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

Le lac de Tonlé Sap (TSL), Cambodge, est un écosystème lac-rivière de forêt alluviale au régime d'écoulement alternatif. Le lac est un déversoir lors de l'inondation saisonnière du Mékong et sert de réservoir en période de basses eaux. La superficie du lac pendant la saison sèche (février à mai), est d'environ 2 700 km2 pour une profondeur d'environ 1 mètre. Cette superficie est pratiquement multipliée par six quand arrive la saison des pluies, pour atteindre près de 16 000 km2 et une profondeur de 9 mètres, noyant rizières et forêts. C'est le plus grand lac d'eau douce d'Asie du Sud-Est. C'est aussi l'une des zones de pêche d'eau douce les plus importantes et productives du monde avec près de 75% du volume annuel de pêche en eau douce du Cambodge, ce qui permet la survie de près de 2,5 millions de personnes. Les changements saisonniers du cycle hydrologique ont une influence sur la structuration des communautés de poissons à l'échelle temporelle et spatiale, mais aussi sur les comportements trophiques des principales espèces qui n'exploitent alors pas les mêmes habitats. Toutefois, le bassin versant du Mékong est en changement constant avec un développement important des infrastructures en lien avec l'eau : production d'hydro-électricité, besoins important en irrigation, maitrise des inondations, eau potable, ... Les changements climatiques accélèrent les modifications du cycle hydrologique annuel. Il est alors supposé que ces modifications ont des effets forts sur les habitats et les proies disponibles et finalement sur la biodiversité, notamment de l'ichtyofaune et sur l'abondance des poissons disponibles pour les pêcheries.Dans un premier temps, nous avons caractérisé les variations spatio-temporelles de la composition taxonomique des poissons et mis en lumière quels sont les déterminants de ces variations. À cette fin, nous avons estimé la diversité bêta comme la variance totale de la matrice site par communauté d'espèce et l'avons divisée en contribution locale à la diversité bêta (LCBD) et contribution des espèces à la diversité bêta (SCBD). Nous avons ensuite effectué plusieurs régressions linéaires pour déterminer si la richesse taxonomique, l'abondance des espèces et le niveau de l'eau expliquaient la variation temporelle de la contribution du site et de l'espèce à la diversité bêta. Nos résultats indiquent une forte variation temporelle de la diversité bêta due aux contributions différentielles des sites et des espèces à la variation spatiale de la composition taxonomique des poissons. Nous avons également constaté que la direction, la forme et l'effet relatif de la richesse spécifique, de l'abondance et du niveau de l'eau sur la variation temporelle des valeurs LCBD et SCBD varient grandement selon les sites. Ces résultats suggèrent ainsi une variation spatiale des processus conduisant à une variation temporelle de la composition de la communauté. Dans l'ensemble, nos résultats suggèrent que la composition taxonomique des poissons n'est pas distribuée de manière homogène dans l'espace et dans le temps et risque d'être affectée à l'avenir si la dynamique saisonnière d'écoulement du système est altérée par les activités humaines et/ou les changements climatiques. Dans un second temps, nous avons cherché à étudier le modèle d'évolution temporel des principales espèces en terme d'occurrence et d'abondance à travers le cycle saisonnier hydrologique. / The Tonle Sap Lake (TSL), Cambodia, is a flood-pulse system. It is the largest natural lake in South- East Asia and constitutes one of the largest fisheries over the world, supporting the livelihood 2.5 million peoples. Seasonal change in annual hydrological cycle appears to have influence on fish community structure, both spatial and temporal variation, particularly on feeding behavior of TSL's fishes. Nonetheless, the Mekong River Basin is changing rapidly due to accelerating water infrastructure development (hydropower, irrigation, flood control, and water supply) and climate change, bringing considerable modifications to the annual flood-pulse of the TSL. Such modifications are expected to have strong impacts on fish biodiversity, abundance, reduced habitat and food availability within the lake. To invest how TSL's fish community structure responds to the seasonal change, how they shift their diet across hydrological cycles and feeding competing for food resource: First, we aim to characterize the spatio-temporal variations of fish taxonomic composition and to highlights the underlying determinants of these variations. For this purpose, we estimated beta diversity as the total variance of the site-by-species community matrix and partitioned it into Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD). We then performed multiple linear regressions to determine whether species richness, species abundances and water level explained the temporal variation in the contribution of site and species to beta diversity. Our results indicate strong temporal variation of beta diversity due to differential contributions of sites and species to the spatial variation of fish taxonomic composition. We further found that the direction, the shape and the relative effect of species richness, abundances and water level on temporal variation in LCBD and SCBD values greatly varied among sites, thus suggesting spatial variation in the processes leading to temporal variation in community composition. Overall, our results suggest that fish taxonomic composition is not homogeneously distributed over space and time and is likely to be impacted in the future if the flood-pulse dynamic of the system is altered by human activities. Second, we aim to investigate the temporal pattern of the most occurrence and abundance species and how their co-occurrence pattern across hydrological cycles. We found that occurrence and abundance patterns were temporally varied at all water level seasons. Strong temporal variation in species occurrence was occurred with visiting species such as Labiobarbus leptocheilus and Poropuntius deauratus while water level starts to fill into the TSL. We further observed that the abundance of 17 species was strongly varied while other 22 species (mainly TSL's residential species) were stable within the year. Positive species co-occurrence pattern was generally higher than negative species co-occurrence at all water level seasons. Highest positive co-occurrence patterns were found during the period of decrease and low water level seasons while fishes are migrating from flooded areas, competing for resource and habitats during low water season. Study on temporal distribution and species co-occurrence of fish and how community responds to the seasonal change in hydrological cycles provides critical information for fisheries management and conservation in the Tonle Sap Lake (TSL) as well as maintaining fish biodiversity in the Mekong system. Third, the implications of seasonality on food web structure have been notoriously understudied in empirical ecology, particularly in TSL's system. The current study, we focus on seasonal changes in one key attribute of a food web, vertical trophic position of consumers.

Interações interespecíficas são consideradas importantes forças estruturadoras da vegetação. Enquanto a competição aparentemente prevalece em ambientes com menor estresse abiótico, a facilitação tende a aumentar em importância em ambientes de maior estresse. Consequentemente, é esperado que a facilitação desempenhe um papel importante em áreas tropicais degradadas, nas quais as condições abióticas, envolvendo altos níveis de irradiação, temperatura e evapotranspiração, são muito distintas das condições ótimas para a maioria das espécies florestais. Além disso, face à complexidade dos processos estruturadores de comunidades florestais tropicais altamente diversas, os ecólogos têm percebido a necessidade de simplificação. Um caminho promissor para isso é por meio do uso de características funcionais, que podem ser medidas para qualquer espécie e comparadas em diferentes sistemas e locais. No entanto, em áreas degradadas ainda é incerta a relação entre as características funcionais e o desempenho das espécies. Neste contexto, planejamos um projeto de restauração na planície costeira do sudeste brasileiro para comparar o crescimento e a sobrevivência de mudas de árvores plantadas em diferentes densidades (sistema isolado ou sistema agregado) em um experimento fatorial com adição de nutrientes. No primeiro capítulo analisamos a sobrevivência, altura, diâmetro ao nível do solo e projeção da copa de 4.132 mudas de 19 espécies de diferentes classificações sucessionais, durante um período de 18 meses. Usamos modelos de efeitos mistos para analisar a relação entre o desempenho de espécies e os tratamentos e selecionamos os melhores modelos utilizando o critério de informação de Akaike (AIC). Verificamos uma maior sobrevivência nos sistemas agregados para as espécies não-pioneiras, indicando o predomínio do processo de facilitação. Em contrapartida, constatamos um menor crescimento em diâmetro nos sistema de plantio agregado, indicando o predomínio de competição. A adição de nutrientes não afetou a sobrevivência nos sistemas agregados, mas, surpreendentemente, teve um efeito negativo sobre as plantas isoladas. Além disso, a adição de nutrientes teve um efeito positivo sobre crescimento, diâmetro e projeção da copa nos sistemas de plantio agregado (indicando a redução da competição), especialmente para espécies pioneiras. Uma vez que o estabelecimento de espécies não-pioneiras em áreas degradadas pode ser bastante difícil, a facilitação para a sobrevivência dessas espécies em sistemas agregados pode ser utilizada como instrumento para melhorar os modelos de restauração. No segundo capítulo utilizamos algumas características funcionais que são facilmente mensuráveis para investigar sua relação com o crescimento e sobrevivência das mudas. Além disso, testamos o efeito das interações interespecíficas na relação das características funcionais com o desempenho das plantas. Para espécies pioneiras, uma maior área foliar específica (SLA - Specific leaf area), foi relacionada com uma maior taxa de sobrevivência. Entretanto, ao considerarmos as relações interespecíficas (sistemas agregados), maior SLA foi relacionada com uma menor taxa de sobrevivência. Em geral, as características funcionais explicaram apenas parcialmente o desempenho de mudas no contexto de restauração de áreas degradadas. Nosso trabalho contribuiu para a discussão sobre o potencial da aplicação prática da abordagem funcional na escolha das espécies para a recuperação de áreas degradadas. O caráter manipulativo da restauração ecológica baseada no plantio de mudas amplia as perspectivas para implementar experimentos que visem testar novas hipóteses em ecologia e refinar modelos de restauração / Interspecific interactions are considered to be important structuring forces in early successional vegetation. Whereas competition seems to prevail in less severe environments, facilitation tends to increase in importance in harsh environments. Hence, facilitation is expected to play an important role in degraded tropical areas with high irradiance, heat loads, and evapotranspiration, where conditions are far from optimum for most forest species. Moreover, in order to understand complex structuring process of high diverse tropical forests, ecologists have realized the need for simplification. A promising way to do that is through the use of functional traits, which can be measured for any species and compared in different systems and different locations around the world. However, in these conditions, little is known about the role of species interaction on the relation of functional traits and species performance. In this scenario, we planned a restoration project on the southeastern Brazilian coastal plain to compare growth and survival of tree seedlings planted at two densities (isolated or aggregated) in a factorial experiment with nutrient addition. In the first chapter we analyzed survival, height, ground level diameter, and crown projection of 4,132 saplings from 19 species that ranged along a successional gradient, over an 18-month period. We used mixed-effect models to analyze the relationship between species performance and treatments, and Akaike\'s information criterion (AIC) to select the models. The best model showed higher survival in aggregated plantations (indicating facilitation) for non-pioneer species. In contrast, we found lower diameter growth in aggregated plantation (indicating competition). Fertilizer addition did not affect survival in clusters, but, surprisingly, it had a negative effect on isolated plants of both pioneer and non-pioneer species. On the other hand, fertilizer addition had a positive effect on diameter and crown projection growth in aggregated plantations (reducing competition), especially for pioneer species. Thus, whether facilitation or competition was the predominant interaction depended on the response analyzed. We concluded that, as establishment of non-pioneer species in disturbed sites can be challenging, restoration designs could take advantage of higher survival rates in clusters and use resource addition to ameliorate growth and decrease competition for limited resources. In the second chapter we used the core simple-measurable traits to investigate whether functional traits were related to growth and survival and whether there was a difference in the effect of the functional traits on plant performance of isolated individuals or of individuals subjected to interaction with neighbors. Our main findings were that for pioneer species, the greater the specific leaf areas (SLA), the greater the survival rates, but, under aggregated conditions, the greater the SLA the lower the survival rates. However, functional traits only partially explained saplings performance in a restoration context and more research is needed to understand its role in predicting seedlings outcomes, especially considering the potential applicability of this methodological approach. The manipulative character of ecological restoration broadens perspectives to use experiments to generate and test new hypotheses in ecology and to refine restoration models

Ubiquitaires et très anciens, les communautés des tapis microbiens font preuve de capacités métaboliques et adaptatives très importantes. Situés en zone côtières, ces écosystèmes peuvent être soumis à des contaminations pétrolières. Dans ce contexte, cette étude vise d’une part à décrire la structure et le fonctionnement de tapis microbiens et d’autre part à comprendre l’impact d’une contamination pétrolière sur ces écosystèmes. Cette étude porte sur deux tapis microbiens de l’étang de Berre aux paramètres physico-Chimiques proches mais présentant des contaminations pétrolières contrastées. Le fonctionnement du système étant tributaire d’autres facteurs tels que la lumière et les saisons, les variations saisonnières et nycthémérales ont été prises en compte dans cette étude. Un accent particulier a également été porté sur le cycle du soufre de par son importance en milieu marin. Les résultats de cette étude mettent en évidence des structures de communautés différentes entre les deux tapis au niveau global, la séparation spatiale prévalant sur la séparation saisonnière. La fraction active de la communauté du site contaminé présente une évolution linéaire tandis que celle du site témoins suit pour sa part les variations saisonnières. Au niveau du site contaminé une augmentation de l’expression des gènes impliqués dans la dégradation des hydrocarbures couplée à une biodégradation des hydrocarbures suggère que le tapis contaminé est adapté à la contamination pétrolière. Malgré les différences de structures et d’activités de dégradation, des profils métaboliques très semblables sont cependant observables entre les deux tapis, avec des fonctions similaires laissant supposer une redondance fonctionnelle. Des variations saisonnières et nycthémérales ont également été observées avec notamment des Desulfobulbaceae plus abondantes au printemps et plus actives en journée. Des études culturales ont été réalisées en parallèle. Elles permettront d’appréhender de manière complémentaire la dynamique des communautés des sulfato-Réducteurs au sein du tapis et de mieux comprendre les variations mises en évidence dans cette étude. / Ubiquist and very ancient, the microbial mats communities demonstrate very important metabolic and adaptive capacities. Located in the coastal area, these ecosystems may be subject to oil contamination. In this context, the aim of this study is on one hand to describe the structure and functioning of microbial mats and on the other to understand the impact of oil contamination on these ecosystems. This study focused on two microbial mats from the Berre lagoon with close physical chemical parameters but with contrasted hydrocarbon contamination levels. The functioning of the system is dependent on other factors such as light and seasons, diurnal and seasonal variations were taken into account in this study. Special emphasis was placed on the sulfur cycle due to its importance in the marine environments. The results of this study highlighted different communities’ structures at the global level between both mats, the spatial variation prevailed on seasonal variation. The active part of the community from the contaminated site shows a linear trend while that one of the uncontaminated site follows the seasonal variations. The contaminated site shows genes involved in hydrocarbon degradation more expressed coupled to a hydrocarbon biodegradation suggesting that the contaminated mat is adapted to the petroleum contamination. Despite these differences in the structure and the degradation capacities, very similar metabolic profiles are observed between the two mats with similar functions, suggesting functional redundancy. Seasonal and diurnal variation was also observed, the Desulfobulbaceae were particularly more abundant in spring and more active during the day. A complementary cultural approach will allow to better understanding the dynamics of sulfate-Reducers communities in the mat and comprehending these variations.

The widespread threat of species extinctions caused by the destruction and degradation of tropical primary forest (PF) could potentially be mitigated by the expansion of regenerating secondary forest (SF). However, the conservation value of SF remains controversial, and is dependent on many site- and landscape-scale factors, such as habitat age and isolation. The aim of this thesis was to assess the role that SF can play in conserving forest bird communities in central Panama. We study a chronosequence of SF aged 20 – 120-years-old, with sites either isolated from or connected to extensive PF. Our results suggest that SF supports high levels of avian species diversity, and similar community composition to PF. Whilst forest age plays a small role in determining compositional similarity to PF, connectivity to extensive PF was the main determinant of community composition. However, despite high species richness and complex community composition, some specialist PF bird species were consistently absent from SF, and isolated PF. The functional diversity of bird communities did not vary substantially across the forest age and isolation gradient, although we did find some inter-guild differences; with distinct responses in communities of avian insectivores and frugivores. Isolation caused shifts in the trophic traits of insectivores, but resulted in alterations in the dispersal traits of frugivores. The response of bird and tree community composition to forest age and isolation was similar, although isolation had a stronger impact on bird communities. Bird diversity and composition tracked changes in forest structure over succession. When examining the role of birds in seed-dispersal networks, we found bird gape width was the key predictor of seed size consumed. Large-gaped birds consume a wider variety of seed-sizes than small-gaped birds, and small-seeded trees attract a greater number of bird species than large-seeded trees. These results imply high levels of redundancy among small-gaped avian frugivores and small-seeded plant species, but low levels of redundancy among large-seeded plant species and their avian dispersers. This suggests that large-seeded plants may be most at risk of dispersal failure following any change in avian frugivore assemblages. Together, these results suggest that SF can play a key role in sustaining most tropical biodiversity, and in maintaining ecosystem services. Our findings emphasise the importance of integrating SF into conservation strategies to support and buffer tropical PF habitats.

Interações interespecíficas são consideradas importantes forças estruturadoras da vegetação. Enquanto a competição aparentemente prevalece em ambientes com menor estresse abiótico, a facilitação tende a aumentar em importância em ambientes de maior estresse. Consequentemente, é esperado que a facilitação desempenhe um papel importante em áreas tropicais degradadas, nas quais as condições abióticas, envolvendo altos níveis de irradiação, temperatura e evapotranspiração, são muito distintas das condições ótimas para a maioria das espécies florestais. Além disso, face à complexidade dos processos estruturadores de comunidades florestais tropicais altamente diversas, os ecólogos têm percebido a necessidade de simplificação. Um caminho promissor para isso é por meio do uso de características funcionais, que podem ser medidas para qualquer espécie e comparadas em diferentes sistemas e locais. No entanto, em áreas degradadas ainda é incerta a relação entre as características funcionais e o desempenho das espécies. Neste contexto, planejamos um projeto de restauração na planície costeira do sudeste brasileiro para comparar o crescimento e a sobrevivência de mudas de árvores plantadas em diferentes densidades (sistema isolado ou sistema agregado) em um experimento fatorial com adição de nutrientes. No primeiro capítulo analisamos a sobrevivência, altura, diâmetro ao nível do solo e projeção da copa de 4.132 mudas de 19 espécies de diferentes classificações sucessionais, durante um período de 18 meses. Usamos modelos de efeitos mistos para analisar a relação entre o desempenho de espécies e os tratamentos e selecionamos os melhores modelos utilizando o critério de informação de Akaike (AIC). Verificamos uma maior sobrevivência nos sistemas agregados para as espécies não-pioneiras, indicando o predomínio do processo de facilitação. Em contrapartida, constatamos um menor crescimento em diâmetro nos sistema de plantio agregado, indicando o predomínio de competição. A adição de nutrientes não afetou a sobrevivência nos sistemas agregados, mas, surpreendentemente, teve um efeito negativo sobre as plantas isoladas. Além disso, a adição de nutrientes teve um efeito positivo sobre crescimento, diâmetro e projeção da copa nos sistemas de plantio agregado (indicando a redução da competição), especialmente para espécies pioneiras. Uma vez que o estabelecimento de espécies não-pioneiras em áreas degradadas pode ser bastante difícil, a facilitação para a sobrevivência dessas espécies em sistemas agregados pode ser utilizada como instrumento para melhorar os modelos de restauração. No segundo capítulo utilizamos algumas características funcionais que são facilmente mensuráveis para investigar sua relação com o crescimento e sobrevivência das mudas. Além disso, testamos o efeito das interações interespecíficas na relação das características funcionais com o desempenho das plantas. Para espécies pioneiras, uma maior área foliar específica (SLA - Specific leaf area), foi relacionada com uma maior taxa de sobrevivência. Entretanto, ao considerarmos as relações interespecíficas (sistemas agregados), maior SLA foi relacionada com uma menor taxa de sobrevivência. Em geral, as características funcionais explicaram apenas parcialmente o desempenho de mudas no contexto de restauração de áreas degradadas. Nosso trabalho contribuiu para a discussão sobre o potencial da aplicação prática da abordagem funcional na escolha das espécies para a recuperação de áreas degradadas. O caráter manipulativo da restauração ecológica baseada no plantio de mudas amplia as perspectivas para implementar experimentos que visem testar novas hipóteses em ecologia e refinar modelos de restauração / Interspecific interactions are considered to be important structuring forces in early successional vegetation. Whereas competition seems to prevail in less severe environments, facilitation tends to increase in importance in harsh environments. Hence, facilitation is expected to play an important role in degraded tropical areas with high irradiance, heat loads, and evapotranspiration, where conditions are far from optimum for most forest species. Moreover, in order to understand complex structuring process of high diverse tropical forests, ecologists have realized the need for simplification. A promising way to do that is through the use of functional traits, which can be measured for any species and compared in different systems and different locations around the world. However, in these conditions, little is known about the role of species interaction on the relation of functional traits and species performance. In this scenario, we planned a restoration project on the southeastern Brazilian coastal plain to compare growth and survival of tree seedlings planted at two densities (isolated or aggregated) in a factorial experiment with nutrient addition. In the first chapter we analyzed survival, height, ground level diameter, and crown projection of 4,132 saplings from 19 species that ranged along a successional gradient, over an 18-month period. We used mixed-effect models to analyze the relationship between species performance and treatments, and Akaike\'s information criterion (AIC) to select the models. The best model showed higher survival in aggregated plantations (indicating facilitation) for non-pioneer species. In contrast, we found lower diameter growth in aggregated plantation (indicating competition). Fertilizer addition did not affect survival in clusters, but, surprisingly, it had a negative effect on isolated plants of both pioneer and non-pioneer species. On the other hand, fertilizer addition had a positive effect on diameter and crown projection growth in aggregated plantations (reducing competition), especially for pioneer species. Thus, whether facilitation or competition was the predominant interaction depended on the response analyzed. We concluded that, as establishment of non-pioneer species in disturbed sites can be challenging, restoration designs could take advantage of higher survival rates in clusters and use resource addition to ameliorate growth and decrease competition for limited resources. In the second chapter we used the core simple-measurable traits to investigate whether functional traits were related to growth and survival and whether there was a difference in the effect of the functional traits on plant performance of isolated individuals or of individuals subjected to interaction with neighbors. Our main findings were that for pioneer species, the greater the specific leaf areas (SLA), the greater the survival rates, but, under aggregated conditions, the greater the SLA the lower the survival rates. However, functional traits only partially explained saplings performance in a restoration context and more research is needed to understand its role in predicting seedlings outcomes, especially considering the potential applicability of this methodological approach. The manipulative character of ecological restoration broadens perspectives to use experiments to generate and test new hypotheses in ecology and to refine restoration models

Le lac Tonle Sap (TSL) est l'un des plus grands lacs du monde et est connu comme un hot-spot de la biodiversité en Asie du Sud-Est. En raison de la grande diversité ainsi que de la productivité élevée de poissons, le lac contribue à un apport important en protéines pour la population cambodgienne. Cette étude vise principalement à étudier (1) la dynamique spatiale et temporelle de la composition des communautés de poissons, (2) les effets des facteurs environnementaux sur la distribution des espèces et (3) l'effet de l'abolition des lots de pêche sur la biomasse, les communautés de poissions et le structure des poissons. En utilisant des méthodes statistiques multivariées sur les données de poissons et de variables environnementales, je suis en mesure de mettre en évidence les principales conclusions suivantes: * Les communautés de poissons du TSL étaient composées de deux assemblages de poissons: l'assemblage du nord, principalement caractérisé par des poissons noirs, et l'assemblage du sud, principalement lié aux poissons blancs, gris et estuariens. Les assemblages de poissons de la période 1994-1995 étaient représentés par l'abondance de tous les groupes fonctionnels, c'est-à-dire les poissons noirs, blancs et gris, et pour la période de 1996 à 1999, les assemblages étaient liés aux poissons blancs et gris. * Les distributions des abondances espèces de poissons n'étaient pas homogènes dans le TSL. De plus, les aires de distributions des espèces étaient différentes et étaient régies par des combinaisons distinctes de caractéristiques de l'habitat et de facteurs climatiques. * H. lobatus et H. siamensis peuvent coexister ensemble, mais la synchronisation et la migration de H. lobatus conduisent toujours à celles de H. siamensis. Ces résultats suggèrent que la population de H. lobatus est plus sensible aux variations d'impulsion de flux que celles de H. siamensis. Ceci indique que les variations des impulsions d'écoulement sont les principaux déterminants responsables de la dynamique temporelle de chaque espèce.[...] / Tonle Sap Lake (TSL) is one of the world's largest lakes and is a biodiversity hotspot in Southeast Asia. It supports high fish productivity which sustains protein supply for millions of people in the region. This study aims to investigate (1) spatial and temporal dynamics of fish community composition, (2) the effects of environmental factors on fish distribution and (3) effects of fishing lot abolishment on fish biomass, community and structure in TSL. By using multivariate statistical methods on fish and environmental data, the thesis highlights that: * There were two fish assemblages in TSL: the northern assemblage, mostly characterised by black fishes, and the southern assemblage, mainly linked to white, grey and estuarine fishes. Fish assemblages from earlier years (1994 and 1995) were represented by the abundances of all functional groups, i.e. black, white and grey fishes, and from 1996 to 1999, the assemblages were linked only to white and grey fishes. * Fish species distributions were not homogeneous within TSL. In addition, species distribution areas were different and were governed by distinct combinations of the local habitat characteristics and regional climatic factors. * H. lobatus and H. siamensis can co-occur together, but synchronisation and migration of H. lobatus always lead those of H. siamensis. These results suggest that the population of H. lobatus is more responsive to flow pulse variations than those of H. siamensis.[...]

Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. Actuellement, les écosystèmes sont soumis à dimportantes pressions anthropiques et environnementales, pouvant aboutir à des pertes massives de biodiversité. Les scientifiques sinterrogent sur limpact de ces perturbations sur la diversité et, par conséquent, sur lactivité des microorganismes du sol. En effet, ceux-ci régulent de nombreux processus du sol. Actuellement, de nombreuses lacunes subsistent dans la connaissance de la diversité microbienne du sol. Celles-ci peuvent être partiellement attribuées aux difficultés méthodologiques associées à l'étude des micro-organismes du sol. Lavènement des techniques moléculaires nous permet de combler ces lacunes. Les avancées réalisées dans l'étude des communautés microbiennes du sol ont mis en évidence le rôle crucial joué par les communautés microbiennes dans le fonctionnement des écosystèmes. De plus, il semblerait que les processus régulés par un groupe restreint dorganismes, tel le processus de nitrification, soient plus sensibles à toute altération de la communauté. Lobjectif de cette thèse était détudier la structure de la communauté ainsi que la richesse (nombre de bandes DGGE) des bactéries oxydant lammoniac (AOB) comme une partie intégrante du fonctionnement des sols. Notre étude se focalisait sur linfluence de (a) différents groupes fonctionnels de plantes (graminées, légumineuses, dicotylédones), (b) communautés de plantes présentant une richesse spécifique croissante et (c) différentes essences forestières, sur la diversité (structure de la communauté et richesse des AOB) et la fonction des AOB. Cette recherche étudiait également limpact dune augmentation de température de 3°C sur ces paramètres. Létablissement dun lien éventuel entre la diversité et la fonction (nitrification potentielle) des AOB a aussi été envisagé. Concernant les écosystèmes prairiaux, nous avons réalisé une étude en microcosmes. Une plateforme expérimentale comprenant 288 communautés artificielles de plantes a été établie à Wilrijk (Belgique). Cette plateforme consistait en 12 chambres, dont une moitié était à température ambiante et la seconde était à température ambiante augmentée de 3°C. Chaque chambre contient 24 communautés de plantes de richesse spécifique variable (9 S=1, 9 S=3 et 6 S=9). Les communautés de plantes sont créées avec 9 espèces de plantes appartenant à trois groupes fonctionnels : 3 espèces de graminées (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), de légumineuses (dicotylédones fixatrices dazote ;Trifolim repens L., Medicago sativa L., Lotus corniculatus L.), et de dicotylédones non fixatrices dazote (Bellis perennis L., Rumex acetosa L., Plantago lanceolata L.). Les sols issus dune chambre à température ambiante et dune chambre à température ambiante augmentée de 3°C ont été échantillonnés, respectivement, 4, 16 et 28 mois après le début de lexpérimentation. Linfluence des groupes fonctionnels de plantes sur le processus de nitrification ainsi que sur la structure de la communauté et la richesse des AOB a été mesuré sur les sols issus des deux premiers échantillonnages (chapitre 2). Nous avons mesuré leffet de la richesse croissante en plantes sur la diversité et lactivité des AOB sur les sols échantillonnés après 16 et 28 mois dexpérimentation (chapitre 3). La structure de la communauté ainsi que la richesse des AOB ont été évaluées à laide dune amplification spécifique par réaction de polymérisation en chaîne (PCR) de lADN génomique extrait du sol suivie par une séparation par électrophorèse sur gel dacrylamide en présence dun gradient dénaturant (DGGE). Nous avons identifié les différentes AOB présentes par séquençage des bandes DGGE excisées. Nos résultats ont montré que les différents groupes fonctionnels peuvent affecter la structure de la communauté des AOB. En particulier, la présence de légumineuses, aussi bien en monoculture quen mélange avec des graminées ou des dicotylédones non fixatrices dazote, provoque des changements au sein de la structure de la communauté des AOB, favorisant la présence de clusters tolérants des concentrations en ammonium plus élevées. Ces changements de la structure de la communauté des AOB sont liés à des augmentations de la production potentielle de nitrates (nitrification potentielle) quand lammonium est supposé être non limitant. Cette étude révèle que la physiologie des AOB ainsi que la disponibilité en substrat peuvent être des facteurs majeurs intervenant dans le contrôle du processus de nitrification. Cette recherche montre que linfluence de la richesse spécifique des plantes sur la nitrification pourrait dépendre des interactions entre les plantes et les AOB via la compétition pour le substrat. Une augmentation de la température de lair de 3°C na pas influencé les richesse, structure de la communauté ou les fonctions des AOB. Pour les écosystèmes forestiers, nous aborderons leffet de différentes essences forestières (Picea abies (L.) KARST, Fagus sylvatica L., Quercus petraea LIEBLEIN ; Pseudotsuga menziezii (MIRB.) FRANCO) dans différents peuplements au Grand Duché du Luxembourg et en Belgique. Nous avons étudié l'influence de ces essences forestières sur les processus microbiens (chapitre 5) liés aux cycles du carbone et de lazote, en particulier leur effet sur le processus de nitrification et la diversité des AOB (chapitre 6). Notre étude révèle que linfluence des essences forestières sur la minéralisation nette de lazote pourrait être attribuable à leur effet sur la biomasse microbienne, reflétant ainsi leur effet sur la teneur en matière organique et la disponibilité en carbone. Limpact des essences forestières sur la nitrification (à la fois sur la nitrification relative et sur la nitrification potentielle) serait conditionné par la présence de végétation au sol, en raison de linfluence de celle-ci sur la disponibilité en ammonium et en carbone labile. Nous avons observé que la structure de la communauté des AOB était plus spécifique aux sites quaux essences forestières. Cependant, au sein dun site, elle différait sous feuillus et sous conifères. Les essences forestières influenceraient la structure de la communauté des AOB au travers de limpact quelles ont sur la minéralisation nette de lazote qui régule, quant à elle, la disponibilité en ammonium. Cette recherche démontre que le lien observé entre la diversité et la fonction dépendrait la fois de labondance, de la structure de la communauté et de la richesse des AOB. Cette thèse na révélé aucune relation claire entre la structure de la communauté ou la richesse des AOB et leur fonction. Par contre, nous avons observé que la richesse spécifique et les groupes fonctionnels de plantes prairiales et les essences forestières affectent la structure de la communauté et la richesse des AOB.

The effects of reafforestation with seedlings of spruce, birch, mountain-ash, beech and larch, partially in combination with liming and removal of the topsoil layer before planting, on the community of saprophagous invertebrates (lumbricids, enchytraeids, oribatids, collembolans) were examined. The study area was located on plateau sites of the eastern Ore Mountains (Saxonia, Germany). Investigations were carried out on study sites exposed to high sulphur dioxide immissions and reforested 3 respectively 10 years ago. Invertebrates were sampled by the extraction of soil cores and by the ?electro-octett-method? (lumbricids). Additionally, the ?minicontainer method? was used to investigate decomposition rates of different types of litter. On the control area, a diedback spruce stand, the decomposer community showed high adaptations to the acidic soil substrate and was dominated by few enchytraeid species. Long-termed loss of tree shelter, liming and topsoil removal before planting resulted in a severe decline of most saprophagous species. However, changes in invertebrate community pattern due to different plantations were not found. A comparison of leaf and needle litter decomposition rates resulted in the following order: birch (k = 0.50) > mountain-ash (0.40) > spruce (0.30) >> larch (0.12). Considering all investigated taxa, the metabolic decomposing capacity of the larch litter reached 39 %, that the spruce litter 54 % of the foliage litter results. / Anläßlich des kompletten Ausfalls der Fichte in den extrem immissionsbelasteten Kammlagen des Osterzgebirges (Sachsen) wurden im Rahmen eines interdisziplinären Verbundprojektes verschiedene Waldbaukonzepte hinsichtlich ihrer Einflüsse auf die saprophage Invertebratenfauna (Enchytraeidae, Lumbricidae, Oribatida, Collembola) untersucht. Zur Disposition standen Verfahren zur Waldneugründung (Kulturparzellen mit Reihenpflanzung von Birke, Eberesche oder Fichte; zusätzlich waldbaulich unbeeinflußte Sukzessionsparzellen) und zum Waldumbau (Kulturparzellen mit Reihenpflanzung von Buche oder Lärche nach Abtrieb und flächigem Oberbodenabschub). Ein absterbender Fichtenreinbestand in fortgeschrittener Auflösung diente als Referenz- bzw. Korrelationsmaßstab. Die Erfassung der Mesofauna erfolgte über die Extraktion von Stechrohrproben. Lumbriciden wurden mit der Elektrooktett-Methode aufgenommen. Neben der flächenbezogenen Datenerfassung wurden 1.200 mit Blattstreu von Birke, Eberesche, Fichte und Lärche befüllte Minicontainer über 19 Monate auf einer Sukzessionsparzelle exponiert, um substratspezifische Abbaugeschwindigkeiten zu ermitteln und faunistische Sukzessionsverläufe zu studieren. Die Referenzfläche zeichnete sich durch eine stark enchytraeendominierte Zersetzergemeinschaft aus, die deutliche Anzeichen einer kalkungsbedingten Überprägung erkennen ließ. Der Enchytraeenanteil an den potentiellen Umsatzleistungen der untersuchten Destruententaxa (berechnet über metabolische Äquivalenzwerte) lag bei über 90 %. Hiervon ausgehend zeigten die Zersetzergemeinschaften der Versuchsanlagen "Waldneugründung" und "Waldumbau" stark divergierende Entwicklungsrichtungen. Als ausschlaggebende Faktoren konnten Schirmverlust, Kalkung und Oberbodenbeseitigung wahrscheinlich gemacht werden. Dagegen waren Einflüsse der unterschiedlichen Kulturbaumarten kaum nachzuweisen. Die streuspezifischen Dekompositionsgeschwindigkeiten unterschieden sich wie folgt: Birke (k = 0,50) > Eberesche (0,40) > Fichte (0,30) >> Lärche (0,12). Diese vergleichsweise geringen Abbauraten stehen überwiegend mit dem rauhen Montanklima in Zusammenhang. Enchytraeen besiedelten alle Streutypen zügig, während Collembolen vor allem die Ebereschenstreu verzögert aufsuchten und mit geringster Dichte bevölkerten. Oribatiden zeigten die geringste Besiedlungsgeschwindigkeit und hatten wie die Enchytaeen in der Laubstreu signifikant höhere Wohndichten. Nur Steganacarus spinosus zeigte eine besondere Affinität für Nadelstreu. Das metabolische Leistungspotential des Destruentenbesatzes der Lärchenstreu erreichte 39 %, das der Fichtenstreu 54 % der Laubstreuresultate.

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