Étude des sédiments quaternaires, de la molasse et sa tectonique, dans le Grand Lac (Léman) à partir de données sismiques 2D et 3D

RESUME L'Institut de Géophysique de l'Université de Lausanne a développé au cours de ces dernières années un système d'acquisition de sismique réflexion multitrace à haute résolution 2D et 3D. L'objectif de cette thèse était de poursuivre ce développement tout améliorant les connaissances de la géologie sous le lac Léman, en étudiant en particulier la configuration des grands accidents sous-lacustres dans la Molasse (Tertiaire) qui forme l'essentiel du substratum des formations quaternaires. En configuration 2D, notre système permet d'acquérir des profils sismiques avec une distance inter-CDP de 1,25 m. La couverture varie entre 6 et 18 selon le nombre de traces et la distance inter-tir. Le canon à air (15/15 eu. in.), offre une résolution verticale de 1,25 ni et une pénétration maximale de 300 m sous le fond de l'eau. Nous avons acquis au total plus de 400 km de sections 2D dans le Grand Lac et le Haut Lac entre octobre 2000 et juillet 2004. Une campagne de sismique 3D a fourni des données au large d'Evian sur une surface de 442,5 m sur 1450 m, soit 0,64 km2. La navigation ainsi que le positionnement des hydrophones et de la source ont été réalisés avec des GPS différentiels. Nous avons utilisé un traitement sismique conventionnel, sans appliquer d'AGC et en utilisant une migration post-stack. L'interprétation du substratum antéquaternaire est basée sur l'identification des sismofaciès, sur leurs relations avec les unités géologiques adjacentes au lac, ainsi que sur quelques données de forages. Nous obtenons ainsi une carte des unités géologiques dans le Grand Lac. Nous précisons la position du chevauchement subalpin entre la ville de Lausanne, sur la rive nord, et le bassin de Sciez, sur la rive sud. Dans la Molasse de Plateau, nous avons identifié les décrochements de Pontarlier et de St. Cergue ainsi que plusieurs failles non reconnues jusqu'ici. Nous avons cartographié les accidents qui affectent la Molasse subalpine ainsi que le plan de chevauchement du flysch sur la Molasse près de la rive sud du lac. Une nouvelle carte tectonique de la région lémanique a ainsi pu être dressée. L'analyse du substratum ne montre pas de failles suggérant une origine tectonique de la cuvette lémanique. Par contre, nous suggérons que la forme du creusement glaciaire, donc de la forme du lac Léman, a été influencée par la présence de failles dans le substratum antéquaternaire. L'analyse des sédiments quaternaires nous a permis de tracer des cartes des différentes interfaces ou unités qui les composent. La carte du toit du substratum antéquaternaire montre la présence de chenaux d'origine glaciaire dont la profondeur maximale atteint la cote -200 ni. Leur pente est dirigée vers le nord-est, à l'inverse du sens d'écoulement actuel des eaux. Nous expliquons cette observation par l'existence de circulations sous-glaciaires d'eau artésienne. Les sédiments glaciaires dont l'épaisseur maximale atteint 150 ni au centre du lac ont enregistré les différentes récurrences glaciaires. Dans la zone d'Evian, nous mettons en évidence la présence de lentilles de sédiments glaciolacustres perchées sur le flanc de la cuvette lémanique. Nous avons corrélé ces unités avec des données de forage et concluons qu'il s'agit du complexe inférieur de la pile sédimentaire d'Evian. Celui-ci, âgé de plus de 30 000 ans, serait un dépôt de Kame associé à un lac périglaciaire. La sismique réflexion 3D permet de préciser l'orientation de l'alimentation en matériel détritique de l'unité. La finesse des images obtenues nous permet également d'établir quels types d'érosion ont affecté certaines unités. Les sédiments lacustres, dont l'épaisseur maximale imagée atteint plus de 225 m et sans doute 400 ni sous le delta du Rhône, indiquent plusieurs mécanismes de dépôts. A la base, une mégaturbidite, épaisse d'une trentaine de mètres en moyenne, s'étend entre l'embouchure de la Dranse et le delta du Rhône. Au-dessus, la décantation des particules en suspension d'origine biologique et détritique fournit l'essentiel des sédiments. Dans la partie orientale du lac, les apports détritiques du Rhône forment un delta qui prograde vers l'ouest en s'imbriquant avec les sédiments déposés par décantation. La structure superficielle du delta a brutalement évolué, probablement à la suite de l'évènement catastrophique du Tauredunum (563 A.D.). Sa trace probable se marque par la présence d'une surface érosive que nous avons cartographiée. Le delta a ensuite changé de géométrie, avec notamment un déplacement des chenaux sous-lacustres. Sur l'ensemble de nos sections sismiques, nous n'observons aucune faille dans les sédiments quaternaires qui attesterait d'une tectonique postglaciaire du substratum. ABSTRACT During the last few years the institute of Geophysics of the University of Lausanne cleveloped a 2D and 3D high-resolution multichannel seismic reflection acquisition system. The objective of the present work was to carry on this development white improving our knowledge of the geology under Lake Geneva, in particular by studying the configuration of the large accidents affecting the Tertiary Molasse that makes up the basement of most Quaternary deposits. In its 2D configuration, our system makes it possible to acquire seismic profiles with a CDP interval of 1.25 m. The fold varies from 6 to 18 depending on the number of traces and the shooting interval. Our air gun (15/15 cu. in.) provides a vertical resolution of 1.25 m and a maximum penetration depth of approximately 300 m under water bottom. We acquired more than 400 km of 2D sections in the Grand Lac and the Haut Lac between October 2000 and July 2004. A 3D seismic survey off the city of Evian provided data on a surface of 442.5 m x 1450 m (0.64 km2). Ship's navigation as well as hydrophone- and source positioning were carried out with differential GPS. The seismic data were processed following a conventional sequence without .applying AGC and using post-stack migration. The interpretation of the pre-Quaternary substratum is based on sismofacies, on their relationships with terrestrial geological units and on some borehole data. We thus obtained a map of the geological units in the Grand Lac. We defined the location of the subalpine thrust from Lausanne, on the north shore, to the Sciez Basin, on the south shore. Within the Molasse de Plateau, we identified the already know Pontarlier and St Cergue transforms Fault as well as faults. We mapped faults that affect subalpine Molasse as well as the thrust fault plane between alpine flysch and Molasse near the lake's south shore. A new tectonic map of the Lake Geneva region could thus be drawn up. The substratum does not show faults indicating a tectonic origin for the Lake Geneva Basin. However, we suggest that the orientation of glacial erosion, and thus the shape of Lake Geneva, vas influenced by the presence of faults in the pre-Quaternary basement. The analysis of Quaternary sediments enabled us to draw up maps of various discontinuities or internal units. The top pre-Quaternary basement map shows channels of glacial origin, the deepest of them reaching an altitude of 200 m a.s.l. The channel's slopes are directed to the North-East, in opposite direction of the present water flow. We explain this observation by the presence of artesian subglacial water circulation. Glacial sediments, the maximum thickness of which reaches 150 m in the central part of the lake, record several glacial recurrences. In the Evian area, we found lenses of glacio-lacustrine sediments set high up on the flank of the Lake Geneva Bassin. We correlated these units with on-land borehole data and concluded that they represent the lower complex of the Evian sedimentary pile. The lower complex is aider than 30 000 years, and it could be a Kame deposit associated with a periglacial lake. Our 3D seismic reflexion survey enables us to specify the supply direction of detrital material in this unit. With detailed seismic images we established how some units were affected by different erosion types. The lacustrine sediments we imaged in Lake Geneva are thicker than 225 m and 400 m or more Linder the Rhone Delta. They indicate several depositional mechanisms. Their base is a major turbidite, thirty meters thick on average, that spreads between the Dranse mouth and the Rhone delta. Above this unit, settling of suspended biological and detrital particles provides most of the sediments. In the eastern part of the lake, detrital contribution from the Rhone builds a delta that progrades to the west and imbricates with the settling sediments. The shallow structure of the Rhone delta abruptly evolved, probably after the catastrophic Tauredunum event (563 A.D.). It probably coincides with an erosive surface that we mapped. As a result, the delta geometry changed, in particular associated with a displacement of water bottom channels. In all our seismic sections, we do not observe fault in the Quaternary sediments that would attest postglacial tectonic activity in the basement.

Decomposition of Arachis pintoi and Hyparrhenia rufa litters in monoculture and intercropped systems under lowland soil

Tropical grasslands under lowland soils are generally underutilized and the litter of forage legumes may be used to recover these degraded pastures. The objective of this work was to study the dynamics of litter decomposition of Arachis pintoi (pinto peanut), Hyparrhenia rufa (thatching grass) and a mixture of both species in a lowland soil. These treatments were analyzed in three areas: grass monoculture, legume monoculture and legume intercropped with the grass during the dry and wet seasons. Litter bags containing the legume, grass or a mixture of both species were incubated to estimate the decomposition rate and microorganism colonization. Decomposition constants (K) and litter half-lives (T1/2) were estimated by an exponential model whereas number of microorganisms in specific media were determined by plate dilution. The decomposition rate, release of nutrients and microorganisms number, especially bacteria, increased when pinto peanut was added to thatching grass, influenced by favorable lignin/N and C/N ratios in legume litter. When pinto peanut litter was incubated in the grass plots, 50% N and P was released within about 135 days in the dry season and in the wet season, the equivalent release occurred within 20 days. These results indicate that A. pintoi has a great potential for nutrient recycling via litter and can be used to recover degraded areas.

Human-to-bovine jump of Staphylococcus aureus CC8 is associated with the loss of a β-hemolysin converting prophage and the acquisition of a new staphylococcal cassette chromosome.

Staphylococcus aureus can colonize and infect both humans and animals, but isolates from both hosts tend to belong to different lineages. Our recent finding of bovine-adapted S. aureus showing close genetic relationship to the human S. aureus clonal complex 8 (CC8) allowed us to examine the genetic basis of host adaptation in this particular CC. Using total chromosome microarrays, we compared the genetic makeup of 14 CC8 isolates obtained from cows suffering subclinical mastitis, with nine CC8 isolates from colonized or infected human patients, and nine S. aureus isolates belonging to typical bovine CCs. CC8 isolates were found to segregate in a unique group, different from the typical bovine CCs. Within this CC8 group, human and bovine isolates further segregated into three subgroups, among which two contained a mix of human and bovine isolates, and one contained only bovine isolates. This distribution into specific clusters and subclusters reflected major differences in the S. aureus content of mobile genetic elements (MGEs). Indeed, while the mixed human-bovine clusters carried commonly human-associated β-hemolysin converting prophages, the bovine-only isolates were devoid of such prophages but harbored an additional new non-mec staphylococcal cassette chromosome (SCC) unique to bovine CC8 isolates. This composite cassette carried a gene coding for a new LPXTG-surface protein sharing homologies with a protein found in the environmental bacterium Geobacillus thermoglucosidans. Thus, in contrast to human CC8 isolates, the bovine-only CC8 group was associated with the combined loss of β-hemolysin converting prophages and gain of a new SCC probably acquired in the animal environment. Remaining questions are whether the new LPXTG-protein plays a role in bovine colonization or infection, and whether the new SCC could further acquire antibiotic-resistance genes and carry them back to human.

Plant growth and phosphorus uptake in mycorrhizal rangpur lime seedlings under different levels of phosphorus

The objective of this work was to evaluate the response of rangpur lime (Citrus limonia) to arbuscular mycorrhiza (Glomus intraradices), under P levels ranging from low to excessive. Plants were grown in three levels of soluble P (25, 200 and 1,000 mg kg-1), either inoculated with Glomus intraradices or left noninoculated, evaluated at 30, 60, 90, 120 and 150 days after transplanting (DAT). Total dry weight, shoot P concentration and specific P uptake by roots increased in mycorrhizal plants with the doses of 25 and 200 mg kg-1 P at 90 DAT. With 1,000 mg kg-1 P, mycorrhizal plants had a transient growth depression at 90 and 120 DAT, and nonmycorrhizal effects on P uptake at any harvesting period. Root colonization and total external mycelium correlated positively with shoot P concentration and total dry weight at the two lowest P levels. Although the highest P level decreased root colonization, it did not affect total external mycelium to the same extent. As a result, a P availability imbalance affected negatively the mycorrhizal symbiosis and, consequently, the plant growth.

Effect of Bacillus thuringiensis on microbial functional groups in sorghum rhizosphere

The objective of this work was to assess the effect of two strains of Bacillus thuringiensis var. kurstaki on sorghum rhizosphere microorganisms. The strains were HD1, that produces the bioinsecticidal protein, and 407, that is a mutant non-producer. The strains do not influence microbial population, but reduce plant growth and improve mycorrhizal colonization and free living fixing N2 community.

Asexual reproduction in introduced and native populations of the ant Cerapachys biroi.

Asexual reproduction is particularly common among introduced species, probably because it helps to overcome the negative effects associated with low population densities during colonization. The ant Cerapachys biroi has been introduced to tropical and subtropical islands around the world since the beginning of the last century. In this species, workers can reproduce via thelytokous parthenogenesis. Here, we use genetic markers to reconstruct the history of anthropogenic introductions of C. biroi, and to address the prevalence of female parthenogenesis in introduced and native populations. We show that at least four genetically distinct lineages have been introduced from continental Asia and have led to the species' circumtropical establishment. Our analyses demonstrate that asexual reproduction dominates in the introduced range and is also common in the native range. Given that C. biroi is the only dorylomorph ant that has successfully become established outside of its native range, this unusual mode of reproduction probably facilitated the species' worldwide spread. On the other hand, the rare occurrence of haploid males and at least one clear case of sexual recombination in the introduced range show that C. biroi has not lost the potential for sex. Finally, we show that thelytoky in C. biroi probably has a genetic rather than an infectious origin, and that automixis with central fusion is the most likely underlying cytological mechanism. This is in accordance with what is known for other thelytokous eusocial Hymenoptera.

Diverging Cave- and River-Dwelling Newts Exert the Same Mate Preference in their Native Light Conditions

When colonizing a new habitat, populations must adapt their sexual behaviour to new ecological constraints. Because caves display drastically different conditions from surface habitats and cave animals are deprived from visual information, hypogean populations are expected to have modified their mate preference and signalling behaviour after cave colonization. Here, we experimentally examined the female preference and the sexual behaviour of brook newts Calotriton asper from different cave and river populations, either in light or in darkness. Our results suggest that females prefer large individuals in both hypogean and epigean populations, but that this preference is only expressed in the light conditions of their native habitat. Hence, some mate choice criteria would be maintained across genetically divergent populations and throughout dissimilar habitats. However, this sexual behaviour is likely to be expressed via a different sensory pathway in the different habitats, suggesting that a sensory shift has occurred in cave populations, enabling animals to communicate through a non-visual channel.

Regulation of antibiotic production in root-colonizing Peudomonas spp. and relevance for biological control of plant disease.

Certain strains of fluorescent pseudomonads are important biological components of agricultural soils that are suppressive to diseases caused by pathogenic fungi on crop plants. The biocontrol abilities of such strains depend essentially on aggressive root colonization, induction of systemic resistance in the plant, and the production of diffusible or volatile antifungal antibiotics. Evidence that these compounds are produced in situ is based on their chemical extraction from the rhizosphere and on the expression of antibiotic biosynthetic genes in the producer strains colonizing plant roots. Well-characterized antibiotics with biocontrol properties include phenazines, 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, lipopeptides, and hydrogen cyanide. In vitro, optimal production of these compounds occurs at high cell densities and during conditions of restricted growth, involving (i) a number of transcriptional regulators, which are mostly pathway-specific, and (ii) the GacS/GacA two-component system, which globally exerts a positive effect on the production of extracellular metabolites at a posttranscriptional level. Small untranslated RNAs have important roles in the GacS/GacA signal transduction pathway. One challenge in future biocontrol research involves development of new strategies to overcome the broad toxicity and lack of antifungal specificity displayed by most biocontrol antibiotics studied so far.

RpoN (sigma54) controls production of antifungal compounds and biocontrol activity in Pseudomonas fluorescens CHA0.

Pseudomonas fluorescens CHA0 is an effective biocontrol agent of root diseases caused by fungal pathogens. The strain produces the antibiotics 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) that make essential contributions to pathogen suppression. This study focused on the role of the sigma factor RpoN (sigma54) in regulation of antibiotic production and biocontrol activity in P. fluorescens. An rpoN in-frame-deletion mutant of CHAO had a delayed growth, was impaired in the utilization of several carbon and nitrogen sources, and was more sensitive to salt stress. The rpoN mutant was defective for flagella and displayed drastically reduced swimming and swarming motilities. Interestingly, the rpoN mutant showed a severalfold enhanced production of DAPG and expression of the biosynthetic gene phlA compared with the wild type and the mutant complemented with monocopy rpoN+. By contrast, loss of RpoN function resulted in markedly lowered PLT production and plt gene expression, suggesting that RpoN controls the balance of the two antibiotics in strain CHA0. In natural soil microcosms, the rpoN mutant was less effective in protecting cucumber from a root rot caused by Pythium ultimum. Remarkably, the mutant was not significantly impaired in its root colonization capacity, even at early stages of root infection by Pythium spp. Taken together, our results establish RpoN for the first time as a major regulator of biocontrol activity in Pseudomonas fluorescens.

Progress in front propagation research

We review the progress in the field of front propagation in recent years. We survey many physical, biophysical and cross-disciplinary applications, including reduced-variable models of combustion flames, Reid's paradox of rapid forest range expansions, the European colonization of North America during the 19th century, the Neolithic transition in Europe from 13 000 to 5000 years ago, the description of subsistence boundaries, the formation of cultural boundaries, the spread of genetic mutations, theory and experiments on virus infections, models of cancer tumors, etc. Recent theoretical advances are unified in a single framework, encompassing very diverse systems such as those with biased random walks, distributed delays, sequential reaction and dispersion, cohabitation models, age structure and systems with several interacting species. Directions for future progress are outlined

Virulent infections due to alpha-haemolytic streptococci in cancer patients and their management

Streptococci of the viridans group have long been considered to be minor pathogens, except in bacterial endocarditis. For some years, however, these microorganisms have been the cause of serious bacteraemia in neutropenic patients receiving intensive chemotherapy. These infections can lead to severe complications such as endocarditis, respiratory distress syndromes or shock, and are associated with a mortality rate ranging from 6-30%. The principal risk factors for these infections are profound neutropenia, antibiotic prophylaxis with quinolones or cotrimoxazole, large doses of cytosine arabinoside, a recent history of chemotherapy, oropharyngeal mucositis and viridans streptococcal colonization. Protective factors are the early administration of parenteral antibiotics during periods of neutropenia, or the prophylactic administration of penicillin. Although the introduction of penicillin to prophylactic antibiotic regimens has led to a decrease in the incidence of these infections, the emergence of strains resistant to beta-lactams is a worrying problem which could compromise this type of treatment.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.

Arbuscular mycorrhizal fungi mediate below-ground plant-herbivore interactions: a phylogenetic study

Ecological interactions are complex networks, but have typically been studied in a pairwise fashion. Examining how third-party species can modify the outcome of pairwise interactions may allow us to better predict their outcomes in realistic systems. For instance, arbuscular mycorrhizal fungi (AMF) can affect plant interactions with other organisms, including below-ground herbivores, but the mechanisms underlying these effects remain unclear. Here, we use a comparative, phylogenetically controlled approach to test the relative importance of mycorrhizal colonization and plant chemical defences (cardenolides) in predicting plant survival and the abundance of a generalist below-ground herbivore across 14 species of milkweeds (Asclepias spp.). Plants were inoculated with a mixture of four generalist AMF species or left uninoculated. After 1month, larvae of Bradysia sp. (Diptera: Sciaridae), a generalist below-ground herbivore, colonized plant roots. We performed phylogenetically controlled analyses to assess the influence of AMF colonization and toxic cardenolides on plant growth, mortality and infestation by fungus gnats. Overall, plants inoculated with AMF exhibited greater survival than did uninoculated plants. Additionally, surviving inoculated plants had lower numbers of larvae in their roots and fewer non-AM fungi than surviving uninoculated plants. In phylogenetic controlled regressions, gnat density in roots was better predicted by the extent of root colonized by AMF than by root cardenolide concentration. Taken as a whole, AMF modify the effect of below-ground herbivores on plants in a species-specific manner, independent of changes in chemical defence. This study adds to the growing body of literature demonstrating that mycorrhizal fungi may improve plant fitness by conferring protection against antagonists, rather than growth benefits. In addition, we advocate using comparative analyses to disentangle the roles of shared history and ecology in shaping trait expression and to better predict the outcomes of complex multitrophic interactions.

Low immunoglobulin levels in patients with cystic fibrosis: reduced inflammation or sign of common variable immunodeficiency syndrome?

Introduction: In children with cystic fibrosis (CF), low immunoglobulin (IgG) levels have been reported to be associated with significantly less severe lung disease. However, decreased IgG can be a sign for common variable immunodeficiency (CVID) and affect clinical outcome. The aim of this study was to analyze clinical and serological data of patients having low IgG levels in routine blood tests at annual assessment, particularly their antibody response to polysaccharide antigens. Method: Retrospective chart review of demographic data of CF patients followed at the pediatric CF clinic throughout 2009. Clinical parameters (genotype, pancreas sufficiency, FEV1), presence of Pseudomonas aeruginosa (PA) and number of exacerbations per year were correlated with immunoglobulin and vaccination antibodies levels (antibodies to pneumococcal serotypes 14, 19, 23, 1, 5 and 7F measured by enzyme-linked immune-sorbent assay). Results: 4 out of 60 patients (6.7%) had lower IgG-levels for age. Ages ranged from 1 year 8 months to 11 years, 2 boys, 2 girls. Three patients were delF508 homozygotes, one heterozygote composite delF508/G542X. All were pancreatic insufficient. FEV1 ranged from 74 to 108%. One patient never had colonization by PA, 2 had intermittent PA colonization and one was chronically infected. After conjugated vaccination all patients had protective antibodies against serotypes 14, 19, 23F. For serotypes not included in the vaccine, only one patient had protective titers for 1 out of 3 serotypes. None of the patients had received unconjugated pneumococcal vaccine. There was no significant clinical difference in FEV1, PA colonization or number of exacerbations according to IgG and vaccination antibody levels. Conclusion: Cystic Fibrosis patients with low immunoglobulin levels have normal antibody response to protein antigens. However, despite recurrent infections, there seems to be delayed or deficient antibody response to polysaccharide antigens. Prospective studies are needed to evaluate the development of polysaccharide antibody responses in CF-patients to monitor for CVID. With early detection of CF by newborn screening program, long term follow up could be started early in childhood.

New isolates of ectomycorrhizal fungi and the growth of eucalypt

The objective of this work was to evaluate the efficiency of ectomycorrhizal isolates on root colonization, phosphorus uptake and growth of Eucalyptus dunnii seedlings. Inocula of ten ectomycorrhizal isolates of Chondrogaster angustisporus, Hysterangium gardneri, Pisolithus spp., and Scleroderma spp. were aseptically produced in a peat-vermiculite mixture supplemented with liquid culture medium. Plants grew in a similar substrate supplemented with macro-and micro-nutrients; treatments were randomly distributed in a greenhouse. After three months, seedlings inoculated with three isolates - UFSC-Sc68 (Scleroderma sp.), UFSC-Ch163 (Chondrogaster angustisporus), and UFSC-Pt188 (Pisolithus microcarpus) - had a phosphorus shoot content and a shoot dry matter higher or equivalent to those of noninoculated controls which had been fertilized with a 16-fold phosphorus amount. These isolates were selected for new studies for establishing inoculum production techniques, in order to be applied in reforestation programmes under nursery and field conditions.