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Zopfi, Jakob

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Zopfi, Jakob
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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
    Discovery of anammox bacteria in terrestrial ecosystems
    (2011)
    Humbert, Sylvia
    ;
    Aragno, Michel 
    ;
    Zopfi, Jakob 
    Avant cette étude, le processus anammox (oxydation anaérobie de l’ammonium) était uniquement étudié dans les usines de traitement des eaux usées et dans les milieux aquatiques, sédiments inclus. Cependant, rien n'était connu encore sur la distribution, la diversité, l'abondance et l'activité des bactéries anammox dans les écosystèmes terrestres. Dans cette étude, nous apportons l’évidence, par approche moléculaire, de la présence de bactéries anammox dans les sols de zones humides, les sédiments des marais, le profil de sol d’un Reductisol, des sols de rives de lacs, un sol sur Permafrost et un aquifère poreux. L'analyse phylogénétique des séquences du gène ARNr 16S a démontrée que les bactéries anammox présentes dans les écosystèmes terrestres sont affiliées à Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’, ‘Jettenia’ and ‘Anammoxoglobus’ ainsi qu’à deux groupes non identifiés. Ces candidats anammox étaient largement distribués dans les différents environnements terrestres indiquant une plus grande diversité que dans les colonnes d’eau des milieux marins. Les bactéries anammox n'étaient pas présentes dans tous les milieux et fractions de sol échantillonnés, l’analyse démontrant leur distribution hétérogène et leurs besoins écologiques spécifiques comme la présence d’interfaces oxique / anoxique à long terme et de composés azotés inorganiques. Nous avons quantifié les bactéries anammox dans ces différents environnements en développant une nouvelle approche qPCR spécifique anammox, et leur abondance variait de 104 à 106 copies / g de sol. Finalement, le Réductisol a été sélectionné pour réaliser une analyse détaillée de l’activité anammox le long du profil de sol par des expériences d'incubation à l’isotope 15N. Pour chaque date d'échantillonnage, une production de 29N2 était observée à toutes les profondeurs du Réductisol, démontrant la présence de bactéries anammox actives. La contribution d‘anammox à la production totale de N2 était inférieure à 14%. Cette étude fournit la première preuve que les bactéries anammox sont présentes, diverses et actives dans les écosystèmes terrestres., Until this study, the anammox (anaerobic ammonium oxidation) process has been only studied in waste water treatment plants and aquatic environments, including sediments. However, nothing is known so far about the distribution, diversity, abundance and activity of anammox bacteria in terrestrial ecosystems. In this study, we provided molecular evidence for the presence of anammox bacteria in wetlands, sediments of marshes, a Reductisol profile, lake shores, a permafrost soil and a porous aquifer. Phylogenetic analysis of the 16S rRNA gene sequences showed that anammox bacteria from terrestrial ecosystems are affiliated to Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’, ‘Jettenia’ and ‘Anammoxoglobus’, as well as two unidentified clusters. They were widely distributed in the different terrestrial environments indicating a higher diversity than in marine water column environments. Anammox bacteria were not present in every sampled environments and soil fractions demonstrating their heterogeneous distribution and their specific ecological requirements as the presence of long term oxic/anoxic interfaces and inorganic nitrogen compounds. We quantified Anammox bacteria using a new developed qPCR approach applied to the different soil environments and their abundance ranged from 104 to 106 copies/g of soil. Finally, the Reductisol has been selected for a detailed analysis of their activity along the soil profile by 15N-isotope incubation experiments. For each sampling date, production of 29N2 was observed at all depths in the soil profile demonstrating the presence of active anammox bacteria. The amount of N2 produced by anammox is less than 14% of the total N2 production. This study provides the first evidence that anammox bacteria are present, diverse and active in terrestrial ecosystems.
  • 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
    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
    Origin and spatial–temporal distribution of faecal bacteria in a bay of Lake Geneva, Switzerland
    (2009)
    Poté, John
    ;
    Goldscheider, Nicola
    ;
    Haller, Laurence
    ;
    Zopfi, Jakob 
    ;
    Khajehnouri, Fereidoun
    ;
    Wildi, Walter
    The origin and distribution of microbial contamination in Lake Geneva’s most polluted bay were assessed using faecal indicator bacteria (FIB). The lake is used as drinking water, for recreation and fishing. During 1 year, water samples were taken at 23 points in the bay and three contamination sources: a wastewater treatment plant (WWTP), a river and a storm water outlet. Analyses included Escherichia coli, enterococci (ENT), total coliforms (TC), and heterotrophic plate counts (HPC). E. coli input flux rates from the WWTP can reach 2.5 × 1010 CFU/s; those from the river are one to three orders of magnitude lower. Different pathogenic Salmonella serotypes were identified in water from these sources. FIB levels in the bay are highly variable. Results demonstrate that (1) the WWTP outlet at 30 m depth impacts near-surface water quality during holomixis in winter; (2) when the lake is stratified, the effluent water is generally trapped below the thermocline; (3) during major floods, upwelling across the thermocline may occur; (4) the river permanently contributes to contamination, mainly near the river mouth and during floods, when the storm water outlet contributes additionally; (5) the lowest FIB levels in the near-surface water occur during low-flow periods in the bathing season.
  • 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
    Characterizing Water Circulation and Contaminant Transport in Lake Geneva Using Bacteriophage Tracer Experiments and Limnological Methods
    (2007)
    Goldscheider, Nicola
    ;
    Haller, Laurence
    ;
    Poté, John
    ;
    Wildi, Walter
    ;
    Zopfi, Jakob 
    Multi-tracer tests with three types of marine bacteriophages (H4/4, H6/1, and H40/1), together with various limnological methods, including physicochemical depth profiling, surface drifters, deep current measurements, and fecal indicator bacteria analyses, have been applied to characterize water circulation and pathogen transport in the Bay of Vidy (Lake Geneva, Switzerland). The experimental program was carried out twice, first in November 2005, when the lake was stratified, and a second time during holomixis in February 2006. The bacteriophages were injected at three points at different depths, where contaminated waters enter the lake, including the outlet pipe of a wastewater treatment plant, a river, and a stormwater outlet. Thereafter, water samples were collected in the lake at 2 m depth during a 48 h sampling campaign. The results demonstrate that (i) contaminated river water spreads rapidly in the bay; (ii) a well-developed thermocline is highly effective in preventing contamination from the depth to rise up to the surface; (iii) rapid vertical mixing and pathogen transport occur under thermally homogeneous conditions; and (iv) repeated multi-tracer tests with bacteriophages are a powerful technique to assess water circulation and contaminant transport in lakes where high dilution occurs.
  • 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.