The evolution of RNA interference system, blue light sensing mechanism and circadian clock in Rhizophagus irregularis give insight on Arbuscular mycorrhizal symbiosis

La symbiose mycorhizienne arbusculaire (MA) est une association formée par les racines des plantes et les champignons mycorhiziens arbusculaires (CMA). Ces champignons sont les plus anciens symbiotes des plantes et ils sont apparus il y a au moins 460 millions d'années avec l'émergence et l'évolution des plantes terrestres. Les CMA sont également les partenaires symbiotiques des plantes les plus répandus dans les écosystèmes et ils peuvent s’associer avec plus de 80% des espèces de plantes vasculaires. Les CMA appartiennent à une lignée fongique primitive dont la position phylogénétique est encore en débat. Les CMA sont des microorganismes biotrophes obligatoires qui dépendent entièrement du carbone provenant de la photosynthèse des plantes hôtes, autrement dit, les CMA ne peuvent assimiler le carbone qu’on association avec les racines des plantes. En échange, les CMA aident les plantes à absorber divers nutriments essentiels du sol, tels que le phosphore. En effet, les CMA absorbent les nutriments et ils les transportent à travers leurs hyphes jusqu’aux cellules des racines dans lesquelles ils forment une structure appelée arbuscule. L'allocation des nutriments et les voies métaboliques interconnectées entre le champignon et l'hôte ont subi une pression sélective en tant que partenaires symbiotiques. En plus, les hyphes de des CMA agissent comme une niche écologique pour divers microbes du sol tels que les bactéries et les champignons, formant ainsi le pivot de la rhizosphère des racines. La symbiose MA est un élément essentiel pour comprendre la physiologie des plantes ainsi que l'écosystème. Malgré les rôles cruciaux des CMA dans les écosystèmes, leur génétique et leur évolution demeure méconnues. Le système d'interférence de l'ARN (ARNi), le mécanisme de détection de la lumière bleue et l'horloge circadienne sont des mécanismes importants qui sont impliqués dans la régulation de l’expression des gènes chez les champignons. Bien que son rôle reconnu dans la régulation des gènes et la traduction des protéines, en particulier dans la symbiose telle que celle des nématodes, le système ARNi n’a jamais été étudié chez les CMA. Pareil pour le cas du mécanisme de détection de la lumière bleue. Seules quelques études ont montré que la lumière bleue peut affecter la germination des spores et la croissance des hyphes des CMA, cependant son mécanisme n'a pas été décrit. Dans le cas de l’horloge circadienne, même si le rythme circadien est omniprésent chez les champignons et que le rythme diurne de la croissance des hyphes a été reporté dans les CMA dans une étude sur le terrain, le mécanisme demeure méconnu. Le génome et le transcriptome du CMA modèle Rhizophagus irregularis isolat DAOM 197198, étaient publiquement disponibles et ils ont été exploité dans mon projet. L'objectif de ma thèse de doctorat visait donc à étudier l'évolution du système ARNi, du mécanisme de détection de la lumière bleue et de l'horloge circadienne dans le génome de R. irregularis à l'aide d'approches biologiques et bioinformatiques. Les objectifs spécifiques étaient de: 1) déterminer si le système ARNi est conservé dans le génome de R. irregularis et d’analyser les traits évolutifs de ses protéines; 2) décrire le mécanisme de détection de la lumière bleue dans le génome R. irregularis ; 3) étudier le mécanisme circadien fongique dans le génome de R. irregularis. J'ai analysé les données génomiques et transcriptomiques pour rechercher les mécanismes conservés du système ARNi de R. irregularis et de certaines espèces de CMA qui lui sont apparentées. Deux phases du cycle de vie de R. irregularis (la phase de la germination des spores et la phase symbiotique avec des racines) ont été utilisées pour déterminer les profils d'expression des gènes en utilisant la PCR quantitative par transcriptase inverse (qPCR). J'ai identifié des traits évolutifs particuliers dans le système ARNi de R. irregularis, tels que le transfert de gènes horizontal (HGT) d’un gène important codant la protéine ribonucléase III, d’origine des cyanobactéries qui n’a jamais été observé chez aucun eucaryote. J'ai également trouvé et identifié un ancien mécanisme de détection de la lumière bleue corrélé à l'horloge circadienne. J’ai trouvé que le gène frequency est conservé dans le génome R. irregularis et que son expression est influencée par l’exposition à la lumière bleue. Ce qui est intéressant est que la protéine la plus importante de l’horloge circadienne (FRQ) n’a jamais été retrouvée dans d’autres lignées primitives fongiques, y compris chez Mucoromycotina, un sous-embranchement fongique considéré comme le plus proche des CMA. Les résultats de mon projet de doctorat a significativement contribuer à la progression de nos connaissances sur les mécanismes importants qui régulent l’expression des gènes chez les CMA qui sont des partenaires symbiotiques des racines des plantes et les plus anciens et les plus répandus dans les écosystèmes. Mes résultats apportent également de nouvelles informations sur le transfert des gènes entre les cyanobactéries et les CMA, et ils ont élargi les connaissances de l'évolution du gène frq chez les champignons. De plus, la présence de gène frq dans le génome de R. irregularis ouvre la voie à l’étude de la chronologique de la symbiose MA, qui peut être le modèle intéressant d’holobiontes des plantes.Arbuscular mycorrhizal (AM) symbiosis is formed by plant roots and arbuscular mycorrhizal fungi (AMF) which are the oldest symbiotic partners of plants and have evolved at least 460 million years ago with the emergence and evolution of land plants. AMF are also the most ubiquitous symbiotic partner of plants as they can colonize more than 80% of vascular plant species. AMF are an early diverged fungal lineage whose phylogenetic position is still under debate. AMF are obligatory plant root symbionts which depend on a source of carbon from the photosynthesis of host plants. In exchange, AMF help plants to absorb various essential soil nutrients, such as phosphorus and transfer these nutrients through their hyphae which have grown into and colonized plant root cells in which they form a structure called an arbuscule. The nutrient allocation and interlocked metabolic pathways between the fungus and the host underwent selective pressure as symbiotic partners. Moreover, AMF hyphae act as an ecological niche for various soil bacteria and other fungi, thus forming the backbone of the rhizospheric part of the plant. AM symbiosis is an essential element to understand plant physiology and ecosystem. Despite the crucial roles of AMF in ecosystems, their genetics and evolution are far from being understood. The RNA interference (RNAi) system, the blue light sensing mechanism and the circadian clock are important mechanisms which regulate expression of various genes in fungi. Although it has an acknowledged role in gene regulation, especially with symbiosis as well as reflected selective pressures on core proteins in the cases of other symbiotic organisms such as nematode worms, the RNAi system has never been considered in AMF. The same is true for the case of blue light sensing mechanisms. Only a few studies showed that blue light can affect spore germination and hyphae growth of AMF, but the mechanism was not addressed. In the case of the circadian clock, even though circadian rhythms are ubiquitous in fungi and a diurnal rhythm of hyphae growth was reported in AMF during a field level study, the mechanism was unknown. Currently, the genome and transcriptome of the model AM fungus Rhizophagus irregularis isolate DAOM 197198, are publicly available and they were used in my studies. The objective of my Ph.D. project was therefore to study the evolution of the RNAi system, blue light sensing mechanisms and the circadian clock in R. irregularis genome using both bioinformatic and molecular biological approaches. The specific objectives of my Ph.D. project were: 1) to investigate whether the RNAi system is conserved in the genome of R. irregularis and explore the evolutionary traits in its core proteins; 2) to describe the blue light sensing mechanism in the genome of R. irregularis; and 3) to search for a fungal circadian mechanism in the genome of R. irregularis. I surveyed genomic and transcriptomic data to search for conserved elements of the RNAi system of R. irregularis and its relatives. Two life stages of the R. irregularis lifecycle (germination of spores without roots and established mycorrhizal symbiosis) were investigated for gene expressional profiles using reverse-transcriptase quantitative PCR (qPCR). I identified particular evolutionary traits in R. irregularis RNAi system, such as horizontal gene transfer (HGT) of its core gene coding ribonuclease III protein from autotrophic cyanobacteria, which has never been reported in any eukaryotes so far. I also found and identified an ancient mechanism of blue light sensing which is related to circadian clock. It was intriguing to find a conserved core gene (frequency) that responds to light exposure in the genome of this underground plant-root symbiont. At the same time, the circadian clock core component (FRQ) was not found in other basal fungal lineages including Mucoromycotina, a fungal subphylum which is considered as the closest relative of AMF. The outcome of my Ph.D. project advanced our knowledge on important mechanisms which regulate the expression of various genes in the oldest and most ubiquitous symbiotic partner of plants. My results also provide new insight on the intimacy between cyanobacteria and AMF which resulted in a unique HGT in the RNAi system. It also expands the knowledge of evolution of the circadian frq gene in fungi. Furthermore, the presence of circadian clock and output genes in R. irregularis opens the door to the chronological study of AM symbiosis, which can be used as a model for the plant holobiont

Quantifying the environmental burdens of the hot mix asphalt (HMA) pavements and the production of warm mix asphalt (WMA)

AbstractAsphalt pavement has significant environmental burdens throughout its life cycle. A life cycle assessment (LCA) model is used to quantify the environmental burdens for material, construction, maintenance and use phases of hot mix asphalt (HMA) pavement. Two peer reviewed journals have been used to collect all of the inventory loadings as an input for the LCA model and ten impact categories have been evaluated as output. The result of the inventory analysis is a summary of all inflows and outflows related to the “functional unit”. The result of each impact category is the total of all the individually characterized inventory loadings in each category. Each life cycle phase of HMA pavement has been quantified on these ten impact categories and a comparison provided among the phases to understand the percentage contribution to the environment. Human and eco toxicity values are higher for the material phase, whereas the rest of the impact categories are significant in the use phase. The material phase contributes 97% of the overall human toxicity in water from standpoint of asphalt pavements, whereas in the material phase the production of bitumen is responsible for 90% human and eco toxicity in terms of air based burden. As a solution, the life cycle inventory of WMA has been estimated and reduction only done in HMA production. From analysis, it was estimated that WMA provides a reduction of 29% on the acidification impact and 25% reduction on both fossil fuel consumption and photo oxidant formation impact of HMA

Investigation of Rheological Properties of Blended Cement Pastes Using Rotational Viscometer and Dynamic Shear Rheometer

To successfully process concrete, it is necessary to predict and control its flow behavior. However, the workability of concrete is not completely measured or specified by current standard tests. Furthermore, it is only with a clear picture of cement hydration and setting that full prediction and control of concrete performance can be generalized. In order to investigate the rheological properties of blended cement pastes, a rotational viscometer (RV) was used to determine the flow characteristics of ordinary and blended pastes to provide assurance that it can be pumped and handled. Additionally, a dynamic shear rheometer (DSR) was used to characterize both the viscous and elastic components of pastes. Ordinary Portland cement paste and blended pastes (slag, fly ash, and silica fume) were investigated in this study. /e stress and strain of the blended specimens were measured by the DSR, which characterizes both viscous and elastic behaviors by measuring the complex shear modulus (the ratio of total shear stress to total shear strain) and phase angle (an indicator of the relative amounts of recoverable and nonrecoverable deformation) of materials. Cement pastes generally exhibit different rheological behaviors with respect to age, mineral admixture type, and cement replacement level

Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties

Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications

A STUDY OF MOTION CHARACTERISTICS LED BY CONNECTION METHODS AND POSITIONS OF A WAVE-ENERGY CONVERTER IN A REGULAR WAVE

The potential of wave power as an alternative energy resource is being studied to address problems associated with fossil fuel exhaustion and environmental pollution. In this paper, to improve the power generation efficiency of a floating-type wave-energy converter that has an activating body, the effects of the positions of a connecting bridge and different connecting methods between a main body and the activating body of the wave-energy converter were studied. In order to research the activating body’s motion characteristics that are caused by the changes of connecting bridge’s position and connecting methods; hinged or fixed connector, the wave-energy converter was modeled and simulated by using a commercial software. The moment and angular velocity of the axis of power generation were measured from the results of simulations and then the power outputs were calculated based on the moment and angular velocity. The outputs, which were analyzed under several regular wave conditions, were compared to each other