No description available.

The ubiquitous nature of microorganisms and their specificity to certain locations make them potentially useful for forensic investigators. Advances in microbial profiling techniques have made it possible to compare microbial community profiles obtained from evidence or crime scenes to individuals and vice versa. Profiling microbial communities associated with cadaver decomposition may provide useful information concerning post-mortem intervals and aid in the identification of clandestine graves. Four experiments using pigs as human decomposition analogues were performed over the course of 2011 and 2012 in southern Ontario to document changes in soil microbiology following decomposition. Studies were conducted in the spring and summer to document the effect of environmental conditions on the decomposition process and subsequent changes in gravesoil microbiology. Microbial activity was measured using a fluorescein diacetate assay as a preliminary indicator of changes within the soil microbial population. Both decreases and increases in microbial activity were observed throughout each decomposition experiment indicating that the microbial response to decomposition is complex. It is believed that environmental conditions and decomposition rates play a role in determining how taphonomic events affect soil microbial activity. Fatty acid methyl esters (FAME) profiling was used document community level changes throughout decomposition. Shifts in FAMEs profiles were brought on by the onset of active decay and persisted through to the dry remains stage. The fatty acids 3OH 12:0, 12:0, 16:0 and 18:0 were frequently found in higher amounts in gravesoils and may prove useful as markers of cadaver decomposition. Metagenomic profiles of soil microbial communities were obtained using Illumina?? sequencing. Decomposition was associated with changes v in microbial community composition. This allowed gravesoil samples to be differentiated from control samples for an extended period of time. Bacteria responsible for the shift in microbial profiles are those commonly associated with cadaver decomposition. Both sets of soil profiles indicated that weather had an effect on microbial community composition. Results highlight the need to document natural changes in microbial communities over seasons and years to establish normal microbial patterns to effectively use soil microbial profiles as post-mortem interval or clandestine grave indicators.

It is well known that the elderly often manifest chronic low-grade inflammation. This phenomenon, called “inflamm-aging,” is postulated to contribute to increased susceptibility towards infectious diseases and an overall increase in frailty. We have proposed examining the gut microbiome as a potential mediator of these changes. Gut microbial communities influence the host immune system; often dictating an individual’s health status. Thus, harmful gut microbiome changes, termed dysbiosis, are associated with poor health in the elderly. We first sought to understand the key immunological, physiological and microbiome changes occurring with age (Chapter 3). Our data reveals immune impairments in aged mice, with increased intestinal permeability, systemic inflammation and alterations in the functions of myeloid cell populations. However, our aged germ-free (GF) mice are protected from these outcomes, indicating that the old microbiome may play a strong role in these age-associated impairments. To study this further, we have colonized young and old GF mice with the “young” or “old” microbiota in order to determine whether the relationship between microbial dysbiosis with age and health status is correlative or causative (Chapter 4). Interestingly, young GF mice colonized with old microbiota have significantly increased permeability, systemic inflammation and an influx of Ly6Chigh monocytes when compared to those colonized with the young microbiota. By using transgenic mice (TNF-/- mice), or by reducing systemic TNF levels via therapeutics, we were able to reduce some aspects of microbial dysbiosis and age-associated inflammation (Chapter 5). Our data suggests that harmful changes to the gut microbiome composition with age initiate a cycle of negative events that ultimately result in increased inflammatory myeloid cell recruitment, increased intestinal permeability and an overall increase in systemic inflammation in old mice. By identifying these key changes, we can work towards developing effective therapeutics that promotes healthy aging and protection against infectious diseases. / Thesis / Master of Science (MSc) / Élie Metchnikoff first coined the term “dysbiosis” when he described the imbalance in microbial populations that could result anywhere in the body. Since then, numerous studies have examined the role of the intestinal microbiota in defense against pathogens. Metchnikoff also suggested that the gut composition and function is altered with age and this can in turn; increase the host’s susceptibility towards infectious diseases. My research aims to characterize the role of microbial dysbiosis on the immune defects with age. To do so, I will be utilizing a unique set of mice, called gnotobiotic mice. These mice are housed under specific germ-free conditions and contain no microbiome. Thus, they provide us with the ideal model to study the effects of the microbiome on immune function. The findings from these studies will help in the development of preventative and therapeutic alternatives to provide the elderly with more years of healthy, independent living.

L’anthropisation est la principale source de perturbations dans les grottes, et dans la grotte de Lascaux cela a entrainé la prolifération de microorganismes et des altérations de paroi menaçant sa conservation. L’objectif de cette thèse était de mieux comprendre l’écologie des microorganismes colonisant la grotte de Lascaux, en identifiant sa communauté microbienne à différentes échelles spatio-temporelles, de caractériser les facteurs qui structurent cette communauté et d’en étudier la dynamique fonctionnelle en utilisant le séquençage à haut débit d’acides nucléiques, une nouvelle approche à Lascaux. Une comparaison à l’échelle régionale de différentes grottes de Dordogne, plus ou moins anthropisées a été réalisée, puis à une échelle locale avec l’étude de salles de Lascaux, le Passage pour évaluer le rôle des substrats minéraux, et l’Abside qui présente deux types d’altérations (taches noires et zones sombres). Nos résultats montrent que les grottes anthropisées (dont Lascaux) ont des communautés microbiennes particulières. Le substrat minéral structure davantage la communauté du Passage que la présence de taches. Dans l’Abside, bien que les zones sombres soient visuellement différentes des taches noires, les communautés microbiennes présentent des similarités fortes, et notamment le rôle des interactions entre les collemboles, les champignons noirs et des bactéries. Enfin, les profils métatranscriptomiques diffèrent en fonction des salles et de la présence de taches. Ce projet a permis de caractériser l’écologie de la communauté microbienne de Lascaux et permet de mieux comprendre le fonctionnement microbien de la grotte / Anthropisation is the main source of disturbance in the caves, and in the cave of Lascaux it has led to the proliferation of microorganisms and alterations of the wall threatening its conservation.The objective of this thesis was to better understand the ecology of microorganisms colonizing the cave of Lascaux, by identifying its microbial community at different spatio-temporal scales, to characterize the factors that structure this community and to study its functional dynamics in using high throughput sequencing of nucleic acids, a new approach to Lascaux.A regional comparison of different Dordogne caves, more or less anthropised was carried out, then at a local scale with the study of Lascaux rooms, the Passage to evaluate the role of mineral substrates, and the Apse which presents two types of alterations (black spots and dark areas).Our results show that anthropogenic caves (including Lascaux) have particular microbial communities. The mineral substrate structures the Passage community more than the presence of spots. In the Apse, although dark areas are visually different from black spots, microbial communities show strong similarities, including the role of interactions between collembolans, black fungi, and bacteria. Finally, the metatranscriptomic profiles differ according to the rooms and the presence of spots.This project has made it possible to characterize the ecology of the Lascaux microbial community and to better understand the microbial functioning of the cave

Objetivou-se com este trabalho avaliar o potencial agrícola do lodo de esgoto produzido no estado de São Paulo, bem como, verificar a possibilidade de interação entre a composição química e a abundância relativa de bactérias no lodo. Foram realizadas coletas de amostra de lodo de esgoto em 19 estações de tratamento de esgoto, em três épocas distintas. Nas amostras provenientes das três épocas foram determinados as concentrações dos 16 hidrocarbonetos policíclicos aromáticos (HPAs) listados como prioritários no monitoramento ambiental pela USEPA (acenafteno, acenaftileno, antraceno, benzo(a)antraceno, benzo(a)pireno, benzo(b)fluoranteno, benzo(ghi)perileno, benzo(k)fluoranteno, criseno, dibenzo(a,h)antraceno, fenantreno, fluoranteno, fluoreno, indeno(1,2,3-cd)pireno, naftaleno e pireno). Nas amostras da segunda época de coleta, além da presença de HPAs, determinou-se as concentrações de poluentes orgânicos emergentes (hormônios, produtos farmacêuticos e produtos de uso industrial), realizou-se a caracterização completa segundo a Resolução CONAMA 375/2006 (umidade, pH, N-Kjeldahl e inorgânico, carbono orgânico, cálcio, potássio, fósforo, magnésio, enxofre, boro, cobre, ferro, níquel, manganês, molibdênio, selênio, zinco, alumínio, arsênio, bário, cádmio, cromo, chumbo, mercúrio e sódio) e a caracterização da comunidade bacteriana através de metodologia independente de cultivo (sequenciamento illumina). Os macronutrientes em maiores concentrações no lodo de esgoto são: N > Ca > S > P > Mg > K. Os elementos inorgânicos Ni e Zn apresentaram concentração superior à máxima permitida para utilização agrícola pela resolução Conama 375/2006 em 1 e 3 amostras, respectivamente. A substância inorgânica que mais limita o enquadramento do lodo de esgoto como adubo orgânico (Instrução Normativa 27/2006) é o Hg. Os compostos benzilparabeno, bisfenol AF (BPAF), ácido perfluorooctanoico (PFOA) e tetrabromobisfenol A (TBBPA) não foram detectados. Por outro lado, cimetidina, metilparabeno, bisfenol A (BPA) e triclocarban foram detectados nas 19 amostras avaliadas. O composto presente em maior concentração é o triclocarban. As concentrações de hidrocarbonetos policíclicos aromáticos são baixas, de acordo com a norma Europeia. Os filos Proteobacteria e Bacteroidetes estão presentes em maior abundância relativa. Existe uma comunidade bacteriana núcleo nas estações de tratamento de esgoto do estado de São Paulo, composta por 81 gêneros, presentes nas 19 ETEs avaliadas, dos quais, os que estão em maior abundância relativa são Treponema, Clostridium, Propionibacterium, Syntrophus e Desulfobulbus. A elevação do pH a valores próximos de 12 reduz a diversidade microbiana. Considerando a abundância relativa e a composição química do lodo de esgoto, as estações podem ser agrupadas em três grupos distintos, sendo que um deles é influenciado principalmente pelos teores de Ca, Zn e Cu, o outro pelos teores de Fe e S e o terceiro grupo que foi influenciado pelos demais fatores avaliados. / The aim of this work was to evaluate the agricultural potential of sewage sludge produced in the São Paulo state - Brazil, as well as to verify the possibility of interaction between the chemical composition and sewage sludge bacterial abundance. Samples were collected from 19 wastewater treatment plants in three different periods. On the samples from the three times were determined the presence and concentrations of 16 polycyclic aromatic hydrocarbons (HPAs) that are listed as priorities in environmental monitoring by the USEPA (acenaphthene, acenaphthylene, anthracene, benzo (a) anthracene, benzo (a) pyrene, benzo (b) fluoranthene, benzo (ghi) perylene, benzo (k) fluoranthene, chrysene, dibenz (a, h) anthracene, phenanthrene, fluoranthene, fluorene, indeno (1,2,3-cd) pyrene, naphthalene and pyrene). On the samples of the second collect time, besides HPAs, were determined the concentrations of emerging organic pollutants (hormones, pharmaceuticals and industrial products). It was performed the complete characterization according to CONAMA 375/2006 (moisture, pH, Kjeldahl and inorganic Nitrogen, organic carbon, calcium, potassium, phosphorus, magnesium, sulfur, boron, copper, iron, nickel, manganese, molybdenum, selenium, zinc, aluminum, arsenic, barium, cadmium, chromium, lead, mercury and sodium); and characterization of bacterial communities through cultivation-independent methods (Illumina sequencing). Macronutrients in higher concentrations in sewage sludge are: N > Ca > S > P > Mg > K. The inorganic elements Ni and Zn showed up in higher concentration than the maximum allowable for agricultural use by CONAMA Resolution 375/2006, at 1 and 3 samples, respectively. The inorganic element that most limits sewage sludge usage as organic fertilizer (MAPA, 2006) is the Hg. The compounds benzylparaben, bisphenol AF (BPAF), perfluorooctanoic acid (PFOA) and tetrabromobisphenol A (TBBPA) were not detected. On the other hand, methylparaben, cimetidine, bisphenol A (BPA) and triclocarban were detected in all 19 samples. The compound present in highest concentration is triclocarban. The concentrations of polycyclic aromatic hydrocarbons are low, according to the European standard. Proteobacteria and Bacteroidetes phyla are present in greatest relative abundance. There is a bacterial core in the sewage sludge treatment plants of the São Paulo State, comprising 81 genera present in all WWTPs evaluated. Those who are at a higher relative abundance are Treponema, Clostridium, Propionibacterium, Syntrophus and Desulfobulbus. The elevation of pH to values close to 12 reduces the microbial diversity. Considering the relative abundance and chemical composition of sewage sludge, the stations can be grouped into three distinct groups, one of which is influenced mainly by Ca, Zn and Cu, the other by Fe and S and the third group that was influenced by the others evaluated factors.

Objetivou-se com este trabalho avaliar o potencial agrícola do lodo de esgoto produzido no estado de São Paulo, bem como, verificar a possibilidade de interação entre a composição química e a abundância relativa de bactérias no lodo. Foram realizadas coletas de amostra de lodo de esgoto em 19 estações de tratamento de esgoto, em três épocas distintas. Nas amostras provenientes das três épocas foram determinados as concentrações dos 16 hidrocarbonetos policíclicos aromáticos (HPAs) listados como prioritários no monitoramento ambiental pela USEPA (acenafteno, acenaftileno, antraceno, benzo(a)antraceno, benzo(a)pireno, benzo(b)fluoranteno, benzo(ghi)perileno, benzo(k)fluoranteno, criseno, dibenzo(a,h)antraceno, fenantreno, fluoranteno, fluoreno, indeno(1,2,3-cd)pireno, naftaleno e pireno). Nas amostras da segunda época de coleta, além da presença de HPAs, determinou-se as concentrações de poluentes orgânicos emergentes (hormônios, produtos farmacêuticos e produtos de uso industrial), realizou-se a caracterização completa segundo a Resolução CONAMA 375/2006 (umidade, pH, N-Kjeldahl e inorgânico, carbono orgânico, cálcio, potássio, fósforo, magnésio, enxofre, boro, cobre, ferro, níquel, manganês, molibdênio, selênio, zinco, alumínio, arsênio, bário, cádmio, cromo, chumbo, mercúrio e sódio) e a caracterização da comunidade bacteriana através de metodologia independente de cultivo (sequenciamento illumina). Os macronutrientes em maiores concentrações no lodo de esgoto são: N > Ca > S > P > Mg > K. Os elementos inorgânicos Ni e Zn apresentaram concentração superior à máxima permitida para utilização agrícola pela resolução Conama 375/2006 em 1 e 3 amostras, respectivamente. A substância inorgânica que mais limita o enquadramento do lodo de esgoto como adubo orgânico (Instrução Normativa 27/2006) é o Hg. Os compostos benzilparabeno, bisfenol AF (BPAF), ácido perfluorooctanoico (PFOA) e tetrabromobisfenol A (TBBPA) não foram detectados. Por outro lado, cimetidina, metilparabeno, bisfenol A (BPA) e triclocarban foram detectados nas 19 amostras avaliadas. O composto presente em maior concentração é o triclocarban. As concentrações de hidrocarbonetos policíclicos aromáticos são baixas, de acordo com a norma Europeia. Os filos Proteobacteria e Bacteroidetes estão presentes em maior abundância relativa. Existe uma comunidade bacteriana núcleo nas estações de tratamento de esgoto do estado de São Paulo, composta por 81 gêneros, presentes nas 19 ETEs avaliadas, dos quais, os que estão em maior abundância relativa são Treponema, Clostridium, Propionibacterium, Syntrophus e Desulfobulbus. A elevação do pH a valores próximos de 12 reduz a diversidade microbiana. Considerando a abundância relativa e a composição química do lodo de esgoto, as estações podem ser agrupadas em três grupos distintos, sendo que um deles é influenciado principalmente pelos teores de Ca, Zn e Cu, o outro pelos teores de Fe e S e o terceiro grupo que foi influenciado pelos demais fatores avaliados. / The aim of this work was to evaluate the agricultural potential of sewage sludge produced in the São Paulo state - Brazil, as well as to verify the possibility of interaction between the chemical composition and sewage sludge bacterial abundance. Samples were collected from 19 wastewater treatment plants in three different periods. On the samples from the three times were determined the presence and concentrations of 16 polycyclic aromatic hydrocarbons (HPAs) that are listed as priorities in environmental monitoring by the USEPA (acenaphthene, acenaphthylene, anthracene, benzo (a) anthracene, benzo (a) pyrene, benzo (b) fluoranthene, benzo (ghi) perylene, benzo (k) fluoranthene, chrysene, dibenz (a, h) anthracene, phenanthrene, fluoranthene, fluorene, indeno (1,2,3-cd) pyrene, naphthalene and pyrene). On the samples of the second collect time, besides HPAs, were determined the concentrations of emerging organic pollutants (hormones, pharmaceuticals and industrial products). It was performed the complete characterization according to CONAMA 375/2006 (moisture, pH, Kjeldahl and inorganic Nitrogen, organic carbon, calcium, potassium, phosphorus, magnesium, sulfur, boron, copper, iron, nickel, manganese, molybdenum, selenium, zinc, aluminum, arsenic, barium, cadmium, chromium, lead, mercury and sodium); and characterization of bacterial communities through cultivation-independent methods (Illumina sequencing). Macronutrients in higher concentrations in sewage sludge are: N > Ca > S > P > Mg > K. The inorganic elements Ni and Zn showed up in higher concentration than the maximum allowable for agricultural use by CONAMA Resolution 375/2006, at 1 and 3 samples, respectively. The inorganic element that most limits sewage sludge usage as organic fertilizer (MAPA, 2006) is the Hg. The compounds benzylparaben, bisphenol AF (BPAF), perfluorooctanoic acid (PFOA) and tetrabromobisphenol A (TBBPA) were not detected. On the other hand, methylparaben, cimetidine, bisphenol A (BPA) and triclocarban were detected in all 19 samples. The compound present in highest concentration is triclocarban. The concentrations of polycyclic aromatic hydrocarbons are low, according to the European standard. Proteobacteria and Bacteroidetes phyla are present in greatest relative abundance. There is a bacterial core in the sewage sludge treatment plants of the São Paulo State, comprising 81 genera present in all WWTPs evaluated. Those who are at a higher relative abundance are Treponema, Clostridium, Propionibacterium, Syntrophus and Desulfobulbus. The elevation of pH to values close to 12 reduces the microbial diversity. Considering the relative abundance and chemical composition of sewage sludge, the stations can be grouped into three distinct groups, one of which is influenced mainly by Ca, Zn and Cu, the other by Fe and S and the third group that was influenced by the others evaluated factors.

Seed germination has many impacts on the uses of seeds, and is an important subject for study. Seed germination is regulated at both transcriptional and post-transcriptional levels. Therefore, it is important to study how polyadenylation regulates gene expression during seed germination. To this end, a modified Illumina GAIIx sequencing protocol (described in Chapter Two) was developed that allows deep coverage of poly(A) site position and distribution. Alternative polyadenylation (APA) regulates gene expression by choosing one potential poly(A) site on a precursor RNA consequentially shortening/lengthening the mRNA relative to other possible sites. To further explore this phenomenon, genes affected by APA during seed germination and other developmental stages were identified (Chapter Three). These genes were categorized based on the location of poly(A) sites. Several genes were chosen to demonstrate how APA, especially that occurring in the coding regions and 5’ untranslated regions, might down regulate gene expression by generating truncated transcripts. In animal oocytes, maternally-derived mRNAs are stored with short poly(A) tails and reactivated by the cytoplasmic polyadenylation complex. It has been reported that seeds also contain stored mRNAs. Moreover, germination and its completion are less sensitive to de novo transcription inhibitors than to poly(A) polymerase inhibitors. Together, these considerations suggest that stored RNA without or with a short poly(A) tail (stored, unadenylated RNA) may be present in dry seed and function in seed germination upon reactivation by cytoplasmic polyadenylation. To further explore this, in Chapter Four, mRNA polyadenylation was studied through the course of germination using a combination of transcriptional inhibitors and the modified sequencing protocol described in Chapter Two. 273 putative stored, unadenylated RNAs were identified. Gene ontology analysis revealed that genes whose products are involved in translation are overrepresented; these genes encode 21 60S- and 10 40S-ribosomal proteins. These results indicate that transcripts whose products are involved in translation might be a major component of the stored, unadenylated RNA pool and, more importantly, translation might be the first cellular process to be activated during seed germination.

RNA-seq transcriptome analysis of Chenopodium quinoa at different water treatment levels was conducted in a greenhouse study using four water treatments (field capacity to drought) on a valley ecotype quinoa (variety Ingapirca) and an Altiplano Salares ecotype quinoa (variety Ollague). Physiological results support the earlier findings that the Salares ecotypes display greater tolerance to drought-like stress conditions than the valley ecotypes (as determined by growth rate, photosynthetic rate, stomatal conductance, and stem water potential). cDNA libraries from root tissue sample for each treatment x variety combination were sequenced using Illumina Hi-Seq technology in an RNA-seq experiment. De novo assembly of the transcriptome generated 20,337 unique transcripts. Gene expression analysis of the RNA-seq data identified 462 putative gene products that showed differential expression based on treatment and 27 putative gene products differential expressed based on variety x treatment, including significant increasing expression in the root tissue in response to increasing water stress. BLAST searches and gene ontology analysis show an overlap with drought tolerance stress and other abiotic stress mechanisms.

No description available.

La connaissance de la diversité microbienne des milieux ultramafiques est essentielle pour établir le fonctionnement écologique de ces milieux, qui présentent de fortes teneurs en Ni et sont caractérisés par une flore particulière, e.g. plantes hyperaccumulatrices de Ni. La rhizosphère des hyperaccumulateurs comporte une forte proportion de bactéries résistantes au Ni, qui peuvent aussi agir sur la nutrition des plantes et sur les propriétés physico-chimiques du sol. Le premier défi de cette thèse a été de cerner le déterminisme de la diversité bactérienne de la rhizosphère d’hyperaccumulateurs de Ni. Le second a été de tester l'intérêt de souches PGPR (Plant Growth Promoting Rhizobacteria) pour optimiser l'agromine à partir d'interactions entre les rhizobactéries et les hyperaccumulateurs de Ni. La démarche s'est appuyée sur un ensemble de prospections dans deux régions climatiques et sur des analyses de séquençage haut débit. Des tests de cultures de plantes hyperaccumulatrices inoculées ont également été conduits. Les résultats montrent que le déterminisme de la diversité bactérienne est variable selon l'échelle spatiale. A l'échelle mondiale, le type de végétation est le facteur majeur structurant les communautés bactériennes, elle-même contrôlée indirectement par le climat. L’influence directe du climat (température et humidité) sur la diversité est significative mais moindre. A l'échelle d'une région climatique, la physico-chimie des sols ultramafiques structure et détermine la diversité des communautés bactériennes rhizosphériques. Enfin, l'inoculation de souches PGPR fortement bioaccumulatrices de Ni modifie la dynamique du Ni dans le sol, ce qui démontre qu'il existe une compétition pour le Ni entre la plante et la bactérie inoculée. En conclusion, le déterminisme de la diversité des communautés bactériennes rhizosphériques est dépendant de l'échelle spatiale considérée. En outre, le choix de la souche PGPR à inoculer, dans un contexte d'amélioration de l'agromine du Ni, est primordial. / Knowledge of the microbial diversity in ultramafic areas is essential to establish the ecological functioning of these environments, which display high level of Ni and are characterized by the presence of particular plants, e.g. Ni hyperaccumulators. The rhizosphere of these plants promotes a high proportion of Ni resistant bacteria that can act on plant nutrition and soil physicochemical properties. The first challenge of this thesis was to understand the bacterial rhizosphere diversity of Ni hyperaccumulators. The second was to test the interest of PGPR (Plant Growth Promoting Rhizobacteria) strains in order to improve agromining based on rhizobacteria and Ni hyperaccumulators interactions. The approach was based on two-contrasted climatic areas prospection and on high-throughput sequencing analyzes. Tests on culture of hyperaccumulator plants inoculated were also conducted. The results show that the determinism of this bacterial diversity is variable according to the spatial scale. On a global scale, the vegetation type, indirectly influenced by the climate, is the major factor structuring bacterial communities. The direct influence of the climate (temperature and humidity) on bacterial diversity is significant but lower. At the scale of a climatic region, the physic-chemistry of ultramafic soils structures and determines the rhizosphere bacterial community diversity. Finally, the inoculation of highly Ni bioaccumulative PGPR strains modifies the Ni dynamic in the soil, demonstrating that there is a competition for this metal between the inoculated bacteria and the hyperaccumulator plant. In conclusion, the rhizosphere bacterial community diversity is dependent on the considered spatial scale. Furthermore, these results emphasize how the choice of the PGPR strain to inoculate is important in order to improve Ni agromining.