The University of South Florida Ecological Research Area (USF Eco Area), located in west central Hillsborough County, is an approximately 306 hectare (756 acre) natural area on the Hillsborough River composed of twelve plant communities. While surrounded on three sides by urbanization, the USF Eco Area makes up the western most section of an extended natural corridor that runs approximately 88 kilometers (55 miles) east and north along the Hillsborough River. An inventory of the vascular flora and the associated ecological communities was developed to better assess the USF Eco Area for educational and research purposes as well as enhance informed decisions when evaluating its status for conservation and management purposes. The study, conducted from June 2001 through August 2005, documented 404 vascular plant taxa in 251 genera and 102 families. Three hundred and seventy-eight taxa (94%) are native to Florida of which 13 are endemic; nine are listed as endangered, threatened, or commercially exploited; four are first time recorded occurrences for Hillsborough County; and ten taxa are listed as Florida Exotic Pest Plant Council’s Category I or II invasive species. Eleven natural plant communities and one ruderal/developed plant community were documented, mapped and characterized by their unique vegetative, topographic, soil, and hydrological components based on qualitative field observations. The blackwater stream, floodplain swamp, floodplain forest, floodplain marsh, hydric hammock, seepage slope, and wet flatwoods are wetland plant communities that cover 65% of the USF Eco Area. Upland plant communities, covering the remaining 35%, are mesic flatwoods, scrubby flatwoods, sandhill, xeric hammock, and ruderal/developed.

Les écosystèmes lacustres sont de plus en plus soumis à de multiples perturbations mais leur réponse est encore trop rarement considérée de façon globale. En effet, au travers d'un jeu d'interactions complexes, chaque perturbation peut moduler l'intensité de l'impact des autres sur les lacs, et de ce fait, leur réponse. Dans ce contexte, ce travail doctoral est axé sur l'approfondissement de notre compréhension de la réponse des lacs à un contexte de perturbations multiples, sur le long terme. Pour cela, trois grands lacs profonds (le lac Léman, du Bourget et d'Annecy), soumis à une perturbation régionale similaire (i.e., le réchauffement climatique) et à deux perturbations locales (i.e., les changements dans le statut trophique et dans les pratiques de gestion piscicole) d'intensités différentes, ont été choisis. La réponse de ces lacs à ces changements a été abordée au travers d'une approche paléolimnologique, basée sur les cladocères. En effet, la capacité de ceux-ci à intégrer les changements temporels dans le réseau trophique pélagique en réponse aux trois perturbations environnementales en fait un modèle adéquat pour reconstruire les changements à l'échelle de la communauté pélagique. Plus précisément, nous avons abordé (i) les changements dans les communautés de cladocères, au cours du siècle dernier, en réponse aux trois perturbations environnementales et (ii) l'impact de ces perturbations sur les stratégies de reproduction des Daphnies. Cependant, le manque de connaissance dans les grands lacs profonds sur la représentativité des communautés sources de cladocères par les assemblages de restes archivés dans les sédiments a tout d'abord conduit à faire un point méthodologique. Ce dernier a abouti à la mise en évidence de différences dans le niveau de représentation de communautés sources de cladocères selon le type de restes utilisés. La composition taxonomique et la structure en taille des restes parthénogénétiques (i.e., exosquelettes) reflètent relativement bien celle des communautés sources. Quant aux éphippies (œufs de dormance), elles se révèlent des indicateurs fiables pour reconstruire les comportements de reproduction. Suite à ces résultats, les reconstructions paléolimnologiques des communautés de cladocères montrent que leur trajectoire écologique était contrôlée par des interactions complexes entre les trois pertubations différentes, selon les périodes de temps et entre les lacs. De plus, la réponse des communautés de cladocères au climat était différente entre les trois lacs comme une fonction de l'intensité des forçages locaux. Ces observations suggèrent qu'il est important d'inclure le rôle des perturbations locales dans la prédiction de l'impact futur des changements climatiques sur les lacs. L'impact des perturbations environnementales sur le comportement de reproduction des Daphnies est tel que des évènements d'hybridation interspécifique ont été observés. Cependant, ces évènements d'hybridation sont issus de sensibilité aux trois perturbations environnementales différentes entre les espèces de Daphnies. / Lake ecosystems are increasingly subjected to multiple perturbations but their response is too rarely considered in overall. But, though a complex set of interactions, each perturbation can modulate the intensity of the impact of each other on lakes, and thus their response. In this context, this work is focused on deepening our understanding of the response of lakes in a context of multiples perturbations, over the long-term. We studied this response performing a paleolimnological approach (based on cladoceran) on three large, deep lakes (Lakes Geneva, Bourget and Annecy) submitted to a similar regional perturbation (i.e., climate warming) and varying intensities of two local perturbations (i.e., changes in nutrient inputs and fisheries managment practices). The ability of cladoceran to integrate the temporal changes in the pelagic food web in response to three environmental perturbations makes them a suitable model to reconstruct changes in the whole pelagic community. Specifically, we addressed (i) changes in cladoceran communities, during the last century, in response to three environmental perturbations and (ii) the impact of these perturbations on reproductive behavior of Daphnia. However, the lack of knowledge in large, deep lakes on the representativity of source cladoceran communitites by fossil assemblages in sediments firstly led to a methodological calibration. This last showed that the represention level of source communities was different according to the type of remain. Parthenogenetic remain assemblages (i.e., exoskeleton) reflect accurately the taxonomical and size structure of source communities in contrast to ephippia which are reliable proxy to reconstruct reproductive behavior. Following these results, the paleolimnological reconstructions of cladoceran communities showed that their ecological trajectories are controlled by complex interactions between the three perturbations, according to time periods and lakes. Moreover, the response of cladoceran communties to climate was different between the three lakes as a function of the intensity of local forcings. These observations suggest that it is important to include the role of local perturbations in predicting the future impact of climate change on lakes. The impact of environmental perturbations on the reproductive behavior of Daphnia is such that interspecific hybridization events were observed. However, these hybridization events were the result of different sensitivity to perturbations among Daphnia species.

Les perturbations anthropiques en Amazonie liées au déboisement de la forêt tropicale conduisent à une mosaïque de paysages constituée de végétations secondaires (forêts secondaires, palmeraies, jachères) et de pâturages. Ces modifications favorisent la prolifération de grands palmiers héliophiles invasifs de la famille Attalea spp., palmiers qui constituent l'écotope principal des espèces de Rhodnius, punaises hématophages vectrices de Trypanosoma cruzi, agent étiologique de la Maladie de Chagas en Amérique Latine. Cette étude a porté sur différentes unités de paysage de trois communautés rurales du bas Tapajós (Amazonie brésilienne) ayant une époque d'installation différente sur le territoire (25-75 ans). Six unités de paysage ont été définies sur le terrain et appliquée via une classification supervisée à une image SPOT 5, afin d'obtenir une cartographie du risque environnemental associé à la présence de palmiers dans la région. Sur les cent trente trois palmiers disséqués appartenant aux trois espèces Attalea maripa, A. phalerata et A.speciosa, 73 (54.88%) étaient infestés par R. robustus (742 insectes récoltés). Des diminutions significatives de densité de triatomes ont été observées chez A. maripa, dans la communauté la plus récemment établie (Araipá) et dans les unités de paysage les plus anthropisées. L'infection des insectes par T. cruzi et T. rangeli a été examinée à l'aide de méthodes moléculaires (mini exon SL_IR and sno-RNA-C11). Respectivement 123 (16.57%) et 69 (9.3%) insectes dans 31 (23.3%) et 17 (13.82%) palmiers ont été identifiés positifs à T cruzi et à T.rangeli. Aucune infection n'a été trouvée dans les insectes collectés à Araipá et aucune différence significative n'a été mise en évidence entre les différentes unités de paysage. Les souches de Trypanosoma cruzi identifiées à l'aide de 4 marqueurs moléculaires (mini exon SL-IR, GPI, HSP60 et D7-24α-rRNA) appartiennent à la lignée TcId et 10 (8.13%) individus présentent une infection mixte TcI-TcII. Vingt espèces d'hôtes réparties en trois classes (mammifères, oiseaux, sauropsidés) ont été identifiées comme sources alimentaires à partir du repas sanguin contenu dans le tube digestif des insectes, à l'aide d'amorces cytochrome b, spécifiques de vertébrés. Quatre-vingts et un pourcent des repas détectés ont été effectués sur des mammifères, hôtes potentiels de T.cruzi dont Tamandua tetradactyla, source alimentaire principale. Cet hôte a été clairement identifié comme réservoir de T.rangeli ainsi que suggéré pour T.cruzi. L'analyse phylogénique réalisée à l'aide de séquences de cytochrome b démontre que les individus de Rhodnius identifiés dans la région du Tapajos appartiennent au clade II, ce qui correspond à une extension de l'aire précédemment décrite pour ce clade. L'utilisation du marqueur mitochondrial cytochrome b a permis de mettre en évidence une structuration phylogénétique (haplogroupes) non retrouvée à l'aide des marqueurs microsatellites. Ce résultat montre que l'histoire des gènes (génome mitochondrial) ne retrace pas l'histoire des individus (microsatellites, 10 locus). L'analyse de génétique des populations conduite à l'aide des deux types de marqueurs n'a pas révélé de structuration génétique au sein de la zone d'étude entre les communautés ou les unités de paysage. Cette étude met en évidence des flux géniques importants peu sensibles à la fragmentation du milieu, la dynamique d'invasion des palmiers assurant aux insectes une connectivité fonctionnelle entre les différentes unités de paysages et les communautés. La prédiction du risque environnemental lié à la situation du Tapajós va vers une augmentation du risque de transmission de la Maladie de Chagas dans cette région, du fait de l'abondance des palmiers, de leur forte connectivité, et de la présence de vecteurs et d'hôtes infectés circulant entre les différentes communautés et unités du paysage / Anthropic disturbances from deforestation of Amazon tropical forest leads to a mosaic of landscapes composed of secondary vegetation (secondary forest, palm groves, fallows) and pasture. These changes result in the proliferation of invasive heliophilous palm trees of the family Attalea spp., the principal ecotope of Rhodnius species, bloodsucking bug vectors of Trypanosoma cruzi, the etiologic agent of Chagas disease in Latin America. The present study focuses on different land cover classes of three rural communities of the lower Tapajós (Brazilian Amazon) with different settlement times (25-75 years). Six different land-cover classes were identified on the field and applied through supervised classification on a SPOT 5 image of the study area in order to cartography environmental risk associated to palm tree presence in the area. Three hundred and thirty palms trees of three species Attalea maripa, A. phalerata and A.speciosa were dissected of which 73 (54.88%) were infested with R. robustus (742 insects collected). The distribution of palm species varied in each community, A.maripa was the only species found in the most recently settled community (Araipá). Significant decreases in bug density were observed in A.maripa, in the community most recently established (Araipá) and in the two most anthropogenic landcover classes.Infection of insects by T. cruzi and T. rangeli was examined using molecular methods (mini exon SL_IR and sno-RNA-C11). Respectively, 123 (16.57%) and 69 (9.3%) insects in 31 (23.3%) and 17 (13.32%) palms were identified as positive for T. cruzi and T. rangeli. A lack of infection was detected in Araipá but no differences were observed between the different land cover classes. The strains of Trypanosoma cruzi were identified using four distinct molecular markers (mini-exon SL-IR, GPI, HSP60 and D7-24α-rRNA) as belonging to the lineage TCI specifically TcId and 10 (8.13%) individuals showed a mixed infection TCI-TCII. Twenty host species divided into three classes were identified (mammals, birds, reptiles) were identified as food source from blood meal from the bug gut with cytochrome b primers, specific for vertebrates (25.74% of meals). Eighty-one percent of meals were conducted on mammals, potential hosts of T. cruzi, specially on Tamandua tetradactyla,identified as the main food source. This host was clearly identified as a reservoir for T.rangeli and also suggested for T. cruzi.Phylogenetic analysis performed using cytochrome b sequences, identified Rhodnius individuals in the Tapajos region within clade II, which represent an extension of the range previously described for this clade. The use of the cytochrome b marker also revealed a phylogenetic structure (haplogroups) not found using microsatellite markers. This result showed that the history of the genes (mitochondrial genome) does not match the history of individuals (microsatellites, 10 loci). Population genetics analysis conducted using both markers did not reveal genetic structure within the study area between the communities or the landcover classes. The study revealed significant gene flow, which was not restricted by the fragmentation of the environment. The invasive dynamics of Attalea palm trees provide a functional connectivity for insects to move between the different landcover classes and communities. Due to the abundance of palm trees and their high connectivity, the presence of vectors and infected hosts moving between the different communities and landcover classes, the environmental risk constituted by Attalea palm tree presence of Chagas disease in Tapajós region will presumably continue to increase

Complex biogenic habitats created by large canopy-forming macroalgae on intertidal and shallow subtidal rocky reefs worldwide are increasingly affected by degraded environmental conditions at local scales and global climate-driven changes. A better understanding of the mechanisms underlying the impacts of complex suites of anthropogenic stressors on algal forests is essential for the conservation and restoration of these habitats and of their ecological, economic and social values. This thesis tests physical and biological mechanisms underlying the impacts of different forms of natural and human-related disturbance on macroalgal assemblages dominated by fucoid canopies along the east coast of the South Island of New Zealand. A field removal experiment was initially set up to test assemblage responses to mechanical perturbations of increasing severity, simulating the impacts of disturbance agents affecting intertidal habitats such as storms and human trampling. Different combinations of assemblage components (i.e., canopy, mid-canopy and basal layer) were selectively removed, from the thinning of the canopy to the destruction of the entire assemblage. The recovery of the canopy-forming fucoids Hormosira banksii and Cystophora torulosa was affected by the intensity of the disturbance. For both species, even a 50% thinning had impacts lasting at least eighteen months, and recovery trajectories were longer following more intense perturbations. Independently of assemblage diversity and composition at different sites and shore heights, the recovery of the canopy relied entirely on the increase in abundance of these dominant fucoids in response to disturbance, indicating that functional redundancy is limited in this system. Minor understory fucoids, which could have provided functional replacement for the dominant habitat formers, had reduced rates of growth or recruitment when the overlying canopy was disturbed. I then used a combination of field and laboratory experiments to test the impacts of physical and biotic stress sources on the dominant fucoids H. banksii and C. torulosa. The large fucoid Durvillaea antarctica was also included in one of the laboratory investigations. I assessed how altered physical and biotic conditions affect these important habitat formers, both separately and in combination. Physical stressors included increased sedimentation, nutrient enrichment and warmer water temperatures. Biotic stress originated from interspecific competition with turfs of articulated coralline algae and ephemeral, fast-growing green and brown algae. Sediment deposition severely reduced the survival and growth of recently settled H. banksii, C. torulosa and D. antarctica germlings in laboratory experiments. In the field, the recruitment of H. banksii on unoccupied substrates was significantly higher than in treatments in which sediments or mats of turf-forming coralline algae covered the substrate. This shows that sediment deposition and space pre-emption by algal turfs can synergistically affect the development of fucoid beds. Further impacts of sediment accumulation in the benthic environment were investigated using in situ and laboratory photorespirometry techniques to assess the contribution of coralline algae to assemblage net primary productivity (NPP), both in the presence and absence of sediment. The NPP of articulated corallines was reduced by sediment. Sediment accumulation among the thalli limited the access of the corallines to the light and induced photoinhibitive mechanisms. In the absence of sediment, however, coralline algae enhanced the NPP of assemblages with a fucoid canopy, showing the importance of synergistic interactions among the components of multi-layered assemblages in optimizing light use. Nutrient enrichment had a less pervasive influence on the dominant fucoids H. banksii and C. torulosa than sedimentation. In laboratory experiments, nutrients stimulated the growth of H. banksii and C. torulosa germlings. However, negative impacts of high nutrient levels were observed for the early life stages of D. antarctica. The abundance of opportunistic, fast-growing algae rapidly increased in response to nutrient enrichment both in the laboratory and in the field. Impacts of ephemeral species on fucoid early life stages were only evident in laboratory contexts, where green algae of the genus Ulva impaired both the settlement of H. banksii zygotes and the growth of its germlings. Fucoid recruitment in the field was not affected by increased covers of ephemeral algae caused by enhanced nutrient regimes, indicating that H. banksii and C. torulosa may be resistant to short-term (one year) nutrient pollution. In the laboratory, increased temperatures within the range predicted for the end of the 21st century caused increased mortality in the H. banksii, C. torulosa and D. antarctica germlings. In a separate experiment, a combination of warmer water temperatures and nutrient enrichment enhanced the growth of ephemeral green algae. These results suggest that opposite responses to altered climate conditions may contribute to shifts from complex biogenic habitats dominated by macroalgal canopies to simplified systems monopolized by a limited number of stress-tolerant species. This research contributes to a clearer mechanistic understanding of biotic and physical mechanisms shaping the structure of coastal marine hard bottom communities under increasingly stressful conditions worldwide. These findings may provide insights for other studies investigating the complex mosaic of challenges facing marine coastal ecosystems.