Dissertations / Theses on the topic 'Biological impacts'

Introduction: My work with the Middlesex University Urban Pollution Research Centre has been conducted in the following areas: 1 Biological Monitoring of Urban Waters (Publications 1, 3, 5, 6, 25) Conventional biological methods and hydrobiological indices used for assessing water quality have been tested in urban streams and rivers and their limitations exposed. The impact of river engineering and physical disturbance on the substrate during storm events has been shown to influence significantly the index scores in addition to pollution impacts. The recommendation to compare biological with physico-chemical assessment of water quality has also been adopted by the National Rivers Authority. A model to predict the community diversity index score for urban stream macro invertebrate biota from recorded physico-chemical parameters was satisfactory for fairly clean waters and for moderate levels of pollution but not for serious levels of pollution (1). Reference streams and ponds in Trent Country Park on the fringe of North London were used for comparison with studies of the biota of urban waters (3,5). A system of river classification using a hydrobiological score system was proposed to complement the existing National Water Council system which was essentially based on chemical criteria (6). A study of the use of indicator organisms to monitor the impact of localised discharges of urban surface runoff and storm sewer overflows was commissioned by the Water Research Centre, the results of which are reported in paper no. 14. A review of the use of macroinvertebrates and plants as bioindicators in urban aquatic systems is included in publication 25. 2 Aquatic Ecotoxicology (Publications 3, 4, 5, 6, 7, 9, 11, 12, 14, 21, 24, 26, 28, 32, 34) 2.1 Heavy Metals Innovative methods have been developed for assessing heavy metal bioaccumulation in selected macro invertebrate species in urban waters. Traditionally, toxicity tests have been conducted in controlled laboratory conditions which do not simulate the natural environment. The use of caged macro invertebrates secured to the substrate in rivers, enables a more realistic determination of bioaccumulation and mortality rates to be made. The impact of storm events and chronic exposure to contaminated water and sediment has been investigated. At a time when new ecotoxicological tests are being introduced to the UK and the EC, the research has considerable potential application as a test for heavy metal impacts and the determination of environmental standards in freshwater. (The research has been sponsored by the Water Research Centre). VI Tissue concentrations of lead, cadmium, copper and zinc in selected macroinvertebrates collected from semi-rural and urban streams and ponds are reported in papers 3, 4 and 5. The relationship between urbanisation and macro invertebrate tissue, sediment and water metal concentrations and their spatial trends along the Salmon's Brook in North London is discussed in publication 6 and compared with the results from the A veiro Lagoon and its feeding rivers in North Portugal in paper 7. Tissue metal bioaccumulation in popUlations of caged Gammarus pUlex, Asellus aquaticus and Lymnea peregra in relation to ambient sediment and water metal concentrations, metal species bioavailability and organism feeding behaviour are discussed in publication 9. A comparison of mortality and metal uptake in aquatic macroinvertebrate species in field studies and laboratory experiments and a recommendation to reduce the length and lethal limit of the traditional 96 hour LC50 test is made in papers 11, 21, 24 and 32. The impact of storm sewer overflows from a sewage treatment works on caged macro invertebrates exposed to the discharges and to the receiving waters immediately downstream is reported in publications 12, 14 and 24. Principal component analysis was used to determine combinations of caged Aselius aquaticus tissue, sediment and water metal concentrations, precipitation volumes and antecedent dry periods which explained much of the variation in organism mortality and weight (28, 34). 2.2 Hydrocarbons (Publications 15 - 20, 29) Caged macro invertebrate species have also been used to determine hydrocarbon bioaccumulation in an urban stream and the Welsh Harp reservoir, a site of special scientific interest. Sediment and water hydrocarbon concentrations and macro invertebrate community diversity have been monitored along the stream and in the reservoir to investigate the impact of an oil boom. The development of biological and chemical techniques in this unique study of an urban freshwater wetland has led to considerable interest and further publications are planned. (The research has been sponsored by English Nature, formerly the Nature Conservancy Council). Publications 15 and 16 describe a baseline study of the ecotoxicological impacts resulting from oil pollution on the Welsh Harp and one of its receiving streams. Sediment and water concentrations of alkanes and P AHs and the tissue concentrations and temporal and spatial trends in selected caged macro invertebrates and fish are reported in publications 17, 18 and 19. The bioaccumulation of hydrocarbons by macro invertebrate species in laboratory tests and the corresponding mortality rates and their comparison with the results of field studies and controlling factors are discussed in publication 20. The results of the study are summarised in paper 29. vii 3 Aquatic Macrophyte Pollution Control (Publications 10, 13, 22, 23, 27, 31, 33, 35) Heavy metal uptake by the reedmace Typha latifolia, an aquatic plant species, has been investigated in urban wetlands and in greenhouse based studies. The research has shown a high level of tolerance by Typha to heavy metals and its biofiltration ability and creation of a sediment metal sink. It has led to the introduction of Typha in pioneering designs of constructed wetlands for highway runoff treatment in the UK. (The research is ongoing and is receiving sponsorship from industry and PCFC). A comparison of the water pollution control performance of Typha latifolia in the UK and Eicchomia crassipes in China is discussed in publication 10. Further details of the study of metal uptake in Typha latifolia and its associated sediment in the Welsh Harp and two ornamental ponds and a comparison with the results of a greenhouse based metal dosing experiment are given in papers 13 and 27 and summarised in 23 and 31. An analysis of the metal and hydrocarbon uptake and biofiltration ability of different species of aquatic macrophyte in an experimental pond receiving runoff from a car park in Washington State, USA is described in report 33.

The consequences of predation have become a central focus of marine ecological research. Numerous studies have emphasized the importance of apex predators in structuring assemblages at various organisational levels and in determining how ecosystems function. However, less appreciated currently is the fact that predators display multiple foraging behaviours, thereby allowing them to overcome problems associated with unpredictability of food resources in space and time. The primary goal of this dissertation is to contribute to growing understanding of the ecological causes and consequences of foraging plasticity displayed by Greater Flamingo Phoenicopterus ruber roseus in intertidal sandflat ecosystems in Langebaan Lagoon, South Africa. P. roseus feeds by either (1) creating pits, which involves flamingos stirring up deep sediments with their feet or (2) creating channels, in which their inverted bills are swept from side-to-side on the sediment surface. The first objective of the study was to quantify the ecological drivers of decisions made by flamingos to feed, and to implement either pit- or channel-foraging strategies. The latter was achieved through RandomForest modelling techniques that identified the prominent ecological drivers from a suite of biotic and abiotic variables. Results indicate that biotic variables, i.e. those associated with flamingo prey assemblages, were key in driving choices made by flamingos to forage and to implement either pit- or channel-foraging strategies. The second aim of this dissertation was to quantify the repercussions of the two different foraging behaviours on benthic assemblages. Comparisons of benthic assemblages in flamingo foraging structures (pits and channels) with adjacent non-foraged sediments (controls) indicated differential effects of both flamingo foraging methods on benthic communities, with channel-foraging eliciting a greater negative impact compared to pit-foraging, for which impacts were negligible. Abundance of macrofauna and surface-dwelling taxa such as micro-algae and the amphipod Urothoe grimaldii were all negatively impacted by channel-foraging. Sizes of channels constructed by flamingos were inversely related to their impacts, with impacts on macrofaunal abundance being greater in smaller channels. Overall, this study has shed light on the differential effects of foraging plasticity on prey assemblages and its importance in enhancing spatio-temporal heterogeneity in intertidal sandflats. The study also emphasizes the need to incorporate foraging plasticity into current thinking and conceptual models of predation in marine soft sediments, in order to appreciate the full spectrum of predation effects on assemblages.

The impacts of biological invasions on native avian diversity have been the subject of many studies in Africa. However, a holistic synthesis of available information from different taxa and their impacts on native birds is lacking. From published information, I analysed the negative and positive effects of biological invaders on native African birds from five taxa: plants, invertebrates, fish, mammals and birds. In order to assess functional gains and losses, native birds were categorized into their functional guilds defined by their primary diet. I limited my scope to mainland Africa at the biome level. ArcView GIS 3.3 software was used to map locational data of impacts within the major biomes. The results indicate that a minimum of 572 native birds are negatively impacted by invasive species from the five taxa. This represents ca 29% of all the bird species in Africa. In contrast, only 191 species of native birds benefited from such invasions. Birds whose diet was primarily insects were disproportionally impacted. The majority of the impacts were caused by invasive plants. At the biome level, the greatest numbers of native birds impacted were in the Montane grassland and shrubland biome. It is predicted that native birds will continue to lose more than they gain from biological invasions in the continent.

Elephant are renowned for their ability to substantially alter vegetation. However, as they need to drink regularly, surface water exerts a strong influence over the distribution and magnitude of elephant impacts on vegetation. This study was conducted in Zambezi National Park, a 560 km2 unfenced protected area in northwest Zimbabwe. It aimed to investigate the impacts of elephant on woody vegetation, particularly in relation to artificial waterholes. Sampling plots were located at different distances from four pumped waterholes in teak (Baikiaea) and Terminalia woodlands, the two main woody vegetation types recognised in the study area. Plots were set at 200, 500, 1000, 2000 and 4000 m from waterholes in the teak woodland. Due to the close proximity of waterholes, a lower maximum distance of 2500 or 3000 m from waterholes had to be used in the Terminalia woodland, but sampling intervals from 200-2000 m were otherwise the same. Assessment of elephant browsing and a series of measurements were performed on trees and shrubs within these plots, with plants assigned to one of three height classes (0.2 - < 1 m; 1 - <3 m and ≥3 m). Elephant dung counts were also conducted in these plots, to provide a measure of elephant occupancy. A clear decline in elephant browsing with distance from waterholes was evident in both the teak and Terminalia woodlands. However, elephant browsing was consistently higher in the latter woodland type. Averaged across all plant height classes, elephant had removed 30-45% of plant canopies in most Terminalia woodland plots. More moderate canopy removal of 10- 30% was found in most teak woodland plots. Plants ≥3 m were particularly highly browsed in the Terminalia woodland, with over 50% of their canopy volume removed in most plots. Elephant browsing impacts were also considered at the species level, which revealed clear differences in browsing levels among species. Some uncommon and highly browsed species were flagged as being potentially vulnerable to disappearance from the area, even in the teak woodland where overall elephant browsing was lower. The effects of elephant browsing on vegetation structure at different distances from artificial waterholes were also investigated. Little change was apparent in the teak woodland, where the only noted impact was a reduction in the density and canopy volume of plants 1 - <3 m tall, limited to within 1 km of waterholes. More pronounced structural impacts were evident in the Terminalia woodland. Substantial declines in the basal area and canopy volume of trees (i.e. plants ≥3 m) occurred closer to waterholes, with widespread conversion of woodland to shrubland evident. Reductions in both tree and shrub canopy volumes closer to waterholes also suggested a reduction in browse availability in the Terminalia woodland. Finally, elephant dung declined with distance to waterholes, confirming that elephant were found in higher densities closer to waterholes. However, dung counts did not reveal different levels of elephant occupancy between the two vegetation types, despite higher browsing in the Terminalia woodland. This finding suggests elephant might be using the teak woodland for purposes other than just browsing, such as for shade. The study thus provided evidence that waterholes have had a significant impact on vegetation in the area, particularly on the favoured Terminalia woodland. Acknowledging the tourism value of retaining waterholes in the area, it is suggested that distances between waterholes should be increased, through only continuing pumping at waterholes with viewing platforms. This could result in a more heterogeneous elephant browsing regime across the highly impacted Terminalia woodland in particular, and lessen further homogenisation of this vegetation type towards a shrubland.

Traditionally, hypoxia has been defined as the situation where DO levels have fallen below 2.0 mg O2 L-1, but increasing evidence suggests that this low level of DO is inadequate to describe the onset of hypoxia impacts for many organisms. Consequently, there is a need for a greater understanding of how ‘moderate’ alterations in DO levels will affect ecosystem processes and functionality, specifically through behavioural and physiological alterations at the organism and community level. This thesis reports on mesocosm experiments which were conducted to examine the effects of moderate ( > 3.0 mg O2 L-1) hypoxia on firstly, a key ecosystem engineer, the brittlestar Amphiura filiformis, and secondly, on the Station L4 infaunal macrobenthic community. Station L4 is a longstanding marine biodiversity and MSFD reference site and forms part of the Western Channel Observatory. At the organism level, short-term (14 d) exposure to moderate hypoxia significantly reduced oxygen uptake rates, oocyte diameter and oocyte development in A. filiformis. However, these physiological affects occurred irrespective of brittlestar population density. Additionally, moderate hypoxia reduced brittlestar activity, in terms of bioturbation behaviour, consequentially having an effect on ammonium and silicate fluxes. These observations were only detected when brittlestar population density was high. It was concluded that denser populations of A. filiformis may therefore exhibit the greatest changes in behaviour and shifts in ecosystem function as competition for resources and oxygen heightens. The benthic community at Station L4, displayed considerable tolerance to medium-term (6 wk.) exposure to moderate hypoxia, in terms of structure, diversity and bioturbatory behaviour, but these results may be different if exposure was longer or more severe. Alterations in nutrient fluxes were detected, but there was little evidence to suggest these changes were due to macrofaunal behavioural alterations. Additionally, results from this study revealed that bringing complex natural communities into the mesocosm caused a substantial loss of individuals and species, mainly due to translocation and disturbance effects. This important insight into the effects of bringing community assemblages into the mesocosm confirms that even with a loss of diversity, the L4 community maintained functionality and was resilient to alterations in DO. This suggests that the L4 benthic community does not depend on any one specific species for the provision of important ecosystem processes, resulting in considerable functional resilience within the L4 system. However, vulnerability to benthic systems may increase if functionality is dominated by species such as A. filiformis. Consequently, moderate hypoxia may not immediately affect benthic communities in terms of structure and diversity, but the physiological effects on individuals, especially to reproductive development, may cause alterations in the quality and quantity of planktonic propagules supplied by benthic species to the pelagic environment. This could affect benthic community diversity and functionality in the long term if repeated hypoxic events occur.

In 1997, land reclamation works began in the coastal area of Mukim Lekir. Ultimately, an area of 8,094 ha was planned to be reclaimed along Lekir's coastline, but to date; only Phase 1 of the project has been completed. The Phase 1 project of 405 ha, created a man-made island for the location of a 2,100MW, coal-fired power plant; a first of its kind in Malaysia. Although the reclaimed land was only 5 % of the total intended area, its impacts on the livelihoods of the coastal communities, especially fishers, were serious and nearby mangroves were degraded. The effect of this intervention was observed to be long-term, contrary to the claims made by the project proponents. Fishers and other coastal inhabitants incurred monetary losses, which were neglected by the project proponents, who also failed over the issue of compensation. This study attempts to establish evidence that the project caused hardship to coastal population, especially fishers who depended on fishery resources that were found to decline after the commencement of the project. It began by assessing the status of fish stock, analysing its catch-rates trend and comparing them with resource status before the project. A socio-economic survey by face-to-face questionnaires interview was carried out on the population to obtain information on how the project had affected their livelihoods in terms of incomes, job opportunity, fishing activities, pollution, etc. The research design intended to prove that environmental degradation was caused by the project by comparing the status of resources before and after the intervention. On the issue of compensation, losses were valued in monetary terms, so that it was easily understood and appreciated. The purpose of valuing damages was to allow affected persons to claim compensation in monetary terms. This study emphasized losses through mangrove degradation and losses as result of fishery resources declining. In addition, losses incurred by cockle farmers and the government were also gauged. For mangrove degradation, a survey using the Contingent Valuation Method was carried out to estimate people's willingness to pay (WTP) on a hypothetical project aiming to protect the mangroves. The amount they were WTP was the benefit loss of not being able to use the mangroves. Other losses valuation was straightforward since it involved marketable or tangible goods. The standing of fishers and other affected communities claiming compensation in the court of laws was discussed. Fish stock assessment done in 2002 and 2003 in the Lekir waters indicated that the resource showed a declining trend since 1996. Commercial fish declined at a greater rate in sub-area A, which was closer to the impacted area, than in sub-area B; located further away. Subarea A was also found to loose its potential as breeding and nursery grounds, since fewer juveniles and fingerlings were caught compared with the 1996 survey. The decline in the fisheries indicative from the surveys was verified by fishers who complained of reduced catches and incomes. In the socio-economic survey, fishers were found not to benefit from the development since the project did not provide them with employment opportunity or generate other kinds of income-induced opportunity. The degradation ofthe mangroves and the fishery were proven to be caused by the present of the project since the control areas, in the absence of perturbation did not show similar characteristic as the impacted areas. The benefit loss of mangrove use was estimated at RM 81,959/year whereas other society losses were RM 118,333,321 in the six years since the perturbation. If fishers were to claim compensation, they have to prove that their losses were above and over the general public and preferably under the rule of Rylands V Fletcher. Other segments of the society may need government intervention since they were claiming pure economic loss, which is unrecoverable in the Common Laws. This study does not advocate monetary compensation to each affected individual but prefers long-term aid to regenerate rural livelihoods. Economic projects are proposed involving active participation of the community. Further researches are also suggested to improve data collection, developing comprehensive stock assessment and improving EIA procedures.

As trends in urbanisation continue globally, there is a growing need to understand the impacts of urban development on wildlife. Whilst urban impacts on patterns of diversity and abundance of species have been well-studied, there remains a distinct lack of understanding around the impacts on ecological interactions. Different species have different levels of tolerance to urban disturbance, some species even appear to thrive in urban areas and make use of human-subsidised resources; but the physiological costs and trade-offs faced by urban-dwelling species are poorly understood. Given that their range in South Africa has only recently expanded into the human-dominated landscapes of the Western Cape, the Black Sparrowhawk (Accipiter melanoleucus) provides an excellent opportunity to explore some of these questions. In this study we explored how urbanisation may affect the health of this raptor on the Cape Peninsula, South Africa. If the health of this species is negatively influenced by levels of urbanisation, this might be driven by differences in diet and prey availability across the urban spectrum. Thus, we explored this potential mechanism by examining diet composition and assessing prey abundance within different territories and habitat types. The health of nestling Black Sparrowhawks was evaluated through their immune response (Heterophil/Lymphocyte ratio in white blood cell counts), body condition (based on morphometric measurements) and blood parasite infection (presence and abundance of Haemoproteus and Leucocytozoon). Trends in diet composition along a gradient of urban cover were determined through the analysis of prey remains collected in the immediate nest surroundings and differences in prey abundance were determined through point counts in different habitat types.

Thesis advisor: Hilary Palevsky
The ocean plays a key role in global carbon cycling, taking up CO2 from the atmosphere. A fraction of this CO2 is converted into organic carbon through primary production in the surface ocean and sequestered in the deep ocean through a process known as the biological pump. The ability of the biological pump to sequester carbon away from the atmosphere is influenced by the interaction between the annual cycle of ocean mixed layer depth (MLD), primary production, and ecosystem processes that influence export efficiency. Gravitational sinking of particulate organic carbon (POC) is the largest component of the biological pump and the aspect that is best represented in Earth System Models (ESMs). I use ESM data from CESM2, an ESM participating in the Coupled Model Intercomparison Project Phase 6 (CMIP6), to investigate how a high-emissions climate change scenario will impact POC flux globally and regionally over the 21st century. The model simulates a 4.4% decrease in global POC flux at the 100 m depth horizon, from 7.12 Pg C/yr in the short-term (2014-2034) to 6.81 Pg C/yr in the long-term (2079-2099), indicating that the biological pump will become less efficient overall at sequestering carbon. However, the extent of change varies across the globe, including the largest POC flux declines in the North Atlantic, where the maximum annual MLD is projected to shoal immensely. In the future, a multi-model comparison across ESMs will allow for further analysis on the variability of these changes to the biological pump
Thesis (BS) — Boston College, 2021
Submitted to: Boston College. College of Arts and Sciences
Discipline: Departmental Honors
Discipline: Earth and Environmental Science

Oysters are important to estuarine ecosystems because of the functions they provide. Thus, oyster restoration projects are undertaken in areas where natural populations have declined. However, restoration techniques can impact sediment organic matter and benthic invertebrates that provide trophic support for important species. This study assesses the impacts of a constructed shell bed on associated sediment and invertebrate communities in a southern California bay. Within the bed site, organic matter, invertebrate abundance, and invertebrate species richness are lower only under the oyster bed. The alteration in the community under the shell is driven by a reduction in species. Tubificidae were the only remaining species under the shell. These results may be explained by the shells’ action as a barrier to the mud-water interface. While significant, impacts of oyster bed construction are spatially restricted to just under the bed. Longer-term studies should be conducted to address effects of the oysters themselves.

Includes abstract.
Includes bibliographical references.
Impacts of invasive predators may be influenced by whether or not native predators which function in the same way as the invasive predator exist in the recipient system. Impacts are expected to be strong in isolated systems lacking functionally similar predators because native species will be naïve to the foraging behaviour of the introduced predator, and because the invasion is likely to change the role which the native predator assemblage performs. In this thesis I studied how the introduction of a functionally novel predatory fish, rainbow trout Oncorhynchus mykiss, has affected native fish, and how changes in the functioning of the predator assemblage have influenced lower trophic levels, in headwater streams in a catchment area within the Cape Floristic Region, South Africa. Fish populations, benthic invertebrate assemblages, benthic algae and particulate organic matter were surveyed in each of 24 minimally-disturbed headwater streams in the upper Breede River catchment, and relevant environmental variables in each stream measured, over one summer.

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Tese (Doutoramento)
IPEN/T
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Donkeys are used extensively in Namaqualand and other rural areas in South Africa for pulling carts, carrying loads, ploughing and threshing grain. There is, however, an ongoing debate among farmers, agriculturalists and the wider population about the implications of keeping donkeys, particularly on communal lands. Donkeys are reported to cause more damage to the veld than other animals, and it is commonly said that one donkey eats as much as seven goats. This project was initiated as a case study to investigate the impacts of donkeys in a communal area in the succulent shrublands of Namaqualand, and to generate suggestions for the management of donkey populations. The degree of competition between goats and donkeys was investigated by predicting daily food intake using a model based on ruminant and non-ruminant digestion, which takes into account the animal's body weight and digestibility characteristics of its diet. The ratio predicted food intakes is discussed in the light of the degree of dietary and habitat overlap, which were obtained from field observations. Habitat use was scored using dung frequency transects, and feeding was directly observed. It was found that in the wet season, one donkey eats as much as 5 / 7.6 goats (donkey weight set at 200 and 250 kg respectively). In the dry summer, this ratio increases to 7.6 / 8.6 because in ruminants, the passage of food through the gut slows down as the digestibility of the diet decreases. Habitat overlap is concentrated in the riverine areas and sandy pediments, which make up 15 % of the landscape and are strongly favoured by donkeys. No significant differences were found to exist between the intensities of goat use of the different habitats. The botanical composition of the diets of donkeys and goats were found to be similar, but there is a great difference in the quality of the diet consumed by each species as goats are able to select plant parts of a higher quality. The implications of this are that whereas a donkey takes in as much dry matter as 5 - 8.6 goats, the diet of this food is not high enough to satisfy the dietary requirements of goats, and hence fewer goats than predicted can be supported for every donkey that is eliminated. Donkeys are commonly reported to have destructive feeding habits; little of this was directly observed, but donkeys were found to bite deeper into the wood of shrubs, which may damage the plants in the long term. There are two main management measures that should be applied. The feral donkey population in Paulshoek, estimated at 50-100 animals, must be eliminated - even at a conservative estimate, these animals could be replaced with 250 goats. However, one must look beyond the number to the processes taking place to make management effective. Even if one donkey can be replaced with fewer than 5 goats, the vegetation is relieved of the indirect effects donkeys have through their feeding habits. Control of working donkeys should focus on the riverine and flat, sandy areas, as they are potentially of high nutritional importance (especially the riverine areas which support grass throughout the year), and which are also the most susceptible to erosion due to their sparse vegetation cover. These areas are small and valuable, and plans should be made to protect some areas through the growing season.

Invasive species are of particular concern as they have the potential to alter community structure and food web relationships within their invaded habitats. African sharptooth catfish Clarias gariepinus, a generalist predator, was introduced through an inter-basin water transfer scheme into the Great Fish and Sundays Rivers, Eastern Cape, South Africa, where it threatens the native riverine biota. This thesis assessed its impact from a trophic perspective. Patterns in catfish distribution and abundance revealed an upstream to downstream gradient that was associated with spatial distribution of most species within the mainstream, and a mainstream to tributary gradient that was associated with the spatial distribution of native minnows. The catfish was predicted to occur widely within the mainstem habitats and to decrease progressively along the mainstrem to tributary gradient with the physico-chemical environment being a good proxy for predicting both its occurrence and abundance. The results suggest the catfish proliferated within mainstem habitats where invasion resistance was possibly reduced due to alteration of flow. Population dynamics and size structuring of two native cyprinid minnows Pseudobarbus afer and Barbus anoplus, threatened by catfish, were examined within uninvaded headwater streams in relation to their proximate physical habitats. Their habitats were characterised by seasonal variation in physico-chemical conditions and a spatial variation in substrata compositions. No evidence of differences was found between seasons for density and capture probability for either species. The population size and density for P. afer was found to increase with increasing proportion of boulders. In comparison, B. anoplus population size and probability of capture increased with increasing proportion of bedrock and bank vegetation, respectively. Size structuring was explained predominantly by seasonality and habitat variables for P. afer and B. anoplus, respectively. Stable isotope ratios of carbon and nitrogen were used to compare the spatial variation in both the community-wide and catfish-specific niches and to estimate catfish prey sources from different habitats within the invaded systems. Aquatic community and catfish niches were statistically different among localities, suggesting that each locality had a distinct community-wide trophic structure. Dispersion metrics indicated no evidence of differences in the clustering among individuals, but provided evidence of differences in path trajectories for the comparisons of catfish populations that suggested dietary plasticity within different localities. Dietary studies revealed both ontogenetic shift and omnivory that suggested that catfish may exhibit less pronounced top-down effects within its invaded habitats. Manipulative experiments were used to test the response of benthic macroinvertebrates within two rivers that were differentially impacted by catfish as a presstype disturbance. Macroinvertebrates were non-responsive to catfish presence within a system where catfish had previously been established. In contrast, excluding catfish in this system indicated a response that suggested the importance of refuge within invaded habitats and the possible recovery pattern of certain macroinvertebrate taxa. By comparison, introduction of catfish within previously uninvaded localities provided evidence of direct catfish impact through elimination of conspicuous taxa. Acoustic telemetry was used to investigate catfish movement patterns within an invaded lentic habitat and provided evidence that habitat utilisation was non-random. The shallow and structured river mouth habitat, which was most utilised, was probably the most ideal for its breeding and feeding. This inferred potential overlap with native species and suggested the risk of predation and competitive interference. Catfish also exhibited both nocturnal and diurnal activity patterns that were probably related to feeding.

Coastal anthropogenic infrastructure has significantly modified nearshore environments. Because these structures often have a strong association with shipping as would be found in ports and harbors, they have been identified as invasion hotspots. Due to propagule pressure from shipping and recreational boating and suitable uncolonized substrate that provides a refuge from native predators, a greater number of non-native species have been found on these structures compared to nearby natural substrate. The mechanisms that limit the spread of non-native species from anthropogenic structures to natural substrate have been explored for several taxa at a species-specific level, but less so from an overall community perspective. Predation has been identified as one of the biotic interactions limiting invasion success. In addition to predation, dispersal ability may also prevent the spread of non-native species from anthropogenic structures to natural substrate. This thesis addresses how these two mechanisms interact to limit the spread of non-native species from anthropogenic structures to natural substrate and how that alters overall community composition. I aimed to explore differences between communities inside and outside of a marina and determine the extent to which predator and dispersal limitation were structuring these communities. I used a three-factor design, deploying seven unglazed ceramic tiles per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators greater than the mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus suspended 1 meter below the surface. I also transplanted caged, suspended tiles of either adults or recruits from inside the marina to benthic and suspended caging treatments outside of the marina. These tiles allowed me to examine predation when dispersal limitation was not a factor for the community inside the marina, i.e. what happens to both recruits and adults if they can get outside of the marina. I found that the communities inside and outside of the marina were different and the data suggest that both predation and dispersal limitation interact to limit the spread of non-native species. Additionally, I found that mesopredators that could fit through the caging may be influencing predation results and community structure. This research addresses gaps in scientific knowledge regarding the mechanisms that prevent or facilitate the spread of non-native species. Future work could include the further exploration of mesopredation as an important factor in limiting the spread of non-native species and exploring dispersal limitation more in depth as well as broadening the geographic scope to see if the same trends hold true across bays and bioregions.

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Dissertacao (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Atlantic bluefin tuna (Thunnus thynnus) are targeted by recreational anglers along the east coast of the United States, and the fishery is thought to be of considerable economic value. However, limited knowledge of the preferences and values of fishery participants impedes the ability of managers to maximize fishery benefits and predict harvest patterns, while an incomplete understanding of post-release mortality hinders efforts to estimate total mortality resulting from the fishery. This dissertation used a multidisciplinary approach that relied heavily on cooperative research with the recreational fishing community to examine these questions. A stated choice survey of private anglers permitted to target bluefin tuna (Chapter II) estimated a fishery consumer surplus of over $14 million in 2015 while revealing striking heterogeneity in angler preferences. Respondents placed a high value on harvesting bluefin tuna, but about half of anglers also valued non-consumptive aspects of bluefin tuna fishing such as catch-and-release. Preference segmentation was largely driven by income and recent bluefin tuna targeting behavior, with high-income anglers who had recently targeted bluefin tuna more likely to belong to the non-consumptive group. These results indicate that liberalization of harvest regulations could result in significant, non-linear increases in effort and harvest should consumptive-oriented anglers decide to re-enter the fishery. A second survey, of Atlantic bluefin tuna fishermen who possess a permit enabling them to fish either commercially or recreationally on a trip-by-trip basis, applied an online contingent sequential stated choice approach to better understand the decision-making of this unique group (Chapter III). Responses indicated that, while some permit holders consistently fish either recreationally or commercially, a substantial proportion of participants change trip type depending on fishery conditions such as prevailing fish size or regulations. The changing behavior of this latter group could potentially result in large shifts in targeting and lead to overages for the commercial handgear sector or recreational sector, and potentially the U.S. bluefin tuna quota as a whole. Lastly, post-release mortality was estimated for juvenile bluefin tuna caught in the increasingly popular light-tackle recreational fishery while also beta testing a newly developed, solar-powered pop-up satellite archival tag designed to enable large-scale, high-precision mortality studies (Chapter IV). Data were only obtained for 15 of 22 deployed tags, with 14 fish demonstrating behavior consistent with survival. One fish was predated upon, likely by a shortfin mako shark, after 17 days, and this was considered a natural rather than a fishing mortality. The low level of estimated post-release mortality, consistent with results from previous studies on different size classes of bluefin tuna caught with various angling gear types, suggests that catch-and-release angling, which Chapter II showed to be highly valued by some anglers, is a viable conservation strategy. Overall, this dissertation provides information regarding both angler preferences and fishery impacts that are of direct relevance to management. Future efforts should be directed to further engaging the recreational bluefin tuna fishing community in order to improve buy-in to management strategies and improve the ability of the United States to maintain fishing mortality within internationally prescribed limits.

Changement climatique, urbanisation, invasions biologiques et hybridation interspécifique constituent des menaces majeures pour la biodiversité. L'objectif de cette thèse a été d'évaluer leurs effets interactifs sur les fourmis du genre Tetramorium de la vallée du Rhône, France. Près de 2000 colonies de 5 espèces de Tetramorium ont été étudiées. Les résultats démontrent que le climat et l'urbanisation limitent leurs aires de répartition et que l'urbanisation impacte leurs distributions simultanément à plusieurs échelles spatiales. Les probabilités d'occurrence de T. immigrans dépendent de l'interaction entre facteurs climatiques et urbains. Quatre populations génétiques de T. immigrans résultent de plusieurs introductions de sources externes, ce qui signifie que cette espèce n’est pas indigène dans les zones urbaines du nord. T. immigrans et T. caespitum produisent des hybrides dans les zones de sympatrie. La détection de rétrocroisements et de discordances entre ADN mitochondrial et nucléaire suggère que cette hybridation conduit à une descendance fertile, donc de l’introgression. Les profils d'hydrocarbures cuticulaires sont bien différenciés entre les deux espèces et sont corrélés à une agression forte contre les hétérospécifiques. Ces espèces présentent un système d'accouplement monogyne polyandre, dans lequel les reines hybrides mais pas les pères hybrides contribuent à la descendance hybride. Les études sur l'hybridation interspécifique n'ont qu'occasionnellement concerné les changements globaux ou invasions biologiques. Ces concepts eux-mêmes sont peu étudiés ensemble et leurs effets interactifs sont négligés dans la littérature actuelle. La prise en compte de ces interrelations et l'exploration de plusieurs échelles sont essentielles pour mieux comprendre les processus qui génèrent des modèles d'échange génétique
Climate change, urbanization, biological invasions and interspecific hybridization are major current threats to biodiversity. The objective of this thesis was to assess their interactive effects in Tetramorium ant species from the Rhône-Saône valley in France. Using a broad array of tools from several fields of biology, I worked on almost two thousand colonies from five Tetramorium species including T. immigrans and T. caespitum. Both climate and urbanization limited the ranges of these species, and urbanization impacted their distributions simultaneously at several spatial scales. The occurrence probabilities of T. immigrans depended on the interaction between climatic and urban factors. Several introductions from external sources seemed to have given rise to four genetically distinct populations of T. immigrans, making it likely that it is not native to the northernmost urban areas. Hybridization and introgression between T. immigrans and T. caespitum was frequent in zones of sympatry, and the detection of nuclear DNA backcrosses and mitochondrial-nuclear DNA discordance between the two species suggested that hybridization lead to fertile offspring (i.e. introgression). Cuticular hydrocarbon profiles were clearly differentiated between the two species and were correlated to heightened interspecific aggression against heterospecifics. Both species presented a monogyne polyandrous mating system, in which hybrid queens but no hybrid fathers contributed to hybrid offspring. Few studies on interspecific hybridization have addressed global change or biological invasions. These concepts are infrequently studied together, and their interactive effects are overlooked in the current literature. Taking these interrelationships into account and exploring multiple scales are essential to better understand the processes that generate patterns of genetic exchange

1. Plant quality (bottom-up effects) and natural enemies (top-down effects) affect herbivore performance. Furthermore, plant quality can also influence the impact of natural enemies. 2. Lower plant quality through reduced irrigation increased the abundance of the cryptic species from the Bemisia tabaci complex [hereafter B. tabaci Middle East Asia Minor 1 (MEAM1)], but not its natural enemies on cotton. It was therefore predicted that lower plant quality would diminish the impact of natural enemies in regulating this herbivore. 3. Over three cotton seasons, plant quality was manipulated via differential irrigation and natural enemy abundance with insecticides. Life tables were used to evaluate the impact of these factors on mortality of immature B. tabaci (MEAM1) over nine generations. 4. Mortality of B. tabaci (MEAM1) was consistently affected by natural enemies but not by plant quality. This pattern was driven by high levels of sucking predation, which was the primary (key) factor associated with changes in immature mortality across all irrigation and natural enemy treatments. Dislodgement (chewing predation and weather) and parasitism contributed as key factors in some cases. Analyses also showed that elimination of sucking predation and dislodgement would have the greatest effect on overall mortality. 5. The top-down effects of natural enemies had dominant effects on populations of B. tabaci (MEAM1) relative to the bottom-up effects of plant quality. Effects were primarily due to native generalist arthropod predators and not more host-specific aphelinid parasitoids. The findings of this study demonstrate the important role of arthropod predators in population suppression and validate the importance of conservation biological control in this system for effective pest control.

Survival, growth, aboveground biomass production, belowground biomass production, sediment accretion, soil surface elevation dynamics, sediment carbon and C/N ratio, sediment N and P, sediment 13C and 15N, sediment texture and macrofauna community structure, were studied in experimental treatments planted with four different densities (6.96, 3.26, 1.93 and 0.95 seedlings m-2) of the mangrove Rhizophora mucronata in Palakuda, Puttalam Lagoon, Sri Lanka. The first three parameters were also studied at a replicated experiment at Rekawa Lagoon, Sri Lanka. For both Palakuda (1,171days) and Rekawa (702 days) sites, the highest tree density (6.96 seedlings m-2) showed significantly higher % survival: means (±S.E.) of 93.4 (± 1.1) and 91.2 (± 1.38) respectively. The measures of individual trees (tree height, stem diameter, number of leaves, leaf area, number of branches, number of prop roots ) did not differ among treatments (p>0.05) for both sites. In contrast, the aboveground biomass responded significantly to planting density with higher plantation densities equating to greater biomass: 10772 ± 24 and 9904 ± 18.1g dry weight m-2 for Palakuda (1,171days) and Rekawa (702 days) respectively. The belowground biomass at Palakuda (1370 days) varied significantly between the densities with the highest belowground biomass (105.41 ± 6.98 g m-2) in the highest tree density. The same tree density had the highest numbers of fine roots m-2 for efficient absorption of nutrients. Higher tree densities accumulated more N in their sediments while the sediment phosphate was not different between the densities. Sediment ‰ 13C, ‰ 15N and C/N ratios ranged between -16.41 to -14.58, 2.80 to 2.40 and 9.32 to 7.85 respectively and were independent of the planting density. The 13C values indicated a potential mix of seagrass C and mangrove C in sediments of the treatments; the highest tree density (6.96 seedlings m-2) had significantly higher % sediment carbon (0.68 ± 0.04) compared with the unplanted controls (0.46 ± 0.05). Rates of surface accretion were 13.0 (± 1.3), 10.5 (± 0.9), 8.4 (± 0.3), 6.9 (± 0.5) and 5.7 (± 0.3) mm year-1 at planting densities of 6.96, 3.26, 1.93, 0.95, and 0 (unplanted control) seedlings m-2 respectively, showing highly significant differences among treatments. Mean (± SE) rates of surface elevation change were much lower than rates of accretion at 2.8 (± 0.2), 1.6 (± 0.1), 1.1(± 0.2), 0.6 (± 0.2) and -0.3 (± 0.1) mm year-1 for 6.96, 3.26, 1.93, 0.95, and 0 seedlings m-2, respectively. The community structure of the sediment macrofauna was unchanged between the treatments; that is likely to be the result of unchanged sediment texture and unavailability of mangrove derived carbon as the major food source. This study demonstrated the role of higher mangrove densities in enhancing the rates of sediment accretion and surface elevation processes that may be crucial in mangrove ecosystems' adaptation to sea-level rise. There was no evidence that increasing plant density evoked a trade-off with growth and survival of the planted trees during their early 1171 days of growth. While these potential processes need further research, the enhanced survival at high densities suggests the potential to use high plantation densities to help mitigate sea-level rise effects by encouraging positive sediment surface elevation. Higher biomass production in higher densities would also help faster sequestration of atmospheric carbon dioxide.

Tsuga canadensis (L.) Carr. (eastern hemlock), a long lived and shade tolerant coniferous tree species native to eastern North America, is currently threatened by the hemlock woolly adelgid (Adelges tsugae Annand, HWA). This exotic, invasive insect poses a serious threat to T. canadensis stands throughout their native range. The loss of this unique tree species is often coupled with numerous ecological consequences. HWA-induced mortality has exceeded 95% in some forest types, and will likely continue to decimate T. canadensis populations in the coming years. Shortly after HWA was found in Great Smoky Mountains National Park (GSMNP), long-term monitoring plots were established across a gradient of T. canadensis associated forest communities to monitor HWA impacts and stand decline. Our objectives were to (1) determine how T. canadensis populations have changed in conjunction with HWA infestation, and (2) document how HWA has affected vegetative community dynamics following five to six years of infestation in GSMNP. We assessed T. canadensis associated overstory communities and determined that crown density, top dieback, and T. canadensis stem density has significantly declined over the observational period. Furthermore, we found that midstory T. canadensis trees were experiencing greater rates of decline than those of the overstory. Even with these losses, overstory and midstory community composition did not significantly change from 2003 to 2008/09. Many studies have documented rapid pulses of understory vegetative productivity in conjunction with T. canadensis defoliation, which often allows increased amounts of solar radiation to reach the forest floor. Although we observed significant T. canadensis mortality at most plots sampled, understory species composition did not significantly change following HWA infestation. We attribute this lack of species response to the overwhelming abundance of Rhododendron maximum in the mid/understory, which restricts increased light from reaching the forest floor despite the formation of small overstory gaps. However, we found that understory composition significantly varied among ecological groupings, and differences were largely associated with soil properties and elevation. Overall, results of this project suggest that T. canadensis may largely disappear from southern Appalachian forests resulting from infestations of HWA. Although community composition of T. canadensis associated stands has not yet been altered, changes are likely to occur as duration of infestation progresses.

Lily leaf spot, a fungal foliar disease caused by Pseudocercosporella inconspicua, leads to premature senescence of aboveground tissues in Lilium grayi. At Roan Mountain, North Carolina/Tennessee, the disease was most prevalent and most severe in seedlings and juveniles. In the two growing seasons assessed, 59 and 70% of mature plants experienced disease-induced premature senescence. Plants with disease lesions on seed capsules matured fewer capsules and had fewer seeds per capsule, and seeds had reduced viability. Disease prevalence over the growing season followed a sigmoidal pattern typical of polycyclic epidemics. Plants with low and high disease severity occurred in clusters whose locations were stable across growing seasons. Prior to the recent description of lily leaf spot, L. grayi was already considered threatened or endangered in each of the three states where it naturally occurs. Therefore, this infectious disease poses conservation and management difficulties because increases in plant density can be expected to lead to enhanced disease transmission. Lily leaf spot of L. grayi is best characterized as an annually recurring epidemic because of high prevalence rates, strong impacts on all life stages, and reductions in seed production and viability.

The Southern Ocean (ca. 20% of the world ocean surface) is a key place for the regulation of Earth climate thanks to its capacity to absorb atmospheric carbon dioxide (CO2) by physico-chemical and biological mechanisms. The biological carbon pump is a major pathway of absorption of CO2 through which the CO2 incorporated into autotrophic microorganisms in surface waters is transferred to deep waters. This process is influenced by the extent of the primary production and by the intensity of the remineralization of organic matter along the water column. So, the annual cycle of sea ice, through its in situ production and remineralization processes but also, through the release of microorganisms, organic and inorganic nutrients (in particular iron)into the ocean has an impact on the carbon cycle of the Southern Ocean, notably by promoting the initiation of phytoplanktonic blooms at time of ice melting.

The present work focussed on the distribution of organic matter (OM) and its interactions with the microbial network (algae, bacteria and protozoa) in sea ice and ocean, with a special attention to the factors which regulate the biological carbon pump of the Southern Ocean. This thesis gathers data collected from a) late winter to summer in the Western Pacific sector, Western Weddell Sea and Bellingshausen Sea during three sea ice cruises ARISE, ISPOL-drifting station and SIMBA-drifting station and b) summer in the Sub-Antarctic and Polar Front Zone during the oceanographic cruise SAZ-Sense.

The sea ice covers were typical of first-year pack ice with thickness ranging between 0.3 and 1.2 m, and composed of granular and columnar ice. Sea ice temperature ranging between -8.9°C and -0.4°C, brines volume ranging between 2.9 to 28.2% and brines salinity from 10 to >100 were observed. These extreme physicochemical factors experienced by the microorganisms trapped into the semi-solid sea ice matrix therefore constitute an extreme change as compared to the open ocean. Sea ice algae were mainly composed of diatoms but autotrophic flagellates (such as dinoflagellates or Phaeocystis sp.) were also typically found in surface ice layers. Maximal algal biomass was usually observed in the bottom ice layers except during SIMBA where the maxima was localised in the top ice layers likely because of the snow and ice thickness which limit the light available in the ice cover. During early spring, the algal growth was controlled by the space availability (i.e. brine volume) while in spring/summer (ISPOL, SIMBA) the major nutrients availability inside sea ice may have controlled algal growth. At all seasons, high concentrations of dissolved and particulate organic matter were measured in sea ice as compared to the water column. Dissolved monomers (saccharides and amino acids) were accumulated in sea ice, in particular in winter. During spring and summer, polysaccharides constitute the main fraction of the dissolved saccharides pool. High concentrations of transparent exopolymeric particles (TEP), mainly constituted with saccharides, were present and their gel properties greatly influence the internal habitat of sea ice, by retaining the nutrients and by preventing the protozoa grazing pressure, inducing therefore an algal accumulation. The composition as well as the vertical distribution of OM in sea ice was linked to sea ice algae.

Besides, the distribution of microorganisms and organic compounds in the sea ice was also greatly influenced by the thermodynamics of the sea ice cover, as evidenced during a melting period for ISPOL and during a floodfreeze cycle for SIMBA. The bacteria distribution in the sea ice was not correlated with those of algae and organic matter. Indeed, the utilization of the accumulated organic matter by bacteria seemed to be limited by an external factor such as temperature, salinity or toxins rather than by the nature of the organic substrates, which are partly composed of labile monomeric saccharides. Thus the disconnection of the microbial loop leading to the OM accumulation was highlighted in sea ice.

In addition the biofilm formed by TEP was also involved in the retention of cells and other compounds(DOM, POM, and inorganic nutrients such as phosphate and iron) to the brine channels walls and thus in the timing of release of ice constituents when ice melts. The sequence of release in marginal ice zone, as studied in a microcosm experiments realized in controlled and trace-metal clean conditions, was likely favourable to the development of blooms in the marginal ice zone. Moreover microorganisms derived from sea ice (mainly <10 µm) seems able to thrive and grow in the water column as also the supply of organic nutrients and Fe seems to benefit to the pelagic microbial community.

Finally, the influence of the remineralization of organic matter by heterotrophic bacterioplankton on carbon export and biological carbon pump efficiency was investigated in the epipelagic (0-100 m) and mesopelagic(100-700 m) zones during the summer in the sub-Antarctic and Polar Front zones (SAZ and PFZ) of the Australian sector (Southern Ocean). Opposite to sea ice, bacterial biomass and activities followed Chl a and organic matter distributions. Bacterial abundance, biomass and activities drastically decreased below depths of 100-200 m. Nevertheless, depth-integrated rates through the thickness of the different water masses showed that the mesopelagic contribution of bacteria represents a non-negligible fraction, in particular in a diatom-dominated system./

L’océan Antarctique (± 20% de la surface totale des océans) est un endroit essentiel pour la régulation du climat de notre planète grâce à sa capacité d’absorber le dioxyde de carbone (CO2) atmosphérique par des mécanismes physico-chimique et biologique. La pompe biologique à carbone est un processus majeur de fixation de CO2 par les organismes autotrophes à la surface de l’océan et de transfert de carbone organique vers le fond de l’océan. Ce processus est influencé par l’importance de la production primaire ainsi que par l’intensité de la reminéralisation de la matière organique dans la colonne d’eau. Ainsi, le cycle annuel de la glace via sa production/reminéralisation in situ mais aussi via l’ensemencement de l’océan avec des microorganismes et des nutriments organiques et inorganiques (en particulier le fer) a un impact sur le cycle du carbone dans l’Océan Antarctique, notamment en favorisant l’initiation d’efflorescences phytoplanctoniques dans la zone marginale de glace.

Plus précisément, nous avons étudié les interactions entre le réseau microbien (algues, bactéries et protozoaires) et la matière organique dans le but d’évaluer leurs impacts potentiels sur la pompe biologique de carbone dans l’Océan Austral. Deux écosystèmes différents ont été étudiés :la glace de mer et le milieu océanique grâce à des échantillons prélevés lors des campagnes de glace ARISE, ISPOL et SIMBA et lors de la campagne océanographique SAZ-Sense, couvrant une période allant de la fin de l’hiver à l’été.

La glace de mer est un environnement très particulier dans lequel les microorganismes planctoniques se trouvent piégés lors de la formation de la banquise et dans lesquels ils subissent des conditions extrêmes de température et de salinité, notamment. Les banquises en océan ouvert étudiées (0,3 à 1,2 m d’épaisseur, températures de -8.9°C à -0.4°C, volumes relatifs de saumure de 2.9 à 28.2% et salinités de saumures entre 10 et jusque >100) étaient composées de glace columnaire et granulaire. Les algues de glace étaient principalement des diatomées mais des flagellés autotrophes (tels que des dinoflagellés ou Phaeocystis sp.) ont été typiquement observés dans les couches de glace de surface. Les biomasses algales maximales se trouvaient généralement dans la couche de glace de fond sauf à SIMBA où les maxima se trouvaient en surface, probablement en raison de l’épaisseur des couches de neige et de glace, limitant la lumière disponible dans la colonne de glace. Au début du printemps, la croissance algale était contrôlée par l’espace disponible (càd le volume des saumures) tandis qu’au printemps/été, la disponibilité en nutriments majeurs a pu la contrôler. A toutes les saisons, des concentrations élevées en matière organique (MO) dissoute et particulaire on été mesurées dans la glace de mer par rapport à l’océan. Des monomères dissous (sucres et acides aminés) étaient accumulés dans la glace, surtout en hiver. Au printemps et été, les polysaccharides dissous dominaient le réservoir de sucres. La MO était présente sous forme de TEP qui par leurs propriétés de gel modifie l’habitat interne de la glace. Ce biofilm retient les nutriments et gêne le mouvement des microorganismes. La composition et la distribution de la MO dans la glace étaient en partie reliées aux algues de glace. De plus, la thermodynamique de la couverture de glace peut contrôler la distribution des microorganismes et de la MO, comme observé lors de la fonte de la glace à ISPOL et lors du refroidissement de la banquise à SIMBA. La distribution des bactéries n’est pas corrélée avec celle des algues et de la MO dans la glace. En effet, la consommation de la MO par les bactéries semble être limitée non pas par la nature chimique des substrats mais par un facteur extérieur affectant le métabolisme bactérien tel que la température, la salinité ou une toxine. Le dysfonctionnement de la boucle microbienne menant à l’accumulation de la MO dans la glace a donc été mis en évidence dans nos échantillons.

De plus, le biofilm formé par les TEP est aussi impliquée dans l’attachement des cellules et autres composés aux parois des canaux de saumure et donc dans la séquence de largage lors de la fonte. Cette séquence semble propice au développement d’efflorescences phytoplanctoniques dans la zone marginale de glace. Les microorganismes originaires de la glace (surtout ceux de taille < 10 μm) semblent capables de croître dans la colonne d’eau et l’apport en nutriments organiques et inorganiques apparaît favorable à la croissance des microorganismes pélagiques.

Enfin, l’influence des activités hétérotrophes sur l’export de carbone et l’efficacité de la pompe biologique à carbone a été évaluée dans la couche de surface (0-100 m) et mésopélagique (100-700 m) de l’océan. Au contraire de la glace, les biomasses et activités bactériennes suivaient les distributions de la chlorophyll a et de la MO. Elles diminuent fortement en dessous de 100-200 m, néanmoins les valeurs intégrées sur la hauteur de la colonne d’eau indiquent que la reminéralisation de la MO par les bactéries dans la zone mésopélagique est loin d’être négligeable, spécialement dans une région dominée par les diatomées.

Doctorat en Sciences agronomiques et ingénierie biologique
info:eu-repo/semantics/nonPublished

[Truncated abstract] Weeds which invade native communities can have major impacts on biodiversity and ecosystem processes. However, these impacts are rarely quantified, and the mechanisms behind these impacts are rarely investigated. Asparagus asparagoides (L.) Druce (Asparagaceae; common name: bridal creeper), a plant native to southern Africa, is a significant environmental weed in southern Australia. Bridal creeper can invade both disturbed and undisturbed native ecosystems and then dominate native communities. As is the case for many environmental weeds, there has been little work conducted on the impacts of this plant. This lack of knowledge has hampered restoration efforts of invaded areas because very little is known about the potential for invaded communities to recover prior to undertaking weed management. There is a need to improve our understanding of how to manage ecosystem recovery during and after weed control. This can be achieved by (i) determining the impacts caused by the weed; (ii) assessing the condition of invaded communities; and (iii) predicting the impacts that weed management itself will have on the native communities. These three prerequisites to environmental weed control have been determined across sites invaded by bridal creeper in southern Australia. The impacts of this invasive geophyte have been determined through multi-site comparisons, weed removal experiments and controlled glasshouse and laboratory experiments. ... Without additional restoration, we will see those species that readily germinate and those that respond positively to increased soil fertility, replacing bridal creeper after control. This will be dominated by other weeds as the invaded sites have large exotic seed banks that will readily germinate. The tuberous mats of older bridal creeper plants will also leave a legacy as they will remain many years after control and still impact on vegetation, even if control has killed the plant. These impacts will be highest at sites where bridal creeper has dominated over the longer term. Environmental weeds, such as bridal creeper, that are capable of altering ecosystem functions can lead to substantial declines in biodiversity. Therefore, it was fortunate that bridal creeper became a target for biocontrol in Australia even though the impacts of the weed were not quantified when this decision was made. There are areas in southern Australia that are still free of bridal creeper or have sparse populations, and it is highly likely that this biological control programme has lead to the protection of these areas. This protection would not have been possible if other control measures were chosen over biological control, given that biocontrol agents can self-disperse and are able to give continuous control. This means that biological control of weeds in conservation areas can be very effective and is the only economically viable option for the control of widespread environmental weeds such as bridal creeper.

Invasive species are significant drivers of global environmental change, altering the stability and functioning of numerous ecosystems. The exotic shrub Lonicera maackii is an aggressive invader throughout much of the eastern United States. While much is known about its population and community impacts, little is known about effects on ecosystem processes. This dissertation documents changes in ecosystem processes associated with L. maackii growing beneath three native tree species (Fraxinus quadrangulata, Quercus muehlenbergii, Carya ovata) in a savanna in Kentucky. Like many invasive plants, L. maackii litter decomposed and lost nitrogen (N) rapidly, especially in comparison with native tree litter. In comparison to the soils beneath the trees where the exotic shrub was absent, soils beneath L. maackii had a lower bulk density, elevated soil organic matter, C:N, and total soil N and a modified soil microbial community. Inorganic N deposition from spring throughfall was also altered by L. maackii, with higher NO3-N deposition beneath shrubs located beneath the tree canopy relative to canopy locations without L. maackii. While many exotic plant species have been shown to alter ecosystem processes, their impact is often not uniform. This variability is attributed to among-site differences (soil, climate, plant community): within site variability is often ignored. While many of L. maackii’s alterations to ecosystem processes were uniform across the site, several were dependent upon interactions between the exotic and the native tree species. Litter from L. maackii decomposed and lost N more rapidly under C. ovata than under the other native tree species. Soils beneath L. maackii shrubs located under C. ovata also had a greater fungal:bacterial ratio and a greater abundance of the saprophytic fungal lipid biomarker 18:1ω9c. These results demonstrate that L. maackii’s impact extends to ecosystem processes and suggests that invasive plants may have variable effects within a given environment depending on their interactions with the dominant native species. Identifying native species or communities that are more vulnerable to alterations of ecosystem function upon invasion may prove useful to land managers and foster a better understanding of the role that community dynamics play in moderating or enhancing invasive species impacts.

The Maptaphut Industrial Estate is located on the Gulf of Thailand, Rayong Province. The area, which has been designated as a main centre for the petrochemical industry currently occupies 16 sq km and comprises petrochemical plants, chemical and fertilizer plants, refineries, construction plants, and steel industry; there are also residential and commercial areas (IEAT, 2004). There is a significant population around the site, with 24,000 inhabitants in the immediate vicinity according to Jadsri et a/ (2006). The estate has been held responsible for deaths and hospital admissions due to leaks and accidents dating back as far as 1997. Whilst the environmental and health and safety performance of the estate as a whole has significantly improved over recent years, there are still significant outpatient admission rates to Maptaphut hospital for respiratory illness, as recently reported by Jadsri et al. (2006), raising the question of whether local emissions are significantly contributing to ill health, or whether general background concentrations of pollutants from nearby road sources and from Rayong City are the main contributions. The main aim of this research, therefore, was to accurately model the dispersion of pollutants from the estate, and to attempt to quantify the health impacts of these emissions. The specific objectives of this study were to (a) to characterise meteorological conditions in the Maptaphut area; (b) to develop a multiple linear regression statistical model to characterise and predict atmospheric pollutant concentrations in Maptaphut; (c) to investigate the relationship between air pollution and ill health in Maptaphut using a multiple linear regression statistical model; (d) to evaluate the effectiveness of Gaussian and Computational Fluid Dynamics atmospheric dispersion modelling software packages in predicting ground level pollutant concentrations at points around the industrial estate and (e) to use the results of the dispersion modelling studies to assess the contribution of the industrial estate to the overall atmospheric pollutant load in the Maptaphut area, and from published health impact factors, to assess the overall health impact of the estate. The first objective was to characterise the environmental status, trend, and impacts of air pollution during the period 1998 to 2007. The estate is located in the coastal area; thus, the role of the sea-land breeze has a significant role in the dispersion of air pollutants harmfulness. Data collected for the Maptaphut Industrial Estates area, including regional, temporal and spatial considerations included: meteorological data from 100-metres tall meteorological mast; ambient air quality data from three ambient air quality monitoring stations; industrial emissions data; traffic volume on nearby major roads; and outpatient admissions data at the Maptaphut and Rayong hospitals. Comparisons with the ambient air quality in the Bangkok area were made, and the daily and yearly trends in concentrations of the main air pollutants were analysed. Multiple linear regression models correlating pollutant concentrations with respiratory outpatient admissions rates showed that 03, PMio and NO were statistically significant determinants. The overall correlation had a coefficient of Determination (R2) of 41.4% for one week average data, increasing to 51.2% when air temperature and %RH were included. Accumulation effect of pollutants up to four weeks period exposure does not appear to have an effect. A basic health impact analysis study using the ADMS modelled concentrations and the WHO AirQ tool, along with default risk factors, showed that emissions from the Maptaphut industrial estate account for almost all of the NO2 and SO2 related respiratory illness and between 10 and 27% of the PMio related admissions; this actually represents less than 2% of the total respiratory admissions for this area.

Many freshwater ecosystems sustain several invasive species. Here I examine multiple invasions in two highly invaded and well catalogued catchments; Lake Naivasha, Kenya and River Thames, England. New metrics, derived from stable isotope analysis, are used to provide measures of trophic diversity and to examine dietary interactions among species. I test the hypothesis that functionally similar sympatric species will occupy a smaller niche than their allopatric counterparts. Additionally, I quantify the impact of multiple invasive species on ecosystem structure and functioning in order to address the question; do interactions among species amplify or mitigate one another's impact? In Lake Naivasha, the stable isotope metrics revealed serial replacement of invasive species due to dietary interactions. Invasive red swamp crayfish were eventually excluded from the lake due to niche restriction in the presence of a more recent invader, the common carp. Now, the crayfish have migrated into the catchment where they overlap with a species of native river crab. Here, I found a novel mechanism of invasion, whereby the crayfish restricted their niche at the invasion front in order to reduce competition with crabs. Crayfish also caused significant changes in invertebrate community structure and increased decomposition rates, which indirectly resulted in displacement of the crabs. In the Thames catchment, I catalogue the non-indigenous species and show how invasion rates have increased significantly since 1800 due to globalisation. Using the four species of invasive crayfish present (red swamp, signal, Turkish and virile), I demonstrate their extensive diet plasticity using novel measures of niche width and individual specialisation based on stable isotope data. Interactions among the crayfish were examined and this revealed that each species has varying and independent impacts on invertebrate community structure, algal standing stock and decomposition rates. Hence, interactions among invaders are not expected to amplify or mitigate one another's impact and instead, the combined impact will be the sum of their allopatric impacts.

Mining has caused ecosystem losses worldwide, with surface mining disturbing >2.4 million hectares in the United States since 1930. The Appalachian region of the US is home to extensive temperate deciduous forests that provide many ecosystem services and economic benefits. However, >400,000 hectares of forest have been lost due to surface coal mining, with most not being restored back to native forests or other productive land uses. These areas are left fragmented, heavily modified, unmanaged, and densely invaded by non-native plants. Autumn olive (Elaeagnus umbellata) is one of the most prevalent invasive species on reclaimed mines in Appalachia and viewed as one of the main hindrances to the successful reclamation of mined land to restore native forests. In order to better assess the impact autumn olive can have on reclamation success, we characterize autumn olive's performance in various reclamation scenarios and also how the management of autumn olive affects hardwood tree establishment. We review how exotic species impact restoration outcomes, and advocate for a better understanding of how these species could contribute towards a more ecological understanding of reclamation. Reclamation goals are currently assessed after 5 years, prioritizing short-term goals (e.g. erosion control) instead of longer-term goals such as the return of ecosystem function. With a better understanding of plant function and ecological processes, we hope to continue to advance successful reclamation on surface mined lands.
Master of Science in Life Sciences

Invasive species represent a major concern; they can result in serious ecological and economic losses and are recognised as one of the most serious threats to global species diversity. Plant invasions are of particular concern in New Zealand, which has high proportions of both naturalised and endemic plant species. In this thesis I focussed on the invasive plant Hieracium lepidulum, an exotic weed introduced from Europe to New Zealand prior to 1941. It is invasive in a variety of habitats in the South Island, where it has steadily increased in distribution and abundance over the last 50 years, and is thought to have detrimental impacts on native plant communities. I investigated factors influencing its invasion success and tested for impacts on native plant communities, making extensive use of existing plots into which H. lepidulum was experimentally introduced in 2003. I examined how community richness, turnover, resource availability and propagule pressure of the invader interacted to determine the invasion success of H. lepidulum. Results differed markedly above and below treeline. Above treeline, plots with higher richness and turnover were more invaded; below treeline, plots with higher available light were more invaded. In both habitats, these findings were modified by the influence of propagule pressure; at low propagule pressure, site characteristics were non-significant in explaining invasion success, while at higher propagule pressure these effects became significant. To test for impacts resulting in altered community composition and structure, I looked for changes in community richness, diversity and evenness subsequent to H. lepidulum introduction. As impacts may be more apparent at fine spatial scales, I made measurements at a 5 x 5 cm cell scale in addition to the established 30 x 30 cm plot scale. Plot species richness increased from 2003 to 2009 and a component of this increase was associated with H. lepidulum density. Other relationships between the plant community and H. lepidulum were generally non-significant. Results showed that H. lepidulum has had no negative effects on community richness, evenness or diversity. Despite being able to opportunistically colonise grassland sites with high turnover, and forest sites subject to canopy disturbance, dependant on propagule pressure, it appears H. lepidulum has not impacted community composition or structure.

Made available in DSpace on 2014-10-09T12:27:30Z (GMT). No. of bitstreams: 0
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Dissertacao (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Rapid Bioassessment Protocols integrate a suite of community, population, and functional metrics, determined from the collection of benthic macroinvertebrates or fish, into a single assessment. This study was conducted in Dallas County Texas, an area located in the blackland prairie eco-region that is semi-arid and densely populated. The objectives of this research were to identify reference streams and propose a set of metrics that are best able to discriminate between differences in community structure due to natural variability from those caused by changes in water quality due to watershed impacts. Using geographic information systems, a total of nine watersheds, each representing a different mix of land uses, were chosen for evaluation. A total of 30 metrics commonly used in RBP protocols were calculated. Efficacy of these metrics to distinguish change was determined using several statistical techniques. Ten metrics were used to classify study area watersheds according to stream quality. Many trends, such as taxa presence along habitat quality gradients, were observed. These gradients coincided with expected responses of stream communities to landscape and habitat variables.

Increasing rates of overweight, obesity, and related metabolic diseases documented among refugee communities across the United States necessitate greater attention to how processes of integration impact refugee health. These nutritional health trends (e.g., increasing rates of obesity) suggest potential disconnects between refugees' past environments and their conditions after re-settlement, which may contribute to adverse changes in energy balance (diet and exercise). While Bhutanese refugees were among the largest refugee groups entering the US during the five years leading up to this research, very few studies have examined how they have responded to integration and the impact of this transition on their health. Grounded in human adaptability and political economic theories, and adopting a biocultural approach, this dissertation investigates how Bhutanese refugees in “Prospect City” (pseudonym) negotiate changing and unfamiliar structural and sociocultural conditions after resettlement and the consequences for energy balance and nutritional status. The results reveal high rates of overweight and obesity compared to US averages. Age and caste related differences in nutritional status were also found. High rates of overweight and obesity corresponded with an energy imbalance due to over consumption of energy dense traditional foods and limited understanding of the importance of regular exercise. Over consumption of energy dense traditional foods stemmed from several interrelated factors: the abundance of foods in the US, prior experiences with food deprivation, a history of political exile that reinforced desires to preserve cultural food preferences, and joint family efforts to accommodate work-related time constraints by increasing food production and availability. Decreases in exercise appeared to stem from more sedentary lifestyles in the US as a result of work environments and available transportation, coupled with a lack of health knowledge regarding health benefits of physical activity. This dissertation’s findings are being reported to Prospect City’s Bhutanese Community Organization to help develop strategies for improving nutritional health in the community.

Trois modèles invasifs à large répartition en Europe, le long d'un gradient latitudinal Norvège-Portugal, ont été choisis : Sargassum muticum, Codium fragile et Gracilaria vermiculophylla. Cette thèse a pour objectif l'étude de la phénologie, de l'écophysiologie et du métabolome de ces macrophytes invasifs face à une variation de facteurs environnementaux 1) à une échelle locale, 2) à l'échelle du gradient latitudinal (en lien avec le changement climatique global) ainsi que l'étude 3) des voies de valorisation possibles des métabolites de stress par bio-inspiration. Le gradient latitudinal, se traduisant par un gradient thermique, permet de mimer le réchauffement climatique car les conséquences de ce changement climatique sur les espèces en milieu naturel ne sont généralement appréciables qu'à l'échelle de dizaines d'années. Les suivis de l'écologie, dumétabolome ainsi que des impacts potentiels de ces espèces à une échelle locale en France, a permis d'étudier le développement et le cycle de vie des espèces. En particulier, G. vermiculophylla se caractérise par une phénologie spécifique (avec la prépondérance de petits fragments végétatifs, <3cm) en Rade de Brest et par une tolérance accrue à l'envasement jusqu'à 12 cm de profondeur en acclimatant son métabolome tout en maintenant une physiologie dormante. Cette espèce ingénieur impacte en profondeur l'écosystème vaseux de la Rade. Le suivi le long du gradient latitudinal a permis d'illustrer la plasticité phénologique des espèces et notamment un potentiel invasif contrasté de C. fragile entre les différentes latitudes. Lors de marée basse de vives eaux, les espèces présentent une acclimatation de leur photo-physiologie en fonction de la latitude avec la mise en évidence d'une photoinhibition du PSll, lié au stress engendré par les conditions environnementales.Enfin, ce travail a illustré les propriétés multifonctionnelles d'extraits enrichis en composés phénoliques, présentant des activités antioxydantes mais également photoprotectrices ou ostéogéniques, soulignant l'émergence de voies de valorisation originales par bio-inspiration pour divers secteurs tels que la cosmétologie et les biomatériaux en santé humaine
Three model species with a large distribution along European coasts, along a latitudinal gradient from Norway to Portugal was chosen: Sargassum muticum, Codium fragile and Gracilaria vermiculophylla. The aims of this PhD thesis were to study the phenology, ecophysiology and the metabolom of these non-native marine macrophytes and their ability to cope with a variation of environmental factors 1) at a population scale, 2) along the latitudinal gradient (in relation with the global climatic change) and to propose 3) bio-inspired molecules for industrial purposes. The latitudinal gradient corresponding to a thermic gradient, allows to imitate the global warming as climatic change ¡mpacts are most of the time only visible at decennial scale.Monitorings of ecology, metabolome and potential impacts of these macroalgae, at a population scale, allowed to study the development and life cycle of these models. In particular, G. vermiculophylla exhibited a specific phenology (with a majority of small vegetative fragments, <3cm) in the Bay of Brest and a highly tolerance to burial until 12 cm depth in the sediment by acclimatizing its metabolome together with the ability to maintain a dormancy physiology. This engineer species modifies deeply muddy shores of this Bay. Latitunal gradients's monitoring highlighted the phenological plasticity and a contrasted invasive potential of C.fragile between latitudes. During low spring tides, species exhibited an acclimation of their photophysiology between latitudes with photoinhibition process related to induce environmental stress. Furthermore, this work showed the multifunctional properties of polyphenols enriched extracts with antioxidant, photoprotective or osteogenic activities, highlighting the emergence of original bio-inspired pathways for cosmetic or biomaterial applications

Abstract My main objectives in this thesis were to explore general patterns and mechanisms driving salmonid invasions globally and, more specifically, to examine the invasion dynamics and impacts of the North American brook trout in North European stream systems. Non-native salmonids have often spread extensively and caused many harmful impacts on their native counterparts. Among the three globally introduced salmonids, the European brown trout appeared as the 'worst' alien species (strongest impact on native fish), followed by the North American rainbow trout and brook trout. Brook trout, which is widely established in European streams, was found to be a non-aggressive species. Moreover, the growth of brown trout was unaffected by brook trout, indicating negligible interspecific interactions between the two species. Habitat niche segregation between brook trout and brown trout was evident, with brook trout occupying mainly low-velocity pool habitats, whereas brown trout resided in fast-flowing riffles. At the river-wide scale, brook trout occurred mainly in small, slightly acid headwater streams, whereas brown trout was found primarily in larger downstream river sections. Evidently, North European streams with a very low number of native fish species offer underutilized niche space for tolerant headwater specialists such as brook trout. However, the habitat niche filled by brook trout was not completely vacant, as brown trout co-occurred with brook trout in numerous small and mid-sized (3–16 m wide) streams. In these streams, brown trout reproduction was negligible presumably related to the presence of brook trout. Brook trout had also increased in density relative to brown trout during the 10-yr study period (1994 vs. 2004). Moreover, the growth rate and population densities of brook trout were high and the species had spread extensively towards the upmost headwater streams during the 10-yr study period. Thus, harmful effects on the native brown trout by brook trout are likely to occur in the core habitat of the invader, i.e. headwater streams, leaving populations of the native species unaffected elsewhere. Due to the high conservation value of the potentially impacted populations of brown trout, I strongly caution against further stocking of brook trout in European watersheds.

Made available in DSpace on 2014-10-09T12:41:24Z (GMT). No. of bitstreams: 0
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Dissertação (Mestrado)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

Les invasions biologiques produisent des assemblages d'espèces souvent inédits et sources de nouvelles interactions spécifiques. L'impact écologique d'une invasion peut être : (i) indirect si l'espèce envahissante entre en compétition avec une ou des espèces résidentes, et (ii) direct si l'espèce envahissante consomme ou parasite une ou des espèces résidentes. Ces deux types d'impacts sont susceptibles de s'appliquer aux insectes envahissants du genre Megastigmus (Hymenoptera: Torymidae), qui exploitent généralement une niche étroite partagée avec d'autres espèces résidentes, et contribuent à d'importantes mortalités dans les populations d'hôtes du fait de leur spécialisation sur les graines. L'objectif de cette thèse est de tester ces prédictions à travers l'étude de l'impact de l'invasion en France de Megastigmus schimitscheki sur : (i) M. pinsapinis, un compétiteur résident, et (ii) les populations en expansion de son hôte obligatoire, le cèdre de l'Atlas (Cedrus atlantica).Un suivi spatio-temporel des populations françaises de Megastigmus spp. révèle que l'expansion rapide de M. schimitscheki est associée à un déclin important de M. pinsapinis. Un modèle mécaniste et statistique a été développé afin de déterminer la contribution relative de la variabilité temporelle de la disponibilité en graines et des divergences de traits d'histoire de vie dans la dynamique de coexistence-exclusion de M. schimitscheki et M. pinsapinis. Nos résultats montrent que la phénologie plus précoce de M. schimitscheki est le principal facteur déterminant le succès de l'invasion de M. schimitscheki et l'exclusion compétitive de M. pinsapinis dans les zones de sympatrie des deux espèces.Nous avons développé une approche théorique de l'impact indirect de M. schimitscheki sur C. atlantica basée sur les modèles de réaction-diffusion. Nos résultats montrent qu'un effet Allee résultant de la prédation des graines sur un front d'expansion peut accroître la contribution des hôtes situés à l'arrière de ce front au pool génétique de la population. Ce phénomène a pour conséquence de freiner l'érosion de la diversité génétique au cours du processus de colonisation.Les approches expérimentales et théoriques développées au cours de cette thèse montrent que l'invasion de M. schimitscheki a un impact indirect négatif sur la démographie d'une espèce résidente occupant la même niche écologique, alors qu'elle pourrait favoriser directement le maintien de la diversité génétique des populations d'hôtes en pleine dynamique de régénération naturelle
Biological invasions produce novel species assemblages in communities that likely result in novel interspecific interactions. Ecological impacts of invasions may be: (i) indirect, if the invader enters competition with resident species, and (ii) indirect if the invader is a predator or a parasite of resident species. Both indirect and direct ecological invasion impacts are likely to apply to invasive wasps of the Megastigmus genus (Hymenoptera: Torymidae), which exploit narrow ecological niches that overlap with those of resident insect species, and contribute to high mortality levels in host plant populations due to their high specialization on seeds. This thesis aimed at testing such predictions by studying the impacts of the invasion of M. schimitscheki on: (i) its resident competitor for the seed resource M. pinsapinis, and (ii) the expanding populations of its obligatory host the Atlas cedar (Cedrus atlantica) in southeastern France.An extensive spatio-temporal survey of Megastigmus spp. populations indicated that the rapid expansion of M. schimitscheki was associated with a strong decline of M. pinsapinis. A mechanistic-statistical modelling approach allowed us to show that an earlier phenology of M. schimitscheki had a stronger explanatory power of both invasion success and the competitive exclusion of the resident than temporal variation in resource supply.A theoretical approach of the indirect impact of M. schimitscheki on C. atlantica expansion dynamics was based on reaction-diffusion models. We showed that an Allee effect resulting from seed predation at the expansion front of a host population may increase the genetic contribution of host individuals situated in the bulk of the expansion front. Interestingly, this phenomenon results in a limited erosion of genetic diversity during the expansion phase of the host population.The empirical and theoretical approaches developed showed that the invasion of M. schimitscheki in French cedar forests had a strong and negative indirect impact on the demography of a resident species, but, parallely, such invasion may directly favour the maintenance of genetic diversity in expanding host plant populations

A growing human population accompanied by urbanisation and industrialisation have led to over exploitation and pollution of freshwater resources and have consequently impacted on aquatic ecosystem health. The Swartkops River in the Eastern Cape of South Africa is no exception. It drains a heavily industrialised catchment which has led to deterioration of its water quality due to pollution. Integrated water resources management (IWRM) requires the concurrent sustainable use of water resources and the protection of aquatic ecosystem health. Macroinvertebrates are well known for their ability to reflect the health of the environment in which they live, thus they were used to assess anthropogenic impacts in the Swartkops River for this study. Macroinvertebrate based biomonitoring approaches, including the South African Scoring System version 5 (SASS5); a multimetric approach involving 19 metrics; Chironomidae community assessments and screening of morphological deformities in Chironomidae larvae, were applied at four selected sampling sites to assess environmental water quality in the Swartkops River. Macroinvertebrates were sampled us ing the SASS5 protocols. Chironomidae were mounted and identified as far as practically possible using available keys. Mentum, ligula, mandible, paraligula and antenna in Chironomidae larvae were screened for deformities. Physical and chemical water quality variables were measured at each of the selected sampling sites. All data were subjected to relevant statistical analyses. Of the four sites sampled during the study period, results revealed that water quality at site 1 was the least impacted with highest SASS5 scores, average score per taxa (ASPT) values, richness, diversity, equitability and Ephemeroptera –Plecoptera-Trichoptera (EPT) richness, as well as least incidences of chironomid deformities. Water quality at site 2 was considered the next least impacted with higher SASS5 scores, A SPT values, richness, diversity and equitability, and lower incidences of deformities compared to sites 3 and 4. SASS5 scores and ASPT values revealed that both sites 3 and 4 were critically modified but the multimetric analysis, Chironomidae community assessment and incidences of deformities in Chironomidae larvae indicated that site 3 is the most impacted of the four sampling sites, with least species diversity, richness, equitability and highest incidences of deformities. The study revealed the importance of multicriteria approach to environmental biomonitoring as an integrated water resources management tool, and based on the results, site 3, as the most impacted, could be prioritised for restoration intervention.

Many virus infections induce a transient state of immune suppression in the infected host. Virus-induced T cell suppression can be caused by T cell activation-induced cell death (AICD), dendritic cell (DC) apoptosis, DC dysfunction, and/or the enhanced expression of immune-suppressive cytokines. It has been previously demonstrated that naïve bystander CD8 T cells derived from hosts experiencing an acute virus-specific T cell response underwent AICD when polyclonally activated by anti-CD3 in vitro (Zarozinski et al., 2000). Susceptibility of naïve bystander T cells to AICD could prevent the development of a new T cell response during an ongoing immune response, and thus render infected hosts immune suppressed. Although immune suppression could result in an enhanced susceptibility to superinfections, virus-infected individuals are more commonly resistant to superinfecting pathogens. Because of these seemingly contradictory conditions, we sought to investigate how acute viral infections impact naïve bystander CD8 T cells in vivo. More specifically, we asked whether bystander CD8 T cells are susceptible to immune suppression or whether they can contribute to the resistance to superinfections. In order to address this, we examined the responses of bystander CD8 T cells activated with cognate antigen during acute viral infections in vivo. We generated several in vivomodels using P14 (LCMV glycoprotein-specific), HY (male antigen-specific), and OT-I (ovalbumin-specific) transgenic CD8 T cells, which we defined as bystander during acute infections with lymphocytic choriomeningitis virus (LCMV), Pichinde virus (PV), vaccinia virus (VV), and murine cytomegalovirus (MCMV). Consistent with the enhanced susceptibility to cell death noted in vitro, we found that bystander CD8 T cells activated with cognate antigen in vivo during acute viral infections underwent markedly reduced proliferation. Virus-induced transient T cell suppression in vivo was not exclusively mediated by Fas-FasL- or TNF-induced AICD or due to an enhanced susceptibility to apoptosis. Instead, immune suppression in vivowas associated with a delayed onset of division, which we found not to be due to a defect in antigen presentation, but rather due to a T cell intrinsic defect. Despite the suppressed proliferation of TCR-stimulated bystander CD8 T cells in vivo, we found an enhancement of the effector functions exerted by bystander CD8 T cells activated during acute viral infections. During acute viral infections or after stimulation with type 1 IFN (IFN-αβ) inducers, some bystander CD8 T cells were sensitized to immediately exert effector functions such as IFN-γ production and degranulation upon stimulation with high affinity cognate antigen. Sensitization of naïve CD8 T cells required self-MHC I and indirect effects of IFN-αβ, while IL-12, IL-18, and IFN-γ were not individually required. IL-15 was not required for the rapid expression of IFN-γ, but was required for up-regulation of granzyme B (GrzB). P14 and OT-I CD8 T cells, which are capable of homeostatic proliferation, could be sensitized by poly(I:C), but HY CD8 T cells, which are poor at homeostatic proliferation, could not, suggesting that the requirement for MHC I may be to present low affinity cryptically cross-reactive self antigens. Sensitized naive CD8 T cells up-regulated the t-box transcription factor Eomesodermin (Eomes), which can regulate these rapid effector functions. In conclusion, we demonstrate in this thesis that acute viral infections impact naïve bystander CD8 T cells such that their response to cognate antigen is altered. Prior to cognate antigen engagement, bystander CD8 T cells up-regulated Eomes, CD122, and GrzB. Following cognate antigen engagement, bystander CD8 T cells rapidly degranulated and expressed the effector cytokine IFN-γ. The ability of bystander CD8 T cells to rapidly exert effector functions may contribute to the resistance of virus-infected individuals to superinfections. Despite these rapid effector functions, the proliferation of TCR-stimulated bystander CD8 T cells was markedly inhibited. This reduced proliferation was found not to be a defect in antigen presentation, but was a T cell intrinsic defect in initiating division. Thus, bystander CD8 T cells were also susceptible to virus-induced immune suppression. It is also likely that virus-specific CD8 T cells that are not activated until later in the response, so-called latecomer CD8 T cells, may also be susceptible to immune enhancement and suppression. Thus, latecomer CD8 T cells would be able to rapidly exert effector functions at the expense of proliferation. Taken together, we propose that during an immune response, due to spatial and temporal gradients of antigen and inflammation, it is likely that a combination of heterogeneous T cells with different signal strengths and sequences of exposure from cytokines and peptide-MHC constitute the total T cell response to pathogens.

Les changements climatiques et leurs impacts sur la biodiversité font aujourd'hui l'objet d'une attention croissante de la part de la communauté scientifique et des gestionnaires des écosystèmes naturels. En effet, le climat influence la biologie et l'écologie des espèces animales et végétales, depuis leur physiologie jusqu'à leur répartition. Les modifications climatiques pourraient donc avoir des répercussions importantes sur les espèces et les assemblages. Au sein des écosystèmes aquatiques continentaux, les poissons de rivière sont des organismes incapables de réguler leur température corporelle et soumis à une variabilité hydrologique importante ainsi qu'à de fortes pressions anthropiques. Leur réponse aux modifications du climat actuelles et à venir a pourtant été encore peu abordée. L'objectif de ce travail de thèse est donc d'évaluer les impacts potentiels du changement climatique sur les poissons des rivières françaises, et plus particulièrement sur la distribution des espèces et la structure des assemblages. Des données fournies par l'Office National de l'Eau et des Milieux Aquatiques ainsi qu'une approche de modélisation basée sur les niches écologiques des espèces (i.e., modèles de distribution) ont été utilisées. Différentes sources d'incertitude ont également été testées dans une approche d'ensembles afin de prendre en compte la variabilité entre les impacts projetés et fournir ainsi une évaluation robuste de ces impacts. La première partie de ce travail a consisté en l'identification des principaux déterminants environnementaux qui structurent la répartition spatiale des espèces de poisson au sein des réseaux hydrographiques. Globalement, il apparaît qu'une combinaison de facteurs climatiques et de variables décrivant l'habitat local et la position des habitats au sein des réseaux hydrographiques est importante pour expliquer la distribution actuelle des espèces. De plus, les espèces ont toutes des réponses différentes aux facteurs de l'environnement. Dans un second temps, nous avons mis en évidence que le choix de la méthode statistique de modélisation de la niche écologique est crucial, les patrons actuels et futurs de distribution prédits étant fortement contrastés selon la méthode de modélisation considérée. Cette dernière s'avère même être la principale source d'incertitude dans les projections futures, bien plus encore que les modèles climatiques de circulation générale et les scénarios d'émission de gaz à effet de serre. La variabilité entre les prédictions issues de plusieurs techniques de modélisation peut être prise en compte par une approche de consensus. Un modèle consensuel basé sur la valeur moyenne de l'ensemble de prédictions est capable de prédire correctement la distribution actuelle des espèces et la composition des assemblages. Nous avons donc choisi de retenir cette approche pour évaluer au mieux les impacts potentiels du changement climatique sur les poissons des rivières françaises à la fin du 21ème siècle. Nous avons montré que la majorité des espèces de poisson pourrait être affectée par les futures modifications du climat. Seules quelques espèces d'eau froide (e.g. truite fario, chabot) pourraient restreindre leur distribution aux parties les plus apicales des réseaux hydrographiques. Au contraire, les espèces tolérant des températures plus élevées pourraient coloniser de nouveaux habitats et étendre ainsi leur répartition. Ces modifications de la distribution des espèces pourraient conduire à un réarrangement des assemblages au niveau taxonomique et fonctionnel. Une augmentation de la diversité locale et de la similarité régionale (i.e., homogénéisation) sont ainsi prédites simultanément. L'ensemble de ces résultats apporte donc des éléments sur la compréhension de la distribution des poissons d'eau douce et sur les conséquences du changement climatique qui peuvent être envisagées. Ce travail fournit ainsi une base aux acteurs de la gestion de la biodiversité afin d'initier des mesures de conservation concrètes. De plus, les considérations méthodologiques développées dans cette thèse sont une contribution importante à l'amélioration des projections issues de modèles statistiques de distribution et à la quantification de leur incertitude
Climate change and its impact on biodiversity are receiving increasing attention from scientists and people managing natural ecosystems. Indeed, climate has a major influence on the biology and ecology of fauna and flora, from physiology to distribution. Climate change may thus have major consequences on species and assemblages. Among freshwater ecosystems, stream fish have no physiological ability to regulate their body temperature and they have to cope with streams' hydrological variability and strong anthropogenic pressures. Yet their response to current and future climate change has been poorly studied. The aim of this PhD thesis is to assess the potential impact of climate change on fish in French streams, mainly on species distribution and assemblages' structure. Data provided by the Office National de l'Eau et des Milieux Aquatiques combined with a modelling approach based on species' ecological niche (i.e., distribution models) have been used. Several sources of uncertainty have also been considered in an ensemble modeling framework in order to account for the variability between projected impacts and to provide reliable estimates of such impact. First, we have identified the main environmental factors that determine the spatial distribution of fish species within river networks. Overall, it appears that a combination of both climatic variables and variables describing the local habitat and its position within the river network is important to explain the current species distribution. Moreover, each fish species responded differently to the environmental factors. Second, we have highlighted that the choice of the statistical method used to model the fish ecological niche is crucial given that the current and future patterns of distribution predicted by different statistical methods vary significantly. The statistical method appears to be the main source of uncertainty, resulting in more variability in projections than the global circulation models and greenhouse gas emission scenarios. The variability between predictions from several statistical methods can be taken into account by a consensus approach. Consensual predictions based on the computation of the average of the whole predictions ensemble have achieved accurate predictions of the current species distribution and assemblages' composition. We have therefore selected this approach to assess the potential impacts of climate change on fish in French streams at the end of the 21st century with the highest degree of confidence. We have found that most fish species could be sensitive to the future climate modifications. Only a few cold-water species (i.e., brown trout, bullhead) could restrict their distribution to the most upstream parts of river networks. On the contrary, cool- and warm-water fish species could colonize many newly suitable habitats and expand strongly their distribution. These changes of species distribution could lead to a rearrangement of fish assemblages both at the taxonomic and functional levels. An increase in local diversity together with an increase in regional similarity (i.e., homogenization) are therefore expected. All these results bring new insights for the understanding of stream fish species distribution and expected consequences of climate change. This work thus provides biodiversity managers and conservationists with a basis to take efficient preservation measures. In addition, methodological developments considered in this PhD thesis are an important contribution to the improvements of projections by statistical models of species distribution and to the quantification of their uncertainty