Дисертації з теми "Diversità intraspecifica"

L'objectif de cette thèse a été de caractériser les patrons spatiaux de diversité inter- et intraspécifique au sein des réseaux dendritiques, d'expliciter les processus évolutifs et écologiques qui les sous-tendent, et d'isoler les possibles covariations spatiales et interactions existant entre ces différentes facettes de biodiversité. Pour cela, j'ai tout d'abord développé de nouvelles méthodes statistiques permettant l'analyse, par des modèles causaux, de données sous la forme de matrices de distances, afin de pouvoir analyser plusieurs facettes de biodiversité dans un unique cadre statistique au niveau alpha et bêta. J'ai par la suite étudié de manière intégrative les patrons de diversité interspécifique et intraspécifique génétique d'une part, et intraspécifique génétique et intraspécifique phénotypique d'autre part, au sein du bassin versant Garonne- Dordogne. Enfin, j'ai utilisé un modèle de dynamique éco-évolutive afin d'étudier l'impact de la structure et des gradients environnementaux caractérisant les réseaux dendritiques sur l'adaptation locale au sein de ces réseaux
The aim of this thesis was to characterized the spatial patterns of inter- and intraspecific diversity within riverine networks, to better understand the ecological and evolutionary processes underlying them and to explore how the different facets of biodiversity interact with one another. First, I developed novel statistical approaches allowing the application of causal modeling to data in the form of pairwise matrices, thus allowing the study within integrative frameworks of several biodiversity facets at the alpha and beta levels. I then studied integratively the patterns of interspecific and intraspecific genetic diversity and of intraspecific genetic and intraspecific phenotypic diversity within the Garonne-Dordogne river basin. Finally, I used an eco-evolutionary metapopulation dynamics model to assess the impacts of the structure and environmental gradients that characterize riverine networks on local adaptation

Listeria monocytogenes est un pathogène d'origine alimentaire à multiples facettes caractérisé par sa capacité d'adaptation dans des conditions défavorables et par sa prolifération dans une vaste gamme d'environnements, du sol aux cellules hôtes des mammifères. L'hétérogénéité génétique de L. monocytogenes se reflète dans sa structure clonale diversifiée, ce qui corrèle, dans une certaine mesure, avec des traits phénotypiques tels que la virulence ou la résistance au stress. La thèse portait sur deux phénotypes les plus éminents, la formation d'un biofilm et le potentiel de virulence, sous différents angles et à l'aide des technologies les plus récentes. Tout au long des études, des grands panels d'isolats ont été utilisés pour représenter la diversité intraspécifique. Stimulants défavorables tels que le choc froid et la privation d'éléments nutritifs induits par l'étape d'adhésion bactérienne. L'ajout de NaCl aux cultures de croissance a stimulé la production de biofilm et, de manière surprenante, il a considérablement intensifié la maturation du biofilm de cellules privées de nutriments. Un degré élevé de variation de la productivité relative du biofilm a été observé parmi les sérotypes, les génotypes, de même que les isolats selon les conditions de culture. Cependant, un certain génotype (complexe clonal 26) a révélé de manière caractéristique une production de biofilm plus élevée à froid (10°C), suggérant une association du génotype avec le phénotype du biofilm. Pan-GWAS a identifié un certain nombre de gènes parmi lesquels ceux impliqués dans des fonctions telles que la ‘transformation/compétence’, les ‘gènes liés aux phages’ et le ‘métabolisme du phosphate’ devront faire l'objet d'études plus approfondies sur leur rôle dans la formation du biofilm. L'analyse du séquençage de l'ARN a révélé une grande hétérogénéité intraspécifique dans les profils de transcriptome basal qui mettaient en évidence le rôle du réseau de régulation, y compris certains facteurs transcriptionnels avec des rôles clés dans la virulence tels que σB, PrfA, et CodY. La plasticité transcriptomique entre les lignées I et II ainsi que les génotypes hyper et hypovirulents ont confirmé les caractéristiques évolutives et épidémiologiques de L. monocytogenes. De plus, la voie métabolique centrale a été impliquée dans l'infection dans le système modèle de Galleria mellonella. En conclusion, la thèse a exploré la diversité intraspécifique de L. monocytogenes et a donné lieu à de nombreux résultats phénotypiques, génomiques et transcriptomiques. Grâce à l'approche intégrative des omiques en listeriologie, le présent travail contribuera à dévoiler la physiologie et la pathogenèse de la bactérie
Conditions and proliferation in a wide range of environments from soil to mammalian host cells. The genetic heterogeneity in L. monocytogenes is reflected on its diversified clonal structure which correlates, to some extent, with phenotypic traits such as virulence or stress resistance. The thesis investigated two most prominent phenotypes, biofilm formation and virulence potential, from various perspectives using state-of-the art technologies. Throughout the studies, large panels of isolates were used to represent the intraspecific diversity. Unfavourable stimuli such as cold shock and nutrient deprivation induced bacterial adhesion step. Addition of NaCl to growth cultures stimulated biofilm production and, surprisingly, it significantly intensified biofilm maturation of nutrient-deprived cells. High degree of variation in relative biofilm productivity was observed among serotypes, genotypes, as well as isolates across culture conditions, however, certain genotype (clonal complex 26) revealed distinctively higher biofilm production under cold temperature (10°C) suggesting an association of genotype with biofilm phenotype. Pan-GWAS identified a number of genes among which those implicated in functions such as ‘transformation/competence’, ‘phage-related genes’, and ‘metabolism of phosphate’ will need further investigations for their roles in biofilm formation. RNA sequencing analysis revealed high intraspecific heterogeneity in basal transcriptome profiles that featured the role of regulatory network including certain transcriptional factors with key roles in virulence such as σB, PrfA, and CodY. The transcriptomic plasticity between lineage I and II as well as hyper- and hypovirulent genotypes supported the evolutionary and epidemiological characteristics of L. monocytogenes. Moreover, the central metabolic pathway was implicated in the infection in Galleria mellonella model system. Conclusively, the thesis explored intraspecific diversity in L. monocytogenes and resulted in ample phenotypic, genomic, and transcriptomic findings. With the integrative omics approach in listeriology, the present work will contribute to unveiling the physiology and pathogenesis of the bacterium

Species vary phenotypically and genetically across their environmental range limits, and this variation can influence ecological processes. Ecologically meaningful intraspecific variation might be particularly important in the context of agricultural weeds and exotic invaders, because intraspecific variation in these species might allow them to rapidly adapt to their unusually dynamic and variable environments. In a greenhouse study, we explored intraspecific variation in the size, rhizome production, and competitive ability of the global invader, Johnsongrass (Sorghum halepense), representing populations from agricultural and non-agricultural habitats across its introduced North American range. We also used these populations to explore the relationship between phenotypic variation and genomic endoreduplication responses to the common stresses herbicides, competition, and clipping. Endoreduplication occurs when plants increase their genome size by increasing their nuclear chromosome number, with some evidence showing correlations with stress response. We found that Johnsongrass plants from agricultural habitats were larger than plants from non-agricultural habitats, but there was no difference between habitats in either rhizome production or competitive ability. Two of the five herbicides we tested, primisulfuron and imazethapyr, had the strongest suppressive effects on Johnsongrass, and also stimulated the greatest rates of endoreduplication. Furthermore, agricultural populations showed higher levels of endoreduplication. We found no overall effect of competition on endoreduplication, although endoreduplication was higher for non-agricultural populations than agricultural populations. When competing with corn, but not with conspecifics, Johnsongrass roots increased endoreduplication by 13%. Clipping induced substantial endoreduplication, but there was no difference between agricultural and non-agricultural populations. Our results suggest that endoreduplication may play a role in some, but not all, stress responses in Johnsongrass. Furthermore, our results indicate that Johnsongrass has adapted in some phenotypic and genomic ways to agricultural habitats in North America. Such adaptation may play a role in this species' success as both an agricultural weed and an exotic invader.
Master of Science in Life Sciences

O presente trabalho analisou as fases gametofítica e tetrasporofítica de morfos verde, vermelho e marrons de Gracilaria domingensis em laboratório. A capacidade reprodutiva foi testada considerando-se: i, número de cistocarpos diferenciados; ii, número de carpósporos e tetrásporos liberados; iii, diâmetro desses esporos; e iv, sobrevivência de carpósporos e tetrásporos, esse último em diferentes condições de irradiância, nutrientes, e radiação ultravioleta. A capacidade somática foi testada em diferentes fases do desenvolvimento por meio da análise dos seguintes parâmetros: i, taxas de crescimento em diferentes condições nutricionais; ii, taxas de crescimento em diferentes condições de radiação ultra-violeta; iii, atividade da enzima nitrato redutase em diferentes condições nutricionais; iv, taxas de fotossíntese; e v, síntese de aminoácidos semelhantes a micosporinas (MAAs) em diferentes condições de radiação UV-B. Uma das únicas diferenças observadas na capacidade reprodutiva entre as linhagens foi o maior período de liberação de carpósporos derivados dos cruzamentos envolvendo apenas gametófitos vermelhos. Essa característica disponibilizaria uma maior quantidade de propágulos dessa linhagem, trazendo vantagens competitivas em relação às demais no ambiente natural. Plantas verdes mostraram maiores valores de fotossíntese máxima, maior síntese de MAAs quando expostas à radiação UV-B, e maior teor de proteínas solúveis totais quando comparadas às plantas vermelhas. Essas respostas sugerem adaptações a ambientes oligotróficos e com intensa luminosidade. Foi observada heterose nas linhagens de tetrasporófitos marrons (VmVd ou VdVm) com relação a pelo menos um dos seguintes parâmetros: fotossíntese máxima e eficiência fotossintetizante; taxas de crescimento; conteúdo de proteínas solúveis totais; atividade da NR; e sobrevivência de carpósporos. Esse vigor híbrido, pelo menos quanto a alguns aspectos, favoreceria a manutenção do alelo verde na natureza. As linhagens de tetrasporófitos marrons apresentaram desempenho distinto quando comparadas entre si com relação a sobrevivência de esporos e taxas de crescimento, indicando que os dois genótipos se expressam de forma diferente frente a condições abióticas distintas. O número de carpósporos liberados foi semelhante ao de tetrásporos considerando-se a massa fresca das plantas férteis, porém, a sobrevivência desses últimos foi sempre maior. O desempenho somático e reprodutivo de tetrasporófitos foi maior que o de gametófitos na maior parte das condições testadas, independentemente da linhagem. Esses resultados demonstraram que as diferentes fases do histórico de vida de G. domingensis têm características metabólicas distintas, o que confere às plantas uma maior plasticidade fenotípica. As diferenças detectadas entre as linhagens no presente trabalho foram discretas. Caso as vantagens proporcionadas pelo alelo verde fossem muito superiores às apresentadas pelo alelo vermelho, ou vice-versa, seria esperado que, ao longo do tempo, uma das duas formas excluísse a outra. A coexistência dos morfos, porém, indica que cada um deles deve ocupar um nicho ligeiramente distinto do outro, o que confere à espécie vantagens frente a ambientes heterogêneos e/ou mudanças ambientais, possibilitando uma maior capacidade de adaptação.
This work investigated gametophytic and tetrasporophytic phases of green, red and brown morphs of Gracilaria domingensis in laboratory. The reproductive performance was tested considering the following: i, number of cystocarps produced; ii, number of carpospores and tetraspores released; iii, diameter of these spores; and iv, survival of carpospores and tetraspores in different nutrient, irradiance and UV-B conditions. The somatic performance of different life phases was tested considering the following: i, growth rates on different nutritional conditions; ii, growth rates on different UV-B conditions; iii, nitrate reductase (NR) activity on different nutritional conditions; iv, photosynthetic rates; and v, mycosporine-like amino acids (MAAs) synthesis on different UV-B conditions. Carpospores originated by the cross of red males x red females were released by a longer period of time when compared to the other carpospores strains. This was almost the only difference found in the reproductive performance among different strains, and could make a greater number of the red strain propagules available for settling. This result could represent competitive advantages in the natural environment. Green plants showed greater values of maximum photosynthesis, a greater MAAs synthesis when exposed to UV-B radiation, and greater amounts of total soluble proteins when compared to the red plants. These responses suggest adaptations to high irradiances and oligotrophic environments. Heterosis was observed in one of the two brown tetrasporophyte strains considering, at least, one of the following parameters: maximum photosynthesis and photosynthetic efficiency; growth rates; total soluble proteins content; NR activity; and survival of carpospores. The heterosis related to these aspects could favor the maintenance of the green allele in nature. The two brown tetrasporophytic strains showed different performance considering the survival of spores and growth rates, which indicates that the two genotypes are expressed in different ways depending on the abiotic conditions. The number of spores released was the same for carpospores and tetraspores when expressed by the fresh biomass of the fertile plants. However, survival of tetraspores was always higher. The somatic and reproductive performance of tettrasporphytes were higher than the gametophytes ones for most of the conditions tested, regardless the strain. These results demonstrate that the different life phases of G. domingensis have specific metabolic characteristics, which contributes to a higher phenotypic plasticity of this species. The differences found among the strains were slight. If the green allele promoted very superior advantages when compared to the ones promoted by the red allele, or vice-versa, it would be expected that, within time, one of the two morphs would exclude the other. The coexistence of the morphs, however, indicates that each one of them must occupy a slightly different niche, which provides advantages to the species concerning heterogonous environments, and /or environmental changes, and enable it with a greater adaptative capacity.

Le déclin actuel de la biodiversité a poussé un grand nombre d’études à s’intéresser aux relations entre la biodiversité et le fonctionnement des écosystèmes. La diversité intraspécifique est une facette centrale de la biodiversité qui permet aux espèces de s’adapter aux variations environnementales et dont l’importance écologique est de plus en plus examinée. A l’aide d’une méta-analyse synthétisant des données sur plusieurs espèces et écosystèmes, nous avons démontré qu’un changement de la diversité intraspécifique peut avoir des conséquences écologiques aussi fortes qu’un changement de la diversité spécifique. Ensuite, au travers d’études empiriques nous avons étudié la diversité fonctionnelle et trophique de populations sauvages de vairons (Phoxinus phoxinus), une espèce de poisson abondante en rivière. Une forte variabilité fonctionnelle et trophique a été montrée entre populations de vairons. Cette diversité était structurée de manière complexe du fait de l’action jointe des conditions environnementales, de facteurs évolutifs et des multiples liens existants entre les traits et la niche trophique. Par ailleurs, nous avons montré expérimentalement que les différences fonctionnelles entre populations de vairons pouvaient engendrer des conséquences écologiques aussi fortes qu’une augmentation de la température. De plus, des populations plus diversifiées génétiquement soutenaient des diversités spécifiques élevées puis augmentaient l’intensité des processus écosystémiques. Ces travaux mettent en évidence que la diversité intraspécifique est une composante essentielle de la biodiversité qui doit être considérée comme un facteur majeur affectant la structure des communautés et le fonctionnement des écosystèmes

The trait based approach has been proposed as a way to reconcile community ecology. Despite recent advances in trait based ecology, such as the development of global trait databases and standardized methodology for trait collections, it remains unclear to what degree traits vary across individuals, species, and communities. In addition, the drivers of trait variation may shed light on the underlying processes that maintain species diversity and community assembly at local to continental scales yet these have been poorly studied. In this study, I examine both the magnitude of trait variation as well as the patterns of trait variation at local to continental scales in order to understand the drivers of diversity patterns across environmental gradients. First, I quantified the magnitude of trait variation at local scales in a dry tropical forest and determined that intraspecific variation is not negligible and can be quite large for compound-leaved species. However, I showed that the sample sizes necessary for quantifying trait variation are tractable and should encourage the adoption of trait variation in trait based ecology. Second, I tested whether climatic variables are predominantly responsible for observed trait variation across dry tropical forests in the Americas. I showed that climatic variability, specifically variability in precipitation, explained a large degree of observed trait variation across dry tropical forests and may provide a unique approach for classifying dry tropical forests based on their inherent degree of climatic seasonality. Third, I quantified patterns of trait variation at continental scales across elevational gradients at high to low latitudes. I showed that climatic variables largely drive patterns of trait variation at high latitudes while biotic factors largely drive patterns of trait variation at low, tropical latitudes. This finding has implications for understanding large-scale patterns of species diversity across elevational and latitudinal gradients. Finally, I apply trait variation to life history theory by quantifying variation in two life history traits (growth and reproduction) in a tropical tree species using a legacy dataset. I showed that variation in these two life history traits is due to both resource availability and allometric related effects on both traits. In sum, this study advances our understanding of the magnitude and underlying drivers of trait variation at local to continental scales.

Fusarium avenaceum est un champignon filamenteux pathogène de nombreuses plantes et est un des acteurs majeurs de la fusariose de l’épi chez le blé et l’orge. Durant l’infection, des métabolites secondaires toxiques pour l’homme et les animaux (mycotoxines) telles que les enniatines sont produites par ce champignon. Les enniatines appartiennent au groupe de mycotoxines dîtes « émergentes » : même si connues depuis 1950, leur présence en quantités importantes et croissantes dans les aliments n’a été mise en évidence que depuis une vingtaine d’année. Actuellement la présence d’enniatines n’est pas surveillée de manière systématique dans les récoltes céréalières, les enniatines ne sont pas soumises à réglementation alors qu’elles sont omniprésentes dans les récoltes et parfois à des concentrations élevées. La diversité des souches productrices ainsi que les mécanismes par lesquels la biosynthèse d’enniatines peut être modulée au cours de l’infection de la plante et/ou en réponse aux conditions environnementales sont mal connus. Ce manque de connaissances constitue un frein à la mise au point d’outils de contrôle et de gestion de l’état sanitaire des récoltes. C’est pourquoi cette étude s’est attachée à apporter de premiers éléments de réponse sur la diversité phénotypique au sein de l’espèce F. avenaceum. Un des facteurs étudiés a concerné la réponse aux variations de pH en termes de croissance et de toxinogénèse et a mis en évidence des comportements très différents entre les isolats. Pour aller plus loin, le rôle de FavPac1, l’homologue de pacC/RIM101 codant un facteur de régulation de l’homéostasie du pH chez les champignons, a été étudié. Des mutants délétés pour ce gène, mutants Fav∆Pac1, ont été construits pour quatre souches de F. avenaceum et ont permis de suggérer l’implication de ce facteur de transcription non seulement dans la régulation de l’expression des gènes de biosynthèse, mais aussi dans la modulation de la production d’enniatines en réponse au pH. Enfin, dans le cadre de la recherche d’inhibiteurs naturels pouvant se substituer aux fongicides de synthèse, nos travaux ont démontré la capacité de certains composés phénoliques à inhiber la production d’enniatines associée à un contrôle transcriptionnel des gènes de biosynthèse et ont mis en évidence l’efficacité élevée de l’acide férulique
Fusarium avenaceum is a filamentous fungus infecting many plants and is one of the causal agents of the Fusarium Head Blight disease in wheat and barley. During plant infection, the fungus can produce secondary metabolites that are toxic for human and livestock (mycotoxins), among which the enniatins. Enniatins belong to the group of “emerging mycotoxins”: first identified as early as 1950, the increasing occurrence of enniatins has only been documented over the last twenty years. Currently, enniatins are neither routinely analysed in grain harvests nor legislatively regulated, even though they are widespread and can be encountered in high concentrations. Diversity of enniatin-producing strains as well as the mechanisms by which their biosynthesis can be modulated during plant infection and/or in response to environmental conditions are poorly known. These gaps of knowledge hinder the development of tools for controlling and mitigating their presence in crops. In the present study, a comprehensive characterisation of the phenotypic diversity within the F. avenaceum species has been carried out. One of the studied phenotypic traits was the effect of pH variations on the fungal growth and toxin production, which has led to evidence various response profiles between strains. To go further, the role of FavPac1, the homologue of pacC/RIM101 encoding a transcriptional factor involved in the response to ambient pH in fungi, has been studied. Construction and phenotyping of deleted mutants, Fav∆Pac1, for four different F. avenaceum isolates have allowed suggesting an involvement of FavPac1 in the modulation of enniatin production and of the expression of biosynthetic genes induced by pH variations. Lastly, with the aim to identify alternatives to synthetic fungicides, the capacity of plant phenolic compounds to inhibit the yield of enniatins has been investigated. The antifungal and anti-mycotoxin properties of hydroxycinnamic acids have been shown; ferulic acid has been highlighted as the most potent compound

Les patrons de diversité caractérisent la structure de la diversité des communautés, c'est-à-dire sa valeur, sa distribution et son changement dans l'espace et le temps. Leur étude peut amener des informations importantes sur les processus écologiques qui en sont à l'origine. Cependant de nombreuses hypothèses de travail sont faites lors de leur analyse. L'idée générale de cette thèse est qu'en remettant en cause ces hypothèses, un certain nombre de développements liés aux indices de diversité et aux modèles nuls deviennent possibles et permettent de mieux comprendre les processus écologiques à l'origine des patrons de diversité fonctionnelle ou phylogénétique. Le premier chapitre est consacré à l'étude des patrons de diversité fonctionnelle des communautés végétales alpines à de multiples échelles spatiales et organisationnelles. Le second chapitre s'intéresse aux perspectives méthodologiques amenés par les nombres de Hill. Dans le dernier chapitre, on s'intéresse aux enjeux méthodologiques d'un nouveau type de données de communautés : l'ADN environnemental
Patterns of community diversity refers to the structure of diversity, i.e. its quantification, its distribution and its turnover in space and time. Its study is likely to shed the light on the assembly rules that determined the structure of communities. However, numerous ecological assumptions are often made when studying diversity patterns. What motivated the work was the perspective that by relaxing these assumptions, a number of developments linked to diversity indices and null models are possible and can help to understand the impact of multiple ecological processes on phylogenetic and functional diversity patterns. In a first part we studied the pattern of functional diversity of alpine plant communities as a function of spatial and organizational scales. In the second part, we studied the methodological perspectives brought by the Hill numbers. In a third part, we addressed the main methodological issues of a new type of community data: environmental DNA

P. roqueforti est une moisissure connue comme contaminant des ensilages et des aliments, mais aussi utilisée comme ferment pour la production de fromages à pâte persillée. Cette espèce est également connue pour son potentiel de production de métabolites secondaires à impact positif, comme les arômes, mais aussi à impact négatif, tels que des mycotoxines (dont la roquefortine C -ROQC- et l’acide mycophénolique -MPA-). Dans la première partie de ce travail, l’occurrence de la ROQC, du MPA et de l’aflatoxine M1 (seule mycotoxine réglementée dans les produits laitiers), dans une collection de 86 fromages à pâte persillée de différentes variétés et origines géographiques (15 pays), a été réalisée. Il apparaît que, si l’aflatoxine est inférieure au seuil de détection (LOD) de la méthode, les concentrations en ROQC et MPA sont quant à elles très variables et qu’une co-occurrence de ces mycotoxines existe dans 51% des échantillons testés. Dans la seconde partie, la toxicité de ces mycotoxines sur modèles cellulaires intestinal ou monocytaires a été évaluée. L’étude de cytotoxicité en mono-exposition a permis d’établir des valeurs de référence (CI50); d’autre part, un effet synergique des deux mycotoxines aux plus fortes concentrations testées a été révélé sur la lignée cellulaire intestinale (Caco-2). L’implication du mécanisme apoptotique après une exposition précoce (3 et 6 heures) à la ROQC et/ou au MPA a aussi été mise en évidence sur le modèle THP-1 ainsi qu’une absence d’implication de l’apoptose après 24 heures de mono ou de co-exposition sur modèle intestinal Caco-2. Enfin, dans la troisième partie, une étude de facteurs biotique ou abiotiques pouvant potentiellement moduler la production de ROQC et de MPA a été réalisée. L’évaluation du potentiel mycotoxigénique de 96 souches de P. roqueforti a mis en évidence que le milieu cheese-agar (mimant la composition physico-chimique du fromage) était beaucoup moins favorable que le milieu YES pour la production des deux mycotoxines et une grande variabilité dans la capacité de production des souches a été observée. L’étude de l’influence des facteurs abiotiques a montré qu’une température de 12°C ou une concentration en NaCl de 8% ou encore une atmosphère contenant 5% d’O2 diminuait significativement la production de ROQC et de MPA indépendamment de la croissance, alors que les autres facteurs (pH et présence de précurseurs de la ROQC) n’avaient pas d’effet dans les conditions testées
P. roqueforti is a mould associated with silage and food contamination but also used as a ripening culture for the production of blue-veined cheese. Moreover, this species is also known for its potential to produce secondary metabolites. These metabolites can have a positive impact (e.g. aromas) or a negative impact (e.g. mycotoxins, including roquefortine C -ROQC- and mycophenolic acid -MPA-). In the framework of this work, we first studied the occurrence of MPA, ROQC and aflatoxin M1 (the only regulated mycotoxin in dairy products) within an 86 blue-veined cheese collection (representing 15 countries). Aflatoxin contents were always below the method detection limit. For MPA and ROQC, concentrations were highly variable and a co-occurrence of both mycotoxins was observed in 51% of the tested samples. Then, the toxicity of the 2 mycotoxins was established on various cell models (intestinal and monocytic). Mono-exposure studies allowed IC50 determination. Moreover, a synergistic effect was observed on Caco-2 cells when MPA and ROQC were used for co-exposure at the highest tested concentrations. While an apoptotic mechanism was observed at early THP-1 exposure stages (3 and 6h), no apoptose occurred for Caco-2 cells after 24 h of mono or co-exposure. Finally, a study of the biotic and abiotic factors potentially modulating P. roqueforti MPA and ROQC production was performed. Mycotoxigenic potential evaluation of 96 de P. roqueforti strains highlighted that a cheese-agar medium (mimicking cheese physico-chemical composition) was less favourable than the synthetic YES medium for mycotoxin production. A large variability in terms of mycotoxin production was also observed among the tested strains. Besides, while a significant effect of the temperature (12°C) and NaCl (8%) and O2 (5%) concentrations was observed on ROQC and MPA production, no significant effect of pH and ROQC amino-acid precursor addition could be detected on the production of both mycotoxins

Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 28, 2008) Vita. Includes bibliographical references.

Meloidogyne graminicola est un nématode à galle du genre Meloidogyne spp. (RKN) qui est prépondérant dans les rizières d’Asie du Sud-Est et qui provoque des pertes significatives chez le riz. Malgré son impact négatif sur le rendement, les moyens de control et les méthodes d’identification de cette espèce sont encore limités. Dans cette étude, nous avons évalué l'incidence et la prévalence des RKN dans les rizières du Cambodge, du Laos et du Vietnam grâce à des marqueurs moléculaires développés dans cette étude. Nous avons de plus évalué, sur une séquence de deux ans, les effets de l'Agriculture de conservation (CA) sur la présence et la dynamique des nématodes parasites des racines (RPN) du riz, en relations avec le rendement et la qualité du sol, dans un champ d’expérimentation sableux de bas fond au Cambodge. Nous avons parallèlement évalué la susceptibilité à M. graminicola de 13 plantes adventices couramment utilisées en CA, ainsi que celle de trois variétés de riz, et identifié des plantes réservoir poussant dans les rizières Cambodgiennes. Dans une autre partie, nous avons validé des marqueurs intraspécifiques pour M. graminicola et étudié sa diversité génétique en Asie du Sud-Est. Par des approches de génomique comparative nous avons discuté des relations évolutives qu’il y aurait pu potentiellement y avoir entre M. graminicola et les espèces génétiquement proches
The rice Root-knot nematode (RKN), Meloidogyne graminicola, reduces significantly rice yield in Southeast (SE) Asia and is prevalent in rice fields in this region. Despite its negative impact on yields, suitable methods of controls and current molecular markers used for M. graminicola identification are still limited. In this study, we evaluated the current occurrence of RKN in rice fields of Cambodia, Laos and Vietnam, and identified those RKN species using molecular markers developed in this study. We then evaluated, during two years sequences, the effects of the Conservation agriculture (CA) on the occurrence and dynamics of root-parasitic nematodes (RPN) of rice, in relation with yields and soil nutrients, in a lowland-sandy field in Cambodia. Host response to M. graminicola of 13 selected cover crops commonly used in CA, of three rice cultivars as well as rice weeds as reservoirs for M. graminicola, were evaluated. Furthermore, we validated intraspecific markers for M. graminicola, studied its genetic diversity in SE Asia, and discussed the potential evolutionary relations of Meloidogyne species using comparative genomics approaches

Invasive plants can displace native species, deteriorate native forest, and change plant communities and ecosystem functions. Native plant populations are fundamentally impacted by invasive species because of the interactions between invasive species and native plants. This study focuses on understanding the extent, mechanisms and consequences of interaction between a non-indigenous invader Ailanthus altissima and its functionally similar native species Robinia pseudoacacia in the Mid-Appalachian region, from an individual scale to a regional scale. These two subject species are common and coexist in early-successional eastern deciduous forest. The interactions between these two common species are important to community structure and canopy tree regeneration. To address the type and extent of interactions of these two species, a greenhouse experiment utilizing various species proportions, nutrient levels and seed sources was performed. In addition, a common-garden experiment with various species densities and proportions over three consecutive growing seasons was performed in a more natural condition than that of the greenhouse experiment. We found at the seedling stage, the dominant interaction was competition, and R. pseudoacacia was the winner both above- and belowground. The allelopathic compounds of A. altissima may have inhibited nodulation of R. pseudoacacia. Ailanthus altissima seedlings from its native region had slightly stronger competitive abilities compared with the seedlings from its invaded range. In the common garden experiment, R. pseudoacacia plants grew quicker than A. altissima, but A. altissima inhibited the growth of R. pseudoacacia by interspecific competition. The negative impact of A. altissima on R. pseudoacacia became larger as time progressed. To assess the community-level consequences of the two species, we conducted a forest mapping and a complete target-tree-based forest survey, and analyzed regional-scale data from the Forest Inventory Analysis Data Base. The two target species were significantly associated with themselves and with each other. Community species composition and diversity were significantly different across sites. A negative impact of both species on the understory community diversity and tree regeneration at the neighborhood scale was detected; while at a regional level, tree diversity in the FIA plots with either A. altissima or R. pseudoacacia was higher than the reference plots.
Ph. D.

Biodiversity is determined by a myriad of complex processes acting at different scales. Given the current rates of biodiversity loss and change, it is of paramount importance that we improve our understanding of the underlying structure of ecological communities. In this thesis, I focused on Species Abundance Distributions (SAD), as a synthetic measure of biodiversity and community structure, and on Beta (β) diversity patterns, as a description of the spatial variation of species composition. I systematically assessed the effect of scale on both these patterns, analysing a broad range of community data, including different taxa and habitats, from the terrestrial, marine and freshwater realms. Knowledge of the scaling properties of abundance and compositional patterns must be fully integrated in biodiversity research if we are to understand biodiversity and the processes underpinning it, from local to global scales. SADs depict the relative abundance of the species present in a community. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, the existence of multiple modes in SADs has largely been overlooked, assumed to be due to sampling errors or a rare pattern. Thus, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here, I provided the first global empirical assessment of the prevalence of multimodality across a wide range of taxa, habitats and spatial extents. I employed an improved method combining two model selection tools, and (conservatively) estimated that ~15% of the communities were multimodal with strong support. Furthermore, I showed that the pattern is more common for communities at broader spatial scales and with greater taxonomic diversity (i.e. more phylogenetically diverse communities, since taxonomic diversity was measured as number of families). This suggests a link between multimodality and ecological heterogeneity, broadly defined to incorporate the spatial, environmental, taxonomic and functional variability of ecological systems. Empirical understanding of how spatial scale affects SAD shape is still lacking. Here, I established a gradient in spatial scale spanning several orders of magnitude by decomposing the total extent of several datasets into smaller subsets. I performed an exploratory analysis of how SAD shape is affected by area sampled, species richness, total abundance and taxonomic diversity. Clear shifts in SAD shape can provide information about relevant ecological and spatial mechanisms affecting community structure. There was a clear effect of area, species richness and taxonomic diversity in determining SAD shape, while total abundance did not exhibit any directional effect. The results supported the findings of the previous analysis, with a higher prevalence of multimodal SADs for larger areas and for more taxonomically diverse communities, while also suggesting that species spatial aggregation patterns can be linked to SAD shape. On the other hand, there was a systematic departure from the predictions of two important macroecological theories for SAD across scales, specifically regarding logseries distributions being selected only for smaller scales and when species richness and number of families were proportionally much smaller than the total extent. β diversity quantifies the variation in species composition between sites. Although a fundamental component of biodiversity, its spatial scaling properties are still poorly understood. Here, I tested if two conceptual types of β diversity showed systematic variation with scale, while also explicitly accounting for the two β diversity components, turnover and nestedness (species replacement vs species richness differences). I provided the first empirical analysis of β diversity scaling patterns for different taxa, revealing remarkably consistent scaling curves. Total β diversity and turnover exhibit a power law decay with log area, while nestedness is largely insensitive to scale changes. For the distance decay of similarity analysis, while area sampled affected the overall dissimilarity values, rates of similarity were consistent across large variations in sampled area. Finally, in both these analyses, turnover was the main contributor to compositional change. These results suggest that species are spatially aggregated across spatial scales (from local to regional scales), while also illustrating that substantial change in community structure might occur, despite species richness remaining relatively stable. This systematic and comprehensive analysis of SAD and community similarity patterns highlighted spatial scale, ecological heterogeneity and species spatial aggregation patterns as critical components underlying the results found. This work expanded the range of scales at which both theories deriving SAD and community similarity studies have been developed and tested (from local plots to continents). The results here showed strong departures from two important macroecological theories for SAD at different scales. In addition, the overall findings in this thesis clearly indicate that unified theories of biodiversity (or assuming a set of synthetic minimal assumptions) are unable to accommodate the variability in SADs shape across spatial scales reported here, and cannot fully reproduce community similarity patterns across scales. Incorporating more realistic assumptions, or imposing scale dependent assumptions, may prove to be a fruitful avenue for ecological research regarding the scaling properties of SAD and community similarity patterns. This will allow deriving new predictions and improving the ability of theoretical models to incorporate the variability in abundance and similarity patterns across scales.

Zooplankton community structure (composition, diversity, dynamics and trophic relationships) of Mediterranian marshes, has been analysed by means of a size based approach.
In temporary basins the shape of the biomass-size spectra is related to the hydrological cycle. Linear shape spectra are more frequent in flooding situations when nutrient input causes population growth of small-sized organisms, more than compensating for the effect of competitive interactions. During confinement conditions the scarcity of food would decrease zooplankton growth and increase intra- and interspecific interactions between zooplankton organisms which favour the greatest sizes thus leading to the appearance of curved shape spectra.
Temporary and permanent basins have similar taxonomic composition but the latter have higher species diversity, a more simplified temporal pattern and a size distribution dominated mainly by smaller sizes. In permanents basins zooplankton growth is not only conditioned by the availability of resources but by the variable predation of planktivorous fish, so that the temporal variability of the spectra may also be a result of temporal differences in fish predation.
Size diversity seems to be a better indicator of the degree of this community structure than species diversity. The tendency of size diversity to increase during succession makes it useful to discriminate between different succession stages, fact that is not achieved by analysing only species diversity since it is low both under large and frequent or small and rare disturbances.
Amino acid composition differences found among stages of copepod species indicate a gradual change in diet during the life cycle of these copepods, which provide evidence of food niche partitioning during ontogeny, whereas Daphnia species show a relatively constant amino acid composition. There is a relationship between the degree of trophic niche overlap among stages of the different species and nutrient concentration. Copepods, which have low trophic niche overlap among stages are dominant in food-limited environments, probably because trophic niche partitioning during development allow them to reduce intraspecific competition between adults, juveniles and nauplii. Daphnia species are only dominant in water bodies or periods with high productivity, probably due to the high trophic niche overlap between juveniles and adults. These findings suggest that, in addition to the effect of interspecific competition, predation and abiotic factors, the intraspecific competition might play also an important role in structuring zooplankton assemblages.
L'estructura de la comunitat zooplanctònica dels Aiguamolls de l'Empordà, composició específica, dinàmica, diversitat i relacions tròfiques, s'ha estudiat a partir d'una aproximació basada en la mida.
L'aproximació s'ha basat en la modelització de l'espectre de mida-biomassa de la comunitat zooplanctònica a partir de la distribució de Pareto. S'ha observat que la forma de l'espectre de mida-biomassa del zooplàncton canvia segons les condicions ambientals: en situacions d'entrada d'aigua són més freqüents els espectres lineals ja que les entrades de nutrients causen un creixement dels organismes de mida petita de manera que es sobrecompensa l'efecte de les interaccions competitives. Els espectres corbats són més freqüents en situacions de confinament quan els recursos són escassos i les interaccions ecològiques entre els organismes prenen més rellevància de manera que es veuen més afavorides les espècies de mida gran que les de mida petita.
Les comunitats zooplanctòniques de les diferents llacunes de la maresma tenen una composició taxonòmica similar però una diversitat d'espècies, un patró estacional i una distribució de mides diferents. En el patró estacional de les llacunes temporànies es poden distingir sis situacions que estan condicionades per el cicle hidrològic i dominades per les següents espècies: Synchaeta spp, Diacyclops bicuspidatus, Eurytemora velox. Calanipeda aquae-dulcis, Cletocamptus confluens i Brachionus plicatilis. La llacuna permanent, tot i presentar una diversitat més alta que les temporànies, té un patró estacional més simple, amb només dues situacions: la situació de Synchaeta spp. i la de C. aquae-dulcis. Aquest patró estacional més reduït i una distribució de mides dominada principalment per organismes de mida petita s'explicarien per la pressió de depredació dels peixos en aquesta llacuna. Així, la variació en la forma de l'espectre de mida-biomassa de les comunitats zooplanctòniques de la llacuna permanent no està únicament relacionat amb el cicle higrològic sinó amb la pressió de depredació dels peixos.
La distribució de Pareto es pot utilitzar per calcular un índex de diversitat de mides (μs'). En el cas de la comunitat de zooplàncton la diversitat de mides ha resultat ser un millor indicador del nivell d'estructuració que la diversitat d'espècies, els augments de la qual moltes vegades no són deguts a una elevada estructuració de la comunitat. La tendència a augmentar al llarg de la successió fa que la diversitat de mides pugui discriminar entre diferents estadis de la successió, en canvi això no es possible a partir de la diversitat d'espècies ja que pot assolir valors elevats tant en moments de pertorbacions elevades i freqüents com en moments de pertorbacions petites i escasses. En llacunes temporànies, valors alts de diversitat de mides coincideixen en períodes de dominància d'una espècie de calanoid, períodes que representen les situacions més estables en aquestes llacunes.
L'anàlisi de la composició d'aminoàcids (AAC) ens demostra que les espècies de copèpodes dominants als Aiguamolls de l'Empordà mostren un canvi gradual en la seva composició bioquímica al llarg de la seva ontogènesi. Aquestes diferències en la AAC entre estadis no són degudes a diferències filogenètiques ni a les condicions ambientals, sinó a variacions en la dieta. Així, les diferents espècies de copèpodes mostren una repartició del nínxol tròfic entre els seus estadis de desenvolupament. Pel que fa a les espècies de dàfnids, mostren una AAC relativament constant durant el seu desenvolupament, fet que indicaria que tot els estadis s'alimenten del mateix recurs, és a dir, que juvenils i adults mostren un solapament del nínxol tròfic. La relació trobada entre la concentració de nutrients de les llacunes i el grau de solapament entre estadis de les espècies dominants mostra que la repartició del nínxol tròfic entre joves i adults és un possible mecanisme per tal d'evitar la competència intraespecífica. Els copèpodes, que tenen un baix solapament entre estadis, dominen en ambients on el recurs és limitat ja que la repartició del nínxol tròfic durant el desenvolupament els permet reduir la competència per l'aliment entre estadis. En les espècies de dàfnids, l'elevat solapament entre joves i adults els restringeix en llacunes o períodes amb elevada productivitat per tal d'evitar la competència intraespecífica. Així doncs, la competència intraespecífica juga un paper important a l'hora d'estructurar la comunitat de zooplàncton, juntament amb els dos altres factors que sovint són citats, la depredació i la competència interspecífica.

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Universidade Federal de Sao Carlos
The genetic diversity of the cattle egret (Bubulcus ibis) was analyzed to investigate reproductive behavior and characterize Brazilian populations of the species. Genotypes at seven microsatellite loci were used to investigate the occurrence of more than one female laying eggs in the same nest, characterizing the occurrence of multiple maternity. DNA was extracted from swabs collected from the outer surface of eggs and sexed; males were excluded. Forty-eight clutches from two breeding seasons (2010 and 2011) were genetically analyzed. Thirty-nine eggs laid by a second or third female were recorded. In five nests, the first egg of the clutch was from a different female, the laying happening prior to that of the incubating female. Suggesting nest takeover by another pair of egrets that kept the pre-existing eggs together with its own clutch. In the other 43 nests, the hypothesis of brood parasitism was posed to explain why one or two additional females were found laying eggs in a nest. A 463-bp fragment of the mitochondrial DNA control region Domain I was amplified for 148 individuals from seven Brazilian populations to investigate genetic-population and demographic parameters. Genetic diversity indices, the population structure tests Fst and AMOVA, a haplotype network, mismatch distribution and neutrality tests (Tajima s D, Fu s Fs, Fu and Li s D* and F*, Ramos-Onsins and Rozas R2) revealed the following: i) a high level of diversity was recorded for the cattle egret in Brazil in comparison to other closely related species studied in the country; ii) genetic diversity levels determined for the Brazilian regions are similar; iii) genetic structuring was not observed between the seven studied populations; and iv) the different tests performed to determine demographic expansion revealed no significant results. This is the first genetic characterization study for Bubulcus ibis to date and the findings indicate a high degree of plasticity in reproductive behavior and confirm a marked dispersion behavior of the species, leading to the homogenization of Brazilian populations.
A diversidade genética da garça-vaqueira (Bubulcus ibis) foi utilizada para se investigar o comportamento reprodutivo e para se caracterizar populações brasileiras da espécie. Genótipos em locos de microssatélites foram utilizados na detecção da presença de mais de uma fêmea ovipositando em um mesmo ninho, o que pode caracterizar a ocorrência de maternidade múltipla. O DNA extraído dos swabs coletados na superfície externa dos ovos foi sexado e eventuais amostras de machos foram excluídas. Quarenta e oito ninhadas, de duas temporadas reprodutivas (2010 e 2011) foram analisadas geneticamente. Foram registrados 39 ovos ovipositados por uma segunda ou terceira fêmea. Em 33 ninhos foram encontrados genótipos distintos de duas fêmeas e em seis ninhos genótipos de três fêmeas. Em cinco ninhos o primeiro ovo na sequência de oviposição mostrou-se ser de uma fêmea diferente, tendo a oviposição acontecido previamente àquela da fêmea incubante. Esse achado foi explicado supondo a tomada de ninho por um segundo casal de garças, com a manutenção do ovo pré-existente juntamente com os da própria ninhada. Nos outros 43 ninhos, a presença das fêmeas extras foi explicada hipotetizando a ocorrência de parasitismo de ninho intraespecífico. Um fragmento de 463 pb do Domínio I da região controladora do DNA mitocondrial foi amplificado para 148 indivíduos para a investigação de parâmetros genéticopopulacionais e processos demográficos nas sete populações estudadas. A estimativa de índices de diversidade genética, testes de estruturação populacional Fst e AMOVA, a construção de uma rede de relação entre haplótipos, a análise de mudanças no tamanho populacional pela mismatch distribution e a realização de testes de neutralidade (D de Tajima, Fs de Fu, D* e F* de Fu e Li, R2 de Ramos-Onsins e Rozas) permitiram identificar: i) um nível alto de diversidade genética para B. ibis no Brasil, quando comparado a espécies proximamente relacionadas estudadas no país; ii) níveis semelhantes de diversidade genética determinados para as regiões brasileiras; iii) ausência de estruturação genética entre as sete populações estudadas; e iv) ausência de sinais de expansão demográfica pelos testes realizados. Os resultados aqui apresentados são os primeiros resultados genéticos na espécie até o momento e apontam para uma alta plasticidade no comportamento reprodutivo e confirmam a dispersão bastante acentuada da espécie, levando a homogeneização das populações brasileiras.

Les traits hydrauliques sont reliés aux fonctions fondamentales du transport de l’eau dans la plante et de la résistance à la sécheresse, déterminant l’écologie, l’évolution, et les processus en lien avec le changement climatique pour les plantes. Cependant, ces traits restent que peu documentés pour les forêts tropicales humides, empêchant de mieux comprendre l’écologie des arbres tropicaux et le futur des forêts tropicales. À partir d’une approche générale s’intéressant à la structure (morphologie et anatomie) et au fonctionnement (physiologie) de la pousse feuillée au sein des arbres, cette thèse analyse la structure et le fonctionnement de la pousse feuillée des arbres, notamment dans la perspective de la résistance à la sécheresse. Cette thèse s’appuie sur un jeu de données général qui concerne 42 espèces d’arbres de canopée échantillonnées en forêt tropicale humide de Guyane, et qui illustre une large gamme de tailles de feuilles. Un second jeu de données, destiné à mieux comprendre les sources de variabilité intraspécifique, porte de l’espèce pionnière Cecropia obtusa Trécul (Urticaceae). Une première partie de la thèse vise à comprendre la coordination entre la feuille et la tige pour une large gamme de dimension foliaire, en analysant les changements morpho-anatomiques et fonctionnels soulignant la relation entre dimensions de la feuille et dimensions de la tige à l’échelle interspécifique. Ce cadre est aussi appliqué à l’échelle intraspécifique pour le modèle C. obtusa pour la relation pétiole-limbe. Comprendre les changements liés aux dimensions de la feuille permet ainsi d’investir correctement les effets ontogénétiques et saisonniers sur les traits foliaires vasculaires et hydrauliques pour C. obtusa. La seconde partie vise à mieux comprendre les mécanismes de résistance à la sécheresse de la pousse feuillée. En retenant 25 espèces, les déterminants anatomiques de la résistance à l’embolie par sécheresse des tiges et sont étudiés. Les différentes propriétés et mécanismes déjà connus pour des plantes tempérées sont abordés conjointement afin de conforter ou non leur existence et comprendre leurs contributions relatives. La segmentation de vulnérabilité (c.-a.d. la différenciation de résistance à l’embolie) à l’interface tige-feuille est également étudiée pour 20 espèces. Sa coordination avec la segmentation hydraulique (c.-à-d. différenciation de résistance hydraulique), qui est dérivée des études anatomiques réalisées dans la première partie, est étudiée. Je montre ainsi (i) un large spectre de variation pour la segmentation de vulnérabilité entre espèces, (ii) une relation positive avec la segmentation hydraulique, suggérant qu’il y a des espèces promouvant à la fois la segmentation hydraulique et la segmentation de vulnérabilité pour découpler le fonctionnement la feuille de la tige du point de vue hydraulique, et (iii) que la segmentation de vulnérabilité a un impact important sur le temps de dessiccation théorique de la pousse feuillée, confirmant que la segmentation de vulnérabilité est un mécanisme de résistance à la sécheresse. Dans une dernière partie, je teste le pouvoir prédictif des différents traits hydrauliques étudiés sur la distribution hydro-topographique des espèces, ainsi que l’impact du stress hydrique sur la croissance des arbres, à une échelle locale. Dans la Discussion générale, je discute de la signification fonctionnelle de la surface de la feuille et des traits de résistance à la sécheresse en forêt tropicale humide, ainsi que la relation potentielle entre la surface de la feuille et la résistance à la sécheresse
Hydraulic traits are related to the fundamental functions of conduction and drought resistance, driving plant ecology, evolution, and processes related to climate change. However, these traits are still poorly documented for tropical rainforest, hindering our understanding of tropical tree ecology and the future of tropical forests. Through a trait-based approach combining leaf and stem in-depth anatomy and physiology, this thesis analyses the structure and the functioning of tree leafy shoots, a compartment exposed to the most severe water stress within a tree. This thesis is based on a dataset of 42 canopy tree species sampled in a rainforest in French Guiana, exemplifying a large range of leaf size. A second dataset, aiming at better understanding the sources of intraspecific variability, focus on the pioneer tree species Cecropia obtusa Trécul (Urticaceae). The first part aims at understanding the coordination between leaf and stem across a large leaf size range, by analysing the morpho-anatomical and functional changes underlying the leaf size-stem size relationship for 42 tropical rainforest canopy trees. This framework is also applied at the intraspecific level for the model C. obtusa, for the petiole-lamina relationship. Understanding leaf size-related changes allows to properly investigate ontogenetic and seasonal effects on leaf vascular and hydraulic traits for C. obtusa. The second part aims at better understanding the drought resistance of the leafy shoot. By retaining 25 species, the anatomical determinants of drought-induced embolism resistance for stems are studied. The different properties and mechanisms already known for temperate plants are investigated jointly to consolidate or not their existence, and understand their relative contribution. Vulnerability segmentation (i.e. differentiation of embolism resistance) at the leaf-stem interface is investigated across 20 species. I further evidenced (i) a large spectrum of variation for vulnerability segmentation across species, (ii) a positive relation with hydraulic segmentation (i.e. differentiation of hydraulic resistance), suggesting that some species promote both hydraulic and vulnerability segmentations to decouple hydraulically leaf and stem, and (iii) that vulnerability segmentation has a massive role in enhancing the theoretical desiccation time of shoots, confirming vulnerability segmentation as a drought resistance mechanism for tropical trees. In a final part, all traits are merged to test their predictive power for species hydro-topographic distribution and growth-mediated response to water stress, at a local scale. In the general discussion, I discuss the functional signification of leaf size and drought resistance traits for tropical rainforest, as also potential relation between leaf size and drought resistance

Oenococcus oeni è un batterio lattico importante dal punto di vista applicativo poiché rappresenta il principale microrganismo responsabile della fermentazione malolattica del vino (Lonvaud-Funel, 1999). Dal momento che il vino è una peculiare nicchia in cui molti fattori, quali il basso pH e la presenza di etanolo, agiscono come stress sulle cellule batteriche, lo studio della risposta a stress in O. oeni è di particolare interesse, specialmente per lo sviluppo di nuove colture starter (Beltramo et al., 2006). Inoltre, O. oeni presenta un genoma di piccole dimensioni (circa 1,8 Mbp), come mostrato dai 14 genomi sequenziati disponibili (Mills et al., 2005; Borneman et al., 2010; Borneman et al., 2012a), e un’ulteriore peculiarità genomica, cioè la mancanza del sistema di riparazione dei mismatch, che probabilmente è responsabile dell’alto livello di diversità all’interno della specie (Makarova et al., 2006; Marcobal et al., 2008). Perciò, O. oeni costituisce una specie interessante sia per scopi applicativi che per la ricerca di base. In letteratura la risposta ai fattori stressanti del vino ha riguardato principalmente l’analisi di espressione di pochi geni (circa 30). D’altra parte, la disponibilità delle sequenze genomiche per alcuni ceppi fornisce un’importante risorsa di informazioni sulla distribuzione di specifici tratti genetici che possono essere legati al diverso comportamento di ceppi differenti. Nella presente tesi la risposta allo stress e la sua correlazione con la diversità intraspecifica sono state investigate in O. oeni. Diverse tecniche sono state applicate e integrate: la trascrittomica basata sull’intero genoma mediante DNA microarray, l’analisi di espressione di singoli geni, la genomica comparativa, gli screening genetici in una collezione di ceppi con differenti proprietà enologiche, e infine, la caratterizzazione genetica e fisiologica di alcuni di questi ceppi. Il primo capitolo ha riguardato un’analisi trascrizionale globale del ceppo O. oeni PSU-1, che ha offerto un quadro più ampio sulla risposta a stress rispetto alla precedente letteratura. Questo esperimento ha delineato un pan transcriptome di 766 geni differenzialmente espressi in almeno una condizioni delle quattro testate (pH 3,5, 10% EtOH, pH+EtOH, e 42°C applicati per 6 ore), e un core transcriptome di 28 geni, modulati in tutti i quattro stress. In particolare, tra questi ultimi geni erano inclusi un regolatore trascrizionale (OEOE_0412) e una tioredossina (OEOE_1702). La presenza di un regolatore differenzialmente espresso in tutte le condizioni applicate ha motivato l’approfondimento dei regolatori trascrizionali, elementi chiave nella risposta a stress, all’interno della specie O. oeni. Infatti, nel secondo capitolo, sono stati identificati tutti i regolatori predetti nel genoma di PSU-1, e circa la metà sono risultati essere modulati in almeno una condizione di stress. Oltre al già conosciuto ctsR, e a OEOE_0412, presente nel core transcriptome, sono emersi altri due interessanti regolatori: OEOE_0878 e OEOE_1398, che fanno parte di un operone e di un regulone, rispettivamente. Questi geni sono stati descritti per la prima volta come coinvolti nella risposta a stress di O. oeni. Poiché l’espressione in risposta a stress dipende dalla presenza di uno specifico background genetico, e data l’elevata diversità all’interno di O. oeni (de las Rivas et al., 2004; Bilhère et al., 2009; Bridier et al., 2010), un ceppo non può essere considerato rappresentativo dell’intera specie. Pertanto, nel terzo capitolo, lo studio si è focalizzato su una collezione di 38 ceppi, costituita dai 14 ceppi sequenziati, e da 24 isolati da vini italiani che hanno mostrato differenti comportamenti in esperimenti di microvinificazione (fermentazione malolattica completa, crescita ma fermentazione incompleta, oppure riduzione di vitalità). In questa collezione sono stati investigati vari aspetti di diversità genetica, e ne è stata valutata la correlazione con lo stress response. Oltre all’identificazione di due nuove regioni di flessibilità, i risultati hanno mostrato che le differenti proprietà enologiche dei ceppi derivano da caratteristiche più complesse della presenza/assenza di specifici geni. È stato comunque possibile osservare che la maggior parte dei ceppi da Amarone (vino con circa il 15% di etanolo) presentava geni relativi ad un’isola genomica o a plasmidi. Quindi, questi elementi sembrano essere importanti, non solo per la diversità dei ceppi, ma anche per l’adattamento e la resistenza alla nicchia ecologica, soprattutto nel caso di questo particolare vino. L’interesse per i geni codificanti tioredossine è derivato sia dall’analisi del core transcriptome di O. oeni PSU-1 (OEOE_1702) che da quella della diversità genetica (OEOE_0350), quindi questi tratti genici, insieme alle tioredossine reduttasi, sono stati approfonditi nel quarto capitolo. La loro distribuzione è stata valutata in tutta la collezione, e inoltre la loro espressione è stata analizzata durante la fermentazione malolattica di sei ceppi con diverse caratteristiche. Il gene trxA OEOE_1702 ha mostrato una marcata sovra-espressione nella maggior parte dei ceppi considerati, pertanto sembra avere una funzione cruciale durante la fermentazione e soprattutto nella sua fase finale. Il ceppo con le peggiori proprietà enologiche (Rz81) ha presentato un profilo di espressione completamente diverso per tutti geni trx, ciò suggerisce che il sistema Trx abbia un’importante ruolo nella risposta a stress. Tra i 24 ceppi da vini italiani considerati in questo lavoro, una sotto-collezione è stata rappresentata da 13 isolati derivanti da una singola fermentazione malolattica spontanea in Amarone. Nel quinto capitolo questi ceppi sono stati caratterizzati geneticamente e fenotipicamente mediante saggi enzimatici e di crescita. Dall’analisi di questa popolazione naturale di O. oeni è emersa un’elevata biodiversità intraspecifica. In particolare, è apparsa variabilità anche nella distribuzione di geni relativi alla produzione di esopolisaccaridi, che possono favorire la sopravvivenza in un ambiente stressante come l’Amarone. In conclusione, lo studio della risposta a stress nella specie O. oeni, affrontato in questo progetto di tesi, ha impiegato un’integrazione di trascrittomica, genomica, e analisi di una collezione di ceppi. Questo approccio ha permesso di ottenere una migliore conoscenza del macchinario di risposta di questa specie e maggiori informazioni sulla sua biodiversità.
Oenococcus oeni is a lactic acid bacterium with an applied importance because it is the main microorganism responsible for the malolactic fermentation of wine (Lonvaud-Funel, 1999). Since wine is a peculiar niche in which many factors, such as low pH and ethanol, act as stresses on bacterial cells, the study of stress response in O. oeni is of particular interest, especially for developing novel starter cultures (Beltramo et al., 2006). Furthermore, O. oeni has a small genome size (about 1.8 Mbp), as shown by the 14 available sequenced genomes (Mills et al., 2005; Borneman et al., 2010; Borneman et al., 2012a), and another genomic peculiarity, i.e., the lack of the mismatch repair pathway, which is probably responsible for the high diversity within this species (Makarova et al., 2006; Marcobal et al., 2008). Therefore O. oeni is an interesting species both for applied purposes and for basic research. In the literature, the response to the stress factors of wine has been mainly addressed with the analysis of the expression of only few genes (about 30). On the other hand, the availability of genome sequences for some strains provides a valuable source of information about the distribution of specific genetic traits that could be linked to the different behaviour of diverse strains. In the present thesis, stress response and its correlation with intraspecific diversity were investigated in O. oeni. Different techniques were applied and integrated: whole-genome transcriptomics with DNA microarray, single gene expression analysis, comparative genomics, genetic screenings on a collection of strains presenting different oenological properties, and, moreover, some of these strains were genetically and physiologically characterized for the first time. The first chapter regarded a global transcription analysis of strain O. oeni PSU-1, which offered a wider picture on stress response compared to the previous literature. This experiment delineated a pan transcriptome of 766 genes, differentially expressed in at least one condition of the four tested (pH 3.5, 10% EtOH, pH+EtOH, and 42°C applied for 6 hours), and a core transcriptome of 28 genes, modulated in all the four stresses. In particular, among these latter genes a transcriptional regulator (OEOE_0412) and a thioredoxin (OEOE_1702) were included. The presence of a regulator differentially expressed in all the applied conditions motivated the further analysis of the transcriptional regulators, key elements in the stress response, within O. oeni species. Indeed, in the second chapter, all the predicted regulators in PSU-1 genome were identified, and about half of them resulted modulated in at least one stress condition. Besides the known ctsR, and OEOE_0412, the unique present in the core transcriptome, other two interesting regulators emerged: OEOE_0878, and OEOE_1398, which were part of an operon and a regulon, respectively. All these genes were described for the first time as involved in the stress response of O. oeni. Since the expression in response to stress depends on the presence of a specific genetic background, and, given the high diversity within O. oeni (de las Rivas et al., 2004; Bilhère et al., 2009; Bridier et al., 2010), one strain cannot be considered representative of the whole species. Therefore, in the third chapter, the study focused on a collection of 38 strains, constituted by the 14 sequenced strains, and 24 isolates from Italian wines showing different behaviours in microvinification experiments (complete malolactic fermentation, growth but incomplete fermentation, or reduction of vitality). In this collection, different aspects of genetic diversity were investigated, and the correlation with stress response was evaluated. Besides the identification of two new flexibility regions, the results showed that the different oenological properties of strains could not be clearly linked to presence/absence of specific genes, but derive from a more complex genetic background. However, it was possible to observe that the majority of the analyzed strains from Amarone wine (with about 15% of ethanol) presented island or plasmid-related genes. Therefore, these elements seemed to be important, not only for strain diversity, but also for adaptation and resistance to the ecological niche, especially for strains from this peculiar wine. Interest in thioredoxin genes derived from both the analyses of the core transcriptome of O. oeni PSU-1 (OEOE_1702) and of genetic diversity (OEOE_0350), therefore these genetic traits, together with thioredoxin reductases, were investigated in the fourth chapter. The distribution of those genes was assessed in the whole collection of strains, and, moreover, their expression was analyzed during the malolactic fermentation of six strains with different characteristics. The trxA OEOE_1702 showed a marked upregulation in most of the strains considered, thus it seemed to have a crucial function during malolactic fermentation, especially in its final phase. The strain with the worst oenological properties (Rz81) presented a completely different expression profile for the trx genes, suggesting that the Trx system plays an important role in stress response. Among the 24 strains from Italian wines considered in this study, a sub-collection was represented by 13 isolates deriving from a single spontaneous malolactic fermentation in Amarone wine. In the fifth chapter these strains were genetically and phenotipically characterized taking into account enzymatic activity and growth assays. A high intraspecific biodiversity emerged from the analysis of this O. oeni natural population. In particular, variability appeared also in the distribution of genes related to the exopolysaccharide production, which may favor the bacterial survival in a stressful environment such as Amarone wine. In conclusion, the investigation of stress response in the species O. oeni, carried out in this thesis project, used an integration of transcriptomics, genomics, and strain collection analysis. This approach allowed to achieve an improved knowledge of the stress response machinery of this species and more information on its biodiversity.

碩士
國立臺灣大學
植物學研究所
88
Arbuscular mycorrhizal fungi (AMF) are one of the most widespread group of fungi on earth. Taxonomists have described three families, six genera and approx. 150 species. This taxonomy is based on morphological characters, and especially on features of asexual spores. These characteristics may be difficult to discern and are subjected to alterations during spore ontogeny or by parasitism. And the morphological similarity might conceal physiological diversity in these fungi. There are two kinds of sporocarp of Sclerocystis sinuosa collected from Taiwan. The size and shape of two sporocarp types are similar; however, they differ in the presence or lacking of sporocarp peridium. The present investigation employed 18S ribosomal DNA sequences, sporocarp ontogeny and pot inoculation test to explore their identity. Numbers and ratios of sporocarp with different mode of peridium formation were varied according to time change after inoculation either by naked sporocarps or sporocarps with peridium. Two types of sporocarps were reproduced at maturity by inoculating solely naked sporocarps in root of sorghum seedlings in the sand pot culture. In contrast, only sporocarps covered peridium were reproduced solely at maturity by inoculating with peridial sporocarps in the same host and environment. As the result of 18S ribosomal DNA sequence, there is no difference between two sporocarp types. But slight variation in sequence compared with Glomus sinuosum were observed. The two sporocarp types of S. sinuosa collected from Taiwan are thus identified as the same species with G. sinuosum, but can be treated as a different strai

Biodiversity is determined by a myriad of complex processes acting at different scales. Given the current rates of biodiversity loss and change, it is of paramount importance that we improve our understanding of the underlying structure of ecological communities. In this thesis, I focused on Species Abundance Distributions (SAD), as a synthetic measure of biodiversity and community structure, and on Beta (β) diversity patterns, as a description of the spatial variation of species composition. I systematically assessed the effect of scale on both these patterns, analysing a broad range of community data, including different taxa and habitats, from the terrestrial, marine and freshwater realms. Knowledge of the scaling properties of abundance and compositional patterns must be fully integrated in biodiversity research if we are to understand biodiversity and the processes underpinning it, from local to global scales. SADs depict the relative abundance of the species present in a community. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, the existence of multiple modes in SADs has largely been overlooked, assumed to be due to sampling errors or a rare pattern. Thus, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here, I provided the first global empirical assessment of the prevalence of multimodality across a wide range of taxa, habitats and spatial extents. I employed an improved method combining two model selection tools, and (conservatively) estimated that ~15% of the communities were multimodal with strong support. Furthermore, I showed that the pattern is more common for communities at broader spatial scales and with greater taxonomic diversity (i.e. more phylogenetically diverse communities, since taxonomic diversity was measured as number of families). This suggests a link between multimodality and ecological heterogeneity, broadly defined to incorporate the spatial, environmental, taxonomic and functional variability of ecological systems. Empirical understanding of how spatial scale affects SAD shape is still lacking. Here, I established a gradient in spatial scale spanning several orders of magnitude by decomposing the total extent of several datasets into smaller subsets. I performed an exploratory analysis of how SAD shape is affected by area sampled, species richness, total abundance and taxonomic diversity. Clear shifts in SAD shape can provide information about relevant ecological and spatial mechanisms affecting community structure. There was a clear effect of area, species richness and taxonomic diversity in determining SAD shape, while total abundance did not exhibit any directional effect. The results supported the findings of the previous analysis, with a higher prevalence of multimodal SADs for larger areas and for more taxonomically diverse communities, while also suggesting that species spatial aggregation patterns can be linked to SAD shape. On the other hand, there was a systematic departure from the predictions of two important macroecological theories for SAD across scales, specifically regarding logseries distributions being selected only for smaller scales and when species richness and number of families were proportionally much smaller than the total extent. β diversity quantifies the variation in species composition between sites. Although a fundamental component of biodiversity, its spatial scaling properties are still poorly understood. Here, I tested if two conceptual types of β diversity showed systematic variation with scale, while also explicitly accounting for the two β diversity components, turnover and nestedness (species replacement vs species richness differences). I provided the first empirical analysis of β diversity scaling patterns for different taxa, revealing remarkably consistent scaling curves. Total β diversity and turnover exhibit a power law decay with log area, while nestedness is largely insensitive to scale changes. For the distance decay of similarity analysis, while area sampled affected the overall dissimilarity values, rates of similarity were consistent across large variations in sampled area. Finally, in both these analyses, turnover was the main contributor to compositional change. These results suggest that species are spatially aggregated across spatial scales (from local to regional scales), while also illustrating that substantial change in community structure might occur, despite species richness remaining relatively stable. This systematic and comprehensive analysis of SAD and community similarity patterns highlighted spatial scale, ecological heterogeneity and species spatial aggregation patterns as critical components underlying the results found. This work expanded the range of scales at which both theories deriving SAD and community similarity studies have been developed and tested (from local plots to continents). The results here showed strong departures from two important macroecological theories for SAD at different scales. In addition, the overall findings in this thesis clearly indicate that unified theories of biodiversity (or assuming a set of synthetic minimal assumptions) are unable to accommodate the variability in SADs shape across spatial scales reported here, and cannot fully reproduce community similarity patterns across scales. Incorporating more realistic assumptions, or imposing scale dependent assumptions, may prove to be a fruitful avenue for ecological research regarding the scaling properties of SAD and community similarity patterns. This will allow deriving new predictions and improving the ability of theoretical models to incorporate the variability in abundance and similarity patterns across scales.
A biodiversidade é determinada por uma miríade de processos complexos que actuam a escalas diferentes. Face às actuais taxas de perda e alteração da biodiversidade, é vital melhorar a nossa compreensão da estrutura subjacente das comunidades ecológicas. Esta tese focou-se na análise de Species Abundance Distributions (SAD; Distribuição das abundâncias relativas das espécies), enquanto medida sintética de biodiversidade e da estrutura das comunidades, e de padrões de Beta (β) diversidade, enquanto medida de descrição da variação espacial na composição específica das comunidades. Os efeitos de escala nestes dois padrões de biodiversidade foram sistematicamente avaliados, analisando uma grande variedade de comunidades, incluindo diferentes taxa e habitats, dos reinos terrestre, marinho e água doce. O conhecimento sobre as propriedades de escala dos padrões de abundância e de composição específica das comunidades deve ser totalmente integrado na investigação da biodiversidade, no sentido de a podermos compreender melhor, bem como aos processos que a sustentam, desde escalas locais à escala global. As SADs descrevem a abundância relativa das espécies presentes numa comunidade. Apesar de serem tipicamente descritas por distribuições unimodais, como a logseries ou a lognormal, SADs empíricas podem também exibir várias modas. No entanto, a existência de múltiplas modas em SADs tem sido largamente ignorada, sendo normalmente assumida como um padrão raro ou atribuído a erros de amostragem. Desta forma, a frequência de multimodalidade em SADs é desconhecida, bem como os factores que podem levar à sua ocorrência. Nesta análise, efectuei a primeira avaliação empírica global da frequência de multimodalidade, analisando várias comunidades de differentes taxa, habitats e extensões espaciais. Usando um método melhorado que combina dois critérios de selecção de modelos, estimei (conservadoramente) que cerca de 15% das comunidades analisadas eram multimodais com grande suporte. Além disso, demonstrei que a multimodalidade é mais comum em comunidades com maior extensão espacial e com maior diversidade taxonómica (isto é, comunidades filogeneticamente mais diversas, uma vez que a diversidade taxonómica foi medida como o número de famílias). Estes resultados sugerem uma ligação entre SADs multimodais e heterogeneidade ecológica, aqui amplamente definida para incorporar a variabilidade espacial, ambiental, taxonómica e funcional dos sistemas ecológicos. Ainda não possuímos uma compreensão empírica de como a escala espacial afecta a forma das SADs. Nesta análise, estabeleci um gradiente de escala espacial abrangendo várias ordens de magnitude, começando por decompor a extensão espacial total de várias comunidades em secções menores. Este gradiente foi usado para realizar uma análise exploratória de como a forma das SADs é afectada pela área amostrada, riqueza específica, abundância total e diversidade taxonómica. Mudanças claras na forma das SADs podem fornecer informações sobre mecanismos ecológicos e espaciais relevantes que afectam a estrutura das comunidades. Esta análise demonstrou um efeito claro da área, riqueza específica e diversidade taxonómica na forma das SADs, enquanto que a abundância total não exibiu um efeito direccional. Estes resultados apoiam as conclusões da análise anterior, mostrando uma maior prevalência de SADs multimodais para áreas maiores e para comunidades mais diversas taxonomicamente. Adicionalmente, estes resultados sugerem que os padrões de agregação espacial das espécies influenciam a forma das SADs ao longo do gradiente espacial. Por outro lado, esta análise identificou diferenças sistemáticas relativamente às previsões de duas importantes teorias macroecológicas para as SAD a escalas diferentes, especificamente o facto de a logseries apenas ter sido seleccionada para escalas menores e quando a riqueza específica e o número de famílias eram proporcionalmente muito menores do que para a extensão total. A β diversidade quantifica a variação na composição específica entre locais. Apesar de ser um componente fundamental da biodiversidade, conhecimento sobre a variação das suas propriedades com a escala espacial ainda é escasso. Nesta análise, testei se dois tipos conceptuais de β diversidade apresentam variação sistemática com a escala, considerando também explicitamente os dois componentes de β diversidade: turnover e nestedness (aninhamento) – substituição de espécies vs diferenças na riqueza específica entre locais, respectivamente. Efectuei a primeira análise empírica de padrões de escala de β diversidade para diferentes taxa, revelando que as curvas de escala são notavelmente consistentes para as comunidades analisadas. A β diversidade total e a componente de turnover exibem um declínio segundo uma power law com o logaritmo da área, enquanto a componente de nestedness é basicamente insensível às mudanças de escala. Relativamente à análise do declínio da similaridade com a distância geográfica, enquanto a área amostrada afectou significativamente os valores de dissimilaridade total, as taxas de mudança na similaridade foram consistentes para grandes variações entre áreas amostradas. Finalmente, em ambas as análises, o turnover foi o principal contribuinte para as diferenças composicionais. Estes resultados sugerem que as espécies estão espacialmente agregadas ao longo das escalas espaciais analisadas (de locais a regionais). Adicionalmente, os resultados ilustram que mudanças substanciais na estrutura das comunidades podem ocorrer, apesar de a riqueza específica permanecer relativamente estável. A análise sistemática e abrangente de SADs e de padrões de similaridade nesta tese identificou a escala espacial, a heterogeneidade ecológica e padrões de agregação espacial das espécies como componentes críticos subjacentes aos resultados encontrados. Esta investigação expandiu as escalas às quais tanto teorias que derivam SAD, como estudos de similaridade têm sido desenvolvidos e testados (desde plots locais a continentes). Estes resultados identificaram claros desvios face a duas importantes teorias macroecológicas para SAD a diferentes escalas. Adicionalmente, os resultados gerais desta tese indicam claramente que teorias unificadas da biodiversidade (ou assumindo um conjunto mínimo de pressupostos sintéticos) não são capazes de, por um lado, acomodar a variabilidade na forma das SADs a escalas espaciais diferentes aqui reportada, e, por outro lado, reproduzir totalmente os padrões de similaridade a todas as escalas espaciais. A incorporação de pressupostos mais realistas, ou a imposição de pressupostos dependentes da escala, pode revelar-se uma linha de investigação produtiva para as propriedades de escala das SADs e de padrões de similaridade, permitindo derivar novas previsões e melhorar a capacidade dos modelos teóricos em incorporar a variabilidade nos padrões de abundância e de similaridade a várias escalas.
Apoio financeiro do POCTI no âmbito do III Quadro Comunitário de Apoio. Apoio financeiro da FCT e do FSE no âmbito do III Quadro Comunitário de Apoio
Programa Doutoral em Biologia e Ecologia das Alterações Globais