Pierre Rossi | EPFL - Academia.edu (original) (raw)
Papers by Pierre Rossi
Hydrogeology Journal, 2006
The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in ... more The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in a review, which also discusses their relevance for questions of groundwater protection. Aquifers are heterogeneous on all scales and structured in a variety of habitats. The void spaces in many aquifers are small. The biocenoses are thus predominantly composed of microorganisms and, often, microinvertebrates. Larger voids and macroorganisms occur in karst cavities. Due to the absence of light, the biocenoses depend on chemical energy resources, which are, however, scarce in non-contaminated groundwater. The microorganisms thus show small cell sizes, low population densities and reduced activity; they developed specific strategies to survive oligotrophic conditions. The review also discusses the impact of contamination on the biocenoses, and the potential use of the biocenoses or specific organisms as indicators for groundwater quality, and the limits of this approach. Bacteria are either planktonic or attached to aquifer material, which requires both fluid and solid phase sampling. Most groundwater bacteria are viable but non-culturable. Consequently, cultivation techniques give an incomplete picture of the biocenoses, while methods from molecular microbiology provide genetic fingerprints of the entire community. Different analytical methods are available to count microorganisms, identify species, characterise microbial diversity, and measure activity.
La ville d'Aix-en-Provence se trouve dans une cuvette remplie de dépôts sédimentaires miocène... more La ville d'Aix-en-Provence se trouve dans une cuvette remplie de dépôts sédimentaires miocènes, située à l'ouest du massif calcaire de la Sainte-Victoire. Des eaux thermales de 26 à 35° C, à faciès bicarbonaté calcique et magnésien, émergent en différents endroits du centre-ville sous la forme de sources anciennes et de forages récents avec un débit total estimé à 25 m 3 /h. Actuellement, elles sont exploitées sur le site historique des Thermes de Sextius par pompage dans le forage F4 (35° C) à une profondeur de 70-79 m. La zone productive se situe dans des calcaires fracturés du Crétacé supérieur. Suite à une contamination bactériologique par des Légionelles et des Pseudomonas et à une baisse de productivité de l'un des forages (F3), une étude globale sur la ressource hydrothermale d'Aix-en-Provence a été entreprise. L'étude se donnait pour double objectif de parvenir, d'une part à une connaissance générale du circuit hydrothermal régional et des interaction...
... tL: Time till the first arrival of the ... Photo-decomposition, biodegradation by micro-organ... more ... tL: Time till the first arrival of the ... Photo-decomposition, biodegradation by micro-organisms (release of bromine atoms by eosin for example) and chemical reactions with other substances present in the aquifer (the chloration of waters as well) are all susceptible of resulting in ...
Science of The Total Environment
Mine tailings are a serious threat to the environment and public health. Remediation of these res... more Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur-and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / s c i t o t e n v remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands.
With the goal of a better understanding of the fate of methane in the deep layers of peat bogs, w... more With the goal of a better understanding of the fate of methane in the deep layers of peat bogs, we analysed the microbial 16S rDNA gene pool and measured the stable carbon isotope composition of bulk peat of a deep (6 m) peat bog profile (Etang de la Gruyère, Switzerland). Both Bacterial and Archaean communities were assessed using respectively TTGE (Temporal Temperature Gradient Electrophoresis) and SSCP (Single Strand Conformation Polymorphism), with fragments of the V1-V3 region of the 16S rDNA gene. The "relative diversity" shown in the TTGE AND SSCP gel patterns is presented using indices and band numbers per sample (Simpson evenness). PCA was calculated on the basis of the intensities of all bands found in the TTGE and SSCP fingerprinting profiles. These DNA fingerprinting patterns reveal the presence of a structured microbial community throughout the whole depth profile. Clear differences can be observed between the communities found in the near surface layers and those found at depth. Surprisingly, for both Archaean and Bacterial communities, the deepest samples display a high similarity level with those found in the first 20 centimeters. The delta 13 C values of the peat are relatively constant from the surface of the bog down to a depth of 5 m (values between 25.5 ppm and 26.5 ppm). Below 5 m the values decrease considerably with depth ( 28.5 ppm). As a working hypothesis to explain the two observations, we consider the possibility of the presence of methanotrophs in the deepest parts of the bogs. The electron acceptors needed for methane oxidation could be derived from lateral advection of less reducing groundwater. However, available pore water analyses suggest that neither molecular oxygen, nor sulfate or nitrate are present. One possible oxidising agent would be trivalent iron (solid or colloidal). Indeed are the iron concentrations in the deeper pore waters are elevated. Such deep methanotrophic microbial community could be similar to those found near the surface, and the addition of isotopically light biomass of methanotrophs to the bulk peak could explain the lower delta 13 C values.
Journal of Hydrology, 2005
The bacteria Escherichia coli and Pseudomonas putida, and the bacteriophage virus H40/1 are exami... more The bacteria Escherichia coli and Pseudomonas putida, and the bacteriophage virus H40/1 are examined both for their transport behaviour relative to inert solute tracers and for their modelability under natural flow conditions in a gravel aquifer. The microbes are attenuated in the following sequence: H40/1≥P. putida≫E. coli. The latter is desorbed almost completely within a few days. Breakthrough and recovery
Hydrogeology Journal, 2006
The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in ... more The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in a review, which also discusses their relevance for questions of groundwater protection. Aquifers are heterogeneous on all scales and structured in a variety of habitats. The void spaces in many aquifers are small. The biocenoses are thus predominantly composed of microorganisms and, often, microinvertebrates. Larger voids and macroorganisms occur in karst cavities. Due to the absence of light, the biocenoses depend on chemical energy resources, which are, however, scarce in non-contaminated groundwater. The microorganisms thus show small cell sizes, low population densities and reduced activity; they developed specific strategies to survive oligotrophic conditions. The review also discusses the impact of contamination on the biocenoses, and the potential use of the biocenoses or specific organisms as indicators for groundwater quality, and the limits of this approach. Bacteria are either planktonic or attached to aquifer material, which requires both fluid and solid phase sampling. Most groundwater bacteria are viable but non-culturable. Consequently, cultivation techniques give an incomplete picture of the biocenoses, while methods from molecular microbiology provide genetic fingerprints of the entire community. Different analytical methods are available to count microorganisms, identify species, characterise microbial diversity, and measure activity.
La ville d'Aix-en-Provence se trouve dans une cuvette remplie de dépôts sédimentaires miocène... more La ville d'Aix-en-Provence se trouve dans une cuvette remplie de dépôts sédimentaires miocènes, située à l'ouest du massif calcaire de la Sainte-Victoire. Des eaux thermales de 26 à 35° C, à faciès bicarbonaté calcique et magnésien, émergent en différents endroits du centre-ville sous la forme de sources anciennes et de forages récents avec un débit total estimé à 25 m 3 /h. Actuellement, elles sont exploitées sur le site historique des Thermes de Sextius par pompage dans le forage F4 (35° C) à une profondeur de 70-79 m. La zone productive se situe dans des calcaires fracturés du Crétacé supérieur. Suite à une contamination bactériologique par des Légionelles et des Pseudomonas et à une baisse de productivité de l'un des forages (F3), une étude globale sur la ressource hydrothermale d'Aix-en-Provence a été entreprise. L'étude se donnait pour double objectif de parvenir, d'une part à une connaissance générale du circuit hydrothermal régional et des interaction...
... tL: Time till the first arrival of the ... Photo-decomposition, biodegradation by micro-organ... more ... tL: Time till the first arrival of the ... Photo-decomposition, biodegradation by micro-organisms (release of bromine atoms by eosin for example) and chemical reactions with other substances present in the aquifer (the chloration of waters as well) are all susceptible of resulting in ...
Science of The Total Environment
Mine tailings are a serious threat to the environment and public health. Remediation of these res... more Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur-and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / s c i t o t e n v remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands.
With the goal of a better understanding of the fate of methane in the deep layers of peat bogs, w... more With the goal of a better understanding of the fate of methane in the deep layers of peat bogs, we analysed the microbial 16S rDNA gene pool and measured the stable carbon isotope composition of bulk peat of a deep (6 m) peat bog profile (Etang de la Gruyère, Switzerland). Both Bacterial and Archaean communities were assessed using respectively TTGE (Temporal Temperature Gradient Electrophoresis) and SSCP (Single Strand Conformation Polymorphism), with fragments of the V1-V3 region of the 16S rDNA gene. The "relative diversity" shown in the TTGE AND SSCP gel patterns is presented using indices and band numbers per sample (Simpson evenness). PCA was calculated on the basis of the intensities of all bands found in the TTGE and SSCP fingerprinting profiles. These DNA fingerprinting patterns reveal the presence of a structured microbial community throughout the whole depth profile. Clear differences can be observed between the communities found in the near surface layers and those found at depth. Surprisingly, for both Archaean and Bacterial communities, the deepest samples display a high similarity level with those found in the first 20 centimeters. The delta 13 C values of the peat are relatively constant from the surface of the bog down to a depth of 5 m (values between 25.5 ppm and 26.5 ppm). Below 5 m the values decrease considerably with depth ( 28.5 ppm). As a working hypothesis to explain the two observations, we consider the possibility of the presence of methanotrophs in the deepest parts of the bogs. The electron acceptors needed for methane oxidation could be derived from lateral advection of less reducing groundwater. However, available pore water analyses suggest that neither molecular oxygen, nor sulfate or nitrate are present. One possible oxidising agent would be trivalent iron (solid or colloidal). Indeed are the iron concentrations in the deeper pore waters are elevated. Such deep methanotrophic microbial community could be similar to those found near the surface, and the addition of isotopically light biomass of methanotrophs to the bulk peak could explain the lower delta 13 C values.
Journal of Hydrology, 2005
The bacteria Escherichia coli and Pseudomonas putida, and the bacteriophage virus H40/1 are exami... more The bacteria Escherichia coli and Pseudomonas putida, and the bacteriophage virus H40/1 are examined both for their transport behaviour relative to inert solute tracers and for their modelability under natural flow conditions in a gravel aquifer. The microbes are attenuated in the following sequence: H40/1≥P. putida≫E. coli. The latter is desorbed almost completely within a few days. Breakthrough and recovery