Dissertations / Theses on the topic 'Freshwater ecosystems'

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L'objectiu d'aquesta tesi és contribuir a l'ús dels peixos continentals com a indicadors de l'estat ecològic a la conca Mediterrània. En el primer treball es va detectar que encara que tots els índex biològics estaven correlacionats significativament, els peixos integren i expressen els estressos de manera i a una escala diferents, aportant una informació complementària als altres índexs. Al segon article es van estudiar els cabals de sis conques catalanes. S'ha mostrat que els règims hídrics estan alterats amb una tendència a la disminució del cabal i del nivell dels aqüífers. S'ha detectat quatre mètriques de peixos que es troben significativament afectades en zones més castigades per manca d'aigua degut a l'activitat humana. Es discuteix la necessitat de conèixer en profunditat el règim hídric de cada conca abans d'utilitzar els índex biològics. Al tercer article es va detectar que la composició d'espècies capturades va variar significativament al llarg del buidat amb un augment de l'alburn (A. alburnus) a les aigües pelàgiques durant els dies de pitjor qualitat de l'aigua, confirmant que l'alburn és més tolerant a la mala qualitat de l'aigua que la madrilleta vera (R. rutilus) i suggereix el seu potencial com a bioindicador. La condició d'aquestes dues espècies va canviar significativament al llarg del buidat de manera molt estreta amb la qualitat de l'aigua. Al quart capítol es va estudiar la biologia dels peixos d'un embassament altament contaminat (Flix). El percentatge de DELT anomalies i la presència de paràsits externs era major en la zona impactada que als punts de control i els valors més alts de pes eviscerat i pes del fetge estaven als punts de control. Les respostes van ser diferents per cada espècie i la carpa va ser la que va mostrar més clarament els impactes.
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The aim of this thesis is to contribute to the use of freshwater fish as ecological indicators in the Mediterranean basin. In the first article we found that although most biological indices were correlated, fish reflected different ecological aspects due to their particular features. In the second article the stream flow regimes of six Mediterranean basins were studied. A decrease of streamflow and aquifer levels was detected, despite no observed decrease of rainfall precipitation. Of the thirty metrics tested to detect sites impacted by water abstraction, we detected four significant fish metrics. Furthermore, the role of biotic indices when the river is artificially dry is discussed. In the third article we found that species composition in the pelagic zone varied significantly during the drawdown with higher proportion of bleak (A. alburnus) during the days of worst water quality, confirming that bleak is more tolerant than roach (R. rutilus) to poor water quality. The weight-length relationship of roach and bleak also varied significantly during the drawdown with close relationship between water quality and fish condition. In the fourth article the condition and fecundity of freshwater fishes were assessed in a highly polluted reservoir (Flix reservoir). We have shown significant increases of DELT anomalies and ectoparasite prevalences and decreases in condition and fecundity of several freshwater fish at the impacted area. The responses to the pollutants were species-specific and common carp was the species that showed more markedly the effects.

Doutoramento em Biologia
The projections made by the International Panel on Climate Changes (IPCC) until the year 2100 foresee scenarios of increased sea level rise and extreme weather events. As a consequence of these changes it is anticipated that coastal ecosystems (both terrestrial and freshwater) will suffer from seawater (SW) intrusions and, consequently, become impacted with salinization. Such salinization, caused by SW intrusion, may occur through surface flooding (for example due to violent storms, which may lead to pulses of SW intrusion with high peaks of salinity that, most probably, will cause lethal effects on biota) and/or groundwater intrusion (which may occur more gradually, and, most likely starts by inducing sublethal effects in the ecological receptors). In this context, the present work intended to evaluate the adverse effects that salinization, due to SW intrusion, may cause to coastal ecosystems. For this, several specific goals were identified: (i) to determine if sodium chloride (NaCl) may be used as a surrogate of SW at early stages of ecological risk assessment frameworks. This possibility would be advantageous since many toxicity data exist for NaCl and, therefore, it would reduce the number of toxicity assays needed to be carried out; (ii) to identify the ecological receptors most sensitive to salinization, by using standard approaches; (iii) to establish if biota is capable of acquire an increased tolerance to low levels of salinization through mechanisms of phenotypic plasticity; (iv) to assess the effects of increased salinity on interspecies relationships; and (v) to identify the effects of salinization for freshwater and soil communities under realistic exposure scenarios. These objectives were addressed along seven chapters by using standard and non-standard ecotoxicological approaches from the individual (by exposing organisms, from species belonging to different trophic levels, to increased salinity levels) to the community level (by performing multispecies exposures under more realistic scenarios of exposure). Obtained results revealed that, in general, NaCl exerted a similar or higher toxicity than SW, both to freshwater and terrestrial species. These results, suggest that NaCl could be used as a surrogate of SW at early stages of ecological risk assessment of salinization caused by SW intrusion. However, caution must be taken since there were a few species for which SW revealed higher toxicity, and multigenerational exposures showed an increase in the sensitivity to SW for microalgae species. Within the freshwater compartment, cladocerans and rotifers were the two taxonomic groups exhibiting the highest sensitive to salinization (both for NaCl and SW) while fish and macrophytes showed to be the most tolerant groups. Ecotoxicity data obtained for terrestrial plants and fungi (generated in the present work) was integrated with data obtained from literature, allowing to identify microinvertebrates (Folsomia candida and Enchytraeus crypticus) as the most sensitive group to salinization while fungi and plants were the most tolerant ones. The toxicity data generated from standard assays (or in part compiled from literature for terrestrial species) was used to compute the hazard concentrations that allowed protecting 95% of species (HC5), on the basis of species sensitive distribution curves. The values of HC5 were computed for freshwater and terrestrial species and for NaCl and SW; all of these values were very low (HC5 ≤ 2.26 mScm-1) when compared to the conductivity of natural seawater (≈ 52 mScm-1), foreseeing that coastal ecosystems will be at a high risk due to salinization. Experiments involving a pre-short and long-term (multigerational) exposure to low levels of salinity, overall, did not caused a change in the tolerance of biota to this stressor. However, some species revealed an increased tolerance (either associated with physiological acclimation or other mechanisms of phenotypic plasticity) to salinity after short (the amphibian species Pelophylax perezi) and multigenerational exposure (the cyanobacteria Cylindrospermopsis raciborskii and the cladoceran Daphnia longispina) to low levels of salinity. Contrarily to this, it was also observed that a few species revealed a higher sensitivity to salinization after multigenerational exposure (the microalgae Raphidocelis subcapitata and the macrophyte Lemna minor). These diverse results may be due to differences in the intensity of salinity stress and to the duration of the periods of exposure to low levels of salinization. To more accurately understand the influence of prolonged exposure to low levels of salinity in biota tolerance to this stressor, further studies should be carried out involving multigenerational exposure to sublethal levels of salinization. Regarding the specific objective (iv), the obtained results revealed that sublethal salinization levels influenced interspecific relationships. For freshwater microalgae, it was observed that, at low levels of salinity, a shift in the competition between the two microalgae species occurred. Adding to the direct effect that these changes will caused in the structure of microalgae community, indirect effects on other species (e.g. cladoceran species that feed on them) are also foresee. For terrestrial plants in the absence of salinization, a lower productivity was registered for some tested plants when exposure occurred under polyculture conditions comparatively to monoculture conditions. However, exposure to the salinity threshold of 4 mScm-1 under such conditions seemed not to alter the pattern of responses. Finally, exposure under more realistic scenarios (outdoor mesocosms) suggested a much lower toxicity of salinization to freshwater ecosystems than that predicted from standard approaches, suggesting a higher resilience of communities to salinization under more complex and relevant scenarios of exposure. These results suggest that risk of salinization to freshwater ecosystems may be overestimated when using standard methodologies and that ecologically relevant scenarios at higher stages of ecological risk assessment for this stressor should be considered.
Os relatórios de avaliação do Painel Intergovernamentl para as Alterações Climáticas (IPCC) baseados nas últimas décadas preveem, até 2100, cenários de contínua subida do nível médio da água do mar e eventos climatéricos extremos. Como consequência destas alterações prevê-se a ocorrência de intrusões de água do mar e subsequente salinização destes ecossistemas costeiros (tanto terrestres como dulçaquícolas). A salinização destas regiões costeiras pode ocorrer diretamente por inundações de superfície pela água do mar, por exemplo, devido a tempestades costeiras violentas (provavelmente, causando sobretudo efeitos letais), mas também pode ocorrer por intrusão de água do mar nos sistemas subterrâneos de água doce (o que pode ocorrer de forma mais gradual, provavelmente causando efeitos subletais). Tendo em conta estes aspectos, o presente trabalho pretendeu avaliar os efeitos adversos que tal salinização pode causar nos ecossistemas costeiros. Para tal, foram delineados os seguintes objectivos específicos: (i) determinar se o cloreto de sódio (NaCl) pode ser utilizado como substituto da água do mar, em avaliações preliminares de risco ecológico. Esta alternativa seria vantajosa uma vez que existem muitos dados de toxicidade para NaCl e, portanto, reduziria o número de ensaios de toxicidade que seria necessário realizar; (ii) identificar quais os receptores ecológicos mais sensíveis à salinização, utilizando protocolos padronizados; (iii) estabelecer se a biota é capaz de aumentar a sua tolerância a baixos níveis de salinização através de mecanismos de plasticidade fenotípica; (iv) avaliar os efeitos do aumento da salinidade nas relações interespecíficas; e (v) identificar os efeitos de salinização nas comunidades dulçaquícolas e terrestres em cenários de exposição mais realistas. Estes objetivos foram abordados ao longo de sete capítulos, recorrendo a abordagens ecotoxicológicas padronizadas e não padronizadas desde o nível de organização biológica indivíduo (expondo organismos, de espécies pertencentes a diferentes níveis tróficos, a níveis de salinidade crescentes) até ao nível da comunidade (realizando exposições com várias espécies em cenários mais realistas de exposição). Os resultados obtidos revelaram que, de um modo geral, o NaCl exerceu uma toxicidade similar ou superior à provocada pela água do mar, quer nas espécies dulçaquícolas quer nas terrestres. Esses resultados sugerem que o NaCl pode ser usado como substituto da água do mar nos primeiros estágios de avaliação do risco ecológico de salinização causada pela intrusão de água do mar. No entanto, o seu uso deve ser cauteloso, uma vez que houve algumas espécies para as quais a água do mar apresentou maior toxicidade, e no caso de exposições multigeracionais de espécies de microalgas, estas mostraram um aumento na sensibilidade à agua do mar. No compartimento dulçaquícola, os cladóceros e os rotíferos foram os dois grupos taxonómicos que apresentaram maior sensibilidade à salinização (tanto para NaCl como para água do mar), enquanto que os peixes e as macrófitas mostraram ser os grupos mais tolerantes. Os dados de ecotoxicidade obtidos para plantas terrestres e fungos (gerados no presente trabalho) foram integrados com dados recolhidos da literatura, permitindo identificar os microinvertebrados terrestres (Folsomia candida e Enchytraeus crypticus) como o grupo mais sensível à salinização, enquanto que os fungos e as plantas demonstraram ser os mais tolerantes. Os dados de toxicidade gerados a partir de ensaios padronizados (ou em parte compilados a partir de literatura para espécies terrestres) possibilitaram calcular as concentrações de risco que permitem proteger 95% das espécies num ecossistema (HC5), com base em curvas de distribuição de sensibilidade das espécies. Os valores de HC5 foram calculados para espécies dulçaquícolas e terrestres e para NaCl e água do mar; todos esses valores revelaram-se muito baixos (HC5 ≤ 2,26 mScm-1) quando comparados com a condutividade da água do mar natural (≈ 52 mScm-1), o que faz prever que os ecossistemas costeiros estarão em alto risco devido a salinização. De um modo geral, a pré-exposição a curto e a longo (multigeracional) prazo a baixos níveis de salinidade, não causou uma alteração significativa na tolerância da biota à salinização. No entanto, algumas espécies revelaram uma maior tolerância (associada à aclimatação fisiológica ou outros mecanismos de plasticidade fenotípica) à salinidade após curta exposição (espécie de anfíbio Pelophylax perezi) e exposição multigeracional (a cianobactéria Cylindrospermopsis raciborskii e o cladócero Daphnia longispina) a baixos níveis de salinidade. Contrariamente, observou-se também que algumas espécies apresentavam uma maior sensibilidade à salinização após exposição multigeracional (a microalga Raphidocelis subcapitata e a macrófita Lemna minor). Estes resultados diversos podem ser devidos a diferenças na intensidade de salinidade e à duração dos períodos de exposição a baixos níveis de salinização. Para compreender com maior exactidão a influência da exposição prolongada a baixos níveis de salinidade na tolerância da biota à salinidade, devem ser realizados estudos adicionais que envolvam exposição multigeracional a níveis subletais de salinização. Em relação ao objetivo específico (iv), os resultados obtidos revelaram que os níveis de salinização subletal influenciaram as relações interespecíficas. Para as microalgas dulçaquícolas, observou-se que, a baixos níveis de salinidade, ocorreu uma alteração na competição entre as duas espécies estudadas. Adicionando ao efeito direto que estas alterações irão provocar na estrutura da comunidade de microalgas, também se preveem efeitos indiretos em outras espécies (por exemplo, espécies de cladóceros que se alimentam delas). Para as plantas terrestres, na ausência de salinização, foi registada uma menor produtividade para algumas plantas testadas quando as mesmas se apresentavam num cenário de policultura comparativamente às condições de monocultura. A exposição ao limiar de salinidade de 4 mScm-1 pareceu não alterar este padrão de respostas. Finalmente, a exposição em cenários mais realistas (mesocosmos) sugeriu uma toxicidade inferior da salinização nos ecossistemas dulçaquícolas do que aquela prevista através de abordagens padronizadas, sugerindo uma maior resiliência das comunidades à salinização em cenários de exposição mais complexos e relevantes. Esses resultados sugerem que o risco de salinização para os ecossistemas dulçaquícolas pode ser sobrestimado quando se utilizam metodologias padrão e que cenários ecologicamente relevantes devem ser considerados em estágios avançados do processo de avaliação do risco ecológico para salinização.

Over the last 10-15 years pharmaceuticals have been identified as a widespread pollutant in freshwater systems having entered the environment predominantly via the domestic sewage system where removal by treatment systems is often poor. This thesis provides detailed reviews and meta-analyses of existing data regarding pharmaceutical pollutants, examines the occurrence of five pharmaceuticals in semi-rural and urban catchments of West Yorkshire and their effects on freshwater ecosystems using both laboratory and field experiments. A critical review and meta-analysis of 155 published pharmaceutical papers found 204 pharmaceuticals were present in rivers across large parts of Europe, North America and Asia. However, spatial and methodological gaps were identified in the research body with almost no research evident in Africa, South America, the Middle East and large parts of Asia. Furthermore, research effort was focused around a small number of commonly studied compounds often employing poorly representative grab sampling techniques. Treated and untreated effluent of sewage treatment plants, combined sewer overflows and their receiving freshwaters were monitored for five pharmaceuticals (diclofenac, erythromycin, ibuprofen, mefenamic acid and propranolol). All compounds were detected at very high frequencies across all samples confirming them as a ubiquitous and widespread pollutant in freshwaters. Data showed pronounced seasonal (winter maxima) and diurnal (late morning and late evening) peaks in concentrations. Periods of high flow were characterised by reduced concentrations, possibly due to dilution within receiving waters. No appreciable attenuation of pharmaceuticals was observed across an intensively sampled 5 km study reach of the River Aire in Leeds suggesting the pollution burden placed on rivers by pharmaceuticals extends well downstream of individual waste water point sources. Laboratory experiments revealed significant increases in mortality of the freshwater shrimp Gammarus pulex were observed during extended exposures to environmental levels of erythromycin and when combined in mixture with propranolol. A first application of 1H NMR environmental metabolomics to the study of pharmaceutical effects on freshwater biota was coupled with this experiment highlighting its potential use in ecotoxicological research. Sublethal, metabolic changes associated with energy storage and metabolism were observed with potential future applications for biomarker development centred on the osmolyte TMAO. The pharmaceuticals studied here were found to pose no detectable risk to leaf litter decomposition in streams although a further experiment demonstrated a reduction in organic matter processing of freshwater sediments, coupled with some complex stimulatory and inhibitory effects on respiration and nutrient cycling at environmentally relevant concentrations. Taken as a whole this work has added substantial knowledge to this growing research area and has allowed the construction of a conceptual framework that links measured environmental concentrations with effects at the sublethal and individual organism level mediated to the ecosystem and functional level via complex interactions between macroinvertebrates and microbial communities. Overall, this body of research has demonstrated that pharmaceuticals should be treated as a widespread pollutant of on-going major concern capable of eliciting significant effects on freshwater ecosystems. Therefore, they require substantial further research and scrutiny from regulators and policy makers if the negative consequences of their presence in rivers are to be avoided or mitigated.

Evolutionary change has largely been ignored in ecology because it has traditionally been considered too gradual a process to alter ecological patterns. Recent evidence that evolution can occur rapidly has challenged this notion. Understanding when evolution is likely to alter ecological processes and how evolution changes ecological dynamics could improve our understanding of community and ecosystem ecology and lead to greater predictability. In chapter 2 I present the results of an experiment investigating how local adaptation in two species alters community structure and ecosystem function. I found that intraspecific variation between these two taxa can interact to alter both the ecological community and some ecosystem functions. In chapter 3 I focus on understanding how rapid evolution from introgressive hybridization alters ecology in both a mesocosm experiment and a comparative field study. I found that introgressive hybridization lead to a phenotypic shift and predictable changes in community structure and ecosystem function based on trophic cascade theory. In chapter 4 I detail the findings from a large-scale piscivorous fish trophic cascade experiment. In this study I found that the addition of a piscivore alters the movement of invertebrates from aquatic environments to terrestrial environments. In addition, the results support previous findings that non-consumptive effects of predators may play an important role in determining the strength of the trophic cascade in the aquatic system. In chapter 5 I explore the role of rapid evolution in enhancing and maintaining ecosystem services. I create a quantitative criteria for assessing the importance of rapid evolution to ecosystem services, review cases where rapid evolution may already be playing an important role, and suggest ways to manage for the conservation of ecosystem services.
Science, Faculty of
Zoology, Department of
Graduate

Agriculture is the primary cause of sedimentation, nutrient enrichment, and insecticide contamination of freshwater ecosystems. Despite the widespread co-occurrence of these ecological stressors, little is known about their potential interactive effects. I conducted three experiments manipulating combinations of these stressors in order to evaluate their cumulative effects on freshwater ecosystems at different scales of biological organization (community, ecosystem, meta-ecosystem). First, I evaluated stream invertebrate community responses to sedimentation, nutrient enrichment, and the insecticide chlorpyrifos using laboratory microcosms with distinct microhabitats. I demonstrated that chlorpyrifos can interact non-additively with fine sediment (reversal) and nutrients (antagonism), with potentially deleterious impacts on small-sized invertebrates. Furthermore, invertebrates in gravel microhabitats were more severely affected than those in leaf packs. Second, I manipulated levels of nutrients, sediment, and the insecticide imidacloprid in experimental pond ecosystems. I demonstrated these stressors had antagonistic effects on pelagic and benthic invertebrate diversity. Moreover, the results suggested imidacloprid increased ecosystem metabolism indirectly, through negative effects on invertebrate consumers. Finally, I explored processes at the scale of the river network meta-ecosystem. Using a network of experimental channels, I investigated how multiple-stressor interactions within tributaries affected downstream ecosystems. My results indicated that complex nutrient-sediment interactions within tributaries could strongly alter the flux of organisms from tributaries to downstream ecosystems. Furthermore, I observed that at small spatial scales, these alterations of within-network migration patterns could be more influential than the transport of the stressors from headwaters to recipient ecosystems. My research contributes novel evidence suggesting that complex interactions among nutrient enrichment, sedimentation, and insecticide contamination are frequent in freshwater ecosystems, and have distinct mechanisms operating at different scales. In particular, these findings underscore the importance of considering multiple-stressor interactions in insecticide environmental risk assessments; even at low concentrations, interactions with other stressors may result in unexpected negative effects for aquatic biota and ecosystem processes.
Forestry, Faculty of
Graduate

Les microorganismes constituent la forme de vie la plus abondante et diverse sur Terre et ils présentent une grande diversité phylogénétique et métabolique. Ils sont donc impliqués dans les cycles biogéochimiques et les réseaux trophiques, ce qui en fait des acteurs clés du fonctionnement des écosystèmes. Pour décrypter l'écologie des microorganismes, il est essentiel de prendre en compte les échelles spatiales, temporelles et taxonomiques. Bien que des paramètres abiotiques et biotiques aient été identifiés comme influençant la composition des communautés microbiennes dans les écosystèmes aquatiques (e.g. la température, la prédation), des études complémentaires sont nécessaires pour mieux comprendre la structure des communautés microbiennes. Cependant, l'étude des interactions biotiques entre microorganismes est difficile en raison de leur petite taille, de la grande diversité et du peu d’individus cultivés. Cette thèse de doctorat vise à décrire la diversité microbienne au sein de deux types d'écosystèmes d'eau douce encore peu étudiés, et à identifier les facteurs qui déterminent la composition de leurs communautés microbiennes. La première partie de cette thèse vise à décrire la distribution spatiale (horizontale et verticale) des protistes planctoniques du lac Baïkal (Sibérie, Russie). Nous nous sommes intéressés à des échantillons collectés en été 2017 le long d'un transect de ~600 km couvrant les trois bassins du lac, de la surface aux profondeurs (~1500 m) et du littoral au pélagique. Les trois autres parties présentent une étude de huit ans de la composition et de la dynamique temporelle des communautés microbiennes des trois domaines du vivant, à la surface de cinq petits écosystèmes d'eau douce (sud-ouest de Paris, France). Les échantillons ont été collectés à deux fréquences, mensuelle (2011-2013) et saisonnière (2011-2019). Les communautés planctoniques ont été caractérisées par le séquençage des gènes ARNr 16S et 18S. Dans tous les écosystèmes, les communautés microbiennes sont très diverses, couvrant tous les super-groupes eucaryotes et procaryotes connus. Elles incluent des lignées typiquement marines (e.g. diplonémide, MAST), ce qui suggère que la frontière entre le marin et l'eau douce pourrait être plus fine que prévu. Des taxons encore peu connus ont aussi été détectés, tels que des bactéries du Candidate Phyla Radiation. Des analyses multivariées ont montré que seule une faible fraction de la variance des communautés peut être expliquée par les paramètres abiotiques étudiés. Pour les variations spatiales, nous avons constaté une faible variabilité des communautés du lac Baïkal dans les différents bassins, mais avec une forte stratification le long de la colonne d'eau. La profondeur, qui traduit les variations environnementales (e.g. la lumière) dans la colonne d'eau, semble influencer significativement les communautés. Les petits écosystèmes abritent différentes communautés microbiennes malgré leur proximité géographique. Pour les variations temporelles, deux dynamiques ont été identifiées. À l'échelle intra-annuelle, les communautés sont caractérisées par une forte saisonnalité. Cependant, moins de 2% des unités taxonomiques opérationnelles présentent une récurrence saisonnière. Cela suggère que les écosystèmes ont un fonctionnement saisonnier, malgré des dynamiques individuelles imprévisibles. À l'échelle interannuelle, les communautés microbiennes sont de plus en plus différentes au cours des huit années, indiquant des changements continus dans leur composition. Enfin, l’inférence des interactions microbiennes grâce aux réseaux de cooccurrence reflète les variations spatio-temporelles précédemment observées. En effet, les communautés sont plus complexes à la surface du lac Baïkal qu'en profondeur. De plus, les petits écosystèmes partagent des topologies similaires pour chaque saison. Cela souligne l'importance des interactions écologiques chez les communautés microbiennes, dans l'espace et le temps
Microorganisms are the most abundant and diverse forms of life on Earth and are characterized by high phylogenetic and metabolic diversities. They are thus involved in biogeochemical cycles and trophic webs, which make them key players in ecosystem functioning. To decipher the ecology of microorganisms, it is crucial to include spatial, temporal and taxonomic scales. Although several abiotic and biotic parameters have been identified as drivers of microbial community composition in aquatic ecosystems (e.g. temperature, orthophosphate concentration, predation, symbiosis), more investigations are needed to better understand how microbial community structure is shaped. However, investigating biotic interactions involving microbes is challenging because of microbial features (e.g. small size, high diversity, low cultivation efficiency). This PhD thesis aims at describing the microbial diversity inside two overlooked types of freshwater ecosystems and at identifying the factors driving microbial community composition. The first section of this thesis aims at comprehensively describing the spatial distribution (horizontal and vertical) of planktonic microbial eukaryotes in Lake Baikal (Siberia, Russia). We focus on samples collected in summer 2017 along a transect of ~600 km across the three basins of the lake, from the surface to the deepest areas (~1500 m) and from littoral to open waters. The three other sections present an eight-year investigation of the composition and temporal dynamics of microbial communities belonging to the three domains of life at the surface of five small freshwater ecosystems (located in the South West of Paris, France). Samples were collected at two different frequencies, monthly (2011-2013) and seasonally (2011-2019). The composition of planktonic communities was assessed by the sequencing of the phylogenetic marker genes 16S and 18S rRNA. In all the ecosystems studied, the microbial communities were diverse, covering all eukaryotic and prokaryotic supergroups. Moreover, they included typically marine lineages, especially in Lake Baikal, (e.g. diplonemid, MAST) which suggested that the frontiers between marine and freshwater systems may be thinner than previously thought. They also included taxa that remain enigmatic, such as bacteria of the Candidate Phyla Radiation. Multivariate analysis showed that only a low fraction of the variance can be explained by the measured physico-chemical parameters. In terms of spatial variations, there was a weak variability of communities in Lake Baikal in summer across sampling basins, but a strong stratification along the water column. Depth, which is a proxy and a summary of the variations of the environmental conditions (e.g. light) along the water column, appeared to be a major driver of community composition. The small freshwater ecosystems harbored different microbial communities despite their geographic proximity. In terms of temporal variations, two types of patterns were detected. At the intra-annual scale, global communities were characterized by a strong seasonality. However, at the Operational Taxonomic Unit level, less than 2% of the community were characterized by recurrent seasonal patterns. This suggests that ecosystems have a yearly seasonal functioning, despite the presence of some unpredictable microbial dynamics. At the inter-annual scale, microbial communities experienced an increase of dissimilarities over the eight years, indicating turnovers in community composition. Finally, the structure of the communities studied through co-occurrence network inference reflected the spatio-temporal variations previously observed. Indeed, communities were more connected at the surface of Lake Baikal compared to the bottom. Moreover, ecosystems shared similar structural properties at each season. This underlines the importance of ecological interactions in the composition of microbial community over space and time

Freshwater ecosystems and their associated landscape features found in developing cities and urban protected areas are essential components of urban social-ecological systems providing city residents with cultural, provisioning and regulating services, all of which hold value. Understanding these values requires overcoming conceptual and methodological challenges so that the multi-dimensional nature, relating to the varying values, benefits, and trade-offs are understood. Understanding values, benefits and trade-offs is essential for ensuring informed and effective management of these services and the landscapes that provide them. This requires the development of tools and methods to predict how changes in land-use and management practices might affect the provision of such services. This study contributes to both the methodological and empirical literature by developing integrated and multidisciplinary approaches to assessing the beneficiaries of freshwater ecosystem services in an urban context and recognising the ecological, social and economic values assigned to ecosystem services over multiple spatial and temporal scales. The aim of this thesis was to assess how beneficiaries, stakeholders and managers within a developing city context, recognise, value and manage the multiple diverse ecosystems services associated with freshwater ecosystems as provided by different landscape features originating in an urban protected area. This aim was achieved by establishing who the beneficiaries of freshwater ecosystem services are, uncovering the spatial and temporal relationships these beneficiaries have with landscape features, determining the nature of ecosystem service values, benefits, impacts and trade-offs as experienced by the different users, as well as analysing the management policies and practices associated with urban ES. Drawing on accumulated as well as existing data sets, newly developed methods and approaches were implemented in this study. This work was primarily undertaken in Table Mountain National Park and in Cape Town, South Africa. A comparative analysis of the perceptions of park managers toward ecosystem service governance and management was undertaken in Table Mountain National Park and in Tijuca National Park, in Rio de Janeiro, Brazil. Natural freshwater ecosystems (e.g. rivers), particularly when combined with built infrastructure (e.g. dams), provide highly valued features in landscapes, delivering multiple cultural services to city residents. Recreation, aesthetic and existence services were valued highest by respondents. People who live closer to the park use, and benefit from, the park's freshwater ecosystems more frequently than those living further away. Park visitors want ease of access in terms of distance to specific freshwater ecosystems, and then once there they want a diversity of activity options, such as recreation opportunities as well as places to reflect and meditate. The outcomes of the cultural-service study in this thesis have important management implications where insights gained can guide management to ensure equitable and sustainable ecosystem service provision to all city residents. To enhance the management of ecosystem services in urban protected areas, it is important to understand the level of inclusion of the ecosystem-service concept in park policy and daily practice. Although management perceptions correspond well with park policy, the concept of ecosystem services is still narrowly developed and needs to be better integrated into the management structures and activities of Table Mountain National Park and Tijuca National Park. Outcomes from this study show that management attention relating to fresh water is still primarily focussed on biodiversity conservation and maintaining system processes and functions. Implementing and enacting the ecosystem services concept largely still needs to happen within parks and urban interfaces. The lack of communication between managers and stakeholders of protected areas makes identifying the beneficiaries of fresh water and valuing ecosystem services difficult, especially when water and associated services flow outside of the park boundaries. An important component of this study was to determine the changes to ecosystem service provision as fresh water flows from a protected area into and across an urban landscape. A scoring system was developed to determine whether changes in land use along three case-study rivers in Cape Town, all of which originate in Table Mountain National Park, positively or negatively impact the provision of water-related ecosystem services. Changes in service provision, over time, were compared to changes in long-term water quality data to verify results from the scoring system. Generally, service levels increased over time along the upper river reaches, whereas the middle and lower reaches of the rivers showed overall declines. The changes to service provision influence the value that urban residents assign to rivers. Findings in this study suggest that the provision of cultural ecosystem services as well as the protection of biological diversity were the key factors considered by those living along the case study rivers as reasons for being willing to pay to protect rivers. Provisioning services were shown to be of less value, as were the economic contribution to property values based on river frontage. This study supports the call for more innovative research to be undertaken in developing countries to break new ground and provide more comprehensive analyses to further our understanding of the values of urban ES. The challenge for environmental researchers in this context is to intensify efforts to understand the relationships between specific landscape elements and freshwater ecosystems and human perceptions, feelings and interpretations, and to express these relationships in ways that are useful for environmental policy and management.

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Bacteria are important components of the food web structure in aquatic ecosystems in which they influence the flow of carbon and energy. Populations of bacteria in these ecosystems comprise a diverse spectrum of individual cells able to respond to many factors such as nutrient supply, temperature and virus infection, which regulate bacterial life and death. Bacterial death is a key cellular event involved in the control and production of bacteria in aquatic ecosystems with functional meaning in the carbon and nutrient cycles. Therefore, the study of bacterial structural features and cellular mechanisms underlying bacterial death is crucial to understand processes affecting the entire population. However, both bacterial structure and cellular events of death in aquatic ecosystems are still poorly understood. In the present work, we used single cell approaches to study the structural organization of bacteria as well as to characterize cellular processes of death in these organisms. First, by using fluorescence and transmission electron microscopy (TEM), we provided a general panorama of how microscopy techniques, especially TEM, are powerful tools to understand bacterial structure and their responses to environmental stresses. We showed that bacteria from aquatic ecosystems have remarkable ultrastrutural diversity with components such as bacterial envelope of individual cells differing in structure within the same population. Second, we sought to identify and characterize mechanisms of bacterial cell death. Because our TEM analyses revealed morphological signs of apoptosis, a type of program cell death (PCD), in aquatic bacteria directly collected from natural ecosystems, we applied different techniques to detect apoptosis in bacteria cultured from natural samples. We used TEM as well as different probes to detect this type of PCD in cultured bacteria exposed to increased temperature and viral infection, which are recognized inducers of bacterial death. TEM showed, in both situations, ultrastructural changes indicative of apoptosis, such as cell retraction and condensation, similar to those reported for eukaryotic cells. Assays for membrane permeability, DNA fragmentation, phosphatidilserine exposition and caspase activation were significantly increased in treated bacteria compared to the control group. Altogether, our data demonstrate, for the first time, that PCD occur in aquatic bacteria, and that this event may be a basic mechanism for regulation of bacterial communities in these ecosystems.

2017 - 2018
The concept of integrated environmental monitoring includes the gathering of all the information necessary to obtain a comprehensive view of ecosystem status, processes and functionality, through a classical ecological approach. The present research falls in this context by combining passive and active biomonitoring, sediment mineralogy, element total content analysis and partitioning among sediment fractions, water chemical analyses and biodiversity analysis. The approach was applied to two of the main river systems of the “Cilento, Vallo di Diano e Alburni” National Park (PNCVDA), the Bussento and the Calore Salernitano, in order to obtain clear scenarios of river quality and of the subtended processes, in an area hosting exceptional biodiversity. Specifically, 19 elements among macronutrients (Ca, K, Mg, P, S), micronutrients (Co, Cr, Cu, Fe, Mn, Na, Ni, Si, V, Zn) and nonessential elements (Al, As, Cd, Pb), collectively referred to as Potentially Toxic Elements (PTEs), were analysed in 49 sites along the Bussento and Calore Salernitano rivers for two consecutive years. In order to obtain clear scenarios of stable concentration gradients, an ensemble of two passive biomonitors, Helosciadium nodiflorum (L.) W.D.J. Koch and Mentha aquatica L., and two active biomonitors, Fontinalis antipyretica Hedw. and Chara gymnophylla A. Braun, were employed. Whereas H. nodiflorum and F. antipyretica were already recognized as fine biomonitors of PTEs in freshwater ecosystems, M. aquatica and Ch. gymnophylla were novel, and were preliminary validated using the former biomonitors as references. Since no information on the charophyte flora of the PNCVDA was available, the biodiversity of this group of algae in the area was also investigated, in order to avoid the introduction of allochthonous biomonitors possibly interfering with local communities. Finally, in order to shed light on the possible causes of PTE concentration gradients and to highlight other criticalities, sediment mineralogy, sediment PTE fractionation, the concentrations in water of PTEs, photosynthetic pigments, anions, and several chemical-physical parameters like pH, dissolved oxygen, conductivity and redox potential were also investigated. State-of the art spatial and multivariate statistical techniques, involving methods specifically developed for the project, were employed throughout in the analysis of the complex datasets derived from the experimental activities. Overall, three main criticalities were highlighted in the Bussento and Calore Salernitano rivers: i) the presence of springs occasionally emitting water with high PTE concentrations, ii) the presence of wastewater discharges and iii) the presence of nutrient leaching from agricultural soils. With the exception of the latter, the criticalities appear to be localized to few sites on both the river systems, an occurrence involving also the presence of high Al, As, Co, Fe, and Mn concentrations in a few sites, which are likely related to the presence of metallic structures or wastes in the riverbed. The approach embraced for the research, joining chemical, physical, botanical, zoological, geological, cartographical and statistical skills, represents a true ecological strategy to the study of complex ecosystems, and an example of how multiple activities can be coupled to obtain a comprehensive view of freshwater ecosystem integrity. Despite the enormous efforts required, it is the unique approach capable of dealing with the complexity of ecological systems, and what it is advocated for to cope with the current local and global scale crises of the Anthropocene. [edited by Author]
XXXI ciclo

Benthic algae a re one of the most important primary producers i n lotic ecosystems, and changes i n their community structure and function (e.g., metabolism) will influence other organisms at higher trophic levels or even the entire aquatic ecosystem through bottom-up effects. Since they are known to be sensiti ve to changes i n ambient conditions, benthic algae and especially diatoms have been widely used as i ndicators of environmental changes in aquatic ecosystems, particular ly i n E urope , through developi ng diatom-based indices. However, these indices have not been widely used i n other continents. Applications of such i ndices in Asia and Oceania first require testi ng to see whether the y can perform as reliable bioindicators across time and space, considering that aquatic systems are constantly changing in terms of their ambient environment such as water physical and chemical conditions. Nevertheless, few studies have been carried out to compare the environmental influences on benthic algal communities among different geographic regions, nor the influences at different spatial scales (e.g., catchment, reach, and habitat). F urthermore, few studies have considered how diatom indices perform compare with other commonly used bioindicators of aquatic ecosystem health.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment.
Science, Environment, Engineering and Technology
Full Text

Carp (Cyprinus carpio) are alien freshwater fish that are globally widespread and often associated with highly degraded freshwater ecosystems. This study explored carphabitat interactions that could contribute to the worldwide distribution of, and consequent ecological impacts by, carp. Particular emphasis was placed on the role of carp size in these interactions. One component of this study involved a field experiment that was used to quantify the effects of carp biomass density and size-structure on freshwater invertebrate communities and water quality. The treatments in this field experiment comprised different combinations of large (2 kg) and small (0.7 kg) carp, and low (330 kg.ha-1), intermediate (570 kg.ha-1) and high (650 kg.ha-1) biomass densities. Carp impacts were more carp size-dependent than described in previous studies. In particular, carp size was more important than carp biomass density in determining the concentration of total phosphorus and algal biomass. On the other hand, a more even mix of carp sizes increased total nitrogen. The zooplankton and macroinvertebrate taxa that were more abundant in the presence of carp were the taxa most able to avoid carp predation and tolerate habitat changes caused by carp benthivory. To complement the small-spatial scale field experiment, large-scale patterns of carp distribution, biomass density and recruitment were explored among the rivers of New South Wales (Australia) in relation to their physical habitat. In contrast to expectations, and although most recruitment probably occurred at lower-altitudes, the populations with a size structure and biomass density most likely to cause ecological degradation occurred at intermediate altitudes. Furthermore, the distribution of smaller carp (less than or equal to 100 mm, and less than or equal to 300 mm) indicated that the regulation of river flows does not always favour carp populations, particularly during drought conditions. Nevertheless, it was concluded in a review of the carp literature, which incorporated the findings of this study, that invasion by alien carp is most successful in streams with formerly highly variable flows that are now subject to flow regulation. Moreover, carp are likely to enhance their advantage in these waters through habitat modification.

Esta tesis tiene como objetivo principal contribuir al desarrollo de las mejores prácticas disponibles en la modelización del destino multimedia y de los efectos de compuestos farmacéuticos para evaluar su impacto en los ecosistemas. La distribución de fármacos a través de los distintos compartimentos ambientales representa un riesgo potencial de toxicidad para los ecosistemas acuáticos. La capacidad de ionización de muchos de estos compuestos en el medio ambiente es un reto para la modelización de su destino multimedia, de su exposición y efectos. El uso de modelos convencionales no polares representa un elevado nivel de incertidumbre en la modelización de la movilidad de compuestos orgánicos ionizables, y en la modelización de su biodisponibilidad para la exposición a organismos y para la degradación en el medio ambiente. El desarrollo y la evaluación de modelos alternativos que incluyan estos puntos son esenciales para mejorar la simulación del comportamiento ambiental de microcontaminantes. La comparación de modelos y la cuantificación de la incertidumbre de sus resultados son fundamentales para su correcta interpretación. Además, la cuantificación de estas incertidumbres es necesaria para establecer prioridades de monitoreo y de investigación adicional entre el gran número de fármacos activos en uso actual teniendo en cuenta las diferentes vías de contaminación ambiental. En este contexto, se consideraron los siguientes objetivos específicos: 1. Desarrollo de un modelo de destino multimedia, exposición y toxicidad con base en álgebra matricial y adaptado a compuestos farmacéuticos consistente con modelos de evaluación del impacto de ciclo de vida. 2. Desarrollo de un método para la cuantificación de la incertidumbre del modelo, incluyendo la incertidumbre de los modelos de regresión aplicados, y la identificación de los parámetros más pertinentes a la incertidumbre total. 3. Comparar y cuantificar las incertidumbres de los modelos alternativos en términos de los factores de caracterización y de los resultados finales de impacto, contribuyendo a la identificación de las mejores prácticas de modelización del destino multimedia, exposición y efectos de fármacos con base en los conocimientos científicos actuales. 4 Priorización de compuestos farmacéuticos en términos de su impacto probabilístico en los ecosistemas de agua dulce considerando las emisiones directas y indirectas de plantas de tratamiento de aguas para posterior monitorización e investigación adicional. Capítulo 1 establece el contexto de la tesis y sus objetivos. Capítulo 2 presenta un modelo de destino multimedia, exposición y efectos con base en álgebra matricial, adaptado a fármacos y consistente con el modelo consensual de la UNEP/SETAC, el modelo USEtox. Se presenta un enfoque para cuantificar la incertidumbre de los resultados del modelo usando el análisis de Monte Carlo. El enfoque incluye la incertidumbre asociada a los modelos de regresión utilizados y a los efectos tóxicos, y la variabilidad asociada a los parámetros ambientales y experimentales. El modelo se aplicó a fármacos detectados en lodos de depuradora, posteriormente aplicados a suelos agrícolas. En relación a los compuestos de mayor relevancia, los parámetros más influyentes en la evaluación probabilística de impacto fueron identificados así como temas para investigación futura. El capítulo 3 presenta una comparación detallada entre el modelo USEtox y el modelo alternativo adaptado a compuestos farmacéuticos. Este modelo alternativo incluye modelos de regresión para estimar parámetros teniendo en cuenta la fracción iónica de una molécula. La comparación se hizo al nivel de los factores de caracterización y al nivel de los resultados finales del impacto teniendo en cuenta tres escenarios de emisiones en distintos compartimientos ambientales. Los parámetros más sensibles de los modelos fueron identificados por análisis de Monte Carlo. Los capítulos 4 y 5 presentan una priorización de los fármacos detectados en plantas de tratamiento de aguas residuales europeas al nivel de su monitorización ambiental y de temas para investigación futura. En el Capítulo 4 las emisiones directas de efluentes al compartimiento de agua dulce son estudiadas. En el capítulo 5 se consideran las emisiones indirectas: la aplicación de lodos de depuración y de efluentes en suelos agrícolas como fertilizante y como agua de irrigación, respectivamente. Los temas de investigación futura se definieran tanto por la identificación de lagunas en el conocimiento acerca del comportamiento ambiental de los fármacos, como por la contribución de la incertidumbre de los parámetros estimados del modelo a la varianza de los impactos calculados. En el capítulo 6 se presentan las conclusiones generales y recomendaciones para trabajo futuro. Palabras clave: Modelo de destino multimedia, Análisis de incertidumbre, fármacos, microcontaminantes, compuestos orgánicos ionizables, ecotoxicidad en agua dulce, plantas de tratamiento de aguas residuales, lodos de depuración, agua regenerada, Evaluación de riego, Impacto comparativo probabilístico, Análisis de ciclo de vida, USEtox.
The overall objective of this dissertation is to contribute to the development of best available practices in environmental multimedia fate and effect modelling for ecosystem impacts assessment of pharmaceutical compounds. The distribution of pharmaceuticals through several environmental media poses a potential toxic hazard to freshwater ecosystems, among other endpoints. The ionising properties of pharmaceuticals represent additional challenges when modelling the multimedia fate, exposure, and effect of this class of chemicals. Large uncertainties are expected when modelling the mobility, as well as the bioavailability for uptake by exposed biota and degradation, of ionising organic chemicals using conventional models. The development and evaluation of alternative approaches that include these issues are essential for the improvement of micropollutants environmental behaviour simulation. Model comparison and quantification of uncertainties of model results are vital for their correct interpretation. Furthermore, the quantification of uncertainties of model results is detrimental to establish priorities for further monitoring, as well as research, the wide number of pharmaceutical active compounds currently in use considering the most important pathways of environmental contamination. In order to achieve that, the following specific objectives are addressed: 1. Develop a consistent matrix algebra framework for multimedia fate, multipathway exposure and toxicity effects models adapted for pharmaceutical compounds and consistent with life cycle impact assessment models. 2. Develop an approach to quantify the uncertainty of model results, accounting for regression model uncertainty, and identifying the main contributing parameters to overall uncertainty. 3. Compare and quantify the uncertainty of alternative model approaches on the level of characterisation factors as well as of final impact results, contributing to the identification of the best available practices on multimedia fate, exposure and effect modelling of PCs based on current scientific knowledge. 4. Prioritise pharmaceutical compounds on their probabilistic impact on freshwater ecosystems from both WWTP direct emissions and indirect emissions for further monitoring and research. Chapter 1 puts this dissertation into its context and defines its objectives. Chapter 2 presents a multimedia fate, exposure, and effect model based on matrix algebra adapted for pharmaceutical compounds and consistent with the UNEP/SETAC consensus model USEtox. An approach to quantify the uncertainty of model results using Monte Carlo analysis is presented. The approach accounts for the uncertainty of regression models and toxicity effects, as well as the variability of environmental parameters and experimental parameter values. The framework is applied to pharmaceuticals detected in biosolids following application on agricultural soils. The most influential parameters of the probabilistic comparative impact assessment were identified, as well as topics for further research for the compounds of most concern. Chapter 3 is a detailed comparison of the USEtox model with the alternative framework adapted for pharmaceutical compounds. The alternative framework includes regressions to estimate fate parameters that account for the ionized fraction of a molecule. The comparison has been performed at the level of characterisation factors as well as of final impact results for 3 emissions scenarios into different environmental media. The most sensitive model parameters in the estimation of ecotoxicological characterization factors of micropollutants were evaluated by Monte Carlo analysis in both the default USEtox model and in the alternative approach. Chapter 4 and 5 present a prioritisation of PCs detected in European wastewater treatment plants for further monitoring and research. Chapter 4 presents the pathway of direct discharge of WWTPs emissions to surface waters. In Chapter 5 the indirect emissions pathways to the freshwater compartment are addressed. The indirect emission pathways include the application of biosolids from WWTPs and of effluents as reclaimed water for irrigation, both on agricultural areas and landscapes. Research topics were defined by indentifying important gaps of knowledge as well as by computing the contribution of estimated model parameters’ uncertainty to the impact variance. Chapter 6 presents general conclusions on the research outlined and will provide recommendations for future research. Keywords: Multimedia fate model, Uncertainty analysis, Pharmaceuticals, Micropollutants, Dissociating organics, Freshwater ecotoxicity, Wastewater treatment plants, Biosolids, Land application, Reclaimed water, Probabilistic comparative impact, Risk Assessment, LCA, USEtox.

Freshwater ecosystems are important natural emitters of the greenhouse gas CO₂. The magnitude and direction of the exchange of CO₂ between freshwaters and the atmosphere, or flux, is influenced by the concentration of CO₂ in the water. Every organism within a freshwater ecosystem influences the net CO₂ balance of that ecosystem either through respiration, photosynthesis or both. Thus, large changes in populations due to natural or anthropogenic stressors and the underlying food web structure of the ecosystem have the potential to alter CO₂ fluxes of aquatic ecosystems. To evaluate the influences of species loss on food web structure and CO₂ fluxes of aquatic ecosystems, I experimentally manipulated species from different consumer trophic levels (predator, grazer, or detritivore) and tested the effects of these losses on CO₂ fluxes of experimental streams, ponds and bromeliads. In streams, I found that influences on CO₂ emissions were most sensitive to the loss of a predatory insect compared to other trophic levels, including a tadpole grazer and an insect detritivore. Similarly, the removal of a fish predator to ponds or an insect predator to bromeliads resulted in trophic cascades that significantly influenced the CO₂ flux of the ecosystem. Both the identity of the predator and interspecific competition among predatory insects influenced the strengths of cascading effects of predators on CO₂ emissions from bromeliads. However, across all three ecosystems (streams, ponds, and bromeliads) predators, via trophic cascades, had surprisingly consistent effects on the CO₂ flux of the ecosystem. Finally, as alterations to predator abundance often occurs in concert with increasing water temperatures and nutrient loading, I determined the individual and interactive effects of these stressors on pond communities. I found that nutrients often increased top-down control of predators on CO₂ fluxes, but the individual effect of warming and its combined effects with nutrients had negative effects on both consumers and primary producers making predictions about CO₂ fluxes complicated. My results provide novel insights into the influence of predators and food web structure on CO₂ fluxes and the potential for predator loss to markedly alter CO₂ fluxes of freshwaters.

I investigated effects of environmental change on disease, and effects of disease on ecosystems, using a freshwater zooplankton host and its fungal parasite. This research involved lake surveys, manipulative experiments, and mathematical models. My results indicate that ecosystem characteristics such as habitat structure, nutrient availability, and quality of a host’s resources (here, phytoplankton) can affect the spread of disease. For example, a survey of epidemics in lakes revealed direct and indirect links between habitat structure and epidemic size, where indirect connections were mediated by non-host species. Then, in a mesocosm experiment in a lake, manipulations of habitat structure and nutrient availability interactively affected the spread of disease, and nutrient enrichment increased densities of infected hosts. In a separate laboratory experiment, poor quality resources were shown to decrease parasite transmission rate by altering host foraging behavior. My experimental results also suggest that disease can affect ecosystems through effects on host densities and host traits. In the mesocosm experiment, the parasite indirectly increased abundance of algal resources by decreasing densities of the zooplankton host. Disease in the experimental zooplankton populations also impacted nutrient stoichiometry of algae, which could entail a parasite-mediated shift in food quality for grazers such as the host. Additionally, I showed that infection dramatically reduces host feeding rate, and used a dynamic epidemiological model to illustrate how this parasite-mediated trait change could affect densities of resources and hosts, as well as the spread of disease. I discuss the implications of these ecosystem–disease interactions in light of ongoing changes to habitat and nutrient regimes in freshwater ecosystems.

Would it be possible to go one step further than proposing sustainable development as the ultimate answer where people live within nature harmoniously if natural resources were not managed by central authorities, who mostly are male, aged, middle-class bureaucrats? Bearing in mind that we have reached a stage where ecological credit crunch will define human&rsquo
s limits remarks for non-teleological and eco-friendly ways of conceptualizing the relationship between human beings and nature is explored with an emphasis of &lsquo
who&rsquo
that is local, female, young, social science-based, active in civil movement. The objective of conducting the research is to find out the ways why green approaches in social, political and economic spheres in Turkey are not integrated as a first step to decouple the antagonism in man&rsquo
s relationship with nature. The analysis tried to grasp the discrepancies of conceptualizing human-nature relationship in order to find out which segment of the society would be closer to adopt green values, with the intention of proposing them to be involved in a greater extent to decision-making mechanisms with regards to natural resources management, as well as an attempt to grasp the overall picture in understanding nature-human relationship in Turkey by focusing on wetland management based on the research conducted in Bafa Lake (Aydin), Uluabat Lake (Bursa), Salt Lake (Konya) and Egirdir Lake (Isparta). Thanks to the scale that is constructed by operationalizing the existing debates on environmental ethics, agents that would follow more ecologically sound discipline towards living harmoniously within nature is analysed.

Many experiments show that species diversity at small, local scales affects ecosystems; however, conservation is concerned with extinctions of species across broad landscapes. The relevance of global or regional diversity to ecosystems therefore remains in question. I asked whether regional biodiversity in freshwater zooplankton affects the resilience and resistance of local ecosystems to the multiple stressors of warming and salinization. I hypothesised that dispersal of species from the regional community should buffer ecosystems against environmental change by providing species with traits adapted to the novel conditions. I subjected freshwater zooplankton communities in mesocosms that were either connected to or isolated from the larger regional species pool to a factorial manipulation of experimental warming and increased salinity. Dispersal introduced heat-tolerant regional taxa that were able to compensate for reductions in local taxa under warmed conditions. Dispersal also dampened the effects of warming on net primary productivity, suggesting that regional diversity can provide stability against some aspects of climate change. However, other measures of ecosystem performance like decomposition and sedimentation were affected by warming and salinity but not dispersal. The results indicate that regional biodiversity provides important insurance that can stabilize ecosystems in a dynamic environment. However, compensation by the regional biota could not buffer all ecosystem rates against all sources of stress. My results show that the connectivity of habitats to regional biodiversity introduces species with broad ranges of traits that can maintain some local ecosystem function in the face of environmental changes.

Phytoplankton are single celled organisms capable of phytosynthesis, and are present in all the major oceans and lakes in the world. Phytoplankton contribute to 50% of the total primary production on Earth, and are the dominating primary producer in most aquatic ecosystems. This thesis is based on the 1D deterministic model by Jäger et. al. (2010) which models phytoplankton dynamics in freshwater lakes, where phytoplankton growth is limited by the availability of light and phosphorus. The original model is here extended to two dimensions to include a horizontal dimension as well as a vertical dimension, in order to simulate phytoplankton dynamics under varying lake bottom topographies. The model was solved numerically using a grid transform and a finite volume method in MATLAB. Using the same parameter settings as the 1D case studied by Jäger et. al. (2010), an initial study of plankton dynamics was done by varying the horizontal and vertical diffusion coefficients independently.

Bhutan, a small developing country, is recognised for its pro-environmental and unique development philosophy called Gross National Happiness (GNH). Over the years Bhutan has continually increased the area coverage under protected area (PA) system and probably it is the first country in the world that has achieved a 50% protection target. Going beyond the year 2020, there is a growing call to protect at the least 30% of the World’s terrestrial areas by 2030 with the ultimate goal to protect 50% by year 2050 - a goal commonly termed “Nature Needs Half’ (NNH). However, PAs globally and in Bhutan have been designated to protect terrestrial ecosystems and biodiversity. Although freshwater ecosystems and biodiversity are most threatened, there are very few freshwater specific protected areas while they are included within existing PAs by coincidence. The overall objective of this thesis is to assess the potential of existing terrestrialfocussed protected areas of Bhutan in conserving freshwater ecosystems and biodiversity within the context of nature needs half target and protected area dynamism. To achieve this, I have combined a systematic archival literature review with species distribution modelling and systematic conservation planning techniques to address four main issues: (1) the lack of a country level PA dynamism study and possible link between it and GNH, (2) lack of adequate freshwater species distribution data in Bhutan, (3) the need to assess potential of existing PA system for freshwater protection in the context of NNH, and (4) the need for systematic freshwater conservation planning in the context of NNH and PA dynamism. To address the first issue, I conducted systematic archival literature review on PA dynamism in Bhutan for almost the entire modern conservation history of Bhutan (1966- 2016). PA dynamism can be either of gain or loss events; the latter is termed protected area downgrading, downsizing and degazettement (PADDD). The conservation planning was the main proximate cause for PA degazettement and downsizing. On the other hand, an increase in infrastructure with hydropower development as the specific cause was the proximate cause for proposed PADDD. Overall PA dynamism reflected Bhutan’s commitment to environmental conservation guided by its GNH philosophy. I recorded differences in the number of PADDD events, PADDD types and PAs affected between the current study and those previously recorded for Bhutan from a regional level study. This demonstrated the need for country specific systematic archival literature search to better detect PADDD. To fill in freshwater species data gaps I curated georeferenced occurrence data of fish and odonata from the available literatures till 2017 and also through personal communications. While building SDMs for 10 fish and 28 odonates I compared the performance of four sequential model selection approaches against an expert (EXP) approach in selecting ecologically plausible species models. The sequential approaches using omission rate followed by test AUC (ORTEST) performed better over the sequential approaches that used omission rate followed by difference between training AUC and test AUC, and test AUC (AUCDIFF). ORTEST approaches could be used as a good first line model screening approach to reduce time taken by the EXP approach. This thesis contextualized freshwater biodiversity and ecosystems conservation against NNH by categorizing levels of species habitat, river length and lake surface area percentage protection into four progressive targets based on Aichi target 11 and NNH target. Despite covering 50% of Bhutan’s total land area, many freshwater ecosystems and taxa were inadequately represented within the existing PA system of Bhutan. These gaps could be easily filled employing Marxan, a common systematic conservation planning tool. Even when considering hydropower developments, we found solutions that increased the species coverage significantly. That said, high percentages of selected areas are already protected by the existing PA system. This suggests Bhutan may not need to change drastically the existing PA system if PAs are redesigned to better represent both freshwater species and forest types. This thesis provides the first real world example of inadequacy in protecting freshwater ecosystems and biodiversity by terrestrial-focused PAs even when total area of PA system meets the NNH target. The findings also demonstrate a clear need for freshwater conservation planning. The collated species occurrence data and ecologically plausible SDMs chosen here could be a starting point for freshwater conservation planning in Bhutan. The thesis also showed clear need to conduct country level systematic archival literature review to better detect PADDD. This thesis also linked PA dynamism study with freshwater systematic conservation planning and probably this could be way forward to design robust PA systems.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

The general aim of this thesis was to examine the merits of ex-situ vs. in-situ strategies for the conservation of the endangered freshwater pearl mussel, Margaritifera margaritifera, and to investigate the relationship of the larval parasitic stages of the mussel (glochidia) with the salmonid hosts. To this end, I critically reviewed the literature on conservation of freshwater mussels, developed methods for quantifying the behaviour and activity patterns of adult mussels in captivity, experimentally studied host specificity, and quantified the physiological and behavioural effects of glochidia upon salmonid hosts. The results indicate that the conservation of the freshwater pearl mussel is probably best addressed at the watershed scale, and will benefit from a combination of ex-situ and in-situ techniques, as well as from a more critical assessment of findings, many of which are only reported in the grey literature. Empirical, peer-reviewed data are badly needed to inform current conservation efforts. Novel Hall-effect magnetic sensors were used to quantify and characterise discrete mussel behaviours without adversely affecting the welfare or survival of adult mussels, and these hold considerable potential for determining optimal rearing conditions for ex-situ conservation. Arctic charr was shown to be a potentially suitable host for M. margaritifera, and occupied an intermediate position in host suitability between brown trout and Atlantic salmon. Physiological impacts of glochidia upon brown trout included swelling of secondary lamellae and spleen enlargement, but the latter tended to be slight and was restricted to 1 month post-exposure. Glochidia encystment had no significant effect on blood haematocrit, respiratory performance, or cryptic colouration of brown trout hosts. The behavioural effects were more subtle and glochidiosis made brown trout more risk-averse and less willing to explore a novel habitat, without affecting the host's ability to chemically recognise and avoid cues from a predator. Overall, the results of this thesis indicate that the impacts of glochidia upon salmonid hosts are probably slight and temporally variable, and may perhaps lead to increased host survival, which would support the symbiosis-protocooperation theory of glochidia-salmonid interaction.

Doutoramento em Engenharia Florestal e dos Recursos Naturais - Instituto Superior de Agronomia / UL
Many European rivers and floodplains have been subjected to long periods of anthropogenic degradation. Activities like land drainage, construction of dams and weirs, channelization, water abstraction and pollution, resulted, among others, in the loss of floodplains and wetlands, high sediment runoff, biodiversity losses, lowering of the river and water table levels and increase in peak flows. Thus, this thesis focuses on a multi-level top to bottom approach to freshwater ecosystem restoration, addressing the legislation restoration drivers, as well as the restoration at the basin and river section levels. The main conclusions are: a) to improve freshwater restoration success in Europe it is highly recommended to create more ecosystem restoration soft law and reinforcement mechanisms related with governance, quality, stakeholders, publicity and research; b) there is a joint effect of climate change and land use on river water quality, meaning that proposed environmental conservation measures may be too conservative to have a significant effect in river nitrogen concentration, particularly in a climate change context; c) local population awareness and participation are as essential for habitat restoration success as grazing herbivores exclusion, river pollutant load, water table levels and tree installation techniques; d) the sampling of a river section to assess the influence of the liquid effluent from an acid bisulfite pulp mill on river water quality did not reveal particularly high levels of pollution directly related to the mill, in spite of relevant levels of total phosphorous and dissolved lignin; and e) cork and Tasmanian blue gum bark are capable of enhancing biological denitrification in laboratory batch tests. The implementation of ecologically effective restoration should be flexible to adjust to changing climate and societal priorities, retaining simultaneously the capacity to integrate information from new technologies into site assessment and restoration planning
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Includes bibliographical references (p. 125-140).
Freshwater ecosystems underpin the fabric of society and the environment, providing essential ecosystem services such as water and food, upon which all human beings depend. In order to secure these vital services requires the sustainable management of freshwater ecosystems. At present however, freshwater biodiversity is under severe threat from anthropogenic disturbances, and the situation is expected to worsen due to population growth and global change. Coupled with the threats to freshwater biota are the limited resources available to secure their protection. There is a need to therefore prioritise freshwater ecosystems in a comprehensive, adequate and representative manner to maximise the outcomes of conservation effort. The concept of systematic conservation planning was developed to address this challenge. It offers a suitable framework for achieving conservation goals in the face of other competing land uses. The principles of systematic conservation planning are being widely applied in terrestrial and marine ecosystems, but their application in freshwater ecosystems is still relatively limited. Freshwater ecosystems provide challenges to conservation planning that are unique from those of terrestrial and marine ecosystems, such as the longitudinal nature of river systems and the associated connectivity, and catchment divides that constrain some obligate species. As a result freshwater ecosystems require conservation planning tools and approaches that are specifically geared towards addressing these unique challenges. Progress has recently been achieved in addressing some of these challenges, but there are still other outstanding issues that have not been comprehensively addressed. The aim of this thesis was to develop new frameworks, and test approaches for the application of systematic conservation planning principles in the conservation of freshwater ecosystems in South Africa. The thesis addressed a range of issues along the systematic conservation planning continuum from biodiversity assessment to implementation. I first carried out a focused review of systematic conservation literature between 1987- 2006, to gauge the extent to which freshwater ecosystems have being integrated in conservation assessments. Most of the focus was found to be on terrestrial ecosystems with minimal incorporation of freshwater biodiversity. Wetlands for example, were in most cases incorporated into conservation assessments without taking their diversity into account. This was partly attributed to the difficulty of classifying wetlands. I therefore developed and tested a hierarchical GIS framework for automating wetland classification as a strategy for incorporating wetland biodiversity, functions and benefits into broad scale conservation planning.

Doutoramento em Engenharia do Ambiente - Instituto Superior de Agronomia
In freshwater ecosystems associated with agricultural areas, organisms are exposed to a multitude of toxicologically and structurally distinct pesticides in concentrations that may fluctuate over time. However, the environmental risks of chemicals are traditionally evaluated and regulated on the basis of single substance. Understanding and improving the link between effects and exposure assessment is an important step in the current challenges of risk assessment in order to increase its ecological relevance. To this end, integrated approaches of different hierarchical levels of complexity and ecological realism have been developed and applied, including: exposure modelling, laboratory testing with individual organisms, species sensitivity distribution, ecosystem models and assessment of aquatic community interactions to evaluate the effects of realistic pesticide combinations on water bodies associated with rice, tomato and maize typical agroecosystems of Mediterranean conditions. Contributing to the overall knowledge of the adequacy of the prospective risk assessment and demonstrating that pesticide risk may be underestimated during the actual registration procedure. The data generated in the present study contributed to the derivation of optimized programs of measures under the scope of European legislation; the identification of sites with the highest expected impacts of pesticide mixtures; the evaluation of the major pesticide compounds that contributed mostly to the identified aquatic risks. Furthermore contribute to a deeper knowledge and unravel the effects of co-occurring chemicals, environmental and biological stressors in aquatic ecosystems considering the effects of biotic and abiotic interactions at community and ecosystem levels. The results contribute to reducing the risks of pesticides in freshwater
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Stress-specific expression of cellular proteins in responses to exogenous exposure and resulting physiological alteration provides important insight into the field of ecological research. Due to its habitat, feeding, lifestyle and physiologic properties, mussel has become an important indicative measure of aquatic environment pollution in order to assess effect of these pollution in aquatic life. In order to minimize the threats imposed on the aquatic ecosystem and advancement of sustainable lifestyle for human, recent ecological studies are more concern about monitoring different bioindicative properties. In this study, two widely distributed freshwater bivalve mussel species Anodonta anatina and Unio tumidus was used to conduct comparative study on the transcriptome of these species in order to identify and quantify the expressed transcripts on both species and investigate their biomarker properties in mussels for monitoring heavy metal or toxic exposure. mRNA was isolated and converted to cDNA through reverse transcription PCR. Quality and quantity assessments of purity, fragment size and concentration was performed. Each cDNA sample was barcoded and amplified for cDNA library preparation and nanopore sequencing. Basic bioinformatics tools were used to identify the transcripts for transcriptomic analysis. The findings shows some common mitochondrial and ribosomal transcripts along with a wide range of conserved and abundant transcript variants in mussels with important biomarker properties. Some of the transcripts exhibits expression in multiple samples suggesting characteristic bioindicator properties. Also in this study, a pipeline for transcriptomic analysis was generated and critical steps in the procedure were identified and discussed.

Ecological degradation of rivers and streams resulting from multiple stressors is a big concern in the UK and other countries all over the world. The two largest stressors introduced by agriculture are phosphorus and fine sediment. The combined impacts of the multiple stressor and relative strength of each individual stressor needs to be understand. A Number of ecological response variables were tested through a field mesocosm experiment, including algal and ecosystem variables: (1) The subsidy-stress for phosphorus and sediment (where at first, an ecological variable increases positively with the increased level of phosphorus and sediment until very high levels are reached, when negative effects would be expected); (2) Whether the stressors work individually or as multiple stressors and whether they interact; (2.a) Three ecological guilds of algae (‘low profile’ growth form, ‘high profile’ growth form, ‘motile’ growth form) were used in order to test whether the high profile growth form decreases and motile growth form increases with increase of sediment deposition, or whether (2.b) Both high profile growth form and motile growth form increase with increase concentration of phosphorus. Most species showed subsidy stress responses for the gradient of phosphorus, but for the gradient of sediment the response was negative. Phosphorus and sediment together generally acted as multiple stressors and usually in a simple additive way, but complex interactions were also found. The algal community was impacted synergetically by phosphorus and sediment, as shown by the field study. The combined results from the field study and the mesocosm experiment indicate that phosphorus and sediment should be managed together in view of their acting most of the time as multiple stressors in their impacts on epilithic algae. Finally, in order to have a better evaluation for the possible reasons of a stream health decline, it is strongly recommended to measure routinely both fine sediment and phosphorus in the future.

A majority of carbon in freshwater and marine ecosystems is in the form of ultraplankton, heterotrophic and autotrophic plankton &<&5 &\mu&m including heterotrophic bacteria, Prochlorococcus, cyanobacteria, and autotrophic eucaryotes. However, ultraplankton and subsequently microbial food webs have yet to be incorporated into models of benthic-pelagic coupling despite the preponderance of macroinvertebrates with the capacity to feed on ultraplankton. I have examined the role of microbial food webs in benthic-pelagic coupling in three ecosystems: Lake Baikal, Siberia, Russia; Gulf of Maine, Northwest Atlantic Ocean; and Conch Reef, Florida Keys, USA. Using sponges as a model organism and in situ measurements, I have quantified (1) suspension feeding on ultraplankton and (2) release of dissolved inorganic nitrogen (DIN) and phosphorus (DIP) resulting in direct evidence that benthic macroinvertebrates do occupy the level of primary consumer within the microbial food web. Dual-beam flow cytometry was employed to quantified sponge suspension feeding on five types of ultraplankton: heterotrophic bacteria, Synechococcus-type cyanobacteria, autotrophic picoplankton &<&3 &\mu&m, autotrophic eucaryotes 3-10 &\mu&m, and in marine ecosystems Prochlorococcus. Grazing by the freshwater sponges Baikalospongia intermedia and B. bacilliferia and the boreal marine sponge, Mycale lingua, was unselective for all types of ultraplankton with efficiencies ranging from 63-99%. This is the first time that grazing on Synechococcus-type cyanobacteria and Prochlorococcus by macroinvertebrates has been quantified in freshwater and marine ecosystems. Conversely, the coral reef sponges Ircinia felix and I. strobilina release significant amounts of DIN and DIP as a result of grazing on procaryotic plankton. Using a general model for organism-mediated fluxes, it is conservatively estimated that through active suspension feeding sponges in Lake Baikal retain 1.97 g C day&\sp{lcub}-1{rcub}& m&\sp{lcub}-2{rcub}& and M. lingua retains 29 mg C day&\sp{lcub}-1{rcub}& m&\sp{lcub}-2{rcub}& while at Conch Reef sponges released 204 &\mu&mol DIN day&\sp{lcub}-1{rcub}& m&\sp{lcub}-2{rcub}& and 48 &\mu&mol DIP day&\sp{lcub}-1{rcub}& m&\sp{lcub}-2{rcub}&. A majority of the carbon retained at all three locations was from procaryotic cell types suggesting that ultraplankton are an important overlooked component of benthic-pelagic coupling.

Climate change can have potentially catastrophic effects upon biodiversity and food web structure and according to the fourth IPCC report, ambient temperatures will rise by between 3.0-5.0 °C over the next century, with already an average increase in global surface temperature of ~0.74°C in the past 100 years. This has known implications in ecology from individuals to ecosystems. The microbial loop consists of small organisms ranging in body size from bacteria (1-15 μm), single-celled eukaryotes (10-1000 μm) and multicellular organisms (250 – 1000 μm) that assimilate dissolved organic carbon into the “classical food web”. ! The principal goal of this thesis was to assess how rising global temperatures might impact the natural microbial assemblages in 20 mesocosms under 2 treatments – 10 warmed (in line with IPCC predictions) and 10 ambient. The abundance and body mass of 4 major microbial loop taxa (desmids, flagellates, heterotrophic protists and meiofauna) were quantified at monthly intervals over a 2-year period. Secondly, in a microcosm experiment, the population dynamics of three pure cultures of ciliates were monitored across a temperature gradient; the rate of population decline under starvation and changes in body size were quantified.! Results showed that (1) rising global temperatures alters the size spectrum in the autotrophic protists, (2) temperature interacts with temporal and spatial gradients, resulting in changes in phenology (3) these changes in phenology are observable at both the community level and the population level within the microbial assemblage of the mesocosms and (4) extinction rates and body mass reduction in experimental microcosms were faster at warmer temperatures and partially support predictions of the metabolic theory of ecology.! The implications of these findings are discussed in terms of (1) continued research into the role that small organisms play in community and ecosystem ecologyand (2) the use of these small organisms in experiments as models to inform ecological theory by scaling up from microcosms and finally, (3) I discuss future directions in freshwater microbial ecology, focusing on the increased use of molecular techniques.

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

We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states.

Freshwater ecosystems are among the most threatened habitats on Earth, facing challenges from a range of anthropogenic pressures. Accurate biodiversity assessment is essential to identify these pressures prior to irreversible damage. Current monitoring techniques for freshwater systems rely heavily on capture methods to infer the status of an ecosystem. However, these methods are often inefficient at detecting and identifying all species at a site and often miss those in low abundance. Emerging molecular methods such as environmental DNA (eDNA) could be a “game changer” for freshwater biodiversity monitoring. This thesis focuses on the application of eDNA for detection of invasive non-native species (INNS) and whole macroinvertebrate community assessment. Firstly, targeted eDNA PCR assays were developed for four priority freshwater INNS, and validated in mesocosm experiments and field trials. Targeted (PCR and qPCR) and passive (metabarcoding) eDNA approaches were then compared to traditional methods for detecting quagga mussels, Dreissena rostriformis bugensis. The targeted approaches were the most sensitive for detection of quagga mussels at low densities and both qPCR and metabarcoding showed correlations with mussel density. The power and utility of eDNA metabarcoding for detecting rare or unexpected taxa was then demonstrated by passive detection of a new INNS, Gammarus fossarum, in UK rivers. Finally, metabarcoding of both bulk DNA and eDNA from water and sediment was compared to the traditional method of macroinvertebrate sampling, to evaluate the potential of emerging molecular methods for ecological assessment. The results show metabarcoding approaches are not suitable to retrofit or replace existing methods of assessment, but provide an exciting opportunity for greater taxonomic identification and have the ability to detect a combination of taxa across groups, some of which are not utilised in current ecological assessment methods. This work has demonstrated a huge potential for eDNA methods to be applied to INNS monitoring and further our ability to carry out complete biodiversity assessment of waterbodies.

Achieving global water sustainability through a resilient international legal architecture presents one of the most pressing challenges within our resource finite planet. A staggering 42 percent of the total land area of the earth is covered by transboundary river basins, where more than 40 percent of the global population lives and depends on the ecosystem services of the 286 transboundary river basins and 200 transboundary aquifers stretching across the political boundaries of 151 countries. There is already evidence of water resources becoming a source of conflict in many regions and constraining a whole myriad of securities – climate, human, environmental, food, economic, energy – on various levels of society. The international legal architecture to manage this critical natural resource is the overarching area of inquiry in this thesis, and requires improvement to address current and predicted future transboundary water challenges, conflicts and strengthen cooperation. Despite the establishment of around 690 river basin treaties, many of these agreements completely miss or provide unclear provisions on principles and rules of international water law. Until recently there was no legally binding global treaty on transboundary watercourses and customary international law has provided the default rules in the absence of agreements and facilitated the re-interpretation of older agreements in accordance with the Vienna Convention on the Law of Treaties. Now there are potentially two global treaties, with the recent entry into force of the 1997 UN Watercourses Convention and the global opening up of the 1992 pan-regional United Nations Economic Commission for Europe (UNECE) Water Convention, to all UN member states. There is also a plethora of other international environmental legal and non-legally binding instruments, indirectly addressing international law relevant to transboundary watercourses and freshwater ecosystems. Legal regimes for the protection and use of international river basins cannot be interpreted and applied in isolation from other relevant norms of international environmental and general international law. This thesis seeks to understand the rising role and contribution of regional approaches relevant to international law on transboundary watercourses and freshwater ecosystems. More specifically it explores the contribution of the UNECE Water Convention and other relevant UNECE environmental instruments as a structurally distinctive ‘regime’. This thesis introduces a novel conception of a broader ‘UNECE water regime’ which includes the Water Convention, the Convention on Access to Information, Public Participation in Decision-making and Access to Justice (Aarhus Convention), the Convention on Transboundary Environmental Impact Assessment (Espoo Convention), the Convention on the Transboundary Effects of Industrial Accidents, as well as their protocols and non-binding instruments. This research demonstrates how these instruments and their institutions can be interpreted and understood to form a common framework of rules, principles and approaches which fills critical gaps in basin treaties, and collectively contributes to the clarification and development of international law on transboundary watercourses and freshwater ecosystems. This analysis also explores institutional interaction and coordination between and beyond the UNECE pan-regional agreements, as well as the role of soft law or non-binding instruments, and state and non-state actors in the regime. This thesis seeks to contribute to a more coherent understanding of the relationship between the UNECE water regime, international water law, international environmental law and general international law. The UNECE water regime has contributed to clarifying many of the cornerstone rules and principles of international water law and it is argued that the UNECE water regime is lex specialis, which can and mostly does go beyond the UN Watercourses Convention. The UNECE water regime has also arguably spearheaded a paradigm shift in international water law, which sees it moving beyond its historically predominant focus on issues of transboundary impact and utilisation towards a stronger ecosystem orientated approach to environmental protection and equitable use of transboundary river basins. This research identifies key elements of an ecosystem approach, drawing from international environmental and international water law and demonstrates how the ecosystem approach, including ecosystem services, as supported by the UNECE water regime, affects interpretation of international water law towards enhancing ecosystem protection and intra-state equity. This research also explores how the UNECE regime goes beyond what exists elsewhere in international law and international water law on public participation and access to justice. Finally, this research examines the contribution of the UNECE regime vis-à-vis international and European Union water law, across the spectrum of pan-European river basins, especially focusing on the Danube, Sava and Western Bug basins. The UNECE water regime is the most evolved pan-regional regime of its kind, providing ambitious detailed standards and clarification of rules and principles relevant to transboundary watercourses and freshwater ecosystems. It also provides a valuable model of institutional cooperation, progressively engaging state and non-state actors. As this regime takes steps towards realising its global ambition, with almost all instruments now open to all UN member states, and the recent accession by Chad to the Water Convention, this analysis demonstrates why this is predominantly a positive endeavour but also highlights potential challenges and hurdles. This research thus explores the implications and benefits of the UNECE’s rising role in strengthening the international legal architecture to protect the world’s fragile transboundary watercourses and freshwater ecosystems.

Cross-boundary movements of energy and material are ubiquitous. Freshwater ecosystems receive nutrients, dissolved, and particulate organic matter from adjacent terrestrial ecosystems, whereas terrestrial ecosystems mainly receive prey organisms and detritus deposited by physical processes such as floods from freshwater ecosystems. Within lakes, fish are considered as integrators between habitats due to their high mobility, although they often occupy either near-shore littoral or open-water pelagic habitats and develop habitat-specific morphologies. Such intra-population divergence in morphological traits might limit the use of multiple habitats. In this thesis, I first focused on quantity and quality of reciprocal fluxes of particulate organic matter between freshwater and terrestrial ecosystems and responses of recipient consumers. Freshwater ecosystems generally received higher amounts of externally-produced resources than terrestrial ecosystems. Despite this discrepancy, aquatic and terrestrial consumer responses were similar, likely due to the differences in resource quality. Second, I investigated the potential of particulate organic carbon (POC) supporting benthic food webs in lakes; a pathway that has largely been neglected in previous studies. I found that POC can substantially subsidize the benthic food web and that the effects on the benthic food web were transferred to the pelagic habitat, thus emphasizing the importance of benthic pathways for pelagic production. Third, I examined how water transparency can affect intra-population divergence in perch (Perca fluviatilis). I observed that increased water transparency can considerably increase morphological divergence between littoral and pelagic populations likely due to its effects on foraging. Finally, I investigated the effects of such intra-population divergence on littoral-pelagic food web coupling. I found that low morphological divergence corresponded with high overlap in resource use, whereas strong morphological divergence resulted in low overlap in resource use. Here littoral populations mainly utilized littoral resources and pelagic populations primarily utilized pelagic resources, indicating that habitat coupling might be strongly limited when intra-population divergence is high. In conclusion, although different ecosystems seem separated by distinct physical boundaries, these boundaries are often crossed. However, the development of habitat-specific adaptive traits might limit movement between apparently contiguous habitats.