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Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

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A Terra Preta Antropogênica (TPA) tem essa denominação porque é encontrada em sítios arqueológicos, onde viveram grupos pré-históricos e é considerada um dos solos mais férteis do mundo. Nela é encontrada grande quantidade de material deixado por grupos indígenas como fragmentos cerâmicos, artefatos líticos, e especialmente carvão pirogênico. Estudos realizados com o carvão pirogênico verificaram que ele aumenta a capacidade de trocas catiônicas nesses solos. Por meio de microscopia de fluorencência, foi observada a presença de microrganismos habitando esse carvão, no entanto, não se sabe quais seriam. Devido à falta de informações sobre a diversidade bacteriana nessas estruturas, este trabalho estudou a diversidade bacteriana em amostras de carvão pirogênico de solos TPA coletadas nos sítios Lagoa Balbina (Amazônia Central- Amazonas) e Mina I (Amazônia Oriental - Pará), através de técnicas moleculares independentes de cultivo. O estudo visou também comparar essa diversidade com a encontrada no solo de onde carvão foi isolado. As estruturas de carvão foram separadas fisicamente dos solos e seu DNA genômico total extraído e usado como molde em reação de PCR utilizando oligonucleotídeos do gene 16S rRNA para o Domínio Bacteria. O produto da PCR foi clonado em vetor e os clones foram sequenciados e comparados com o banco de dados de 16S rRNA do RDPX. Com a construção das bibliotecas de clones do gene 16S rRNA a partir das amostras de carvão pirogênico observou-se que existe maior número de bactérias desconhecidas no carvão pirogênico do que no solo onde ele foi isolado. Acidobacteria foi o filo predominante nas bibliotecas de carvão pirogênico das duas localidades de estudo, assim como na biblioteca do solo do sítio Mina I. Já na biblioteca do solo do sítio Lagoa Balbina houve predominância do filo Firmicutes. Por meio do método de rarefação foi possível constatar uma menor riqueza de UTOs nas comunidades bacterianas presentes nas estruturas de carvão pirogênico quando comparado à riqueza de UTOs das comunidades bacterianas cujo habitat é o solo. Mas quando se compara a riqueza de UTOs entre as estruturas de carvão isoladas das duas localidades, observa-se que a riqueza é maior no sítio Mina I. Os valores obtidos com os índices de diversidade revelaram menor diversidade de UTOs nas bibliotecas obtidas para o carvão pirogênico das duas regiões estudadas se comparado dos valores para as bibliotecas obtidas do solo da mesma região. Os valores obtidos com os métodos não paramétricos revelaram maior riqueza de UTOs para as bibliotecas do carvão do sítio Mina I e solo TPA do sítio Balbina. A análise da PCA revelou que as bibliotecas do sítio Balbina mostraram-se altamente similares. Em adição, a análise com S-Libshuff, verificou que todas as bibliotecas comparadas são significativamente diferentes quanto à composição das comunidades bacterianas. O carvão pirogênico não é uma estrutura inerte, pois é capaz de ser habitado por diferentes bactérias e a sua estrutura da comunidade bacteriana é diferente daquela de onde ele foi segregado / Anthropogenic Dark Earth (ADE) has this denomination because it is found at archeological sites, where prehistoric groups lived, and it is considered one of the most fertile soils of the world. In this soil a great amount of material left by indigenous groups was found as ceramic fragments, lithic workmanships, and especially pyrogenic black carbon. Studies accomplished with the pyrogenic black carbon verified that it increases the capacity of cationic changes in soils. Through fluorescence microscopy, the presence of microorganisms was observed inhabiting that black carbon, however, this community is still unknown,due to the lack of information about the bacterial diversity in those structures.This work studied the bacterial diversity in samples of pyrogenic black carbon of ADE soils, collected at the sites Lagoa Balbina (Central Amazon) and Mina I (Oriental Amazon), through molecular techniques independent of cultivation. The study also sought to compare that diversity with the one of the soil where black carbon was isolated. The structures of black carbon were separate physically from the soils and total genomic DNA was extracted and used as template in a PCR reaction, using primers of the 16S rRNA gene for the Bacteria Domain. The PCR product was used for construction of clone libraries and the clones were sequenced and compared with the 16S rRNA of RDPX database. The 16S rRNA gene clone libraries from the samples of pyrogenic black carbon, it shown that is a larger number of unknown bacteria in the black carbon than in the soil where it was isolated. Acidobacteria was the predominant phylum in the pyrogenic black carbon libraries from the both studied places, as well as in the soil library from Mina I site. However in the library Lagoa Balbina site there was predominance of the phylum Firmicutes. Through the rarefaction method it was possible to verify a smaller richness of OTUs in the bacterial communities presents in the pyrogenic black carbon structures when compared to the OTUs richness of the bacterial soil communities.But, when the OTUs richness is compared among the isolated structures of pyrogenic black carbon of the two places, it is observed that the richness is higher in the Mina I site. The values from diversity indexes revealed smaller diversity of OTUs in the pyrogenic black carbon libraries when compared with the soil libraries for the two studied areas. The obtained values with the nonparametric methods revealed larger OTUs richness in the black carbon library of Mina I site and in the ADE soil library of the Balbina site. The PCA analysis showed that the libraries of the site Balbina site were highly similar. In addition, the analysis with S-Libshuff verified that all of the compared libraries were significantly different in bacterial communities composition. The pyrogenic black carbon is not an inert structure, once it is capable of being inhabited by different bacteria, and its bacterial community structure is different from that one where is was segregated

Smooth manifolds have been always understood intuitively as spaces that are infinitesimally linear at each point, and thus infinitesimally affine when forgetting about the base point. The aim of this thesis is to develop a general theory of infinitesimal models of algebraic theories that provides us with a formalisation of these notions, and which is in accordance with the intuition when applied in the context of Synthetic Differential Geometry. This allows us to study well-known geometric structures and concepts from the viewpoint of infinitesimal geometric algebra. Infinitesimal models of algebraic theories generalise the notion of a model by allowing the operations of the theory to be interpreted as partial operations rather than total operations. The structures specifying the domains of definition are the infinitesimal structures. We study and compare two definitions of infinitesimal models: actions of a clone on infinitesimal structures and models of the infinitesimalisation of an algebraic theory in cartesian logic. The last construction can be extended to first-order theories, which allows us to define infinitesimally euclidean and projective spaces, in principle. As regards the category of infinitesimal models of an algebraic theory in a Grothendieck topos we prove that it is regular and locally presentable. Taking a Grothendieck topos as a base we study lifts of colimits along the forgetful functor with a focus on the properties of the category of infinitesimally affine spaces. We conclude with applications to Synthetic Differential Geometry. Firstly, with the help of syntactic categories we show that the formal dual of every smooth ring is an infinitesimally affine space with respect to an infinitesimal structure based on nil-square infinitesimals. This gives us a good supply of infinitesimally affine spaces in every well-adapted model of Synthetic Differential Geometry. In particular, it shows that every smooth manifold is infinitesimally affine and that every smooth map preserves this structure. In the second application we develop some basic theory of smooth loci and formal manifolds in naive Synthetic Differential Geometry using infinitesimal geometric algebra.

Red alder (Alnus rubra) is a tree species with high economic and ecological importance. It is subject to defoliation during unpredictable, episodic outbreaks of tent caterpillars (Malacosoma spp.) that result in reduced growth, decreased wood production, unsightly appearance and mortality in severe cases. Alder trees are weakened by severe and repeated tent caterpillar defoliation, and this can increase the susceptibility of the trees to other pests, diseases and drought. Repeated attack by tent caterpillars can cause decline in red alder populations, which can have potential negative impacts on the ecological and economic benefits of the species. Evidence from other species has shown that plants produce phytochemicals for defense against herbivores at a cost to growth and reproduction, but the relative magnitude of the cost of allocating available resources to defense depends on the level of the resources, and the plant genotype. The quality of a plant as food for herbivores is influenced by leaf physical and biochemical traits, and these traits change during a growing season or upon attack by herbivores. My research aimed to explore the defense mechanisms of red alder against western tent caterpillars (Malacosoma californicum) and determine the resistance variation among and within red alder populations, and to evaluate red alder available resource (nitrogen) allocation to defense and growth. Bioassay feeding trials were conducted in 2014 and 2015 with western tent caterpillars (WTC) (M. californicum) on twenty red alder clones from ten provenances. Phenology and quality of red alder leaves as food for the defoliators were analyzed to determine if budburst, leaf chemical content, water content or physical traits are major determinants of western tent caterpillars preference for red alder leaves. In another experiment, one-year-old seedlings from 100 half-sib red alder families were treated with two levels of ammonium nitrate (NH4NO3) in two growing seasons in a common garden. Growth, herbivore defense-related traits and root nodulation were measured and ranked among the plant genotypes and between the two nitrogen (N) treatments. Leaves from the two N treatments and different alder families were also used for bioassay feeding trials with WTC larvae to determine effects of N and genotype on red alder herbivory resistance. In my final experiments, I harvested and analyzed leaves from three-year-old red alder trees from five different families on eight dates from early April to mid-October 2016 to quantify oregonin and total phenolics concentrations, and wound induction experiments were conducted to determine if the concentrations of the chemicals vary during a growing season and upon attack by insects. Alder clones and families differed in percentage leaf area eaten by caterpillars and in leaf defense traits. The concentrations of foliar phenolic compounds negatively correlated with the percentage leaf area eaten by the caterpillars, but the results suggest a threshold, above which the concentration of each of the chemicals appeared to reduce WTC feeding, individually. Particularly, foliar oregonin concentration above 20 % leaf dry weight consistently appeared to reduce feeding by caterpillars. N availability had significant effects on red alder seedling total dry biomass and leaf N concentration. There was a clear trade-off between red alder seedling growth, and content of the phenolic compounds and leaf thickness, which supports the growth-differentiation balanced hypothesis in relation to resource availability. The concentration of oregonin varied during the growing season and there were no significant responses of any of the measured compounds to wounding. The results suggest that red alder foliar oregonin, condensed tannin and total phenolics are constitutive defenses and are not wound-induced. The effects of leaf total phenolic and condensed tannin concentrations on insect herbivory have been documented by past studies but the effects of oregonin concentration in red alder leaves on tent caterpillar feeding is a novel finding. / Graduate / 2020-04-18

Cyclotides are a family of small and macrocyclic proteins that have been found in Violacaee and Rubiaceae plant species. These proteins contain a cystine knot: two disulfides bonds together with their connecting peptide backbone form an embedded ring which is penetrated by a third disulfide bond. The cyclotides have been attributed a wide range of biological activities, which in combination with their chemical stability and structural plasticity have made them attractive tools for pharmaceutical applications. The sequence of eleven novel cyclotides, vibi A-K, from Viola biflora was determined by the use of both chemical (extraction and characterization) and molecular biology (cDNA analyses) approaches. A clear discrepancy in the results from the two methods was observed. Additionally, one novel cyclotide, vodo O, was isolated from Viola odorata. To correlate cytotoxic potency to sequence, vodo O and vibi D, E, G and H were tested on a lymphoma cell line. Based on the presence or absence of a cis-Pro bond, the cyclotides are divided into the Möbius and bracelet subfamilies. The bracelet proteins have a higher net charge and are more cytotoxic potent than the Möbius ones. To explore these differences, charged and hydrophobic residues in varv A (Möbius) and cycloviolacin O2 (bracelet) were chemically modified and tested for their cytotoxicity. The net-charge of the two proteins was not important for the potency. The Glu residue in cycloviolacin O2 was crucial, while this residue was of minor importance in varv A. Oxidation of the single Trp residue declined the potency significantly in both proteins. To evaluate how the surface properties correlate to the degree of cytotoxic potency, models of all cyclotides hitherto tested were constructed by homology modelling. Calculations showed that the membrane orientation of varv A and cycloviolacin O2 differed significantly, which might explain their difference in potency

Against the background of past, recent and future climate change, the present thesis addresses elevational shifts of alpine treelines in the Swedish Scandes. By definition, treeline refers to the elevation (m a.s.l.) at a specific site of the upper trees of a specific tree species, at least 2 m tall. Based on historical records, the first part of the thesis reports and analyzes the magnitude of treeline displacements for the main trees species (Betula pubescens ssp. czerepanovii, Picea abies and Pinus sylvestris) since the early 20th century. The study covered a large and heterogeneous region and more than 100 sites. Concurrent with temperature rise by c. 1.4 °C over the past century, maximum treeline advances of all species amount to about 200 m. That is virtually what should be predicted from the recorded temperature change over the same period of time. Thus, it appears that under ideal conditions, treelines respond in close equilibrium with air temperature evolution. However, over most parts of the landscape, conditions are not that ideal and treeline upshifts have therefore been much smaller. The main reason for that discrepancy was found to be topoclimatic constraints, i.e. the combined action of geomorphology, wind, snow distribution, soil depth, etc., which over large parts of the alpine landscape preclude treelines to reach their potential thermal limit. Recorded treeline advance by maximum 200 m or so over the past century emerges as a truly anomalous event in late Holocene vegetation history. The second part of the thesis is focused more on long-term changes of treelines and one specific and prevalent mechanism of treeline change. The first part of the thesis revealed that for Picea and Betula, treeline shift was accomplished largely by phenotypic transformation of old-established stunted and prostrate individuals (krummholz) growing high above the treeline. In obvious response to climate warming over the past century, such individuals have transformed into erect tree form, whereby the treeline (as defined here) has risen. As a means for deeper understanding of this mode of positional treeline change, extant clonal spruces, growing around the treeline, were radiocarbon dated from megafossil remains preserved in the soil underneath their canopies. It turned out that Picea abies in particular may attain almost eternal life due to its capability for vegetative reproduction and phenotypic plasticity. Some living clones were in fact inferred to have existed already 9500 years ago, and have thus persisted at the same spot throughout almost the entire Holocene. This contrasts with other tree species, which have left no living relicts from the early Holocene, when they actually grew equally high as the spruce. Thereafter they retracted by more than 300 m in elevation supporting that also on that temporal scale, treelines are highly responsive to climate change. The early appearance of Picea in the Scandes, suggests that Picea “hibernated” the last glacial phase much closer to Scandinavia than earlier thought. It has also immigrated to northern Sweden much earlier than the old-established wisdom. The experiences gained in this thesis should constitute essential components of any model striving to the project landscape ecological consequences of possible future climate shifts.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Clones of the Eucalyptus grandis x Eucayptus nitens (GN) hybrids were produced and selected through the CSIR‟s breeding programmes for colder plantation sites in South Africa. Some GN clones consistently exhibit high and superior pulp properties, which makes them valuable for commercial plantations in South Africa. In nurseries, stockplants are usually seven cm in length and maintained at high (100 x1.5 m-2) planting density. However, rooting frequency varies with season and little is known about the impact of position of cuttings on overall rooting frequency of a clone. The aim of this study was to investigate the effect of size and planting density of stockplants in mini-hedges, on the yield and subsequent rooting of cuttings from various positions of GN clones of known rooting potential (i.e. GN 018B: difficult-to-root and PP 2107: easy-to-root clones). Stockplants (10 cm vs. 20 cm) were established at high (100 x 1.5 m-2) and at low (25 x 1.5 m-2) densities for GN 018B and PP 2107 under commercial nursery conditions in a polyethylene tunnel. Cuttings were harvested every two to three weeks in September-October 2010 (spring), December 2010-January 2011 (summer), April-May 2011 (autumn) and June-July 2011 (winter). The harvested material was 5 – 7 cm in length and the light intensity received by individual stockplants at the two planting density levels was recorded. Harvested cuttings from the three positions (apical, middle and basal shoots) were used for: (i) rooting experiments under nursery conditions, (ii) bio-stimulant analysis using the mung bean bioassay, and (iii) analysis of soluble sugars. Between spring and summer 2010, the two GN clones established at low density yielded a similar number of cuttings, but differences in the rooting frequencies were significant in favour of PP 2107 clone. Similar observations were made at high density in terms of production of cuttings, but the significant differences in the rooting observations were reversed between the clones. The GN 018B clone had low rooting rates in summer under nursery conditions but its tissue extracts promoted higher rooting in the bioassay during that time, when compared to spring. Spring and summer had similar effects on rooting responses of PP 2107 cuttings in nursery and bioassay experiments. For both clones, short stockplants produced fewer cuttings but had a higher rooting frequency than cuttings from tall stockplants, with a high rooting frequency recorded from basal cuttings. Similar results were observed in the bioassay experiments which showed high rooting potential of mung bean hypocotyls cuttings using tissue extracts of PP 2107 cuttings maintained at high planting density. Although apical cutting tissues had high concentration of sugars (i.e. sucrose, glucose and fructose), their rooting rates were usually lower at high and low planting density compared to middle and basal cuttings. Sucrose concentration was the highest sugar present in stockplants grown under low planting density. A higher and lower rooting frequency was also observed in autumn although the two clones responded differently to Quambalaria eucalypti (Sporothrix eucalypti) disease infestations. Position, size and genotype had a significant impact on type and concentration of sugar (i.e. sucrose, glucose and fructose), particularly in PP 2107 clone, although rooting rates in the bioassay did not correlate with sugar contents of Eucalyptus cuttings. High carbohydrate (i.e. soluble sugar) content and auxin concentration increased production and subsequent rooting of cuttings across both clones, particularly in spring. Furthermore, rooting was enhanced by relatively higher light intensity intercepted by individual stockplants and in particular the GN 018B clone. Light intensity in the high and low planting densities caused variation in the rooting frequencies thereby increasing or decreasing soluble sugar and auxin concentrations of the two clones. Light intensity and fertiliser concentration received by tall and short stockplants impacted on endogenous hormone levels thereby increasing or decreasing rooting. High sugar concentration levels of PP 2107 clone increased its susceptibility to fungal infection thereby decreasing its rooting frequency in autumn, as its rooting rates increased in winter. Overall results of the investigation revealed that PP 2107 clone has higher rooting potential than GN 018B clone, in particular at high planting density and if stockplants are not infected by fungal diseases. Higher sugar levels were recorded in spring for PP 2107, although rooting rates of mung bean hypocotyl cuttings were higher in summer for GN 018B, suggesting that sugars have nothing to do with rooting of GN cuttings. Season, planting density and size of stockplants affect the rooting frequency of GN clone. Thus, short stockplants maintained at low and high planting densities are recommended for GN 018B and PP 2107 respectively, although the impacts of fertilisers and pathogen resistance on rooting rates still need to be investigated under similar conditions. / Thesis (M.Sc.Agric.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.