochthonous particles from the swallow hole. Wider peaks of OC and bacteria were observed simultaneously. Applying methods from molecular microbiology (PCR-DGGE) allowed characterisation of the bacterial communities at the swallow hole and the springs. The results demonstrate that the swallow hole is an important source of groundwater contamination, while its contribution to aquifer recharge is insignificant. OC appears to be a better indicator for bacterial contamination than turbidity., Se ha estudiado la dinámica del carbono orgánico, turbiedad, una bacteria indicadora de fecales, y parámetros fisicoquímicos en un sistema kárstico cerca de Yverdon, Suiza. Se realizaron mediciones en línea y muestreo en un sumidero que drena una superficie agrícola (la entrada), y dos grupos de manantiales (las salidas) que frecuentemente muestran contaminación bacterial. Un trazador fluorescente que se inyectó en el sumidero durante condiciones de flujo bajo arribó en los manantiales por vez primera 10–12 días después de que fue inyectado; el ritmo total de recuperación fue de 29%. Las pruebas de trazadores realizadas con anterioridad bajo condiciones de flujo alto aportaron tiempos de viaje más cortos. Después de una tormenta fuerte se observó un pico de turbiedad primario en los manantiales. El pico coincide con el limbo ascendente del hidrograma indicando remobilización de partículas alóctonas provenientes del acuífero. Un pico de turbiedad secundario ocurre varios días más tarde sugiriendo el arribo de partículas alóctonas provenientes del sumidero. Se observaron simultáneamente picos más amplios de carbono orgánico y bacteria. La aplicación de métodos de microbiología molecular (PCR-DGGE) permitieron caracterizar las comunidades de bacteria en el sumidero y los manantiales. Los resultados demuestran que el sumidero es una fuente importante de contaminación de aguas subterráneas mientras que su contribución a la recarga del acuífero es insignificante. El carbono orgánico parece ser un mejor indicador de contaminación bacterial que la turbiedad.
  • Publication
    Accès libre
    Effect of molecule size on carbon isotope fractionation during biodegradation of chlorinated alkanes by Xanthobacter autotrophicus GJ10
    Yumiko, Abe
    ;
    Zopfi, Jakob 
    ;
    Hunkeler, Daniel 
    The effect of the number of carbon and chlorine atoms on carbon isotope fractionation during dechlorination of chlorinated alkanes by Xanthobacter autotrophicus GJ10 was studied using pure culture and cell-free extract experiments. The magnitude of carbon isotope fractionation decreased with increasing carbon number. The decrease can be explained by an increasing probability that the heavy isotope is located at a non-reacting position for increasing molecule size. The isotope data were corrected for the number of carbons as well as the number of reactive sites to obtain reacting-site-specific values denoted as apparent kinetic isotope effect (AKIE). Even after the correction, the obtained AKIE values varied (on average 1.0608, 1.0477, 1.0616, and 1.0555 for 1,2-dichloroethane, chloropentane, 1,3-dichloropentane and chlorobutane, respectively). Cell-free extract experiments were carried out to evaluate the effect of transport across the cell membrane on the observed variability in the AKIE values, which revealed that variability still persisted. The study demonstrates that even after differences related to the carbon number and structure of the molecule are taken into account, there still remain differences in AKIE values even for compounds that are degraded by the same pure culture and an identical reaction mechanism.
  • Publication
    Accès libre
    Fungi, bacteria and soil pH: the oxalate–carbonate pathway as a model for metabolic interaction
    Martin, Gaëtan
    ;
    Guggiari, Matteo
    ;
    Bravo, Daniel 
    ;
    Zopfi, Jakob 
    ;
    Cailleau, Guillaume 
    ;
    Aragno, Michel 
    ;
    Job, Daniel 
    ;
    Verrecchia, Eric 
    ;
    Junier, Pilar 
    The oxalate–carbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.