This thesis investigates the influence of nonrandom species loss on the structure and functioning of trophic floodplain lagoons. Two experiments were conducted based on different realistic scenarios of biodiversity loss using multitrophic fish assemblages derived from long-term survey data. Loss of fish diversity influenced overall ecosystem multifunctionality of these lagoons through complex multitrophic interactions throughout the aquatic food web. These results indicate that biodiversity loss from diverse multitrophic ecosystems can influence ecosystem structure and function and likely deviate from simplified food chain dynamics or patterns that emerged from single trophic level studies.

In the last few decades, a growing literature has examined how biodiversity influences ecosystem functioning. This body of work has greatly improved our understanding of ecosystem functioning and its modulation by biodiversity. In particular, there is nowadays large consensus that biodiversity increases ecosystem productivity, and stabilises ecosystems. Early investigations were largely theoretical or involved simple experiments run in laboratory conditions, but over time biodiversity ecosystem-functioning experiments evolved to more realistic field experiments that better represent the real conditions found in natural ecosystems. In particular, these experiments are often run on larger spatial scales and over longer time frames allowing for the effect of environmental heterogeneity and temporal fluctuations to be explored. The designs of these experiments evolved along with the questions addressed in this field of research. However, the analytical tools used in the analyses of these experiments followed a slightly different path. In particular, most of the metrics currently used to analyse biodiversity ecosystem functioning experiments are not entirely suited to properly deal with the complexity of modern designs as they make a number of assumptions that are not met any more. In my thesis I developed a unified framework, based on the tailored use of Linear Mixed Effects Models, to analyse biodiversity-ecosystem functioning experiments such that the new complexities of these experiments can be taken into account. This thesis aimed to bring the focus of the analysis back to the biological interpretation of the results. I successfully applied my approach to several data sets. The framework developed here is expected to improve greatly our understanding of ecosystem functioning and how biodiversity modulates it. It also sheds new light on past research in this field. The great flexibility of the new approach makes it possible to let these experiments to evolve such that new biological questions can be addressed.

The restoration of degraded tallgrass prairies can mitigate climate change due to the carbon accrued during the development of grasslands. The focal species, dominant grass Andropogon gerardii, can assist the recovery of grassland ecosystem functioning. Climate, local adaptation, and biodiversity have been found to impact the accrual of carbon in grasslands. This study examined the difference in ecosystem functioning between ecotypes along a dry to mesic precipitation scale. The study site for this project was at the Southern Illinois University Agriculture Research Center in Carbondale, Illinois. The field site was planted with seeds originating from dry to mesic ecotypes, and the resulting ecosystem functioning was analyzed. It was found that the Kansas non-local ecotypes had significantly higher biodiversity, while the local Illinois sites demonstrated local adaptation with A. gerardii. Aboveground plant biomass was higher in the local sites, but there was no difference in carbon accrual between any of the ecotypes. While ecotypic variation in a dominant species will usually differentially influence ecosystem functioning, in this case, high biodiversity and local adaptation result in similar carbon inputs in grassland soil. It is necessary to analyze the carbon content of the soil in the drier field sites in order to determine if major differences in rainfall leads to differences in carbon accrual. If the goal of restoring a tallgrass prairie in southern Illinois is to assist with climate change mitigation, then it does not make a significant difference if the dominant species is sourced locally or non-locally.

As a part of Saudi Arabia’s Vision 2030, the Al Wajh Bank will soon undergo major coastal development to be transformed into a sustainable luxury tourist destination, with goals to safeguard the marine and coastal habitats in order to achieve a net conservation benefit of 30%. To realize these objectives, it is essential to establish baseline data on the marine communities to gauge the success of conservation goals. In this study, we evaluated and compared the taxonomic and functional diversity of reef fish assemblages between two areas in the Al Wajh Bank, sites inside the lagoon and those outside of it, in order to establish differences in fish communities across environmental gradients. Conditions within the lagoon, such as temperature and salinity, have been shown to differ from most other Red Sea areas and are thought to result in unique fish assemblages. Underwater assessments of fish communities and benthic composition were conducted throughout the Al Wajh Bank during cruises in 2016 and 2017. We found that of the 168 fish species recorded, 75 species were exclusive outside the lagoon, 22 were exclusive inside the lagoon, and 71 species were shared between inside and outside. Sites within the lagoon had significantly less species richness as well as lower abundances. While taxonomic composition differed between the two areas, functionally they were very similar. Two functional metrics (functional richness and functional dispersion) indicated different levels of functional diversity, while two other metrics (functional evenness and functional specialization) showed no differences in functional diversity. The outside had five groups comprising eleven species with functional redundancy; in contrast, the inside had two species which were functionally redundant. This study was able to establish that the inside and outside habitats are different and have dissimilar species compositions, yet the functional characterization of fish assemblages in conserved. These results advocate for the use of functional diversity metrics as a way to evaluate changes to community composition, and is an initial assessment towards tracking changes in the fish communities as coastal development progresses

Dans le contexte des changements globaux, la biodiversité en Méditerranée est menacée, notamment par une sécheresse plus intense, avec des modifications probables du fonctionnement des écosystèmes. Cette thèse étudie l’effet de la sécheresse accrue sur la végétation et la modulation des effets par la diversité végétale, par une expérimentation d’exclusion de pluie dans une garrigue au nord de Marseille avec un gradient naturel de diversité. Les performances des 4 arbustes dominants, la diversité spécifique et fonctionnelle, les relations interspécifiques et la relation diversité-productivité de la garrigue ont été étudiés sous deux niveaux de pluieAprès 2,5 années, les effets de la sécheresse accrue sur la performance des 4 arbustes dépendent de l’espèce et du paramètre évalués et peuvent être modulés par la diversité des co-dominantes. Q.coccifera parait plus résistante et résiliente, suivie de R.officinalis et finalement de C.albidus et U.parviflorus. Ceci s’explique en partie par leurs différentes stratégies d’acquisition, utilisation et conservation du carbone et de l’eau. Les traits foliaires et la diversité fonctionnelle et spécifique ne sont pas affectés significativement par la réduction des pluies, mais dépendent du nombre, l’identité et le recouvrement des dominantes. Au vu de l’effet différentiel de la sécheresse accrue sur les espèces dominantes, on peut s’attendre à un effet négatif indirect de la sécheresse sur la biodiversité et donc sur le fonctionnement de la garrigue. On confirme l’importance d’intégrer les facteurs biotiques dans les modèles visant à prévoir le fonctionnement et les services des écosystèmes dans le cadre du changement climatique. / In the global change context, the biodiversity in the Mediterranean is under threat, mainly due to the more intense drought, which could lead to modification of ecosystem functioning. This thesis focuses on the effects of higher drought on the aboveground vegetation and the modulation of these effects by plant diversity thanks to a precipitation exclusion experiment in a shrubland in the south of France whith a natural diversity gradient. The 4 dominant shrub species performances, the specific and functional diversity, the interspecific interaction, and the biodiversity-productivity relationship were studied under 2 rain levelsAfter 2,5 years the effects of increased drought on the 4 dominant shrub performances was species- and parameter-dependant and can be modulated by the diversity of the co-dominant species. Q. coccifera seems the most resistant and resilient, followed by R. officinalis and finally by C. albidus and U. parviflorus. This is partly explained by the different strategies of acquisition, utilization and conservation of carbon and water of the four species. The leaf traits, the functional and specific diversity are not significantly affected by the precipitation decrease, but they depend on the number, the identity and the cover of the dominant shrubs. Given the differential effect of higher drought on the dominant species performances, we could expect an indirect negative effect of drought on the shrubland diversity and so on ecosystem functioning. We confirm the importance of taking into account the biotic factors in models aiming to predict the ecosystem functioning and environmental risks and services under future in the climate change context

Bacteria are immensely diverse and hold key-positions in essentially all biogeochemical cycles. In freshwater ecosystems, bacteria degrade and mineralize organic compounds, linking the pool of dissolved organic matter to higher trophic levels. Aware of the global biodiversity loss, ecologists have started identifying the relationship of diversity and ecosystem functioning. Central to this is the question if species can functionally replace other species, hence being functionally redundant. Functional redundancy might allow communities to maintain functioning when diversity is lost. Due to their large numbers and great diversity, bacterial communities have been suspected to harbor large amounts of redundancy. The central aim of this thesis is to investigate the coupling of diversity and ecosystem functioning of bacterial communities and to understand how environmental perturbation affects this relationship. I manipulated the diversity of complex communities by a dilution technique, and measured the performance of bacterioplankton and biofilm-forming communities at different diversities. Reduction of bacterial diversity differently affected different functions, and that the presence or absence of certain species might be causing this pattern. However, for ecosystems to function, the interplay of multiple functions, i.e. multifunctionality, has to be sustained over long periods of time. In bacterial biofilm communities reduced diversity affected multifunctionality, as reflected by extracellular enzyme activities. A continuous cultivation system was used to address the importance of diversity for resistance and resilience upon environmental perturbation. The analysis of co-occurrence of bacterial taxa showed that the communities form a dense network before the perturbation and that these patterns are disturbed by the environmental perturbation. The final chapter of the thesis presents experimental evidence for the positive effects of temporal and spatial refuges for bacterial communities and the functions they provide. Overall, I found several indications for a lower amount of functional redundancy as previously assumed and it becomes apparent from this thesis that a multifunctional perspective and the consideration of environmental heterogeneity is pivotal.

The projected increase of shrubs across the Arctic is expected to alter patterns of snow cover, which may affect the phenology and survival of arthropods such as spiders. In this study, we simulated shrub encroachment on a series of tundra plots and examined the effects on the spider assemblages during the following growing season. Our simulated shrub treatment did not affect the abundance or composition of spider communities over the season; however, adults from the dominant genus Pardosa (Lycosidae) had significantly higher body mass on treatment plots. This difference in mass was observed following snow melt and persisted until halfway through the growing season. Given the importance of spiders as arthropod predators and as food sources for breeding birds, such a change in summer body mass could represent a shift in spiders’ functional contributions to Arctic ecosystems.

The projected increase of shrubs across the Arctic is expected to alter patterns of snow cover, which may affect the phenology and survival of arthropods such as spiders. In this study, we simulated shrub encroachment on a series of tundra plots and examined the effects on the spider assemblages during the following growing season. Our simulated shrub treatment did not affect the abundance or composition of spider communities over the season; however, adults from the dominant genus Pardosa (Lycosidae) had significantly higher body mass on treatment plots. This difference in mass was observed following snow melt and persisted until halfway through the growing season. Given the importance of spiders as arthropod predators and as food sources for breeding birds, such a change in summer body mass could represent a shift in spiders’ functional contributions to Arctic ecosystems.

Bacterial diversity and ecosystem functioning (BEF) relationships have received considerable attention during the last three decades and tend to be positive in most cases. However, most studies were done in closed systems and largely ignored the importance of placing local communities into the metacommunity context, in which dispersal can be a crucial factor modifying community diversity and composition and ecosystem functioning. The aim of this study was to investigate the effects of both diversity and dispersal on the responses of bacterial community to a starvation perturbation. To achieve this, we implemented a batch culture experiment using the dilution-to-extinction approach to create a diversity gradient of local bacterial community richness. Different dispersal rates were manipulated by transferring cells in different quantities from a regional source to the cultures, and they were then exposed to a perturbation by transferring them into water from another lake which differed in organic carbon content and quality. We evaluated the BEF relationship by measuring the bacterial community composition using t-RFLP and multiple ecosystem functions. Generally, our results demonstrated that diversity and dispersal have an interactive and positive effect on ecosystem functioning. In particular, dispersal had a stronger and more pronounced effect on ecosystem functioning when bacterial diversity was low. When evaluating the responses of bacterial community respiration, no significant difference was observed among different treatments, however, there were clear differences in substrate utilization patterns, implying that specific functions, such as decomposing certain substrates, are more sensitive to a perturbation than general functions, such as respiration. Therefore it is important to include multiple functional parameters when studying BEF relationships and, in particular, when applying our knowledge to the conservation of natural environments.

Habitat loss and fragmentation have been identified as the main drivers of biodiversity loss. These drivers increase the proportion of habitat edges and change the configuration of landscapes. Habitat edges are known to affect ecological patterns and processes, however, is still unknown how these boundaries affect the assemblage of interactions among species within a community, and particularly its structure. Food webs depict not only the composition of the community, but also the feeding links, which represent a measure of energy flow. Therefore, they can inform about the relationships among community diversity, stability, and ecosystem functions. This thesis explores the effects of habitat edges across native vs. managed forests on the food web of a tri-trophic system comprising plants, herbivores (Lepidoptera larvae) and predators (parasitoids). Particularly, it addresses three main objectives: 1) how food webs at habitat edges are assembled from the species and interactions present in the adjoining habitats; 2) how phylogenetic diversity and the coevolutionary signal among interacting species change across a habitat edge gradient; and 3) whether the mechanisms driving community-wide consumption rates and the ecosystem service of pest control are related to structural characteristics of the food webs. The key findings of this thesis are that, despite the composition of species and interactions of native and managed habitats merging at their interface, food-web structure did not arise as a simple combination of its adjacent habitat webs, potentially due to differential responses of organisms to habitat edges. Moreover, beyond taxonomic composition, the phylogenetic diversity and signal of coevolution among interacting species also change between habitat types, even though this did not translate to changes in consumption rates. Consumption rates and their stability increased with complementarity and redundancy in resource-use among predators. This reflects how environmental changes such as habitat fragmentation can have an effect beyond composition per se, affecting the assemblage of species interactions and even potentially interfering with natural evolutionary processes. Therefore, using interaction-network approaches for determining the impacts of changes may shed light on the underlying mechanisms driving such changes, and help to develop landscape management plans that reduce negative effects on species assemblages.