The cuticle: Not only a barrier for plant defence: A novel defence syndrome in plants with cuticular defects.

The cuticle is a physical barrier that prevents water loss and protects against irradiation, xenobiotics and pathogens. This classic textbook statement has recently been revisited and several observations were made showing that this dogma falls short of being universally true. Both transgenic Arabidopsis thaliana lines expressing cell wall-targeted fungal cutinase (so-called CUTE plants) or lipase as well as several A. thaliana mutants with altered cuticular structure remained free of symptoms after an inoculation with Botrytis cinerea. The alterations in cuticular structure lead to the release of fungitoxic substances and changes in gene expression that form a multifactorial defence response. Several models to explain this syndrome are discussed.

Relatedness among arbuscular mycorrhizal fungi drives plant growth and intraspecific fungal coexistence.

Arbuscular mycorrhizal fungi (AMF) form symbioses with most plant species. They are ecologically important determinants of plant growth and diversity. Considerable genetic variation occurs in AMF populations. Thus, plants are exposed to AMF of varying relatedness to each other. Very little is known about either the effects of coexisting AMF on plant growth or which factors influence intraspecific AMF coexistence within roots. No studies have addressed whether the genetics of coexisting AMF, and more specifically their relatedness, influences plant growth and AMF coexistence. Relatedness is expected to influence coexistence between individuals, and it has been suggested that decreasing ability of symbionts to coexist can have negative effects on the growth of the host. We tested the effect of a gradient of AMF genetic relatedness on the growth of two plant species. Increasing relatedness between AMFs lead to markedly greater plant growth (27% biomass increase with closely related compared to distantly related AMF). In one plant species, closely related AMF coexisted in fairly equal proportions but decreasing relatedness lead to a very strong disequilibrium between AMF in roots, indicating much stronger competition. Given the strength of the effects with such a shallow relatedness gradient and the fact that in the field plants are exposed to a steeper gradient, we consider that AMF relatedness can have a strong role in plant growth and the ability of AMF to coexist. We conclude that AMF relatedness is a driver of plant growth and that relatedness is also a strong driver of intraspecific coexistence of these ecologically important symbionts.

Coupled reproductive ecologies in a plant-pollinator-seed predator system

Résumé de la thèseBien que le mutualisme puisse être considéré comme une relation harmonieuse entre différentes espèces, son étude révèle plutôt une exploitation réciproque où chaque partenaire tente de maximiser ses bénéfices tout en réduisant ses coûts. Dans ce contexte, l'identification des facteurs qui favorisent ou contrarient, au cours de l'évolution, une issue mutualiste est une étape majeure pour pouvoir reconstruire les étapes clés menant à l'apparition et au maintien des interactions mutualistes. Le but de ce doctorat était l'identification des traits phénotypiques qui permettent à la plante Silene latofolia (Caryophyllacée)et à son pollinisateur - prédateur de graines, la phalène Hadena bicruris (Noctuidé), d'augmenter les bénéfices nets que chacun retire de l'interaction. Ce système d'étude est particulièrement bien approprié à l'étude de ces traits, car on peut assez facilement estimer la qualité et la quantité des descendants (fitness) des deux partenaires. En effet, la femelle papillon pond un oeuf dans la fleur qu'elle pollinise et sa larve se développe dans le fruit, consommant les graines de la plante. Ainsi, sur une même plante, il est possible d'estimer les succès respectifs de la plante et du papillon à obtenir une descendance. De plus, le conflit d'intérêt autour des graines qui sont indispensables, à la fois à la plante et au papillon, peut stimuler l'évolution de traits qui limitent la surexploitation réciproque des partenaires. Dans une première étude, j'ai montré que le papillon mâle était un pollinisateur efficace de S. latifolia et qu'ainsi, il permettait à la plante d'augmenter le nombre de graines produites (i.e.bénéfice) sans pour autant augmenter la quantité de larves sur la plante. Dans ce système, les papillons pondent un seul oeuf par fleur, déposé soit à l'intérieur de la fleur, dans le tube de corolle, soit sur le pétale. Ma seconde étude montre que les plantes répondent différemment à la présence des oeufs suivant leur position. Aussi, quand l'oeuf est placé dans la fleur, la plante a davantage tendance à ne pas développer le fruit de la fleur infesté ou bien à produire des fruits plus petits que lorsque l'oeuf est placé sur le pétale. Enfin, j'ai montré que la femelle du papillon pond plus souvent sur le pétale lorsque elle visite des fleurs dotées d'un long tube de corolle, et que les larves issues de ces oeufs ont moins de chances de réussir à pénétrer dans le fruit que les larves issues des oeufs placés à l'intérieur de la fleur. Aussi, la variation observée du site de ponte pourrait être causé par la morphologie de la fleur qui contraint le papillon à pondre sur le pétale. Vu dans leur ensemble, les résultats obtenus pendant ce doctorat suggèrent que la participation des mâles à la pollination, l'absence de développement des fruits et la profondeur du tube de corolle pourraient réduire les coûts que S. latifolia subit dans son interaction avec H. bicruris. Par ailleurs, je n'ai pas détecté de mécanismes qui permettraient au papillon de réduire les coûts que la plante pourrait lui imposer. La prochaine étape serait de déterminer l'effet des traits identifiés dans ce doctorat sur la fitness globale de la plante et du papillon pour estimer pleinement leur efficacité à réduire les coûts et à favoriser une issue mutualiste. De même, il faudrait évaluer l'effet de ces traits en populations naturelles pour identifier le rôle des facteurs environnementaux sur leur efficacité.AbstractAlthough mutualisms can be regarded as harmonious relationships between the interacting partners, they are best conceptualized as reciprocal exploitations in which each partner attempts to increase its own benefits and decrease its costs. To date, identifying the factors which promote or discourage mutualistic outcomes remains a major goal to reconstruct the ecological conditions leading to mutualisms. The aim of this PhD thesis was to identify phenotypic traits that may increase the net benefits of each partner in the interaction between the plant Silene latifolia (Caryophyllaceae) and its pollinator / seed predator, the moth Hadena bicruris (Noctuidae). This study system is particularly well suited because the fitness of both interacting species can be assessed. The female moth lays its egg in the flower it pollinated, and its offspring grows in the fruit, feeding on the seeds of the plant, which allows for the follow-up of both larva and fruit fates. Furthermore, the inherent conflict of interest over the seeds as plant progeny vs. larval resource may stimulate the evolution of traits that reduce overexploitation in both the moth and plant. In a first study, I show that male moths are efficient pollinators, hence increasing seed production without increasing oviposition. The contribution of male moths to pollination might thus improve the net benefits of the interaction for the host plant. Females of the H. bicruris moth lay a single egg per flower, and place it either inside the corolla tube or on the petal. My second study shows that plants are more likely to abort the infested flower or to produce a smaller fruit when the egg was experimentally placed inside the flower compared to plants that received an egg on the petal. Finally, female moths were found to lay their eggs more frequently on the petal when visiting a flower with a deep corolla tube, and larvae hatching from these eggs less likely to successfully attack the fruit. Variation in egg position on the flower may thus be the result of a constraint imposed by floral morphology. Overall, this PhD work suggests that the pollination by male moths, flower abortion, and deep corolla tube may efficiently reduce the costs experienced by S. latifolia in its interaction with H. bicruris. Interestingly, no apparent mechanism of costs reduction was detected for the moth. Further studies should focus on the effects of these traits (i) in the long term fitness of both the plant and the insect and (ii) their interactions with environmental factors (biotic and abiotic) that may affect their efficiency in natural populations.

A better understanding of ecological conditions for Leontopodium alpinum Cassini in the Swiss Alps

Although Leontopodium alpinum is considered to be threatened in many countries, only limited scientific information about its autecology is available. In this study, we aim to define the most important ecological factors which influence the distribution of L. alpinum in the Swiss Alps. These were assessed at the national scale using species distribution models based on topoclimatic predictors and at the community scale using exhaustive plant inventories. The latter were analysed using hierarchical clustering and principal component analysis, and the results were interpreted using ecological indicator values. L. alpinum was found almost exclusively on base-rich bedrocks (limestone and ultramaphic rocks). The species distribution models showed that the available moisture (dry regions, mostly in the Inner Alps), elevation (mostly above 2000 m.a.s.l.) and slope (mostly >30°) were the most important predictors. The relevés showed that L. alpinum is present in a wide range of plant communities, all subalpine-alpine open grasslands, with a low grass cover. As a light-demanding and short species, L. alpinum requires light at ground level; hence, it can only grow in open, nutrient-poor grasslands. These conditions are met in dry conditions (dry, summer-warm climate, rocky and draining soil, south-facing aspect and/or steep slope), at high elevations, on oligotrophic soils and/or on windy ridges. Base-rich soils appear to also be essential, although it is still unclear if this corresponds to physiological or ecological (lower competition) requirements.

Antimicrobial peptide genes in Bacillus strains from plant environments

The presence of the antimicrobial peptide (AMP) biosynthetic genes srfAA (surfactin), bacA (bacylisin), fenD (fengycin), bmyB (bacyllomicin), spaS (subtilin), and ituC (iturin) was examined in 184 isolates of Bacillus spp. obtained from plant environments (aerial, rhizosphere, soil) in the Mediterranean land area of Spain. Most strains had between two and four AMP genes whereas strains with five genes were seldom detected and none of the strains had six genes. The most frequent AMP gene markers were srfAA, bacA, bmyB, and fenD, and the most frequent genotypes srfAA-bacA-bmyB and srfAAbacA-bmyB-fenD. The dominance of these particular genes in Bacillus strains associated with plants reinforces the competitive role of surfactin, bacyllomicin, fengycin, and bacilysin in the fitness of strains in natural environments. The use of these AMP gene markers may assist in the selection of putative biological control agents of plant pathogens

Evaluation of four whole-plant inoculation methods to analyze the pathogenicity of Erwinia amylovora under quarantine conditions

Four methods were tested to assess the fire-blight disease response on grafted pear plants. The leaves of the plants were inoculated with Erwinia amylovora suspensions by pricking with clamps, cutting with scissors, local infiltration, and painting a bacterial suspension onto the leaves with a paintbrush. The effects of the inoculation methods were studied in dose-time-response experiments carried out in climate chambers under quarantine conditions. A modified Gompertz model was used to analyze the disease-time relatiobbnships and provided information on the rate of infection progression (rg) and time delay to the start of symptoms (t0). The disease-pathogen-dose relationships were analyzed according to a hyperbolic saturation model in which the median effective dose (ED50) of the pathogen and maximum disease level (ymax) were determined. Localized infiltration into the leaf mesophile resulted in the early (short t0) but slow (low rg) development of infection whereas in leaves pricked with clamps disease symptoms developed late (long t0) but rapidly (high rg). Paintbrush inoculation of the plants resulted in an incubation period of medium length, a moderate rate of infection progression, and low ymax values. In leaves inoculated with scissors, fire-blight symptoms developed early (short t0) and rapidly (high rg), and with the lowest ED50 and the highest ymax

Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly

The importance of competition between similar species in driving community assembly is much debated. Recently, phylogenetic patterns in species composition have been investigated to help resolve this question: phylogenetic clustering is taken to imply environmental filtering, and phylogenetic overdispersion to indicate limiting similarity between species. We used experimental plant communities with random species compositions and initially even abundance distributions to examine the development of phylogenetic pattern in species abundance distributions. Where composition was held constant by weeding, abundance distributions became overdispersed through time, but only in communities that contained distantly related clades, some with several species (i.e., a mix of closely and distantly related species). Phylogenetic pattern in composition therefore constrained the development of overdispersed abundance distributions, and this might indicate limiting similarity between close relatives and facilitation/complementarity between distant relatives. Comparing the phylogenetic patterns in these communities with those expected from the monoculture abundances of the constituent species revealed that interspecific competition caused the phylogenetic patterns. Opening experimental communities to colonization by all species in the species pool led to convergence in phylogenetic diversity. At convergence, communities were composed of several distantly related but species-rich clades and had overdispersed abundance distributions. This suggests that limiting similarity processes determine which species dominate a community but not which species occur in a community. Crucially, as our study was carried out in experimental communities, we could rule out local evolutionary or dispersal explanations for the patterns and identify ecological processes as the driving force, underlining the advantages of studying these processes in experimental communities. Our results show that phylogenetic relations between species provide a good guide to understanding community structure and add a new perspective to the evidence that niche complementarity is critical in driving community assembly.

Villisca Municipal Power Plant, Independent Auditor's Reports Financial Statements and Supplemental Information Schedule of Findings, December 31, 2003

Other Audit Report - Utilities

Fluid flow through the sedimentary cover in northern Switzerland recorded by calcite-celestite veins (Oftringen borehole, Olten)

Abundant veins filled by calcite, celestite and pyrite were found in the core of a 719 m deep borehole drilled in Oftringen near Olten, located in the north-western Molasse basin, close to the thrust of the Folded Jura. Host rocks are calcareous marl, argillaceous limestone and limestone of the Dogger and Malm. The delta O-18 values of vein calcite are lower than in host rock carbonate and, together with microthermometric data from fluid inclusions in vein calcite, indicate precipitation from a seawater-dominated fluid at average temperatures of 56-68A degrees C. Such temperatures were reached at the time of maximum burial of the sedimentary pile in the late Miocene. The depth profile of delta C-13 and Sr-87/Sr-86 values and Sr content of both whole-rock carbonate and vein calcite show marked trends towards negative delta C-13, high Sr-87/Sr-86, and low Sr content in the uppermost 50-150 m of the Jurassic profile (upper Oxfordian). The Sr-87/Sr-86 of vein minerals is generally higher than that of host rock carbonate, up to very high values corresponding to Burdigalian seawater (Upper Marine Molasse, Miocene), which represents the last marine incursion in the region. No evidence for internally derived radiogenic Sr (clay minerals) has been found and so an external source is required. S and O isotope composition of vein celestite and pyrite can be explained by bacterial reduction of Miocene seawater sulphate. The available data set suggests the vein mineralization precipitated from descending Burdigalian seawater and not from a fluid originating in the underlying Triassic evaporites.

Predicting global change impacts on plant species' distributions: Future challenges

Given the rate of projected environmental change for the 21st century, urgent adaptation and mitigation measures are required to slow down the on-going erosion of biodiversity. Even though increasing evidence shows that recent human-induced environmental changes have already triggered species' range shifts, changes in phenology and species' extinctions, accurate projections of species' responses to future environmental changes are more difficult to ascertain. This is problematic, since there is a growing awareness of the need to adopt proactive conservation planning measures using forecasts of species' responses to future environmental changes. There is a substantial body of literature describing and assessing the impacts of various scenarios of climate and land-use change on species' distributions. Model predictions include a wide range of assumptions and limitations that are widely acknowledged but compromise their use for developing reliable adaptation and mitigation strategies for biodiversity. Indeed, amongst the most used models, few, if any, explicitly deal with migration processes, the dynamics of population at the "trailing edge" of shifting populations, species' interactions and the interaction between the effects of climate and land-use. In this review, we propose two main avenues to progress the understanding and prediction of the different processes A occurring on the leading and trailing edge of the species' distribution in response to any global change phenomena. Deliberately focusing on plant species, we first explore the different ways to incorporate species' migration in the existing modelling approaches, given data and knowledge limitations and the dual effects of climate and land-use factors. Secondly, we explore the mechanisms and processes happening at the trailing edge of a shifting species' distribution and how to implement them into a modelling approach. We finally conclude this review with clear guidelines on how such modelling improvements will benefit conservation strategies in a changing world. (c) 2007 Rubel Foundation, ETH Zurich. Published by Elsevier GrnbH. All rights reserved.

Cross recurrence quantification for cover song identification

There is growing evidence that nonlinear time series analysis techniques can be used to successfully characterize, classify, or process signals derived from realworld dynamics even though these are not necessarily deterministic and stationary. In the present study we proceed in this direction by addressing an important problem our modern society is facing, the automatic classification of digital information. In particular, we address the automatic identification of cover songs, i.e. alternative renditions of a previously recorded musical piece. For this purpose we here propose a recurrence quantification analysis measure that allows tracking potentially curved and disrupted traces in cross recurrence plots. We apply this measure to cross recurrence plots constructed from the state space representation of musical descriptor time series extracted from the raw audio signal. We show that our method identifies cover songs with a higher accuracy as compared to previously published techniques. Beyond the particular application proposed here, we discuss how our approach can be useful for the characterization of a variety of signals from different scientific disciplines. We study coupled Rössler dynamics with stochastically modulated mean frequencies as one concrete example to illustrate this point.

Predictability of music descriptor time series and its application to cover song detection

Intuitively, music has both predictable and unpredictable components. In this work we assess this qualitative statement in a quantitative way using common time series models fitted to state-of-the-art music descriptors. These descriptors cover different musical facets and are extracted from a large collection of real audio recordings comprising a variety of musical genres. Our findings show that music descriptor time series exhibit a certain predictability not only for short time intervals, but also for mid-term and relatively long intervals. This fact is observed independently of the descriptor, musical facet and time series model we consider. Moreover, we show that our findings are not only of theoretical relevance but can also have practical impact. To this end we demonstrate that music predictability at relatively long time intervals can be exploited in a real-world application, namely the automatic identification of cover songs (i.e. different renditions or versions of the same musical piece). Importantly, this prediction strategy yields a parameter-free approach for cover song identification that is substantially faster, allows for reduced computational storage and still maintains highly competitive accuracies when compared to state-of-the-art systems.

Chroma binary similarity and local alignment applied to cover song identification

We present a new technique for audio signal comparison based on tonal subsequence alignment and its application to detect cover versions (i.e., different performances of the same underlying musical piece). Cover song identification is a task whose popularity has increased in the Music Information Retrieval (MIR) community along in the past, as it provides a direct and objective way to evaluate music similarity algorithms.This article first presents a series of experiments carried outwith two state-of-the-art methods for cover song identification.We have studied several components of these (such as chroma resolution and similarity, transposition, beat tracking or Dynamic Time Warping constraints), in order to discover which characteristics would be desirable for a competitive cover song identifier. After analyzing many cross-validated results, the importance of these characteristics is discussed, and the best-performing ones are finally applied to the newly proposed method. Multipleevaluations of this one confirm a large increase in identificationaccuracy when comparing it with alternative state-of-the-artapproaches.

A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.

Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients.

Understanding drivers of biodiversity patterns is of prime importance in this era of severe environmental crisis. More diverse plant communities have been postulated to represent a larger functional trait-space, more likely to sustain a diverse assembly of herbivore species. Here, we expand this hypothesis to integrate environmental, functional and phylogenetic variation of plant communities as factors explaining the diversity of lepidopteran assemblages along elevation gradients in the Swiss Western Alps. According to expectations, we found that the association between butterflies and their host plants is highly phylogenetically structured. Multiple regression analyses showed the combined effect of climate, functional traits and phylogenetic diversity in structuring butterfly communities. Furthermore, we provide the first evidence that plant phylogenetic beta diversity is the major driver explaining butterfly phylogenetic beta diversity. Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables.