Rozprawy doktorskie na temat „Anthropogenic pressures”

Die Besiedlung von Gewässern durch Fische, ist neben abiotischen Lebensraumbedingungen auch von der Erreichbarkeit d.h. von der art-spezifischen Ausbreitungsfähigkeit sowie von Wanderhindernissen abhängig. Der erste Teil dieser Arbeit bietet die erste umfangreiche quantitative Analyse von Ausbreitungsmustern und -distanzen von Flussfischen. Aus der Fachliteratur wurden 160 empirische Datensätze aus 71 wissenschaftlichen Studien zur Ausbreitung von 62 Fischarten in Flüssen extrahiert und an leptokurse Wahrscheinlichkeits-Dichte-Funktionen (Dispersal kernel) angepasst. Es konnte bei Fischpopulationen zwischen einer stationären (ca. 2/3) und einer mobilen Komponente (ca. 1/3) unterschieden werden deren Ausbreitungsdistanzen von vier Faktoren abhängig sind: Fischlänge, Form der Schwanzflosse, Fließgewässergröße, betrachtete Zeitspanne. Der zweite Teil dieser Arbeit widmet sich dem neu entwickelten Fischausbreitungsmodell FIDIMO einem GIS-Softwareprogramm zur Modellierung und Simulation der räumlichen und zeitlichen Ausbreitungsmuster von Fischen in Flüssen unter Berücksichtigung von Wanderhindernissen. FIDIMO verknüpft konzeptionelle Überlegungen zu Ausbreitungsmodellen in verzweigten Fließgewässernetzwerken mit empirisch bestimmten leptokursen Fischausbreitungskurven unter ausschließlicher Verwendung von Free and Open Source Software. Im dritten Teil der Arbeit wurde FIDIMO zur Modellierung der Ausbreitung von 17 Fischarten angewendet um die Einflüsse von (i) Habitatqualität, (ii) Ausbreitungsfähigkeit und (iii) Fließgewässer-Fragmentierung auf die Besiedlungsmuster durch Fische zu bestimmen. Die Ergebnisse zeigen, dass die artspezifische Habitatqualität und Ausbreitungsfähigkeit die Besiedlung maßgeblich bestimmen. Dagegen wurde kein signifikanter Einfluss von Barrieren auf das Vorkommen einer Art gefunden. Über längere Zeiträume sinkt der Einfluss von Fischausbreitung auf das lokale Vorkommen einer Fischart während die Habitatqualität relativ wichtiger wird.<br>The colonisation of rivers by fishes is directly linked to abiotic habitat conditions but often impaired by dispersal abilities of fishes and movement constraints such as barriers. The first part of this thesis provides the first comprehensive quantitative analysis of freshwater fish movement while considering fish populations consisting of differently mobile specimens. 160 empirical datasets from 71 studies on the movement of 62 riverine fish species were analysed based on refitted leptokurtic probability-density functions (dispersal kernels). A share of one third and two thirds emerged as a general pattern of the mobile and stationary component of a fish population, respectively. Moreover, four variables were identified primarily determining dispersal distances: fish length, aspect ratio of the caudal fin, river size and time. In the second part of the thesis, the novel fish dispersal model FIDIMO is introduced. FIDIMO provides a GIS-tool for predicting and simulating spatio-temporal patterns of fish dispersal in dendritic river networks considering movement barriers. The fish dispersal model FIDIMO links conceptual considerations on dispersal modelling with empirically observed leptokurtic fish movement patterns and the strengths of geographically explicit modelling in Free and Open Source GIS. In the third part of the thesis, FIDIMO was applied for modelling dispersal of 17 fish species to disentangle the effects of (i) habitat suitability, (ii) dispersal constraints and (iii) network fragmentation on the distribution of river fishes. The results show significant positive effects of both, local-scale habitat quality and species-specific dispersal ability on the distribution of river fishes, whereas no significant effect of barriers influencing the presence of a species could be found. Over longer time periods the importance of dispersal decreased in favour of habitat suitability becoming relatively more relevant in determining species'' presence.

Le maintien et le renouvellement des populations de poissons coralliens dépendent en grande partie du recrutement larvaire, c’est-à-dire de l’installation des larves pélagiques dans les habitats récifaux adultes, et de leur survie après s’être métamorphosées en juvéniles. De plus en plus d’études révèlent que les changements de composition de l’eau, causés par le changement climatique et la pollution, peuvent altérer les capacités sensorielles des poissons coralliens, diminuant leurs aptitudes à localiser des habitats propices (maximisant leur croissance et diminuant leur mortalité) lors de l’installation. Cependant, les mécanismes internes à l’origine de ces phénomènes sont méconnus. Lors de cette thèse, j’ai examiné le recrutement larvaire du poisson chirurgien bagnard Acanthurus triostegus et mis en évidence que les changements écologiques, morphologiques, physiologiques et comportementaux qui s’y déroulent correspondent à une métamorphose contrôlée par les hormones thyroïdiennes (HT). J’ai ensuite analysé comment des stress d’origine anthropique, tels que l’élévation des températures de surface et la pollution par un pesticide d’origine agricole, peuvent perturber sa métamorphose. Lors de cette étape clé de leur cycle de vie, ces perturbations diminuent les taux d’HT, altérant la maturation de leurs organes sensoriels, leurs capacités sensorielles, et augmentant leur mortalité. Cette thèse est donc une analyse holistique de l’impact des perturbations anthropiques sur les processus moléculaires, et les changements histologiques, anatomiques et comportementaux du recrutement larvaire des poissons coralliens. Elle souligne l’importance du système thyroïdien, et invite à une meilleure compréhension des processus endocriniens du recrutement larvaire, dans l’optique d’une amélioration de la conservation des récifs coralliens<br>The persistence and sustainability of coral-reef fish populations depends on the continued larval recruitment, i.e. successful settlement by pelagic larvae into adult reef habitats and post-settlement survival through metamorphosis to a juvenile stage. There is growing evidence that changes to water conditions due to global change and waterborne pollution can impair coral-reef fish sensory abilities to locate settlement habitats that maximize growth while minimizing mortality risk. However, the inner mechanisms of such impairments remain unknown. In this thesis, I have examined the recruitment phase of the convict surgeonfish Acanthurus triostegus, and determined that the ecological, morphological, physiological and behavioral changes occurring at recruitment correspond to a metamorphosis mediated by thyroid hormones (TH). Then, I investigated whether this metamorphosis is prone to endocrine disruption under anthropogenic disturbances such as elevated sea water temperature and agricultural pesticide pollution. I demonstrated that such pressures can reduce TH levels at a critical developmental stage in coral-reef fishes, impairing their metamorphic processes such as intestine remodeling, sensory organ maturation, and sensory abilities acquisition, further increasing their mortality rates. Overall, this thesis is a holistic analysis that addresses molecular, histological, anatomical, and behavioral assays of multiple stressors affecting coral-reef fish recruitment. It indicates the importance of a proper endocrine function during coral-reef fish recruitment, highlighting the need for a better understanding of these processes for coral-reef conservation

Thesis (Ph. D.)--Dept. of Geosciences and School of Computing and Engineering. University of Missouri--Kansas City, 2006.<br>"A dissertation in geoscience and software architecture." Advisor: Wei Ji. Typescript. Vita. Title from "catalog record" of the print edition Description based on contents viewed Nov. 13, 2007. Includes bibliographical references (leaves 248-261). Online version of the print edition.

Mestrado em Gestão e Conservação dos Recursos Naturais - Instituto Superior de Agronomia / Universidade de Évora<br>Free-living nematodes have been and are continually considered excellent bioindicators by several authors. Their high structural and functional diversity makes them more diversified and numerically dominant in aquatic habitats, with a wide distribution ranging from untouched habitats to highly polluted habitats. This fact as called the attention of many researchers who in turn motivated and promoted their use in the evaluation of the quality of water bodies. Farther, studies showed that morphometry and biomass are two important aspects to consider in ecological studies of free-living nematodes. The current study focuses on the investigation of the morphometric attributes of the free-living nematodes of the Tagus estuary (Portugal) in order to relate them to the various environmental conditions of the sediment along the estuary. Therefore, the following null hypothesis was tested: There will be no differences in the nematode morphometric parameters (length, width, L / W ratio and biomass) in the different sections of the estuary. Conclusions led to the rejection of the null hypothesis as significant differences were observed along the sections of the estuary for most of the morphometric attributes measurements taking in consideration the six most abundant genera of nematodes in the Tagus estuary (Terschellingia, Sabatieria, Daptonema, Ptycholaimellus, Viscosia and Anoplostoma). Though salinity, depth, grain size variables and organic matter were the environmental variables that were found to be more correlated with the nematode morphometric attributes variance along the estuary, nematode size and shape at investigated sections most likely reflected differences in quality and quantity of organic material and sediment size of the estuary. Most of the variability in terms of nematode morphometry along the Tagus estuary were verified for the genera Terschellingia leading to the conclusion that this genera can provide better information about the different environmental conditions of the sediment along the Tagus estuary<br>Os nemátodes de vida livre foram e são continuamente considerados ótimos bioindicadores por vários autores. A elevada diversidade estrutural e funcional dos nemátodes de vida livre torna-os o grupo mais diversificado e numericamente dominante em habitats aquáticos, com uma ampla distribuição que varia de habitats intocados a habitats altamente poluídos. Este fato chamou a atenção de muitos investigadores que, por sua vez, motivaram e promoveram o seu uso na avaliação da qualidade das massas de água. Além disso, estudos mostraram que a morfometria e biomassa são dois aspectos importantes a serem considerados em estudos ecológicos de nemátodes de vida livre. O corrente estudo foca-se na investigação dos atributos morfométricos dos nemátodes de vida livre do estuário do Tejo de modo a relacioná-los com as várias condições ambientais do sedimento ao longo do estuário. Para este efeito foi testada a seguinte hipótese nula: Não haverá diferenças nos parâmetros de nemátodes (comprimento, largura, relação C/L e biomassa) em diferentes secções do estuário. As conclusões levaram à rejeição da hipótese nula. Diferenças significativas foram observadas ao longo das seções do estuário para a maioria das medições dos atributos morfométricos dos seis géneros mais abundantes de nemátodes no estuário do Tejo (Terschellingia, Sabatieria, Daptonema, Ptycholaimellus, Viscosia e Anoplostoma). Embora a salinidade, profundidade, tamanho do sedimento e matéria orgânica tenham sido as variáveis ambientais mais correlacionadas com a variância dos atributos morfométricos dos nemátodes ao longo do estuário, o tamanho e a morfologia de nemátodes nas seções investigadas refletiram diferenças na qualidade e quantidade de matéria orgânica e tamanho do sedimento do estuário. A maior parte da variabilidade em termos de morfometria dos nemátodos ao longo do estuário do Tejo foi verificada para o género Terschellingia, levando à conclusão de que este género pode fornecer uma melhor informação sobre as diferentes condições ambientais do sedimento ao longo do estuário do Tejo<br>N/A

Mestrado em Engenharia do Ambiente - Instituto Superior de Agronomia<br>The European Union established a framework for Community action in the field of water policy. Considering the need for the natural resources protection and conservation, the Water Framework Directive 2000/60/EC Directive was adopted, involving the efforts of all Member States in the task of achieving good status for all waters, in which the aim of achieving good ecological state for natural ecosystems can be included. Within this context, the main objectives of this study are: the characterisation and quantification of the degradation degree in the fluvial ecosystem of the Alcoa river drainage basin, and to that end it was used the Predictive Ecological State methodology; and planning restoration actions for the most degraded stretches of the river system which deteriorate under the effect of human actions. Based on the results obtained, a Map of River Corridor Conservation Status was developed for the Alcoa river catchment area with the intend of revealing the degree of degradation of the river streams, and a Map of River Restoration Planning was developed which summarizes the restoration actions to be implement in the drainage basin.

Of all anthropogenic pressures, urbanisation is one of the most damaging, and is expanding in its influence throughout the world. In Australia, 90% of the human population live in urban centres along the eastern seaboard. Before European settlement in the early 1800s, much of the Australia's East coast was dominated by forests. Many of the forest dependent fauna have had to adapt to forest fragmentation and habitat loss resulting from clearing for urbanisation. However, relatively few studies have investigated the impact of urbanisation on biodiversity. This is especially true for the remaining fauna in large metropolitan areas, such as Melbourne, Sydney and Brisbane. The physical and conceptual context of this thesis is the increasing impact of urbanisation and the potentially threatening factors to forest dependent fauna. Bats were selected because they comprise a third of Australia's mammal species, and therefore form a major component of Australia's biodiversity. Very little is known about the ecology and conservation biology of hollow-dependent bats in general, but particularly in urban environments. The study was conducted in Brisbane, south-east Queensland, one of Australia's most biodiverse regions. More than a third of Australia's bat species occur in this region. A large insectivorous bat, the white-striped freetail bat (Tadarida australis), was selected to study two key resources in this urban area - hollow availability and foraging habitat. This thesis also examined if artificial roost habitat could provide temporary roosts for white-striped freetail bats and other insectivorous bats and assessed whether these bat boxes can be used as a conservation tool in urban environments where natural hollow-availability is limited. The white-striped freetail bat is an obligate hollow-dweller and roosted largely in hollows of old or dead eucalypts throughout Brisbane's urban matrix. These roost trees harboured significantly more additional hollow-dependent species compared to control trees of similar age, height, and tree diameter. Roost cavities inside trees often exceeded 30 cm in diameter. Furthermore, maternity colonies used cavities of hollow trunks, which often extended into major branches, to roost in big numbers. Therefore artificial alternatives, such as small bat boxes, may provide temporary shelter for small roosting groups, but are unlikely to be suitable substitutes for habitat loss. Although five bat species used bat boxes during this study, the white-striped freetail bat was not attracted into bat boxes. Roost-switching behaviour was then used to quantify associations between individual white-striped freetail bats of a roosting group. Despite differences in gender and reproductive seasons, the bats exhibited the same behaviour throughout three radio-telemetry periods and over 500 bat-days of radio-tracking: each roosted in separate roosts, switched roosts very infrequently, and associated with other tagged bats only at a communal roost. Furthermore, the communal roost exhibited a hub of socialising between members of the roosting group especially at night, with vocalisation and swarming behaviour not found at any of the other roosts. Despite being spread over a large geographic area (up to 200 km2), each roost was connected to others by less than three links. One roost (the communal roost) defined the architecture of the network because it had the most links. That the network showed scale-free properties has profound implications for the management of the habitat trees of this roosting group. Scale-free networks provide high tolerance against stochastic events such as random roost removals, but are susceptible to the selective removal of hub nodes, such as the communal roost. The white-striped freetail bat flew at high speed and covered large distances in search for food. It foraged over all land-cover types found in Brisbane. However, its observed foraging behaviour was non-random with respect to both spatial location and the nature of the ground-level habitat. The main feeding areas were within three kilometers of the communal roost, predominantly over the Brisbane River flood plains. As the only mammal capable of flight, bats can forage above fragmented habitats. However, as this study showed, hollow-dependent insectivorous bats, including free-tailed bats, are specialised in their roosting requirements. The ongoing protection of hollow-bearing trees, and the ongoing recruitment of future hollow-bearing trees, is essential for the long-term conservation of these animals in highly fragmented landscapes. Furthermore, loss of foraging habitat is still poorly understood, and should be considered in the ongoing conservation of bats in urban environments.

Mestrado em Engenharia do Ambiente - Instituto Superior de Agronomia<br>According to the Water Framework Directive (WFD), which requires Member States to take measures in order to protect, enhance and restore the superficial water bodies, looking to attain a good water quality status, the work at hand aims at assessing the ecological status of the Rio Grande water bodies, by implementing the Predicted Ecological State methodology. This methodology allows the division of the fluvial ecosystem in sections with homogenous features, the identification of its degradation level through the measurement of local anthropogenic pressures and plan rehabilitation measures and actions so as to achieve the goal set by the WFD.

Of all anthropogenic pressures, urbanisation is one of the most damaging, and is expanding in its influence throughout the world. In Australia, 90% of the human population live in urban centres along the eastern seaboard. Before European settlement in the early 1800s, much of the Australia's East coast was dominated by forests. Many of the forest dependent fauna have had to adapt to forest fragmentation and habitat loss resulting from clearing for urbanisation. However, relatively few studies have investigated the impact of urbanisation on biodiversity. This is especially true for the remaining fauna in large metropolitan areas, such as Melbourne, Sydney and Brisbane. The physical and conceptual context of this thesis is the increasing impact of urbanisation and the potentially threatening factors to forest dependent fauna. Bats were selected because they comprise a third of Australia's mammal species, and therefore form a major component of Australia's biodiversity. Very little is known about the ecology and conservation biology of hollow-dependent bats in general, but particularly in urban environments. The study was conducted in Brisbane, south-east Queensland, one of Australia's most biodiverse regions. More than a third of Australia's bat species occur in this region. A large insectivorous bat, the white-striped freetail bat (Tadarida australis), was selected to study two key resources in this urban area - hollow availability and foraging habitat. This thesis also examined if artificial roost habitat could provide temporary roosts for white-striped freetail bats and other insectivorous bats and assessed whether these bat boxes can be used as a conservation tool in urban environments where natural hollow-availability is limited. The white-striped freetail bat is an obligate hollow-dweller and roosted largely in hollows of old or dead eucalypts throughout Brisbane's urban matrix. These roost trees harboured significantly more additional hollow-dependent species compared to control trees of similar age, height, and tree diameter. Roost cavities inside trees often exceeded 30 cm in diameter. Furthermore, maternity colonies used cavities of hollow trunks, which often extended into major branches, to roost in big numbers. Therefore artificial alternatives, such as small bat boxes, may provide temporary shelter for small roosting groups, but are unlikely to be suitable substitutes for habitat loss. Although five bat species used bat boxes during this study, the white-striped freetail bat was not attracted into bat boxes. Roost-switching behaviour was then used to quantify associations between individual white-striped freetail bats of a roosting group. Despite differences in gender and reproductive seasons, the bats exhibited the same behaviour throughout three radio-telemetry periods and over 500 bat-days of radio-tracking: each roosted in separate roosts, switched roosts very infrequently, and associated with other tagged bats only at a communal roost. Furthermore, the communal roost exhibited a hub of socialising between members of the roosting group especially at night, with vocalisation and swarming behaviour not found at any of the other roosts. Despite being spread over a large geographic area (up to 200 km2), each roost was connected to others by less than three links. One roost (the communal roost) defined the architecture of the network because it had the most links. That the network showed scale-free properties has profound implications for the management of the habitat trees of this roosting group. Scale-free networks provide high tolerance against stochastic events such as random roost removals, but are susceptible to the selective removal of hub nodes, such as the communal roost. The white-striped freetail bat flew at high speed and covered large distances in search for food. It foraged over all land-cover types found in Brisbane. However, its observed foraging behaviour was non-random with respect to both spatial location and the nature of the ground-level habitat. The main feeding areas were within three kilometers of the communal roost, predominantly over the Brisbane River flood plains. As the only mammal capable of flight, bats can forage above fragmented habitats. However, as this study showed, hollow-dependent insectivorous bats, including free-tailed bats, are specialised in their roosting requirements. The ongoing protection of hollow-bearing trees, and the ongoing recruitment of future hollow-bearing trees, is essential for the long-term conservation of these animals in highly fragmented landscapes. Furthermore, loss of foraging habitat is still poorly understood, and should be considered in the ongoing conservation of bats in urban environments.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>Australian School of Environmental Studies<br>Full Text

The study of ocean sunfishes has for decades been practically synonymous with the study of Mola mola, recently listed as ‘vulnerable’ on a global scale by the International Union for Conservation of Nature. The concerns are high levels of fisheries bycatch worldwide, however sunfish bycatch is rarely identified to species level anywhere, perhaps as a long legacy of taxonomic confusion in the sunfish taxonomy has rendered identification to species level challenging. This includes the Australian and New Zealand longline fisheries, where sunfishes are listed at “High Risk” due to data deficiency. In the popular sunfish SCUBA dive tourism off Bali, Indonesia, another type of anthropogenic pressure is manifested through diver crowding, preventing sunfish from interacting with cleaner-fish on the local reefs. The consequences are difficult to gauge due to a paucity of information on this highly seasonal phenomenon, but have motivated discussions of sunfish protection by Indonesian authorities. In this study, the species identities and zoogeographies of the little studied sunfishes in Australia and New Zealand were explored through biopsy sampling in the longline fisheries, and by reviewing museum collections across both countries. Specimen IDs were established phylogenetically and/or morphologically. Combined, the results revealed a new species of ocean sunfish, Mola tecta, which was diagnosed and described. Furthermore, the results showed that three large species of sunfish dominate the tropical, subtropical/warmtemperate and cold-temperate waters of Australia and New Zealand; Masturus lanceolatus, Mola alexandrini and Mola tecta, respectively. Mola mola appears to be rare. These results imply that the long-term fisheries observer sunfish bycatch data from both countries consists of a mix of species. Bycatch rate analyses within four fishing grounds sub-areas, each presumably dominated by one species of sunfish, did not reveal downwards trends over the 10 - 12 year periods, for which data were available. In the Bali tourism industry, the sunfish species identity was confirmed molecularly and morphologically as Mola alexandrini. The strong seasonality in diver sightings was documented through sunfish encounter rates based on operator logs. The results revealed that the 2015 sunfish season (August – October/November) lagged by ~1 month the seasonal change in intensity of two major oceanographic features of the area, established from in situ and satellite sea surface temperature data. Data from eight satellite tagged sunfish revealed a high affinity by four fish to the dynamic Lombok Straight during the sunfish season, however, at least one other fish left the area. Overall, temperature emerged as an unlikely main driver of the sunfish seasonality, which is instead presumably driven by an increase in sunfish prey availability, associated with the seasonal cold-water upwelling. Overall, these findings have provided much needed clarity to the taxonomy and phylogenetic relationships of the genus Mola, and demonstrated the need for species-level investigations of fisheries bycatch globally to inform fisheries risk assessments. Furthermore, the results provided important information on the sunfish seasonality off Bali to inform tourism management decisions.

Les éléments génétiques mobiles (EGM) sont des structures génétiques fréquemment associées à la dissémination de gènes de résistance aux antibiotiques (GRA). Dans ce travail, nous avons utilisé deux EGM comme « proxies », les intégrons de classe 1 et les plasmides IncP-1, afin de mieux comprendre (i) le devenir possible des GRA une fois relargués dans un écosystème fluvial (l’Orne, France), ainsi que (ii) l’effet des pressions anthropiques sur leur persistance. À partir d'analyses de l'eau des rivières, nous avons pu montrer que les deux EGM ne se comportaient pas de la même manière. L'entrée des intégrons de classe 1 dans le système fluvial semblait être diffuse plutôt que ponctuelle, tandis que l'abondance du plasmide IncP-1 est relativement stable le long de la section de la rivière étudiée (23 km), indiquant ainsi une origine plutôt indigène. Les intrants anthropiques tels que les stations d’épuration des eaux usées ne semblent pas affecter l’abondance des EGM en raison d’un niveau trop élevé de dilution des effluents. Par ailleurs, il est intéressant de noter que les bactéries porteuses d’EGM semblaient être enrichies sur les matières en suspension, susceptibles de servir de véhicule pour amener des communautés de bactéries plus riches en EGM vers les sédiments. L'analyse de deux carottes de sédiment indique clairement que seules les couches supérieures présentent un niveau élevé de bactéries porteuses d’EGM. Ces abondances diminuent dans les couches plus profondes où seules des zones ponctuelles présentent des microréservoirs avec des abondances d’EGM plus élevées. Pour une carotte sédimentaire au moins, nous avons pu montrer que l'abondance relative d’EGM corrèle négativement la présence de polluants tel que le plomb ou certains HAP<br>Mobile genetic elements (MGEs) are genetic structures frequently associated to the dissemination of antibiotic resistance genes (ARGs). In this work, we used two of them as proxies, class 1 integrons and IncP-1 plasmids, to better understand (i) the possible fate of ARGs once released in a river ecosystem (Orne, France), as well as (ii) the effect of anthropogenic pressures on their persistence. From river water analyses, we could show that the two MGEs do not behave the same way. The entry of class 1 integrons in the river system appeared to be diffuse rather than punctual, while the abundance of IncP-1 plasmid is relatively stable along the river section studied (23 km) thus indicating a rather indigenous origin. Anthropic inputs such as wastewater treatment plant did not seem to affect the abundance of MGEs because a too high level of effluent dilution. Interestingly, MGE-bearing bacteria appeared to be enriched on suspended material, which is likely to serve as a vehicle to drive MGE-richer communities of bacteria toward the sediments. The analysis of two sediment cores clearly indicates that only the top layers displayed an elevated level of MGE-bearing bacteria. These abundances decrease in deeper layers where only localized zones display micro-reservoirs of elevated MGE abundances. For one sediment core at least, we could show that the relative abundance of MGE negatively correlates with pollutants such as lead or certain PAHs

Dans la plupart des mers et des océans, la zone littorale est dominée par de grandes Phaeophyceae (Laminariales et Fucales) qui jouent un rôle écologique majeur dans la structuration et le fonctionnement de l’écosystème (fourniture d’habitats, de nourri ture, de frayères et de nurseries pour de nombreuses espèces). En Méditerranée, ce sont les espèces de Fucales appartenant aux genres Cystoseira C. Agardh et Sargassum C. Agardh qui sont les principales espèces structurantes du stade climacique de la végétation photophile de la zone littorale (de la surface jusqu’à 70-80 m de profondeur dans les eaux les plus claires). L’étude diachronique menée dans ce travail de thèse à partir des premières observations scientifiques exploitables (18ème siècle) est une première en Méditerranée sur autant de linéaire de côte (~ 2 970 km à l’échelle 2 500ème). Les résultats obtenus par l’analyse des données historiques et actuelles de distribution des Fucales le long des côtes françaises différent suivant les espèces étudiées, aussi bien en ce qui concerne l’état de conservation des populations que les causes impliquées dans leur régression. Dans l’ensemble, les forêts de Cystoseira et de Sargassum ont régressé de façon drastique en Méditerranée française. L’écosystème a souvent basculé (regime shift) vers un état stable alternatif (Multiple Stable State) de type barren ground, caractérisé par la dominance de macrophytes calcifiés encroûtants (corallinacées) et d’oursins<br>Throughout the world, coastal ecosystems are severely affected by the cumulative impact of increasing human pressure (e.g. destruction of habitats, pollution, non-indigenous species, overfishing, coastal aquaculture and global warming). Different foms of stress act over time and in unison, with a possible synergistic effect, on species, ecosystems and their ability to deliver ecosystem services. Along temperate rocky coasts worldwide, large canopy-forming kelps (Laminariales, Phaeophyceae, Ochrophyta) and fucoids (Fucales, Phaeophyceae, Ochrophyta) represent the dominant species in pristine environments. In the Mediterranean Sea, species of the genus Cystoseira C. Agardh and Sargassum C. Agardh are habitat-forming species dominating several assemblages from the littoral fringe down to the lower sublittoral zone (0 down to 70-80 m depth). The present diachronic study based on the first usable scientific observations (18th century) is the first in the Mediterranean to cover such a long stretch of coastline (~ 2970 km at 1/2 500 scale). The results obtained by the analysis of historical and current data on the distribution of Fucales along the French coast differ according to the species studied, both with regard to the conservation status of populations and the causes involved in their regression. The general loss of habitat-structuring species is worrying. We are witnessing a typical regime shift with a replacement of macroalgal forests by less structured algal assemblages dominated by Corallinales or by barren grounds dominated by encrusting species, filamentous algae and sea urchins

La gestion et la conservation des littoraux exigent la synthèse de données géographiques sur la répartition et l'intensité des activités humaines et sur le cumul de leurs impacts sur les écosystèmes côtiers marins et terrestres. Actuellement, à l’échelle du littoral européen ou français, peu d’études offrent une vision globale des risques sur les habitats terrestres et marins. Comment s’y répartissent les pressions humaines sur la biodiversité ? Comment mieux définir le système littoral et ainsi améliorer la gestion de ce territoire ? A l’échelle européenne, à l’aide de 24 pressions anthropiques issues d’EUROSTAT sur une classification NUTS, nous avons découpé le littoral terrestre européen en bandes de 10 km jusqu’à une limite de 100 km et identifié la répartition et l’intensité relative des pressions sur les environnements côtiers. Nous avons ainsi montré que la grande majorité des pressions se situent directement sur le trait de côte et les 30 premiers kilomètres, puis diminue fortement jusqu’à la limite des 100 km. Ce découpage du littoral européen nous a aussi permis, à l’aide d’analyses factorielles des correspondances couplées à de la classification hiérarchique ascendante, de diviser les territoires littoraux en 4 groupes cohérents présentant les mêmes pressions et intensités relatives à l’échelle de l’Europe. A l’échelle française, nous avons également développé un modèle spatial pondéré par dires d’experts basé sur la géolocalisation de 15 pressions anthropiques pour 81 habitats biophysiques marins et terrestres présents sur les littoraux français métropolitains. L’information est synthétisée sous la forme de score appliqué à un maillage composé de 26000 cellules de 25 km². Cette méthode de scoring cumulative, dans un modèle additif des impacts anthropiques, nous montre les aires à risques à la fois sur le territoire marin et terrestre. Encore une fois, les zones les plus affectées par les perturbations humaines sont les plus proches du littoral. A contrario, les zones les moins affectées sont celles avec une bathymétrie forte et celles avec une élévation importante. Nous avons finalement développé un site web participatif qui comporte de la SIG intégrée pour permettre la collecte et la diffusion de l’analyse de ces pressions anthropiques sur la France métropolitaine en suivant notre modèle additif et permet à des échelles plus locales de restituer notre analyse à tout type d’utilisateur. Au final, peu de zones ne sont pas affectées par les activités humaines (0,1%) et au contraire, une fraction importante présente de très forts risques (4,8%). Les risques sont de plus en plus forts en se rapprochant du trait de côte. Ces analyses et les cartes développées sont des outils permettant de mieux comprendre les enjeux de conservation pour la mise en œuvre d’une gestion des socio-écosystèmes littoraux et permettront de mieux cibler les priorités dans la conservation de notre territoire à échelle continentale, nationale ou locale<br>Coastal management and conservation require the synthesis of geographic data on the distribution and intensity of human activities and their combined impacts on marine and terrestrial coastal ecosystems. Currently, across the European or French coasts, few studies provide a global view of risks on terrestrial and marine habitats. How are human pressures on biodiversity distributed? How to define the littoral system and thus improve management of this territory? At the European level, using 24 human pressures from EUROSTAT across the NUTS classification, we cut the European coasts in strips of 10 km to a limit of 100 km and identified the distribution and relative intensity pressures on coastal environments. We have shown that the great majority of the pressures occurs directly on the coastline and in the first 30 kilometers, then decreases sharply to the limit of 100 km. This division of the European coasts has also allowed us to use factorial correspondence analyses coupled with a hierarchical cluster analysis to divide the coastal territories in 4 coherent groups with the same pressures and relative intensities across Europe. At the French level, we have also developed a spatial model weighted by expert opinions based on geolocation of 15 human pressures on 81 marine and terrestrial biophysical habitats present on the metropolitan French coasts. The information is synthesized in the form of impact score applied to a mesh composed of 26000 cells (25 km²). This method of cumulative anthropogenic impacts scoring in an additive model shows areas with higher risks on both the marine and land territory. Again, the most affected areas by the human disturbances are close to the coast. Conversely, the least affected areas are those with a strong bathymetry and those with a significant elevation. We finally developed a participatory website that includes integrated GIS that allows the collection and dissemination of analysis of these human pressures on France following our additive model and allows at more local scales to return our analysis from any type of user. In the end few areas are not affected by human activities (0.1%) and a rather large fraction present very high risk (4.8%). The nearer the coastline, the more the risks are high. These analyses and maps are tools that give better understanding of conservation issues for the implementation of a socio-ecosystems coastal management and that will target the priorities in the conservation of our territories at a continental, national or local scale

Le déclin mondial des anguilles tempérées est lié aux effets synergiques de multiples pressions anthropiques. Cependant, la complexité du cycle de vie des anguilles et leurs incroyables capacités d’adaptation font qu’il est très difficile de connaître le poids relatif de chacune des pressions. Les anguilles tempérées sont trois espèces catadromes qui ont de très grandes aires de répartition pendant leurs phases de croissance continentales. Leurs panmixies et les longues dérives larvaires passives sont des freins aux adaptations locales, cependant on observe des patrons spatiaux de traits d’histoire de vie corrélés aux gradients environnementaux, à l’échelle du bassin versant et de son aire de répartition. Ce doctorat vise à (i) démontrer si ces patrons spatiaux d’histoire de vie sont le résultat de deux réponses adaptatives : le polymorphisme génétique et la plasticité phénotypique adaptative, et (ii) à réévaluer l’effet des différentes composantes du changement global en prenant en compte ces réponses adaptatives. Dans ce cadre, GenEve el, un modèle d’optimisation individu-centré a été développé. Ce modèle postule que la sélection de l’habitat dépendant du génotype et la plasticité phénotypique sont deux mécanismes permettant de faire face à l’hétérogénéité environnementale. Avec de telles hypothèses, le modèle permet de reproduire les patrons spatiaux observés concernant la longueur à l’argenture, le sexe-ratio et la distribution des écotypes. Par la suite, différents types des pressions anthropiques - les pêcheries de civelles et d’anguilles argentées, les obstacles à la migration de montaison et les mortalités dues aux turbines hydroélectriques - ont été intégrés dans le modèle.L’objectif a été d’évaluer leurs impacts sur l’échappement, à la fois en nombre, mais aussi sur différents attributs comme le sexe-ratio, la répartition entre génotypes, la longueur à l’argenture moyenne, et la production globale d’oeufs. Les résultats montrent que la pression qui induit la plus forte mortalité directe n’a pas forcément la plus forte influence sur la biomasse féconde et n’exerce pas nécessairement la pression sélective la plus forte sur les écotypes. Le modèle met aussi en évidence que la plasticité phénotypique peut être source de résilience pour la population et qu’elle atténue l’effet de certaines pressions, mais pas de toutes. Cela suggère également que la gestion ne doit pas seulement se concentrer sur les nombres de survivants et les mortalités directes, mais aussi sur la protection de la diversité au sein des populations. Finalement, un modèle démo-génétique est décrit pour résumer notre compréhension des populations d’anguilles. Un tel modèle pourra être utilisé à l’avenir pour explorer les conditions écologiques dans lesquelles le polymorphisme génétique et la plasticité phénotypique ont été sélectionnés à travers des générations et fournir de nouvelles recommandations pour la conservation des espèces d’anguilles en voie d’extinction<br>The worldwide decline of temperate eels is due to a synergistic combination of several anthropogenic pressures. However, eels display very specific life-cycles and amazing adaptation capacities that impair our ability to assess the relative effects of each pressure. Temperate eels are three catadromous species with large spatially distribution area during their continental growth stage. Their panmixia and the passive larval drifts impair the possibility of local adaptation; however life history spatial patterns are correlated with environmental gradients at both river catchment and distribution area scales. ThisPhD aims (i) to explore whether these life history spatial patterns may result from two adaptive responses: genetic polymorphism and adaptive phenotypic plasticity, and (ii) to revisit the effect of different components of global change in consideration to these adaptive responses. In this context,GenEveel, an individual-based optimization model was developed. The model postulates that genetic dependent habitat selection and phenotypic plasticity are mechanisms to address environmental heterogeneity. With such assumptions, the model was able to mimic observed spatial patterns in length-at-silvering, sex ratio and distribution of ecotypes. Moreover, different types of anthropogenic pressures (glass eel fishery, silver eel fishery, obstacles to upstream migration, and mortality due to hydropower facilities) were integrated in the model. Then, the model was used to assess their impacts on the number of escapees and their attributes: sex ratio, repartition between genotypes, mean lengthat-silvering, and overall egg production. The results showed that the pressure that induces the highest direct mortality has not necessarily the greatest influence on the spawning biomass and does not necessarily exert the strongest selective pressure on the ecotypes. This demonstrates that phenotypic plasticity can be a source of resilience for the population and mitigates the effect of some but not all the pressures. It also suggests that management should not only focus on numbers and direct mortalitybut on the preservation of diversity within populations. Finally, a demo-genetic model is described summarizing our understanding of eel populations. Such model can be used in the future to explore the ecological conditions in which genetic polymorphism and phenotypic plasticity have been selected through generations and provide new insights for the conservation of endangered eel species

During the past two centuries, human activities have greatly modified the exchange of carbon and nutrients between land, atmosphere, freshwater bodies, coastal zones and open ocean. This PhD thesis focuses on different aspects of carbon cycle, considering three case study for the evaluation of the effects of anthropogenic pressure and of the natural evolution of carbon cycle. The first case study focuses on anthropogenic impacts on contaminated coastal areas. These environments connect terrestrial and oceanic systems, and are highly subjected to anthropogenic pressure. An example of a contaminated coastal area is the Mar Piccolo of Taranto (Ionian Sea) and the results of two published papers are reported. In the first paper, the results of the analysis of nutrients and carbon fluxes at sediment-water interface showed that the multi-contamination of both inorganic and organic pollutants in the sediments is potentially transferable to the water column and to the aquatic trophic chain. On the other hand, in the second paper, the results of the analysis of a long time series of chemical-physical characteristics of the water column highlighted that the implementation of sewage treatment plants has positively affected the trophic status of the Mar Piccolo from being relatively eutrophic to moderately oligotrophic. The increase of atmospheric CO2 concentration has been recognised as one of the main causes of climate change. Carbon capture and storage technology (CCS) is expected to play a key role among mitigation strategies by reducing CO2 emissions into atmosphere from fossil fuel combustion. Although leakages from well-engineered storage sites are not expected, the environmental impacts related to potential CO2 seepages are a major issue for the acceptance of this approach and should be carefully monitored. Since different carbon sources have different δ13C values, the aim of the second case study is the evaluation of phytoplankton stable carbon isotopes as a tool for effective early warning of CO2 leakage from CCS. Two culture experiments were conducted under controlled conditions for monitoring δ13C changes in the diatom Thalassiosira rotula during growth in two different media. The isotopic composition of microalgae grown in natural seawater (NAT) was compared to that of diatoms grown in an artificial seawater (ASW), supplied with industrial CO2 and characterised by strongly 13C-depleted dissolved inorganic carbon values. The uptake of inorganic carbon in ASW resulted in a rapid and significant change in microalgae δ13C values, whereas in NAT phytoplankton δ13C did not show important deviations from the starting value, confirming the effectiveness of phytoplankton δ13C as a tool for detecting different CO2 sources. The third case study aims at a better understanding of carbon cycle, as the rate of changes not only depends on human activities, but also on natural biogeochemical processes. Marine dissolved organic matter (DOM) plays a crucial role in oceanic carbon storage, and the extent of its contribution on carbon sequestration depends on its bioavailability. In this study, a plug-flow bioreactor approach has been tested in order to evaluate DOM availability for microbial community in the Gulf of Trieste (Northern Adriatic Sea) by the analysis of dissolved organic carbon (DOC), nitrogen (DON) and phosphorus (DOP) degradation and nutrient uptake. The bioreactor approach confirmed to be useful for bioavailable DOC assessment, but further research is needed for confirming its effectiveness for defining DON and DOP bioavailability and nutrient utilisation.

L’ichtyofaune est encore peu utilisée en bioindication sur les plans d’eau, alors que la demande des gestionnaires est forte, notamment dans le contexte de la mise en œuvre de la Directive Cadre Européenne sur l’Eau. L’objectif de cette thèse est d’analyser la réponse de l’ichtyofaune à diverses pressions anthropiques, afin de définir des variables biologiques de bioindication et construire un indice rendant compte de l’état écologique des lacs naturels et des retenues français. Plusieurs questions sont successivement abordées.En première analyse, les possibilités de sélection de métriques répondant à des pressions s’exerçant sur le bassin versant sont explorées par une approche typologique. L’analyse consiste à effectuer des classifications des plans d’eau, puis à établir, au sein de chaque groupe homogène d’un point de vue environnemental, des régressions linéaires entre les métriques candidates et les pressions. Les résultats montrent la pertinence de l’ichtyofaune en bioindication sur ces milieux, mais mettent en exergue des limites à cette approche typologique. Ainsi, afin de tester la possibilité de construction d’un bioindicateur commun aux lacs naturels et aux retenues, une méthode alternative dite « site spécifique » a ensuite été développée. Une modélisation statistique a été appliquée pour contrôler l’effet de l’environnement naturel sur les communautés piscicoles lacustres. Cette analyse montre que les métriques piscicoles répondant aux pressions sont différentes entre les deux types de milieux. La dernière étape, explique le développement d’un indicateur, construit sur le principe de la mesure d’un écart à la référence, en se basant sur une approche de type statistique par hindcasting. Cette méthode encore peu utilisée permet de s’affranchir de la sélection de sites de référence en France en modélisant les conditions biologiques de référence, i.e., telles qu’elles seraient en l’absence de pression anthropique. Les caractéristiques des communautés piscicoles des sites non perturbés sont ensuite comparées à celles des sites plus ou moins impactés par des pressions anthropiques. Ont été considérées ici les pressions s’exerçant à l’échelle du bassin versant et localement sur les plans d’eau. Suivant ce protocole, un indice poisson lacustre issu de la combinaison de métriques répondant conjointement à des pressions anthropiques globales et locales est proposé pour les lacs naturels et pour les retenues.Les avancées de ce travail et les perspectives sont ensuite discutées au regard du contexte européen de la gestion des milieux aquatiques<br>Fish communities remain underused in the domain of lentic ecosystem bioindication, even though water managers need such tools in the current context of the Water Directive Framework. The objective of this thesis was to analyse the fish communities’ response to various anthropogenic pressures, in order to define the candidate biological variables in bioindication and to develop an index to evaluate the ecological status of French natural lakes and reservoirs. Several questions are raised.First of all, the means available to select fish-based metrics responding to catchment-scale anthropogenic pressures are analysed using a typological approach. This analysis consists in classifying lentic ecosystems using classifications, and then, within each homogenous group of ecosystems identified based on environmental criteria, performing linear regressions between candidate fish-based metrics and anthropogenic pressures. The results clearly show that fish communities could be used as good bioindicators for the lentic ecosystems, but they also underline the limits of typological approaches.To test how a bioindicator shared by natural lakes and reservoirs could be developed, an alternative site-specific method was subsequently developed. Statistical modeling was applied to control the natural environmental effects on lentic fish communities. This analysis shows that fish-based metrics responding to catchment-scale anthropogenic pressures differ in the two types of lentic ecosystems.The last part reports the development of an index, based on the reference condition approach, using a hindcasting statistical approach. This method, still infrequently used, enables one to sidestep the problem related to the selection of reference sites in France. Furthermore, this method allows modeling biological reference conditions, i.e. conditions without anthropogenic pressures. Fish communities’ characteristics are then compared for both undisturbed sites and sites that are more or less impacted by anthropogenic pressures. Both catchment-scale and local anthropogenic pressures were considered in this analysis. Following this protocol, a lake fish-based index resulting from the combination of metrics that respond jointly to global and local anthropogenic pressures was developed for natural lakes and reservoirs. Finally, the advances made as a result of this research and its perspectives are discussed with regards to the European context of aquatic ecosystem management

La gestion et la conservation des lacs de haute montagne Pyrénéens dans le contexte actuel du changement climatique et de l’augmentation de la pression anthropique nécessitent une connaissance approfondie de leur fonctionnement biogéochimique. Dans cette thèse, cinq campagnes d’échantillonnage ont été réalisées (2017-2019) dans plus de 20 lacs alpins. L’analyse d’échantillons d’eau nous a permis d’étudier les teneurs, les profils en profondeurs, la répartition géographique, et les variations saisonnières de nombreuses caractéristiques physico-chimiques et biogéochimiques. Le cycle du dioxyde de carbone (CO2) et le devenir des Eléments Traces Potentiellement Dangereux (PHTEs) ont été étudiés. Le mercure (Hg) a été particulièrement étudié au travers du développement d’une procédure analytique pour la détermination de concentrations en traces dans les eaux naturelles et de recherches biogéochimiques sur la distribution et le devenir des espèces du Hg dans la colonne d’eau, et dans des archives de sédiments.La procédure développée pour analyser l’alcalinité totale (TA) et le carbone inorganique dissous (DIC) nous a permis de déterminer les autres paramètres du système du CO2, le pH et la fugacité du CO2 (fCO2). Les spécificités du substrat rocheux apparaissent essentielles pour l’état d’acidification des lacs étudiés. De plus, les valeurs de fCO2 obtenues montrent que les lacs sont des sources de CO2 pour l’atmosphère.La mesure de divers paramètres physico-chimiques nous a permis de classer les lacs en fonction de leur géochimie de l’eau mettant en évidence l’importance de l’état trophique des lacs, des caractéristiques géologiques et des apports atmosphériques. La présence, les sources et le comportement des PHTEs ont été étudiés, démontrant un contraste entre les apports géologiques et atmosphériques. Le suivi intensif a démontré que certains PHTEs sont très sensibles aux changements environnementaux comme la température et les conditions redox.La mesure des concentrations de Hg total dans les systèmes aquatiques reste complexe et il est nécessaire de développer des méthodes analytiques moins coûteuses et faciles d’utilisation. La méthode développée et optimisée dans ce travail a été appliquée avec succès et a montré une bonne limite de détection et une excellente répétabilité. La spéciation du Hg dans la colonne d’eau a démontré l’état intact et la dynamique des lacs Pyrénéens. L’homogénéité dans les concentrations de Hg total non-gazeux a confirmé l’absence de sources locales et l’utilisation potentielle de ces écosystèmes en tant que sentinelles de la contamination régionale et globale du Hg. Alors que lemercure inorganique (iHg) n’a pas montré de variations saisonnières, le monométhylmercure (MMHg) a été significativement plus élevé en automne 2018 et le mercure gazeux dissous (DGM) a fortement varié parmi les lacs. Les expérimentation in-situ ont confirmé les conditions qui favorisent la méthylation (eaux anoxiques stratifiées), la déméthylation et la photoréduction (intense lumière UV) du Hg.L’analyse des archives de sédiments a mis en lumière les tendances temporelles des taux d’accumulation du Hg (HgARs), avec une augmentation progressive depuis le 16ème siècle et l’industrialisation, reflétant la production de Hg dans les mines d’Almadén. Les isotopes stables du Hg permettent de tracer certaines sources anthropiques ainsi que les variations climatiques passées.Globalement, les changements environnementaux dans les écosystèmes des lacs, provoqués à la fois par les conditions climatiques (température, intensité lumineuse) et la pression anthropique (apports atmosphériques, eutrophisation, CO2 atmosphérique) sont susceptibles d’entrainer des répercussions importantes parmi le CO2, certains PHTEs et le cycle biogéochimique du Hg dans les écosystèmes montagnards<br>The management and conservation of Pyrenean high mountain lakes within the current context of climate change and increasing anthropogenic pressure require detailed knowledge of their biogeochemical functioning. In this doctoral thesis, five sampling campaigns were carried out (2017-2019) in more than 20 alpine lakes. The analysis of water samples allowed us to study the occurrence, the depth profiles, the geographical distribution and the seasonal trends of a large array of physico-chemical and biogeochemical parameters. Specifically, the cycle of carbon dioxide (CO2) and the fate of Potentially Harmful Trace Elements (PHTEs) were investigated. The mercury (Hg) was specially studied through the development of an analytical procedure for the measurement of trace concentrations in natural waters and through biogeochemical investigations on the distribution and the fate of Hg species in the water column, as well as in sediment archives.The new and robust procedure developed in this work to measure the total alkalinity (TA) and the dissolved inorganic carbon (DIC) allowed us to determine the other two parameters of the CO2 system, the pH and the fugacity of CO2 (fCO2). The bedrock characteristics of the watershed appear to be the most important parameters influencing the acid status of the studied lakes. Moreover, obtained fCO2 values indicate that lakes are sources of CO2 for the atmosphere.The measurement of various physico-chemical parameters allowed us to discriminate and classify the studied lakes according to their water geochemistry, highlighting the importance of the trophic status of the lakes, the geological background and the atmospheric inputs. The occurrence, sources and behaviour of the PHTEs were investigated with evidence of a contrast between geological and atmospheric inputs. Intensive monitoring revealed some PHTEs to be highly sensitive to environmental changes such as temperature and redox conditions.Monitoring natural concentrations of total Hg in aquatic systems remains a difficult challenge and there is a need for the development of low cost and easy handling analytical methods. The method for analysis of trace Hg concentrations developed and optimized in this work was successfully operational and exhibits a suitable limit of detection and an excellent reproducibility. Hg speciation results in the water column demonstrated the pristine state and the dynamic of the Pyrenean lakes. The homogeneity in the non-gaseous total Hg concentrations in the studied lakes confirmed the absence of local sources and the potential use of these ecosystems as sentinels of regional to global Hg contamination. While inorganic mercury (iHg) did not show seasonal variations, monomethylmercury(MMHg) was significantly higher in autumn 2018 and dissolved gaseous mercury (DGM) varied strongly within and among lakes. In-situ experiments confirmed the conditions that promote Hg methylation (stratified anoxic waters), demethylation and photoreduction (intense UV light).The historical Hg record in sediment archives highlighted temporal trends in Hg accumulation rates (HgARs) with a progressive increase since the 16th Century and the industrialization, mirroring the Hg production in Almadén mines (Southern Spain). Besides, Hg stable isotopes allow the identification of distinct anthropogenic sources as well as past climate variability.Overall, environmental changes in lake ecosystems, induced by either climatic conditions (temperature, light intensity) or anthropogenic pressure (atmospheric inputs, eutrophication, atmospheric CO2) are likely to produce significant impacts among CO2, specific PHTEs and Hg biogeochemical cycles in mountainous ecosystems

A method to predict spatial variations in the peak pressure level of impulsive low frequency anthropogenic signal propagating in marine environments is presented. The method is based on the correlation between the peak pressure level and the sound exposure level, and the application of extreme value theory to estimate fluctuations of the peak pressure around its mean value in varying ocean environments. The method was examined using signals from offshore seismic surveys and pile driving.

Робота публікується згідно наказу ректора від 21.01.2020 р. №008/од "Про перевірку кваліфікаційних робіт на академічний плагіат у 2019-2020 навчальному році". Керівник проекту: доцент кафедри екології, к.т.н., Радомська Маргарита Мирославівна<br>Object of research: change in the composition of atmospheric air under the influence of anthropogenic activity Subject of research: the level of air pollution Aim оf research: to assess the ecological state of the city of Kherson, to estimate the anthropogenic load on the city using bioindication methods. Methods of research – information search, analysis and synthesis of information, comparative analysis, mapping, visual observations, method of phytoindication, method of lichen indication. The practical value of the work is to determine the anthropogenic impact on the city and the environment. Creation of a map of anthropogenic load on the city and maps of city pollution. The results of the thesis can be used in the course of research and in practice by both local residents and environmental experts. Information of the thesis can serve the development of the environmental awareness of city residents.

Робота публікується згідно наказу ректора від 21.01.2020 р. №008/од "Про перевірку кваліфікаційних робіт на академічний плагіат у 2019-2020 навчальному році". Керівник проекту: доцент кафедри екології, к.т.н., Радомська Маргарита Мирославівна<br>Object of research: change in the composition of atmospheric air under the influence of anthropogenic activity Subject of research: the level of air pollution Aim оf research: to assess the ecological state of the city of Kherson, to estimate the anthropogenic load on the city using bioindication methods. Methods of research – information search, analysis and synthesis of information, comparative analysis, mapping, visual observations, method of phytoindication, method of lichen indication. The practical value of the work is to determine the anthropogenic impact on the city and the environment. Creation of a map of anthropogenic load on the city and maps of city pollution. The results of the thesis can be used in the course of research and in practice by both local residents and environmental experts. Information of the thesis can serve the development of the environmental awareness of city residents.

Il cambiamento climatico è considerato una delle minacce più gravi per la terra e gli ecosistemi acquatici e cresce la preoccupazione per gli effetti che il riscaldamento globale può avere sulle comunità biologiche. Negli ultimi anni, diversi studi hanno evidenziato la sensibilità dei corpi idrici alle fluttuazioni climatiche. Gli organismi zooplanctonici, caratterizzati da piccole dimensioni e rapido ciclo riproduttivo, sono sensibili ai cambiamenti ambientali. Inoltre, rappresentano dei componenti chiave delle catene trofiche acquatiche, collegando i produttori primari ai grandi consumatori secondari come pesci. Lo scopo della presente ricerca di dottorato è di ampliare le conoscenze sulle comunità zooplanctoniche dei grandi laghi subalpini, rilevando tendenze e cambiamenti nella struttura delle reti trofiche pelagiche e le loro potenziali cause. L’analisi di dati limnologici a lungo termine combinata a uno studio paleolimnologico del lago d’Iseo ha permesso di distinguere gli effetti dovuti al cambiamento climatico a quelli dovuti a impatti più locali, come l’eutrofizzazione. I risultati evidenziano che le rete trofiche dei laghi profondi subalpini sono fortemente influenzate dal clima. In particolare, la variabilità climatica invernale provoca un effetto a cascata che coinvolge l'intero ecosistema lacustre, modificando le caratteristiche chimiche, fisiche e biologiche del lago. Gli effetti del riscaldamento delle temperature invernali possono ripercuotersi sulle dinamiche di popolazione dello zooplancton fino all'estate, influenzando il funzionamento dell’intera catena trofica. L'indagine paleolimnologica, attraverso lo studio combinato di fattori biotici e abiotici, ha permesso di considerare gli effetti dei più importanti fattori di cambiamento negli ecosistemi lacustri, suggerendo che i fattori climatici dovrebbero essere considerati di fondamentale importanza nel determinare le dinamiche di sviluppo delle comunità planctoniche e la struttura e il funzionamento delle reti trofiche pelagiche.<br>Climate change is considered to be one of the most severe threats to earth and aquatic ecosystems and the concern about the effects that global warming can have on biological communities is growing. Even if the number of studies concerning climate change is worldwide increasing the effects of climate change are challenging to monitor and understand because of the multitude of responses within an ecosystem. In the last years, analyses of long-term data sets provide increasing evidence on the sensitivity of water bodies to climatic fluctuation. Small size and fast reproducing zooplankton organisms are sensitive to environmental change. Moreover, they represent key components of aquatic food webs, connecting primary producers to big secondary consumers as fishes. The purpose of the present PhD research is to expand the knowledge on the zooplankton communities of the large and deep lakes south of the Alps, detecting trends and significant change or shift in the pelagic food webs structure due to global or local impacts. The analysis of long-term series of limnological observations and a paleolimnological study on lake sediment have been combined in order to disentangle the effects of climate change from that due to more local and anthropic stressor as eutrophication. The obtained results suggested that in deep subalpine lakes the effect of climate change on pelagic food webs components is complex, including several direct and indirect effects, and it is mediated by nutrient availability. In particular, in deep lakes winter climatic variability trigger a cascading effect that involves the entire lake ecosystems, modifying lake chemical, physical and biological characteristic. The effects of warmer winter temperature can reverberate on zooplankton seasonal patterns until summer, affecting the food webs functioning. The paleolimnological investigation, through the combined study of biotic and abiotic factor, allowed clarifying the synergic effects of the most important drivers of change in lake ecosystems, suggesting that climatic factors should be considered with nutrient availability as a determinant element in controlling the temporal development of plankton communities and pelagic food web structure.

The impact of increased sediment exposure on coastal marine ecosystems is one of the most important contemporary environmental issues. Sediment exposure is defined as the concentrations of sediment particles suspended in the water column and the amount of sediment depositing on the seabed. In addition to natural events, such as land erosion, rainfall, and tidal currents, anthropogenic activities such as land use, road building, logging, mining, port maintenance and dredging, contribute to the discharge of a great amount of sediment in the water column. As sessile suspension-feeder assemblages play a critical role in marine ecosystems through their active transfers of organic and inorganic between the water column and the seabed (i.e. benthic-pelagic coupling), increased sediment exposure generated by anthropogenic activities may negatively impact these organisms. This study set out to evaluate the influence of increased sediment exposure on suspension-feeder assemblages in a temperate seagrass habitat. Most of the research was conducted within Posidonia sinuosa meadows near Woodman Point (32◦7’S, 115◦44’E), south of Fremantle, Western Australia. At this location, persistent sediment plumes from a cement manufacturer’s wash plant provided an opportunity to study the mechanisms through which increased sediment exposure can affect suspension feeder assemblages. This study was examining: the relationship between sediment exposure and suspension feeder assemblage composition; the influence of increased sediment exposure on the contribution of potential food sources to suspension feeder diets; and the influence of sediment exposure on suspension-feeding mechanisms (filtration and retention rates) and strategies (food particle selection). The descriptive work, presented in Chapter 1, revealed a strong gradient in sediment exposure with decreasing sediment deposition with distance from the wash plant. There was little dissimilarity, in term of species diversity and biomass, among suspension-feeder assemblages under high sediment exposure and those experiencing natural sedimentation regimes. These findings indicated that the suspension-feeder assemblages at the study site were resistant to high sediment exposure and that some species could potentially display compensatory mechanisms. Thus, the degree to which increased sediment exposure influences suspension feeders was more likely to be species specific and depend on the resilience of their feeding mechanisms and strategies. Those findings underlined the need to test the causal parameters underlying responses to suspension-feeding activity and selectivity due to increased sediment exposure. Results presented in Chapter 2 indicated that the three most conspicuous suspension feeder in term of biomass and abundances presented distinct isotopic signatures, implying dissimilarities in their diets. Differences in δ13C and δ15N can be explained by consumption of different types of picoplanktonic particles and the degree to which sedimentary organic matter contributed to their diets. Increased sediment exposure had no influence on the natural diets of the ascidian Herdmania momus and the bivalve Pinna bicolor. For the sponge Tethya sp, the contribution of sedimentary organic matter to its diet increased at sites with high sediment exposure, suggesting a potential benefit to its diet. Overall, the influence of sediment exposure on suspension feeder diets was species specific and dependent on the nature (e.g. organically rich versus organically depleted) and concentrations of the sediment. In Chapter 3 data are presented to show that feeding mechanisms and strategies of three species of suspension feeders best representing the benthic assemblages were influenced by sediment exposure. Under high sediment exposure, the ascidian Herdmania momus had lower pumping rates, but maintained a relatively constant food retention rate, and optimised its food intake by expanding its food sources from mainly cyanobacteria (Synechococcus) to a wider range of food sources. The bivalve Pinna bicolor also had lower filtration activity with high sediment exposure, again, maintaining relatively constant total retention rates and displaying a change in particle selection from bacteria and Synechococcus to larger picoeukaryotic cells of higher carbon content. The sponge Tethya sp. appeared to benefit from elevated sediment concentrations, as filtration and retention rates increased, potentially related to a lack of food selectivity. In Chapter 4, a short-term laboratory experiment was combined with a field transplant experiment to investigate the response of suspension feeders to increased sediment exposure. Under elevated sediment exposure, Herdmania momus and Pinna bicolor modulated their particle selection to optimise food intake, while the non-selective suspension feeder Tethya sp increased its particle retention rate and efficiency. Both the laboratory and transplant experiment findings corroborated observations made in Chapters 1 and 2; compensatory adaptations associated with the feeding activity, such as the modulation of pumping rates and the optimisation of food intake by particle selection, help to explain the potential resistance of suspension feeder community structure to high sediment exposure. A major outcome of this research is that it informs shallow coastal ecosystems stakeholders of the possible consequences of anthropogenic activities that increase sediment exposure, particularly those in the order of TSS at 40 mg·l-1 and deposition rates in the order of 10 g·cm- 2·month-1. Despite this magnitude of sediment exposure had little influence on suspension feeder assemblage composition, the effects on the suspension-feeding function, including the increase of the filtration activity and transfers of carbon to the benthos, potentially influence benthicpelagic coupling and other ecosystem-scale processes. Given the variation in sensitivity to sediment exposure among suspension feeder species, meaningful criteria to limit the effects of anthropogenic sediment loading on shallow coastal ecosystems should take into account the whole species assemblage present at any given site.

Tanzania's Ruaha landscape harbours some of the most important carnivore population strongholds in East Africa. However, ongoing human-induced changes of natural habitat expose these carnivore populations to increased anthropogenic pressure, even within protected areas. Such habitat changes can disrupt carnivore distribution and species interactions, which can be detrimental for species conservation. Yet, there is limited understanding about how anthropogenic-related variables influence carnivore occurrence and interspecific interactions in this landscape, which hinders the development of strategies to conserve carnivores. In this thesis, I examined the spatial occurrence of carnivores across the gradient of anthropogenic pressure in the Ruaha landscape and adjacent areas. In the first data chapters I investigated how landscape and human-related variables influenced carnivore site occupancy and interspecific interactions in the Ruaha National Park (RNP), surrounding wildlife management area, and village lands through extensive camera-trapping data. I found a consistent and steady decline in carnivore detections with increasing distance from RNP, especially closer to human households. Large carnivores, specifically, were not detected anywhere in the village lands. There was a notable variation on the influence of anthropogenic and landscape variables to carnivore site use: large carnivores were influenced by prey biomass and anthropogenic variables, whereas mesocarnivores were largely influenced by distance to the Great Ruaha River. In addition, mesocarnivore detections were correlated with those of top-order carnivores. Furthermore, increased probability for interspecific interactions between mesocarnivores was influenced by proximity to households. Overall, I identified that the village lands were likely acting as a hard edge that limited carnivore distribution outside RNP. On my last data chapter, I investigated the determinants of carnivore habitat suitability beyond Ruaha, and generated a predictive map of highly suitable carnivore habitats for the human gradient between the Ruaha and Selous landscapes, using the lion (Panthera leo) as a key-species. Highly suitable habitats were associated with low human population density (< 10 people/km²) and rainfall, and over 75% of these habitats were limited to protected areas, with the remainder patchily distributed across village lands. The results suggested limited potential for landscape connectivity between Ruaha and Selous. Overall, this thesis provides a rigorous assessment of the first comprehensive baseline data of carnivore spatial occurrence within a gradient of anthropogenic pressure in this landscape. The framework presented here can be used to help informing carnivore conservation planning in Ruaha, with applications elsewhere where carnivores and humans overlap.

Depuis quelques dizaines d’années, un intérêt croissant s’est développé pour la protection des espèces et la compréhension des mécanismes qui les conduisent à l’extinction. Actuellement, les causes d’extinction sont pour la grande majorité d’origine anthropique, mais un certain nombre de facteurs intrinsèques, propres à chaque espèce, peuvent interagir avec ces pressions anthropiques, pour aboutir au risque d’extinction. De nombreuses études ont mis en évidence l’impact des traits d’histoires de vie et des caractéristiques écologiques dans la vulnérabilité des espèces à l’extinction, mais très peu se sont penchées sur le rôle du comportement. Or, de par leur nature, tout un ensemble de comportements pourraient constituer des facteurs de vulnérabilité intrinsèques chez les espèces, que ce soit au niveau du risque d’extinction, ou au niveau des principales pressions anthropiques qui existent actuellement. Le but de cette thèse est de déterminer l’impact des caractéristiques du système social et de l’intensité de la sélection sexuelle dans la vulnérabilité des espèces de Primates i) aux principales pressions anthropiques (i.e. chasse, exploitation forestière et agriculture), à un niveau local, en portant une attention spécial au rôle d’infanticide dans la vulnérabilité à la chasse et ii) au risque d’extinction tel que décrit par l’UICN, au niveau global. Ce dernier point nous a amenés à analyser plus spécifiquement l’impact de l’hétérogénéité de l’empreinte humaine dans le risque d’extinction. Toutes nos études reposent sur une approche d’analyses comparatives. Nos différents travaux ont permis de mettre en évidence des effets du comportement à aux différentes échelles spatiales et pour les deux niveaux de vulnérabilité, mais avec des différences dans la nature des variables comportementales impliquées. Nous avons identifié des effets de la taille moyenne des groupes et du système socio-reproducteur dans la vulnérabilité à l’exploitation forestière, mais pas pour les autres menaces testées. De plus, ces effets ont été retrouvés au niveau du risque d’extinction, mais dans des sens différents. Ainsi, les mécanismes impliqués dans la vulnérabilité des espèces diffèrent selon le type de vulnérabilité étudié, faisant intervenir différents effets Allee<br>Improving species protection and better understanding the mechanisms leading to population decline and ultime extinction has become a major research area over the last decades. Nowadays, the causes of extinction are mostly anthropogenic, but some intrinsic factors, specific to each species, can interact with these anthropogenic pressures to determine the extinction risk. Many studies have highlighted the impact of life history traits and ecological characteristics on species vulnerability to extinction, but very few have investigated the role of behaviour. Because of the mechanisms they imply, several behaviours could constitute intrinsic factors of vulnerability among species, at the level of extinction risk, or concerning the main anthropogenic pressures threatening species. The aim of this thesis is to determine the impact of the social system and sexual selection on primate vulnerability i) to the main anthropogenic threats (i.e. hunting, logging and agriculture) and, particularly, the role of infanticide on their vulnerability to hunting, and ii) to the extinction risk as described by the IUCN conservation status. This point has lead us to examine also the impact of human footprint heterogeneity on extinction risk. All our studies are based on a comparative analysis approach. Our different works highlighted several impacts of behavioural variables at the two spatial scales and for the two levels of vulnerability, but with differences in the nature of the behavioural variables. We identified significant effects of the average group size and the socio-reproductive system in species vulnerability to logging, but not in species vulnerability to the other threats. Moreover, these effects have also been found at the level of the extinction risk, but in different ways. Thus, the mechanisms implicated in the vulnerability are different according to the type of vulnerability, and rely on several Allee effects

Abstract Tigers are endangered in the wild and face increasing threats from habitat loss and fragmentation. The majority of their range occurs in the Indian subcontinent, which is therefore a critical area for tiger conservation. Bengal tigers are distributed across many small protected areas in India. Two important Bengal tiger landscapes &#8212; Terai Arc Landscape (TAL) and Sundarbans in India were lacking in basic genetic information and needed to address the impact of anthropogenic pressure and climate change on their genetic makeup in order to identify conservation units. Therefore, I employed nuclear and mitochondrial genetic markers on TAL and Sundarbans tiger individuals to respond these demands for the first time. Thirty-nine heterologous microsatellite loci were screened on Bengal tigers and thirteen of these loci were selected to genotype Bengal tiger samples from western TAL (WTAL) and Sundarbans. After I had genotyped seventy-one Bengal tiger individuals from WTAL, I found cryptic population genetic structure, moderate gene flow and asymmetric migration among the subpopulation. Genetic diversity was moderate and there were no signs of population bottlenecks. In order to maintain the connectivity of subpopulations and avoid human&#8212;wildlife conflict, relocation of villages is necessary. Preventive measures against habitat encroachment and a ban on sand and boulder mining in the corridor area should also be implemented. Noninvasively-collected tiger samples from Sundarbans were analyzed for mitochondrial and microsatellite markers and compared with mainland (northern and peninsular) Bengal tiger populations in India. Sundarbans tigers were found to be genetically distinct and had lower genetic variation in comparison to other mainland tiger populations. Demographic analysis indicated recent historical isolation (600&#8212;2000 years ago) of the Sundarbans tiger from the mainland. Both historical and genetic evidence supported that the Sundarbans tiger was genetically connected to other mainland tigers until recently. Conclusively, genetic isolation from the mainland tiger population and adaptation to the mangrove ecosystem might have jointly shaped the genetic architecture of the Sundarbans tiger. Hence, the Sundarbans tiger needs special conservation attention for the preservation of its unique ability to adapt and for its genetic individuality. It should be managed as an evolutionary significant unit (ESU) under the adaptive evolutionary conservation (AEC) criteria. I also addressed a problem in the previously suggested sex-specific gene flow estimation method and recommended an alternative approach for a more precise estimation<br>Tiivistelmä Tiikeri on nykyisin uhanalainen lajin elinympäristön supistumisen ja pilkkoutumisen vuoksi. Lajin tärkein esiintymisalue on Intian niemimaalla, joka on siten kriittisen tärkeä alue tiikerin suojelun kannalta. Intiantiikereitä esiintyy useilla pienillä suojelualueilla Intiassa. Kaksi tärkeää tiikerin esiintymisaluetta Intiassa ovat Terain kaaren (TAL) alue luoteis-Intiassa sekä Sundarbansin mangrovealue Bangladeshin rajalla. Näiden alueiden tiikereistä ei ole ollut olemassa geneettistä perustietoutta, jota tarvitaan, kun arvioidaan ihmisen toiminnan ja ilmastonmuutoksen aiheuttamia muutoksia tiikeripopulaatioiden geneettisessä koostumuksessa sekä kun määritellään lajin suojelun kannalta merkittäviä luonnonsuojeluyksikköjä. Tässä väitöskirjatutkimuksessa tutkittiin Terain kaaren ja Sundarbansin alueen tiikereiden geneettistä monimuotoisuutta ja rakennetta sekä tuman että mitokondrion geenimerkkien avulla. Tutkimuksessa selvitettiin kolmenkymmenyhdeksän tuman geenimerkin (mikrosatelliitin) soveltuvuutta intiantiikerin geneettisiin tutkimuksiin, ja näistä valittiin kolmetoista käytettäväksi läntisen Terain kaaren ja Sundarbansin alueiden tiikereiden geneettisiin tutkimuksiin. Terain kaaren alueelta tutkittiin seitsemänkymmenentäyksi intiantiikerinäytettä. Tulosten perusteella alueella on aikaisemmin havaitsematonta kryptistä populaatiorakennetta. Geenivirtaa eri alapopulaatioiden välillä oli kohtuullisen paljon, mutta se oli epäsymmetristä. Tiikereiden geneettinen monimuotoisuus oli melko suurta eikä geneettisillä menetelmillä havaittu eri alapopulaatioissa merkkejä populaation koon pullonkauloista. Jotta alapopulaatioiden välinen yhdistyneisyys säilyisi jatkossa, joidenkin kylien siirto toisaalle on välttämätöntä. Ihmisten luvaton levittäytyminen tiikerin elinalueita yhdistävillä käytävillä täytyisi saada hallintaan sekä kieltää hiekanotto ja kivenlouhinta. Sundarbansin alueelta ei-invasiivisesti kerätyt tiikerinäytteet tutkittiin sekä tuman että mitokondrion merkkigeenillä ja alueen tiikereiden geneettistä koostumusta verrattiin manner-Intian tiikeripopulaatioiden koostumukseen. Sundarbansin tiikereiden todettiin poikkeavan geneettisesti manneralueen tiikeripopulaatioista ja niiden geneettinen monimuotoisuus oli alhaisempaa kuin manneralueella. Koalesenssisimulaatiohin perustava demografinen analyysi viittasi Sundarbansin tiikereiden suhteellisen viimeaikaiseen (600&#8212;2000 vuotta sitten) erkanemiseen manneralueen tiikereistä. Sekä historialliset että geneettiset todisteet tukivat teoriaa, jonka mukaan Sundarbansin tiikereillä olisi ollut yhteyksiä mannermaan tiikereihin aivan viime aikoihin asti. Geneettinen isolaatio mannermaan tiikereistä ja adaptaatio mangrove-ekosysteemiin ovat yhdessä muovanneet Sundarbansin tiikereiden geneettistä arkkitehtuuria. Tämän vuoksi Sundarbansin tiikerit vaativat erityistä suojelua, jotta niiden geneettinen ainutlaatuisuus ja kyky sopeutua erityisolosuhteisiin säilyisivät myös tulevaisuudessa. Populaatiota täytyy hoitaa evolutiivisesti merkittävänä yksikkönä (evolutionary significant unit; ESU) adaptiivisen evolutiivisen suojelun (adaptive evolutionary conservation; AEC) kriteeristön mukaisesti. Tutkimuksessa kiinnitettiin huomiota myös ongelmiin, joita saattoi ilmetä aikaisemmin ehdotetuissa menetelmissä eri sukupuolten kautta kulkevan geenivirran määrän arvioimiseksi ja ehdotettiin vaihtoehtoista menetelmää tarkempien arvioiden saamiseksi

L'aire de distribution des espèces est conditionnée à la fois par des facteurs biotiques et abiotiques et ses frontières dépendent généralement des limites physiologiques de l'espèce. Ainsi, en bordure d'aire de répartition, les populations se caractérisent par une diversité génétique moindre ainsi qu'une forte différentiation génétique et leur existence dépend d'un équilibre fragile entre événements de colonisation et d'extinction.Depuis les années 1970, l'augmentation et l'accélération des pressions anthropiques exercées sur les écosystèmes bouleversent ces équilibres et des modifications de l'aire de répartition sont observées chez certaines espèces dont le bivalve Macoma balthica, espèce clé des écosystèmes littoraux en Europe, dont la limite sud de répartition s'est décalée vers le nord-est au cours des quarante dernières années.Afin d'évaluer les capacités adaptatives de M. balthica et dans un but de conservation, deux approches complémentaires ont été menées dans des environnements contrastés qui ont permis de mettre en évidence des signes d'adaptation locale.D'une part, l'étude du génome neutre à l'aide des outils méthodologiques et concepts de la génétique des populations a permis d'inférer l'histoire démographique de l'espèce avec une attention particulière portée sur une baie en limite d'aire de répartition (Baie de Marennes Oléron, France) et sur une baie soumise à de fortes pressions physico-chimiques (Baie de Gdansk, Pologne). Nous avons mis en évidence notamment :(i) un polymorphisme significatif dans les populations en limite d'aire en opposition avec les attendus théoriques(ii) des ruptures au flux de gènes dans le golfe de Gascogne soumis au réchauffement des eaux de surface mais aussi le long d'un gradient environnemental dans la baie de Gdansk. D'autre part, l'étude moléculaire de la sélection a été menée par la méthode de pyroséquençage sur le transcriptome d'individus prélevés en milieux contrastés. Cette étude a permis de mettre en évidence des tendances d'expression différentielle de gènes de réponse générale au stress selon le milieu considéré.

As the acreage of glyphosate-resistant (GR) cropping systems increases, so does the occurrence of herbicide-resistant weeds in the landscape. Biotypes of GR Conyza canadensis were first observed in Delaware, USA, in 2000. Since the first documentation of GR C. canadensis, there have been many instances of independent evolution of GR C. canadensis biotypes. The ecology of GR C. canadensis and any potential fitness consequences of GR trait are still unknown. If there is no fitness cost or a fitness increase associated with the GR trait, GR C. canadensis may increase in prevalence in the landscape even in the absence of glyphosate application. With the consideration that fitness is a difficult parameter to measure, other variables may be used as surrogate measures of fitness, such as reproduction, growth rate, phenology, survivorship, etc. This research seeks to determine if differences exist in surrogate measures of fitness - patterns of growth, reproductive allocation, and competitive ability - and if so, how differences may apply to future population changes, for glyphosate-resistant and -susceptible C. canadensis. The first two experiments presented test two populations of GR plants and two populations of GS plants, first in a greenhouse study of shading effects and intraspecific competition (Chapter 2), and second in a field survivorship study within two habitat types (Chapter 3). The third study tests for the prevalence of GR C. canadensis in field margins of GR cropping systems and seeks correlations in the occurrence of resistance and factors related to geography and field management (Chapter 4). The greenhouse study (Experiment 1, Chapter 2) of surrogate measures of fitness (growth, reproduction) in response to intraspecific competitive ability and shading showed that, while all populations had the same response to shading, there were differences between populations in growth and reproduction. While all measures were greater for individual plants with no competition, plants competing with individuals from one of the GR populations (R2) often had measures that were not different from the no competition treatment or were greater than the other competition treatments (R1, S1, and S2). The field survivorship study compared growth, survival, and reproduction of the previously studied four populations of C. canadensis is two habitats, a old-field in the second year of succession (ruderal) and a soybean field planted with a GR cultivar (agrestal) (Experiment 2, Chapter 3). One of the GR populations (R1) had the highest survivorship of the four populations in the ruderal habitat, while there was no difference in survivorship of the four populations in the agrestal habitat. While there was little difference in growth between ruderal populations, in the agrestal habitat, one GS population (S1) consistently had the smallest diameter, height, and leaf number. One of the agrestal GR populations (R2) was larger than the others, though not always different from R1. R1 was the first population to senesce regardless of habitat. Both agrestal GR populations produced more capitulae (seed heads) than the GS populations, and R1 also showed high reproductive success in the ruderal habitat. A test for the occurrence of GR C. canadensis in field margins of GR cropping systems (Experiment 3, Chapter 4) utilized a discriminating spray test on seed collected from the margins of 17 agricultural fields in 2008 from Illinois, Indiana, and Nebraska. The relationships between the occurrence of GR C. canadensis in 2008 field margins and 1) geography, 2) field management practices, 3) herbicide diversity, 4) weed community diversity, 5) field-interior changes in C. canadensis populations (λ), and 6) knowledge or suspicion of difficult-to-control C. canadensis populations, were tested. Geography was the clearest relationship in these data and was related to geography, with greater, more variable occurrence of GR C. canadensis in 2008 field margins in the southern and eastern sites than the northern and western sites. Management practices in field-interiors from year 2006 to 2008 had little relationship to occurrence of GR C. canadensis in 2008 field margins, except for the increased use of tillage and the increased use of non-glyphosate herbicide modes of action in 2007 field-interiors of fields with the highest occurrence of GR C. canadensis in the field margins in 2008. Additionally, the greatest occurrence of GR C. canadensis was associated with high diversity in the weed community in 2007 field-interiors. These results suggest that GR C. canadensis persisted in 2008 field margins even though there was a perceivable increase in management intensity the previous year. In conclusion, although there were no differences in fitness clearly associated with the GR trait in C. canadensis, GR populations may possess equal or greater vigor in growth, reproduction, and competition as GS populations. Based on these results, GR C. canadensis may persist in agricultural field-margins or other ruderal, unmanaged habitats and act as a seed source for future field-interior infestations. Depending on the characteristics of the GR biotype, GR C. canadensis may increase in frequency in the landscape.

La mer Méditerranée abrite une biodiversité marine importante avec un fort taux d’endémisme. Les poissons représentent 684 espèces dont 9,2 % sont endémiques. Outre le rôle nécessaire des poissons au sein des écosystèmes marins, les sociétés humaines bénéficient également de nombreux services écosystémiques générés par les populations ichtyologiques. Cependant, la biodiversité et le fonctionnement des écosystèmes côtiers méditerranéens, sont parmi les plus touchés à l’échelle mondiale en raison de pressions anthropiques croissantes. Contrairement à la dynamique liée au changement global, les pressions anthropiques locales peuvent être identifiées et gérées plus facilement à l’échelle régionale. Pour cela, il est nécessaire de quantifier et d’évaluer précisément les impacts de ces pressions notamment sur la communauté ichtyologique. Dans ce travail les impacts sur la communauté ichtyologique de quatre pressions anthropiques, communes sur les littoraux méditerranéens, ont été étudiés dans la baie de Calvi en Corse (France) : les effluents de l’émissaire de la station d’épuration, une ferme aquacole, les activités de pêche récréative et, enfin, de plongée sous-marine. L’ensemble des résultats a été discuté dans le contexte du changement climatique qui va induire une modification majeure des écosystèmes méditerranéens dans les décennies à venir. Cette thèse représente une avancée significative dans notre capacité à comprendre, prioriser et anticiper les impacts des pressions anthropiques locales sur les populations ichtyologiques côtières méditerranéennes et préconise des mesures de gestions qui devront être adaptatives en fonction des évolutions futures du changement global<br>The Mediterranean Sea is home to a significant marine biodiversity with a high rate of endemism. The fish population is composed of 684 species, of which 9.2% are endemic. Beyond the fundamental role played by fish populations within marine ecosystems, they also provide human societies with many ecosystem services. However, biodiversity and the functioning of coastal ecosystems, are deeply and increasingly affected by anthropogenic pressures. In contrast with the complex dynamics of global change at a larger scale, local anthropogenic pressures can be identified and managed more easily at the regional scale. To do this, the quantification and evaluation of the consequences of these pressures are necessary, especially regarding the fish community. In this study, we assessed the impacts of four anthropogenic pressures common to the Mediterranean coasts on the ichthyological community present in the Bay of Calvi in Corsica (France). The anthropogenic pressures included effluents from the outfall of the Calvi wastewater treatment plant, an aquaculture farm, recreational fishing activities and scuba diving. The results were discussed in the context of global change and particularly of climate change, which will induce a major evolution of Mediterranean ecosystems in the upcoming decades. This thesis shows the significant progress made in our ability to understand, prioritise and anticipate the impacts of local anthropogenic pressures on Mediterranean coastal fish populations. It further provides management recommendations that will need to be adapted to the human-environment dynamics in the context of global change

Submitted by Fernando Henrique Machado (fernandomtb@hotmail.com) on 2018-04-23T13:30:20Z No. of bitstreams: 1 FHM - Tese 132 [PD].pdf: 9073445 bytes, checksum: 558a93dca350999137782573a2b01e5b (MD5)<br>Rejected by Bruna Bacalgini null (bruna@sorocaba.unesp.br), reason: Prezado, Solicitamos que realize correções na submissão seguindo as orientações abaixo: O pdf não pode estar protegido, por favor, faça a submissão novamente com arquivo pdf não protegido. Agradecemos a compreensão. on 2018-04-23T14:00:52Z (GMT)<br>Submitted by Fernando Henrique Machado (fernandomtb@hotmail.com) on 2018-04-23T14:39:49Z No. of bitstreams: 1 FHM - Tese 132 [PD].pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5)<br>Approved for entry into archive by Bruna Bacalgini null (bruna@sorocaba.unesp.br) on 2018-04-23T14:44:42Z (GMT) No. of bitstreams: 1 machado_fh_dr_soro.pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5)<br>Made available in DSpace on 2018-04-23T14:44:42Z (GMT). No. of bitstreams: 1 machado_fh_dr_soro.pdf: 9054390 bytes, checksum: 858ba049e3608953cf364a4045e9e325 (MD5) Previous issue date: 2018-03-01<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>As bacias hidrográficas localizadas em áreas densamente ocupadas e industrializadas sofrem diferentes pressões antrópicas, situação que compromete a qualidade e quantidade da água. Esse cenário, peculiar nas bacias hidrográficas dos rios Piracicaba, Capivari e Jundiaí (BH-PCJ), reflete também na sub-bacia hidrográfica do rio Jundiaí-Mirim (BH-JM), responsável pelo fornecimento de 95% da água consumida por Jundiaí-SP. Todavia, a vazão produzida nesta bacia é insuficiente para atender as demandas do município, necessitando da reversão sazonal das águas do rio Atibaia. Diante desse quadro de estresse hídrico, este estudo visou propor e analisar um conjunto de indicadores de segurança hídrica visando a melhoria da capacidade de planejamento e gestão dos recursos hídricos da BH-JM. Assim, utilizou-se de uma abordagem metodológica pautada na seleção, validação, aplicação e estruturação de indicadores de segurança hídrica em um modelo de causa-efeito. Os indicadores foram submetidos à avaliação por meio de um painel multidisciplinar de especialistas utilizando-se o método Delphi. Os indicadores validados pelo painel foram discutidos e, posteriormente, sistematizados a fim do estabelecimento das diretrizes. Os indicadores selecionados foram: (i) oferta de água; (ii) reservatórios de água; (iii) rede de distribuição; (iv) perdas na distribuição de água potável; (v) transposição de água; (vi) qualidade físico-química e biológica da água; e (vii) políticas públicas. Os principais resultados foram: (i) a série histórica analisada apontou um crescimento populacional de 1,8% a.a., conquanto a produção de água tratada cresceu a taxas inferiores (1,2% a.a.), onde verificou-se a redução constante do consumo per capta de 248 L hab.-1 dia-1 para 203 L hab.-1 dia-1 em um período de 17 anos; (ii) as áreas ocupadas por lagos e reservatórios foram ampliadas em 703% em um período de 4 décadas, sendo a maior área representada pelo reservatório de abastecimento público, do qual estimou-se receber uma carga de sedimentos de 1,5 mil t ano-1 ; (iii) o crescimento geométrico da rede de distribuição aumentou a taxas de 3,1% a.a., refletindo no aumento linear do número de ligações ativas de água; (iv) as perdas médias do sistema de distribuição de água potável encontra-se na ordem de 34% ao longo de quase duas décadas, representando perdas de aproximadamente 17,6 milhões de m3 ano-1 ou R$ 38,3 milhões ano-1 ; (v) uso cada vez mais frequente das águas revertidas do rio Atibaia, medida que pode emergir inúmeros desdobramentos e conflitos futuros pelo uso da água na região; (vi) alterações adversas na qualidade físico-química da água da BH-JM em decorrência da transposição, como o aumento na concentração de íons metálicos, turbidez, cloreto, dentre outros; (vii) identificou-se um amplo aparato jurídico-ambiental relacionadas à BH-JM, porém com baixa eficácia jurídica em suas aplicações. Em face dos resultados, 49 diretrizes de gestão foram propostas. Desse modo, a abordagem metodológica empregada revelou-se adequada e replicável para outras bacias, uma vez que: a partir do método Delphi foi possível estabelecer critérios de seleção de indicadores considerando a problemática em análise; a discussão individual dos indicadores permitiu uma melhor compreensão das dinâmicas envolvidas em cada indicador; a estruturação dos indicadores em um modelo-causal permitiu a sistematização das informações e, consequentemente, contribuiu para o estabelecimento das diretrizes.<br>The river basins located in densely occupied and industrialized areas are subject to different anthropogenic pressures, a condition that compromises directly the quality and quantity of water resources. This situation is common in the Piracicaba, Capivari, and Jundiaí river basins (BH-PCJ), southwestern Brazil, as well as in the Jundiaí-Mirim river basin (BH-JM) (sub-basin of the Jundiaí river). The BH-JM is a strategic area due to supply 95% of the raw water consumed by Jundiaí-SP. However, the available water flow in this basin is not enough to meet the local demands. This fact led to the need for seasonal interbasin water transfer from the Atibaia river. In view of this water stress scenario, this study aimed to propose and analyze a set of water security indicators for improving the planning and management capacity of the BHJM water resources. Therefore, a methodological approach based in selection, validation, application and structuring of water safety indicators was used in a cause-effect model. The indicators were submitted to the assessment through a multidisciplinary panel of experts using the Delphi method. The valid indicators from the panel were well discussed and, posteriorly, systematized for purpose of establishment of guidelines. The selected indicators were: (i) water supply; (ii) water reservoir; (iii) drinking water distribution system; (iv) drinking water losses in the distribution system; (v) interbasin water transfer; (vi) physical-chemical and biological water quality; (vii) public policies. The main results were: (i) the historical series analyzed showed a population growth rate of 1.8% p.a., while the potable water production was 1.2% p.a., where there was a constant reduction of consumption of 248 L inhabitant-1 day-1 to 203 L inhabitant-1 day-1 in 17 years; (ii) the areas occupied by lakes and reservoirs in BH-JM were increased by 703% in 4 decades, the largest area represented by the public supply reservoir, from which it was estimated that a sediment load of 1,5 thousand tons-1 ; (iii) the geometric growth of the distribution network was of 3.1% p.a., reflecting the linear increase in the number of hydrometric water connections; (iv) the average of drinking water losses in the distribution systems was around 34% over almost two decades, representing losses of about 17.6 million m3 year-1 or R$ 38.3 million year- 1 ; (v) increasingly frequent use of the interbasin water transfer from Atibaia river, a measure that may result in many unfolding and future conflicts over the use of water in the region; (vi) adverse changes in the physical-chemical quality of BH-JM water due to interbasin water transfer, such as the increase in the concentration of metallic ions, turbidity, chloride, among others; (vii) an ample environmental legislative framework related to BH-JM was identified, but with low legal effectiveness in their applications. In view of the results, 49 management guidelines were proposed. Therefore, the methodological approach used demonstrated to be adequate and replicable for other river basins, once that: the Delphi method developed allowed to set up criteria of indicators selection considering the research questions analyzed; the indicators discussion allowed a better understanding of the dynamics involved in each indicator; the indicators structuring in a causal model allowed the information systematization and, thus, it is contributed to the establishment the management guidelines.<br>Capes-DS

Систематизовано і поглиблено теоретико-методичні основи дослідження територіальної організації та комплексно-пропорційного розвитку еколого-економічного комплексу адміністративної області, зокрема уточнено поняття “еколого-економічний комплекс”, обґрунтовано категорії “територіальна організація еколого-економічного комплексу”, “еколого-економічна конверсія господарства”, сформульовано принципи та фактори територіальної організації еколого-економічного комплексу мезорегіону. Запропоновано п’ятисферну структуру еколого-економічного комплексу адміністративної області, зокрема виділено й обґрунтовано існування функціонально-компонентної, функціонально-територіальної, функціонально-управлінської, функціонально-економічної та функціонально-екологічної структур. Розроблено та апробовано на прикладі Волинської області методику суспільно-географічного дослідження територіальної організації еколого-економічного комплексу адміністративної області, зокрема вперше запропоновано методику розрахунку індексу екологічної напруженості геоекосистем, індексу еколого-економічної пропорційності розвитку території, індексу антропогенного навантаження на геоекосистеми, індексу екологічної стійкості геоекосистем, економічних збитків господарства від забруднення довкілля тощо. Виявлено фактори, структурні особливості та закономірності територіальної організації еколого-економічного комплексу Волинської області. Виконано еколого-економічне мікрорайонування Волинської області. Обґрунтовано основні напрями удосконалення територіальної організації еколого-економічного комплексу Волинської області в контексті сталого розвитку.<br>A deep geographical research of the problems of optimization of society ecological-economic parameters within the terms of transition to the sustainable development is carried out in the dissertation. The particular scientific analysis of the factors of the Volyn Region ecological-economic complex formation is given as well as the territorial and constructive peculiarities of the economy influence over the environment are considered. The levers of the economic regulation of the ecological-economic processes adequate for the Region at present are generalized. Both the economic losses from the environment pollution by the economy subjects of the Volyn Region and the indexes of the ecological tension of the administrative districts geoecosystems are calculated. Four ecological-economic zones within the territory of the Region are marked out. The most actual perspective directions of the ecological-economic conversion of the economy are proposed.

Dans le cadre des objectifs définis par la Directive Cadre sur l'Eau, ce travail de thèse porte sur la quantification du transfert de micropolluants organiques à la confluence entre la Fensch et la Moselle. Une nouvelle méthodologie a été développée pour déterminer les niveaux d'anthropisation dans les matrices environnementales. Basée sur la quantification exhaustive des marqueurs moléculaires, cette approche permet de comparer les apports naturels et anthropiques et de différencier les apports anthropiques selon leurs origines (combustion, pétrogénétique, eaux usées). Elle est parfaitement appropriée à l'étude de la matière organique des différentes matrices environnementales fournissant des informations beaucoup plus complètes que le dosage de quelques molécules cibles. Appliquée aux sédiments du système Fensch-Moselle, cette approche a permis d'analyser l'évolution des contributions organiques le long de la Fensch ainsi que leur transfert à la confluence avec la Moselle, tout en déterminant les sources principales de contamination. Ce travail souligne l'importance de l'hydrodynamisme sur la sédimentation et la biodégradation des micropolluants organiques. L'étude de ce système a également été l'occasion de développer deux outils utiles pour répondre à des questionnements environnementaux majeurs. Le premier, basé sur la déconvolution de l'unresolved complex mixture, permet de quantifier la masse de produits pétroliers accumulés dans des sédiments. Le second se base sur l'étude de la répartition des micropolluants organiques en phase aqueuse (dissous, colloïdale, particulaire) lors de la mobilisation de sédiments contaminés, permettant d'évaluer leur biodisponibilité.

Dissertação de Mestrado em Bioquímica apresentada à Faculdade de Ciências e Tecnologia<br>A resistência a antibióticos é um problema crescente a nível mundial associado ao uso abusivo de antibióticos tanto em humanos como animais. Enterobacteriaceae resistentes a cefalosporinas de 3ª geração geram grande preocupação, dado que são fármacos de primeira linha utilizados para tratar infeções causadas por estes agentes infeciosos. A resistência a este tipo de antibióticos é mediada por beta-lactamases de espectro alargado (ESBLs), sendo as CTX-M as mais prevalentes a nível mundial. O rio Lis é um rio com elevados níveis de poluição localizado na região centro de Portugal, sujeito a diversas pressões antropogénicas incluindo descargas ilegais de resíduos provenientes de suiniculturas. Este estudo tem como objetivos: 1) determinar a prevalência de Enterobacteriaceae resistentes a cefotaxima ao longo do rio Lis em dois anos; 2) determinar a afiliação filogenética, clonalidade e perfis de suscetibilidade a antibióticos de bactérias portadoras do gene blaCTX-M isoladas deste rio; e 3) caracterizar a diversidade de genes blaCTX-M, o seu contexto genómico e associação a elementos genéticos móveis. O rio Lis apresentou qualidade da água muito baixa nos 15 locais amostrados, tanto em 2018 como em 2019. Dados recolhidos em 2018 revelaram a presença de bactérias resistentes a cefotaxima em todos os locais, geralmente mais abundantes em locais com menor qualidade da água. Em 2019 foi observada a mesma tendência, mas não foi detetada qualquer bactéria resistente a cefotaxima em três dos locais amostrados. Dos 147 isolados resistentes à cefotaxima distribuídos por 9 géneros, em 68 (46%), pertencentes a 4 géneros, foi detetado o gene blaCTX-M. A tipagem molecular mostrou a presença de isolados provavelmente clonais em diferentes locais e nos dois anos, sugerindo persistência das estirpes no rio e provavelmente fontes de poluição contínuas. Os isolados clonais recolhidos no mesmo local e no mesmo ano foram excluídos da restante análise. Os restantes 54 isolados pertenciam aos géneros Escherichia (n = 32), Klebsiella (n = 18), Enterobacter (n = 3) e Citrobacter (n = 1). Destes isolados, 79,6% mostraram perfis de multirresistência, com 2 isolados a revelarem baixa suscetibilidade ao imipenemo, um antibiótico utilizado em último recurso. Sete variantes diferentes de blaCTX-M foram encontradas, nomeadamente blaCTX-M-1, blaCTX-M-3, blaCTX-M-15, blaCTX-M-32, blaCTX-M-55, blaCTX-M-14, blaCTX-M-27 e blaCTX-M-65, sendo a blaCTX-M-15 a mais prevalente (52,5% dos isolados), tal como descrito mundialmente. A variante blaCTX-M-65 foi detetada pela primeira vez em Portugal. A ISEcp1 foi detetada na região a montante do gene para todas as variantes, e IS903 ou orf477 estavam presentes na região a jusante do gene. Os resultados deste estudo reforçam os graves problemas de poluição no rio Lis. Em locais com mais baixa qualidade da água foram registados os níveis mais elevados de resistência e prevalência do gene blaCTX-M, sugerindo este gene como um marcador de poluição. O número elevado de variantes de blaCTX-M detetadas em Enterobacteriaceae, em contextos frequentemente descritos em isolados clínicos, sugere que a água do rio Lis representa um risco considerável para a saúde humana. Este risco deve ser avaliado em detalhe dado que a água deste rio é utilizada frequentemente para irrigação, pesca e atividades de lazer.<br>Antibiotic resistance is a growing worldwide problem derived from overuse of antibiotics in both humans and animals. Enterobacteriaceae resistant to 3rd generation cephalosporins are a great concern, as these are first-line drugs to treat infections caused by these common pathogens. Resistance to these antibiotics is mainly mediated by extended spectrum beta-lactamases (ESBLs), being CTX-M the most prevalent worldwide. The Lis river is a heavily polluted river in central Portugal, affected by several anthropogenic pressures including illegal waste discharges from piggeries. This study aims are: 1) to determine the prevalence of cefotaxime-resistant Enterobacteriaceae along the Lis river, in two years; 2) to determine the phylogenetic affiliation, clonality and antibiotic susceptibility profiles of blaCTX-M carriers isolated in Lis river; and 3) to characterize the diversity of blaCTX-M genes, their genomic context and association to mobile genetic elements. The Lis river presented a very low water quality in the 15 sampling sites, both in 2018 and 2019. Data from the 2018 campaign revealed the occurrence of cefotaxime-resistant bacteria in all sites, generally with higher rates in sites with lower water quality. In 2019 the same trend was observed but cefotaxime-resistant bacteria were not detected in three sites. From 147 cefotaxime-resistant isolates included in 9 genera, 68 (46%) carried the blaCTX-M gene and affiliated with 4 genera. Molecular typing revealed the presence of potentially clonal isolates in different sites and in the two years, suggesting survival of the strains in the river and probably continuous pollution inputs from the same sources. Clonal isolates collected in the same site and at the same time were excluded from further analysis. The remaining fifty-four isolates affiliated with Escherichia (n = 32), Klebsiella (n = 18), Enterobacter (n = 3) and Citrobacter (n = 1). From these, 79.6% showed a multiresistance profile with 2 isolates with reduced susceptibility to imipenem, a last-resort antibiotic. Seven different variants of blaCTX-M were found, namely blaCTX-M-1, blaCTX-M-3, blaCTX-M-15, blaCTX-M-32, blaCTX-M-55, blaCTX-M-14, blaCTX-M-27 and blaCTX-M-65, with blaCTX-M-15 being the most prevalent (52.5% of the isolates), as reported worldwide. blaCTX-M-65 was detected for the first time in Portugal. ISEcp1 was detected upstream the gene for all variants, and IS903 or orf477 were present in the downstream region. Results from this study reinforce the serious pollution problems in the Lis river. Sites with lower water quality also showed the highest resistance rates and the highest prevalence of the blaCTX-M gene, suggesting this gene as a pollution marker. The high number of blaCTX-M variants detected in Enterobacteriaceae, in contexts frequently reported in clinical isolates, suggest that the Lis river water may present relevant human health risks, which must be further assessed since this water is frequently used for irrigation, fishing and leisure activities.

Official monitoring programs implemented by the Portuguese Environmental Agency (APA), do not fully survey all streams and rivers due to their nationalwide coverage, budget, and practical limitations. Two rivers in the north of Portugal, the Sousa and Ferreira rivers, with a recent past of different types of pollution and that run over areas with a high degree of alteration and dense population, were analyzed ecologically based on biological (diatom communities), physicochemical, and hydromorphological data. Diatoms are excellent ecological indicators of water quality. They are broadly distributed, show high species diversity, and respond rapidly to anthropogenic pressures. The Water Framework Directive (WFD) gives the legal basis for the use of this ecological indicator for water quality assessment, through the calculation of autoecological indexes. Portugal officially adopted the use of the Specific Polluosensitivity Index (SPI), which after determined, is converted into Ecological Quality Ratio (EQR). To determine the SPI, a morphological identification and cunt of diatom species using a microscope is required. This approach requires high taxonomic skills and several hours of analysis. DNA metabarcoding combined with high-throughput sequencing techniques (HTS), offer a promising alternative to classic methodologies, reducing time and costs. The aim of this study was to verify what kind of pressures affect these rivers and streams in the municipality of Paredes, develop plans to improve the sites under study, compare the EQR values obtained for both methodologies, and verify the effectiveness and reliability of DNA metabarcoding on diatoms in the bioassessment of these watercourses. Diatoms were sampled following WFD standards in 2 rivers and streams (21 samples) from the municipality of Paredes, in autumn 2019. All samples were submitted in parallel to the molecular and morphological methodologies. Molecular methodology started with eDNA extraction, followed by DNA sequencing (Illumina MiSeq) using 312 bp rbcL DNA barcode. In the Mothur software, the sequences obtained were analyzed producing Operational Taxonomic Units (OTUs) taxonomically assigned to the R-Syst::diatom reference library. Inventories of diatom communities revealed only 24.2% of the species were common among methodologies, which is explained by the incompleteness of reference library. Regarding the EQR values, the results indicated a good correlation between morphological and molecular methods. PCO analysis revealed a gradient of quality classification in both methodologies, supporting the hypothesis that DNA metabarcoding may be a good option for ecological quality assessment. However, there is work to be done so that this new methodology can integrate in WFD standards. Biological, physical-chemical and hydromorphological data showed negative impacts on watercourses in urbanized and agricultural areas, requiring the implementation of measures and awareness of the population for the dangers involved.<br>Dois rios do norte de Portugal, os rios Sousa e Ferreira, com um passado recente de diferentes tipos de poluição e que percorrem zonas com elevado grau de alteração e densa população, foram analisados ecologicamente com base em dados biológicos (comunidades de diatomáceas), físico-químicos e hidromorfológicos. As diatomáceas são excelentes indicadores ecológicos da qualidade da água. Elas são amplamente distribuídas, apresentam alta diversidade de espécies e respondem rapidamente às pressões antropogénicas. A Diretiva Quadro da Água (DQA) fornece a base legal para a utilização deste bioindicador para avaliação da qualidade da água, através do cálculo de índices autoecológicos. Portugal adotou oficialmente a utilização do Indice de Polluosensibilité Spécifique (IPS), que após determinado, é convertido em Rácio de Qualidade Ecológica (RQE). Para o IPS, é necessária uma identificação morfológica e contagem das espécies de diatomáceas usando o microscópio. Esta abordagem requer alto conhecimento taxonómico e várias horas de análise. DNA metabarcoding combinado com técnicas de sequenciamento de alto rendimento (HTS), oferece uma alternativa promissora às metodologias clássicas, reduzindo tempo e custos. O objetivo deste estudo foi verificar que tipo de pressões afetam os rios e ribeiras no município de Paredes, desenvolver planos de melhoramento dos locais em estudo, comparar os valores de EQR obtidos para ambas as metodologias e verificar a eficácia e fiabilidade do DNA metabarcoding na avaliação biológica destes cursos de água, usando diatomáceas. Diatomáceas foram amostradas seguindo os padrões da DQA em dois rios e suas ribeiras (21 amostras) do município de Paredes, no outono de 2019. Todas as amostras foram submetidas paralelamente aos métodos moleculares e morfológicos. A metodologia molecular começou com a extração de eDNA, seguida pelo sequenciamento de DNA (Illumina MiSeq) usando o barcode de DNA rbcL de 312 bp. No software Mothur, as sequências obtidas foram analisadas produzindo Unidades Taxonómicas Operacionais (OTUs) atribuídas à biblioteca de referência R-Syst :: diatom. Inventários de comunidades de diatomáceas revelaram que apenas 24,2% das espécies eram comuns entre as metodologias, o que é explicado pela falta de espécies na biblioteca de referência. Em relação aos valores de RQE, os resultados indicaram uma boa correlação entre os métodos. A análise de PCO revelou um gradiente de classificação de qualidade em ambas as metodologias, apoiando a hipótese de que o DNA metabarcoding pode ser uma boa opção para avaliação da qualidade ecológica. No entanto, há trabalho a ser feito para que essa nova metodologia possa ser integrada na DQA. Dados biológicos, físico-químicos e hidromorfológicos evidenciaram impactos negativos nos cursos de água em áreas urbanizadas e agrícolas, exigindo a implementação de medidas e a consciencialização da população para os perigos envolvidos.<br>Mestrado em Ecologia Aplicada

Original thesis presented by Andreia Manuela Vieira Garcês at the University of Trás-osMontes and Alto Douro, to obtain the doctor’s degree on Veterinary Science – Biomedical Sciences.<br>Nas últimas décadas, a população humana cresceu exponencialmente e quase três quartos da terra sem gelo são agora dominados por biomas antropogénicos. A presença e A atividade humana provocaram alterações nos ecossistemas, levando à sua destruição ou fragmentação. Estas mudanças têm enormes consequências negativas para as populações selvagens, direta e indiretamente, que em um estadio final podem levar à completa extinção de populações selvagens. Neste estudo, pretendemos obter uma visão geral sobre as consequências das ameaças induzidas pelo homem às populações de vertebrados selvagens (aves, mamíferos, répteis, anfíbios) no norte de Portugal, com base em dados recolhidos num Centro de Reabilitação de Animais Selvagens. O método de Partial Least Squares-Path Modelling (PLSPM) foi utilizado para determinar o impacto das pressões antropogénicas nessas populações. De 2008 a 2017, um total de 6058 aves selvagens nativas, 359 mamíferos selvagens, 66 répteis e 12 anfíbios foram admitidos no Centro de Recuperação de Animais Selvagens do Parque Biológico de Gaia (Portugal), mortos ou que morreram após a sua admissão. As regiões do norte de Portugal mais afetadas pelas pressões antropogénicas e onde foram recolhidos mais animais mortos pelas autoridades ou público foram Vila Nova de Gaia e Porto. A principal causa de internamento ocorreu devido a ferimentos, em todas as classes estudadas. A primavera e o verão foram as estações do ano em que mais animais foram admitidos. A principal causa de mortalidade foi traumatismo (principalmente traumatismo de origem desconhecida). Os resultados do PLS-PM identificaram como pressões mais significativas o número de pequenas e médias empresas nos municípios, tanto em mortes de origem traumática como não traumática. Embora o padrão de pesos seja semelhante, independentemente da causa geral da morte, as causas traumáticas parecem desempenhar um papel mais proeminente, dado os pesos maiores nas causas específicas relevantes (número de empresas). Os altos coeficientes de determinação (R2>0,8) revelam que a variação da mortalidade de aves selvagens é explicada em grande parte pela variação das pressões, o que indica uma relação de causa-efeito entre as variáveis independentes (pressões) e dependentes (mortalidade). O estudo da necropsia e as lesões observadas confirmaram os dados anteriores. No exame post mortem, os principais sistemas afetados foram os sistemas músculo-esquelético e tegumentar. As principais lesões observadas foram relacionadas a traumatismo e a maioria delas teve origem humana. A generalidade das lesões nas aves e morcegos esta relacionada ao impacto com infraestruturas, lesões causadas por armadilhas ou predação de animais domésticos (cão e gato). Em mamíferos estava particularmente relacionado com a colisão com veículos. Numa que realizámos num total de 170 animais selvagens (126 mamíferos e 44 aves) admitidos no Laboratório de Histologia e Anatomia Patológica da Universidade de Trás-os-Montes e Alto Douro de 2009-2019, vítimas de atropelamento, as lesões mais comumente observada foram: hemorragias, fraturas, hematomas e traumatismo craniano. O uso de um sofisticado método estatístico PLS-PM e sua incorporação em um Sistema de Informações Geográficas (SIG) revelou-se uma ferramenta importante para analisar o impacto na fauna silvestre de fatores ambientais e humanos. Os resultados obtidos indicam que há um impacto negativo substancial da atividade humana na mortalidade de animais selvagens. Os dados apresentados constituem uma ferramenta valiosa para promover a conservação da vida selvagem no norte de Portugal. Podem ainda fornecer uma visão da saúde dos ecossistemas, para ajudar a educar as pessoas a valorizarem a biodiversidade existente nessas áreas e encontrar novas estratégias para ajudar a recuperar e proteger muitas dessas espécies. No futuro, estudos mais abrangentes devem ser aprimorados em outras regiões do território nacional, compreendendo diferentes populações, a fim de identificar as principais pressões antropogénicas em diferentes áreas de estudo. É necessário, ao mesmo tempo, a integração de outras áreas do conhecimento, como genética populacional, patologia, ecologia são apenas alguns dos exemplos.<br>In the last decades the human population has grown exponentially and nearly three quarters of the land without ice is now dominated by anthropogenic biomes. Its presence and activity have led to altered ecosystems, leading to their destruction or fragmentation. These changes have enormous negative consequences on the wild populations, both directly and indirectly, that in a final stage can lead to the extinction of entire wild populations. In this study we aim to obtain a general view over the consequences of human-induced threats to the wild vertebrates (birds, mammals, reptiles, amphibians) populations in the Northern of Portugal, based on data collected from a Wildlife Rehabilitation Centre. The method of Partial Least Squares-Path Modelling (PLS-PM) was used to determine the impact of anthropogenic pressures in those populations. From 2008 to 2017 a total 6058 native wild birds, 359 wild mammals, 66 reptiles and 12 amphibians were admitted to the Wildlife Rehabilitation Centre of Parque Biológico of Gaia (Portugal), death or that died after admitted. Vila Nova de Gaia and Porto were the regions on Northern Portugal more affected by anthropogenic pressures and where more death animals were collected. The main cause of admission was due injured animals, in all the classes studied. Spring and summer were the seasons when more animals were admitted. The main cause of mortality was due to trauma (mostly trauma of unknow origin). The PLS-PM results identified as most significant pressures, the number of small and medium companies in the municipalities, both in traumatic and non-traumatic deaths. Although the pattern of weights is similar regardless of the general cause of death, traumatic causes seem to play a more prominent role given the larger weights in the relevant specific causes (number of companies). The high coefficients of determination (R2 > 0,8) reveal that the variance of wild bird mortality is largely explained by the variance of the pressures, which indicates a cause-effect relationship between the independent (pressures) and dependent (mortality) variables. The study of the necropsy and observed lesions confirmed the previous data. In the post-mortem exam the main system affected was the musculoskeletal and integument systems. The main lesions observed were related to trauma and most of them we could related to human origin. The majority of the lesions in the birds and bats were related to the impact with infrastructures, predation by domestic pets’(dog and cat) or entrapment. In mammals it was particularly related to collision with vehicles. In 170 wild animals (126 mammals and 44 birds) admitted to the University of Trásos-Montes and Alto Douro University Laboratory of Histology and Pathology, 2009-2019, victims of being run over, the most commonly observed injuries were: hemorrhages, fractures, bruises and head trauma. The use of a sophisticated statistical method PLS-PM and its incorporation into a Geographic Information System (GIS) revealed to be an important tool for analysing wildlife impacts of environmental and human factors. The results obtained indicate that there is a substantial negative impact of human activity on wild bird mortality. The data presented constitute a valuable tool to promote wildlife conservation in Northern Portugal. It may provide an insight in the health of ecosystems, in order to help educating people to value the biodiversity existent in these areas and find new strategies to help to recover and protect many of this species. In the future, more comprehensive studies should be enhanced within other regions of the national territory comprising different populations in order to identify the main anthropogenic pressures in different study areas. It is necessary at the same the integration of other knowledge areas such as population genetics, diseases, ecology and others.

Resistance to antibiotics is a rising concern in respect to community and personal health, health-access social discrepancy and the future of the natural world. This work aimed to understand the role of environmental bacteria as the origin of the genetic determinants of antibiotic resistance (AR), as well as to explore the impact of anthropogenic pressures on the evolution and spread of AR. Shewanella’s genus role as progenitors and reservoir of AR genes was assessed through the analysis of a collection of environmental isolates and genomes of this genus deposited in public databases. The presence and the genetic context of the gene encoding for carbapenemase OXA-48 and the presence of qnrA-like genes was assessed. These genes were detected in several Shewanella species, in certain cases for the first time, being speciesspecific at times. Furthermore, several new variants were identified in this work. Insertion sequences associated with gene transfer were identified, suggesting its contribution to the spread of these genes to other phylogenetic groups. The impact of human action on the spread of AR in aquatic compartments was addressed through the analysis of groundwater used for irrigation and vegetables consumed raw. Multiresistant strains with virulent characteristics were found, common to both environments, suggesting irrigation water as the source of the contamination detected in the vegetables. Genome analysis of some of these strains revealed virulence determinants, mobile genetic elements and resistance genes, suggesting a potential risk to human health. In addition, the diversity and abundance of bacteria resistant to carbapenems were evaluated in a wastewater treatment plant, throughout the process, which includes an ultraviolet radiation disinfection step. This treatment showed significant results in reducing the number of bacteria, either total and resistant to carbapenems. In untreated samples, Enterobacteriaceae strains were detected carrying blaGES-5 -associated with integrons-, which is rarely found in clinical settings in Portugal. In the final effluent were found bacteria intrinsicallyresistant to carbapenems, namely Stenotrophomonas. The results obtained in this work reveal additional evidence regarding the role of environmental bacteria as progenitors of AR genes, as well as the role of humans in the spread of AR in aquatic compartments. This knowledge is crucial to define mitigation strategies for this problem, both in the environment and in the clinic.<br>A resistência a antibióticos é uma preocupação crescente no que diz respeito à saúde pessoal e comunitária, à discrepância social no acesso à saúde e ao futuro do mundo natural. Este trabalho teve como objetivos compreender a origem dos determinantes genéticos da resistência a antibióticos (RA) em bactérias ambientais, bem como explorar o impacto da pressão antropogénica na evolução e dispersão da RA. O papel do género Shewanella como origem e reservatório de genes de RA foi avaliado através da análise de uma coleção de isolados ambientais e de genomas deste género, depositados em bases de dados públicas. A presença e o contexto genético do gene que codifica para a carbapenemase OXA-48 e a presença de genes qnrA foram avaliados. Estes genes foram detetados em várias espécies de Shewanella, nalguns casos pela primeira vez, sendo específicos para algumas destas espécies. Além disso, várias variantes novas foram identificadas neste trabalho. Sequências de inserção associadas à transferência de genes foram identificadas, fundamentando a sua contribuição na dispersão destes genes para outros grupos filogenéticos. O impacto da ação humana na disseminação da RA em compartimentos aquáticos foi abordado através da análise de vegetais consumidos crus e da água subterrânea utilizada para irrigação. Foram encontradas estirpes multirresistentes e com características de virulência, comuns aos dois ambientes, sugerindo a água de irrigação como origem da contaminação detetada em vegetais. A análise do genoma de algumas destas estirpes revelou determinantes de virulência, elementos genéticos móveis e genes de resistência, sugerindo um risco potencial para a saúde humana. Além disso, a diversidade e abundância de bactérias resistentes a carbapenemos foram avaliadas numa estação de tratamento de águas residuais, ao longo do processo que inclui um passo de desinfeção com radiação ultravioleta. O tratamento reduziu significativamente o número de bactérias, totais e resistentes a carbapenemos. Em águas não tratadas, foram detetadas estirpes de Enterobacteriaceae com o gene blaGES-5 -associado a integrões-, raramente encontrado no contexto clínico em Portugal. No efluente final foram encontradas bactérias intrinsecamente resistentes aos carbapenemos, nomeadamente Stenotrophomonas. Os resultados obtidos revelam evidência adicional no que diz respeito ao papel das bactérias ambientais como progenitores dos genes de RA, tal como o papel do homem na disseminação da RA nos compartimentos aquáticos. Este conhecimento é crucial para definir estratégias de mitigação deste problema, tanto no meio ambiente como na clínica.<br>Programa Doutoral em Biologia e Ecologia das Alterações Globais

University of Technology Sydney. Faculty of Science.<br>Marine coastal systems are threatened by a wide range of anthropogenic pressures. Of particular concern are increased sediment and nutrient runoff. Moreover, hotspots of anthropogenic pressures are also where invasive species tend to be. The spread of invaders can directly translate to a loss of biodiversity and associated ecosystem services. There is a growing awareness that the spread of native species can have similar large impacts on biodiversity and ecosystem function to their famous non-native counterpart. Yet the how, when and why a native species transitions to a ‘native-invader’ (sensu Simberloff and Rejmánek 2010) are poorly known. This is especially true in the marine environment. In New South Wales (NSW), eastern Australia, a native green macroalga from the notorious Caulerpa genus, C. filiformis, has spread both inside and outside its native range. This study investigated the mechanisms that may have promoted the success of C. filiformis. The main aims were to increase our understanding on why this species has become so abundant, the habitat associations of the alga across large and local spatial scales, and the potential impacts on the seaweed community. In Chapter 2, large scale surveys showed that adult population abundance was related to sedimentation at multiple spatial scales, such as Reef Beach Index (RBI), reef width and the presence of a sediment veneer on top of the rocky reef (r+s habitat). In contrast, a low association with turf habitat was found, which is opposite to the observations for several other Caulerpa invaders. A model was proposed where the adult association with r+s represents an end stage of succession after outcompeting turfing alga. Moreover, it was shown that the seaweed community showed reduced morpho-functional richness in presence of C. filiformis. To test the proposed model, habitat association of the recruitment stage was investigated in Chapter 3. Surveys at several locations throughout the alga’s distribution showed that C. filiformis’ recruit abundance was found to be high on turfing algae habitat and not on r+s habitat. This positive association of the recruitment stage was observed for coralline forms of turfing alga, but not for filamentous forms. Those results support the model hypothesized. Additionally, the mechanisms behind this positive association were further explored in this chapter. A laboratory experiment revealed that the high association of C. filiformis’ recruits with coralline alga was explained by the increased attachment performance of C. filiformis fragments on this substrate. Namely, the increased structural complexity of coralline alga aided in rapid and strong attachment of fragments. Finally, mechanisms that may benefit post-recruitment processes of C. filiformis, and in particular the role of turf habitat, were investigated. With the use of long term field observations in Chapter 5, it was shown that established Caulerpa appears a poor competitor, and possibly requires further disturbance to spread. For example, a laboratory experiment showed that C. filiformis is highly tolerant to large sedimentation rates, aided by rapid morphological plasticity (Chapter 4). This may benefit the alga indirectly if sediment more negatively affects competitors. Moreover, increased sediment-nutrient availability was shown to promote growth rates, benefitting the alga’s competitive strength (Chapter 5). Overall, my thesis indicates that disturbance to native macrophytes indirectly promotes recruitment success by promoting turf habitat and that its continued spread is reliant on further disturbance to native communities – a model that has been demonstrated to invasive marine algae but not previously for a rapidly spreading native alga.

Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

Tese de doutoramento em Biociência, na especialidade de Ecologia, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra<br>A Directiva-Quadro da Água reforça o papel dos usos do solo na avaliação da qualidade da água, mas a utilização de dados de ocupação do solo, no que respeita a águas de superfície, restringe-se à estimativa dos padrões de uso do solo para a identificação de pressões provenientes de fontes de poluição difusas. O principal objetivo deste estudo é identificar especificidades da ocupação dos usos do solo na avaliação das mudanças de estado (Capítulo I), pressões (Capítulo I e II) e forças motrizes (Capítulo III e IV) da qualidade das águas de superfície. Para o efeito, usamos dados da bacia hidrográfica do Rio Mondego, uma bacia costeira localizada em Portugal, onde as mudanças socioeconómicas têm sido observadas desde a década de 1990 e que resultaram na perda de representatividade do setor agrícola e ganho do setor da construção. Apesar das mudanças, a agricultura mantém-se como uma fonte de pressão sobre as águas de superfície que, associada a modificações hidromorfológicas, causaram um declínio da qualidade ecológica do estuário do Mondego. Em 1998, a implementação de medidas de mitigação permitiu a recuperação do sistema, mas a monitorização identificou elevadas concentrações de nutrientes que pediam uma avaliação da sua proveniência. Por esta razão, a bacia do Rio Mondego, emerge como um caso de estudo com as condições necessárias para identificar aplicações mais amplas de dados de ocupação do solo no âmbito da identificação de forças motrizes e pressões sobre a qualidade da água. O Capítulo I estabelece a linha de base para este trabalho através da aplicação de indicadores de nutrientes e de substâncias-consumidoras-de-oxigénio para analisar a evolução das concentrações de amónia, nitrato e fosfato no estuário do Mondego entre os períodos 2003-2007 e 2012-2013 (ANOVA no software R); para analisar as diferenças entre as concentrações médias anuais de nutrientes nos rios tributários em 2012-2013 e as concentrações médias anuais encontradas em rios europeus em três períodos diferentes (1992, 2000, 2012); e para avaliar as diferenças na variabilidade das concentrações de nutrientes no estuário e nos tributários em 2012-2013 (ANOVA em software R). Adicionalmente, o Capítulo I avalia a dependência das concentrações de nutrientes estuarinas das entradas de água doce provenientes dos tributários, em dois períodos distintos. Procurou-se a relação linear entre as concentrações de nutrientes e a salinidade, a precipitação e a temperatura (regressão linear no software R). Os resultados revelam diferenças entre os intervalos de tempo e mostram uma dependência das concentrações de nutrientes das entradas de água doce proveniente dos rios, o que indica pressão de cargas de nutrientes sobre o estuário. No Capítulo II a pressão exercida pela descarga de nutrientes nos rios da bacia hidrográfica é avaliada utilizando dados de ocupação do solo. Analisa-se a adequação de métricas de paisagem para descrever a variabilidade espacial de nitratos em toda a bacia do rio Mondego usando dados sazonais de 2001 e 2006 (modelo linear misto - software R). Os resultados revelam que os padrões de ocupação do solo são descritores fracos da variabilidade espacial de nitratos na bacia do rio Mondego. No Capítulo III caracterizam-se as forças motrizes da qualidade da água usando como proxy os processos de mudança da paisagem. Os mapas CORINE de 1990, 2000 e 2006 são utilizados para analisar as mudanças entre oito categorias de ocupação, através de uma análise alargada de matrizes de transição. A magnitude da mudança e a consistência das transições revelam que as forças motrizes mais relevantes incluem categorias com baixa percentagem de ocupação, mas elevado efeito potencial nos processos hidrológicos. No Capítulo IV, reconhecendo que a precisão dos mapas pode influenciar a nossa percepção acerca das forças motrizes que atuam no sistema, aplica-se uma Análise de Intensidade para avaliar a adequação dos mapas CORINE como indicadores de mudanças de ocupação. Transições inconsistentes indicam erros de classificação que se poderiam propagar para outras aplicações que utilizam mapas de mudança de ocupação do solo. Analisando os resultados concluímos que ainda há espaço para o desenvolvimento de indicadores, nomeadamente indicadores de eficácia-de-políticas; que os dados de ocupação do solo como indicadores de pressão podem revelar o efeito, a longo prazo, da implementação de políticas; que a magnitude e a consistência dos processos de mudança de ocupação do solo revelam informações adicionais relativamente à avaliação das forças motrizes de transições de ocupação e que os mapas CORINE, apesar de serem dados de elevada qualidade, têm limitações de precisão facilmente identificadas através de uma Análise de Intensidade. Em relação à concentração de nutrientes, o nosso estudo sugere que são necessárias medidas de mitigação para reduzir as entradas de concentrações de fosfato para o estuário, de preferência por meio de políticas a nível europeu. The European Water Framework Directive enhances the role of land use in determining water quality of all waters, but the use of land cover data, regarding surface waters, is restricted to the estimation of land use patterns for the identification of pressures on surface waters from diffuse source pollution. The main goal of this study is to uncover specificities of land cover in the assessment of state changes (Chapter I), pressures (Chapt er I and II) and drivers (Chapter III and IV) of water quality of surface waters. For this purpose, we use data from the Mondego river basin, a coastal watershed in Portugal , where socio - economic changes observed since the 1990 s resulted in the loss of rep resentativeness from the agricultural sector and gain from the construction sector. Despite the observed changes, agriculture remained a source of pressure on surface waters which, associated with hydro - morphological modifications, caused a decline of the ecological quality of the Mondego estuary. In 1998, the implementation of mitigation measures enabled the recovery of the system but routine monitoring identified high concentrations of nutrients deserving further assessment to understand its sources. For this reason, the Mondego river basin, as a case study, provided conditions to reveal wider applications of land cover data within the assessment of drivers and pressures of water quality. Chapter I establishes the baseline for our research applying indicat ors of nutrients and oxygen - consuming - substances to analyze progress in the concentrations of ammonia, nitrate and phosphate in the Mondego estuary from a former period (2003 - 2007) to a recent period (2012 - 2 2013) (ANOVA in R software); to analyze difference s between the annual mean concentrations of nutrients in the tributary rivers in 2012 - 2013 and the average annual mean concentrations found in European rivers in three different periods (1992, 2000, 2012); and to evaluate differences in the variability of nutrient concentrations between the estuary and the tributaries in 2012 - 2013 (ANOVA in R software). Additionally, Chapter I evaluates the dependency of estuarine nutrient concentration s on riverine freshwater inputs in two different periods. A linear relat ionship between the nutrient concentrations and salinity, precipitation and temperature was sought (linear regression in R software). Altogether the results indicate differences between time intervals and are able to establish a dependency of nutrient conc entrations on riverine freshwater inputs, indicating pressure from nutrient loadings on the estuary. In Chapter II pressure from nutrient flushing on the river basin is evaluated using land cover data as an indicator. The suitability of landscape metrics t o describe the spatial variability of nitrate across the Mondego river basin is assessed using seasonal data from the years 2001 and 2006 (linear mixed model - R software). The results reveal that land cover patterns are weak descriptors of nitrate spatial variability in the Mondego river basin. In Chapter III driving forces of water quality are characterized using processes of landscape change as proxy. CORINE Land cover maps at 1990, 2000 and 2006 are used to analyze changes among eight categories throug h an extended analysis of transition matrices. The magnitude of change and consistency of transitions reveal that the most relevant driving forces from land transitions include categories with low percentage of occupation but high potential effect on hydro logical processes. In Chapter IV, acknowledging that the accuracy of maps may influence our perception of the main driving forces acting in the system, the Intensity Analysis approach is applied to evaluate the suitability of the CORINE land cover maps as indicators of land change. Inconsistent transitions reveal the misclassification errors that could propagate to other land cover change applications, as in the assessment of hydrological processes. Through the analysis of the results we conclude that there is still space for the development of indicators, namely policy effectiveness indicators; land cover data as indicator of pressure may reveal the effect of policies’ implementation in the long - term; the magnitude and con sistency of the processes of land change reveal additional information regarding the assessment of driving Abstract 3 forces from land transitions and that CORINE maps, though being high quality datasets, have accuracy limitations that are easily accessed through Int ensity Analysis. Regarding nutrient concentrations, our study suggests that mitigation measures, preferably through policies at the European level, are needed to reduce the inputs of phosphate concentrations into the estuary.<br>The European Water Framework Directive enhances the role of land use in determining water quality of all waters, but the use of land cover data, regarding surface waters, is restricted to the estimation of land use patterns for the identification of pressures on surface waters from diffuse source pollution. The main goal of this study is to uncover specificities of land cover in the assessment of state changes (Chapter I), pressures (Chapter I and II) and drivers (Chapter III and IV) of water quality of surface waters. For this purpose, we use data from the Mondego river basin, a coastal watershed in Portugal, where socio-economic changes observed since the 1990s resulted in the loss of representativeness from the agricultural sector and gain from the construction sector. Despite the observed changes, agriculture remained a source of pressure on surface waters which, associated with hydro-morphological modifications, caused a decline of the ecological quality of the Mondego estuary. In 1998, the implementation of mitigation measures enabled the recovery of the system but routine monitoring identified high concentrations of nutrients deserving further assessment to understand its sources. For this reason, the Mondego river basin, as a case study, provided conditions to reveal wider applications of land cover data within the assessment of drivers and pressures of water quality. Chapter I establishes the baseline for our research applying indicators of nutrients and oxygenconsuming-substances to analyze progress in the concentrations of ammonia, nitrate and phosphate in the Mondego estuary from a former period (2003-2007) to a recent period (2012) - 2013) (ANOVA in R software); to analyze differences between the annual mean concentrations of nutrients in the tributary rivers in 2012-2013 and the average annual mean concentrations found in European rivers in three different periods (1992, 2000, 2012); and to evaluate differences in the variability of nutrient concentrations between the estuary and the tributaries in 2012-2013 (ANOVA in R software). Additionally, Chapter I evaluates the dependency of estuarine nutrient concentrations on riverine freshwater inputs in two different periods. A linear relationship between the nutrient concentrations and salinity, precipitation and temperature was sought (linear regression in R software). Altogether the results indicate differences between time intervals and are able to establish a dependency of nutrient concentrations on riverine freshwater inputs, indicating pressure from nutrient loadings on the estuary. In Chapter II pressure from nutrient flushing on the river basin is evaluated using land cover data as an indicator. The suitability of landscape metrics to describe the spatial variability of nitrate across the Mondego river basin is assessed using seasonal data from the years 2001 and 2006 (linear mixed model - R software). The results reveal that land cover patterns are weak descriptors of nitrate spatial variability in the Mondego river basin. In Chapter III driving forces of water quality are characterized using processes of landscape change as proxy. CORINE Land cover maps at 1990, 2000 and 2006 are used to analyze changes among eight categories through an extended analysis of transition matrices. The magnitude of change and consistency of transitions reveal that the most relevant driving forces from land transitions include categories with low percentage of occupation but high potential effect on hydrological processes. In Chapter IV, acknowledging that the accuracy of maps may influence our perception of the main driving forces acting in the system, the Intensity Analysis approach is applied to evaluate the suitability of the CORINE land cover maps as indicators of land change. Inconsistent transitions reveal the misclassification errors that could propagate to other land cover change applications, as in the assessment of hydrological processes. Through the analysis of the results we conclude that there is still space for the development of indicators, namely policy effectiveness indicators; land cover data as indicator of pressure may reveal the effect of policies’ implementation in the long-term; the magnitude and consistency of the processes of land change reveal additional information regarding the assessment of driving forces from land transitions and that CORINE maps, though being high quality datasets, have accuracy limitations that are easily accessed through Intensity Analysis. Regarding nutrient concentrations, our study suggests that mitigation measures, preferably through policies at the European level, are needed to reduce the inputs of phosphate concentrations into the estuary.

Le sanctuaire Agoa est une aire marine protégée dans la zone économique exclusive (ZEE) des Antilles françaises qui fut créée en 2010 pour la conservation des mammifères marins et de leurs habitats. Il est connu que le rorqual à bosse fréquente les eaux des Antilles de décembre à mai pour la reproduction et la mise bas. Par contre, peu d’information existe sur l’abondance, le comportement, la distribution et les pressions anthropiques sur cette espèce aux Antilles et encore moins dans le sanctuaire. Cette maîtrise s’intéresse principalement à connaître cette espèce dans un secteur précis de cette aire marine et les liens qu’elle entretient avec certains utilisateurs humains de son habitat. Le tout vise à informer les intervenants en place, autant institutionnels qu’utilisateurs, vers une mise en place de mesures de conservation adaptées. Un suivi terrestre hivernal de plus de 300 heures, en 2012 et 2013, a permis de déterminer l’utilisation de l’habitat et les pressions anthropiques sur une population de rorquals à bosse fréquentant le sud de la péninsule de la Pointe-des-Châteaux en Guadeloupe. Il s’agit du premier suivi terrestre de cette espèce aux Antilles françaises et un des premiers dans l'arc caribéen. La zone d’étude couvre environ 264 km2 et serait une des zones les plus fréquentées de l’archipel guadeloupéen par l’espèce. À l’aide d’un théodolite, la trajectoire de 107 groupes différents (137,8 heures, 699 remontées) a été décrite. Les résultats montrent que la zone d’étude est principalement fréquentée en mars et avril, avec une abondance maximale au début du mois d’avril. La forte présence de baleineaux, particulièrement au mois de mars, pousse à croire que cette zone est utilisée comme pouponnière. Le comportement n’est pas aléatoire dans la zone d’étude et les trajectoires convergent vers certaines zones ayant possiblement un lien avec la bathymétrie. De plus, la zone marine à proximité de la Pointe-des-Châteaux pourrait potentiellement être un lieu de convergence des groupes. Ceux-ci se déplacent à vitesse réduite en direction ENE en général, à l’exception des femelles accompagnées de baleineaux qui prennent une orientation tout autre, c’est-à-dire vers le ONO, et ce à plus grande vitesse. Bien que la pression d’observation soit considérée comme modérée, une forte proportion des remontées se trouve dans les corridors de navigation présents dans la zone d’étude. De plus, le corridor de navigation des navettes entre Saint-François et La Désirade comporte le plus grand risque relatif de collision mortelle. Une réduction de vitesse des embarcations fréquentant le corridor des navettes diminuerait significativement le risque de collision mortelle. Ces pistes de réflexion mèneront sans doute à d’autres études plus poussées afin de continuer à en apprendre sur l’écologie de cette espèce fascinante.<br>The Agoa sanctuary, a marine protected area (MPO) covering the exclusive economic zone (EEZ) in the French Caribbean, was created in 2010 to protect marine mammals and their habitats. It is known that the Caribbean islands are used from December to May by humpback whales (Megaptera novaeangliae) as a reproductive area. However, sparse information exists on the abundance, the behaviour, the distribution and the anthropogenic pressures on this species in the Caribbean and even less in the sanctuary. This thesis focuses on increasing scientific knowledge about this species’ use of a part of the Agoa Sanctuary and their interactions with human users of the MPO. Such knowledge may inform stakeholders’ (institutional and individual) decision-making towards implementation of appropriate conservation measures. A land-based survey of more than 300 hours, in 2012 and 2013, was carried out to determine the habitat use of, and anthropogenic pressures on, a population of humpback whales frequenting the surrounding water of the Pointe-des-Châteaux peninsula in Guadeloupe. This is the first land-based survey of this species in the French West Indies and one of the first in the Caribbean. The study area of approximately 264 square kilometres is one of the most visited areas by this species in the Guadeloupe archipelago. Using a theodolite, 107 trajectories (i.e. groups of whales) were recorded, representing 137.8 hours and 699 surfacings. Results show that the abundance was higher in March and April with a peak in the first week of April. The high proportion of calves in this population, mainly in March, suggest that the study zone is a nursing area. Overall movement patterns are not random and may possibly be dictated by the bathymetry. Furthermore, trajectories seem to converge close to the Pointe-des-Châteaux. The average movement is slow and oriented in the same direction as the dominant current to the west of the Pointe-des-Châteaux (i.e. ENE), except for mother and calf groups that swim faster in the opposite direction (i.e. WNW). Even if the anthropogenic pressure may be consided as moderate, a high proportion of surfacing is located in some of the main maritime traffic corridors. In addition, the shuttle corridor between Saint-Francois and Désirade island has the greatest relative risk of fatal collision. A reduced speed for the shuttle corridor would lower significantly the collision risk. These findings may lead to more extensive studies to better understand the ecology of this fascinating species.