Riverine physical habitats and habitat utilization by fish have often been studied independently. Varying flows modify habitat composition and connectivity within a stream but its influence on habitat use is not well understood. This study examined brown trout (Salmo trutta) and bullhead (Cottus gobio) utilization of physical habitats that vary with flow in terms of size and type, persistence or duration, and frequency of change from one state to another, by comparing groundwater-dominated sites on the River Tern (Shropshire) with surface runoff-dominated lowland, riffle-pool sites on the Dowles Brook (Worcestershire). Mesohabitat surveys carried out at two-month intervals on a groundwater-dominated stream and on a surface runoff-influenced stream showed differences in habitat composition and diversity between the two types of rivers. The temporal variability in mesohabitat composition was also shown to differ between the two flow regime types. In the groundwater-influenced stream, mesohabitat composition hardly varied between flows whereas in the flashy stream it varied to a great extent with discharge. Habitat suitability curves for brown trout and bullhead were constructed to predict the potential location of the fish according to flow. The resulting prediction maps were tested in the field during fish surveys using direct underwater observation (snorkelling). Under the groundwater-influenced flow regime brown trout displayed a constant pattern of mesohabitat use over flows. Mesohabitats with non-varying characteristics over flows and with permanent features such as large woody debris, macrophytes or any feature providing shelter and food were favoured. Biological processes, such as hierarchy, life cycle and life stage appeared to play a key role in determining fish habitat use and to a greater extent than physical processes in these streams. Bullhead observations in the flashy river showed that mesohabitat use varied with flow but that some mesohabitats were always favoured in the stream. Pools and glides were the most commonly used mesohabitat, due to their stability over flows and their role as shelter from harsh hydraulic conditions and as food retention zones. The presence of cobbles was also found to be determinant in bullhead choice of habitat. In this flashy environment, physical processes such as flow and depth and velocity conditions appeared to be a more decisive factor in bullhead strategy of habitat use than biological processes. This research shows that: 1. Though differences in habitat use strategies between the two flow regimes can in part be attributed to differing ecology between the species, flow variability affects fish behaviour. 2. A stable flow regime allows biological processes to be the main driving force in determining fishbehaviour and location. A highly variable environment requires fish to develop behaviour strategies in response to variations in hydraulic conditions, such as depth and velocity, which constitute the key factor in determining fish location.

With the formal adoption of the Water Framework Directive in 2000, into European legislation it committed all member states to ensure that all inland waterbodies should reach good ecological status by 2015. As a result examination of the influence of hydromorphology on the ecological health of riverine ecosystems has become an increasingly important priority for statutory monitoring agencies such as the Environment Agency of England and Wales and equivalents in other parts of the UK. It is anticipated that by increasing our understanding of the role that hydromorphological processes play in shaping river habitats and the ecosystems that they support, river management strategies can be developed that will help lead to waterbodies achieving good ecological status. In this thesis, the influence of river hydromorphology and instream channel management activities on instream macroinvertebrate communities is explored. A two-scale approach was used at a regional macro-scale and local / catchment micro-scale. The macro-scale study examines the ecological, hydrological and geomorphological data for 88 river reaches located within the Environment Agency , Anglian Central and Anglian Northern regions, over a twenty year period (1986-2005). At the micro-scale two sub-catchments were selected, the River Bain and River Lymn, both located in Lincolnshire, England for detailed investigation. The micro-scale study was undertaken using ecological, hydrological and geomorphological data collected over three successive seasons (Autumn 2008, Spring 2009 and Summer 2009) enabling the seasonal variations and the influence of both stream size and habitat biotope on macroinvertebrate community composition and structure to be explored. The hydromorphological characteristics and condition of the rivers were quantified using ecologically relevant hydrological indices, calculated from flow discharge paired with geomorphological indices from River Habitat Survey data. The response of the instream macroinvertebrate communities was examined using a range of ecological indices including the Lotic-invertebrate Index for Flow Evaluation (LIFE). The results of the macro-scale investigation demonstrate that the macroinvertebrate community is directly influenced by instream hydromorphology and the level of anthropogenic modification. The micro-scale study highlights important differences in macroinvertebrate communities associated with instream habitat / biotope composition. The quantification of river hydromorphology, with the use of ecologically relevant hydrological indices and geomorphological indices, derived from River Habitat Survey data, is discussed with regards its ability to help explain the structure and composition of macroinvertebrate communities within highly managed /regulated riverine ecosystems. The implications of this research for river managers and for implementing river restoration and rehabilitation schemes are explored.

No description available.

Floodplain lakes are strongly regulated by river connectivity because floodwaters exert strong influence on the water balance, the physical, chemical and biological limnological conditions, and the influx of contaminants. The Peace-Athabasca Delta (PAD) in northern Alberta (Canada) is a hydrologically complex landscape and is an important node in the upper Mackenzie River Drainage Basin. The ecological integrity of the PAD is potentially threatened by multiple environmental stressors, yet our understanding of the hydroecology of this large floodplain remains underdeveloped. Indeed, ever since the planning and construction of the WAC Bennett Dam (1960s), concerns have grown over the effects of upstream human activities on the lakes of the PAD. More recently, concerns over the health of the PAD have intensified and come to the fore of national and international dialogue due to water abstraction and mining and processing activities by the rapidly expanding oil sands industry centred in Fort McMurray Alberta. Currently, widespread perception is that upstream human activities have reduced water levels and frequency of flooding at the PAD, which have lowered nutrient availability and productivity of perched basin lakes, and have increased supply of pollutants from oil sands. However, these perceptions remain based on insufficient knowledge of pre-impact conditions and natural variability. Current and past relations between hydrology and limnology of PAD lakes are mostly undocumented, particularly during the important spring freshet period when the effects of river flood waters are strongest. Similarly, knowledge of the deposition of oil-sands- related contaminants in the PAD remains insufficient to determine whether anthropogenic activities have increased the deposition of important oil-sands-related contaminants such as polycyclic aromatic compounds (PACs) relative to natural processes. Such knowledge gaps must be filled to achieve effective monitoring, policy and governance concerning impacts of industrial development and the protection of human and environmental health within the PAD and Mackenzie drainage basin. This thesis examines the effects of river flooding (and the lack of) on water clarity, nutrients, chemistry, phytoplankton abundance, epiphyton community composition and the deposition of polycyclic aromatic compounds (PACs) in lakes of the Peace-Athabasca Delta. To determine the role of flooding on contemporary epiphytic diatom communities (an abundant and diverse guild of primary producers in PAD lakes), a field experiment was conducted examining the community composition and abundance of epiphytic diatoms in four PAD lakes. Two of these four lakes had received floodwaters that spring and two had not. Epiphytic diatom communities in each lake were sampled during the peak macrophyte biomass period (summer) from two macrophyte taxa (Potamogeton zosteriformis, P. perfoliatus var. richardsonii) and from polypropylene artificial substrates previously deployed that spring. A two-way analysis of similarity (ANOSIM) test identified that epiphytic diatom community composition differed between lakes that flooded and those that did not flood. From the use of similarity percentage (SIMPER) analysis, diatom taxa were identified that discriminate between flooded and non-flooded lakes. The relative abundance of ‘strong flood indicator taxa’ was used to construct an event-scale flood record spanning the past ~180 years using analyses of sedimentary diatom assemblages from a closed-drainage lake (PAD 5). Results were verified by close agreement with an independent paleo-flood record from a nearby flood-prone oxbow lake (PAD 54) and historical records. Comparison of epiphytic diatoms in flooded and non-flooded lakes in this study provides a promising approach to detect changes in flood frequency, and may have applications for reconstructing other pulse-type disturbances such as hurricanes and pollutant spills. Additionally, this study demonstrates that artificial substrates can provide an effective bio-monitoring tool for lakes of the PAD and elsewhere. To improve our understanding of the hydrolimnological responses of lake in the PAD to flooding, repeated measurements over three years (2003-05) were made on a series of lakes along a hydrological gradient. This allowed the role of river flooding to be characterized on limnological conditions of lakes and to identify the patterns and timescales of limnological change after flooding. River floodwaters elevate lake water concentrations of suspended sediment, total phosphorus (TP), SO4 and dissolved Si (DSi), and reduce concentrations of total Kjeldahl nitrogen (TKN), DOC and most ions. River flooding increases limnological homogeneity among lakes, because post-flood conditions are strongly affected by the river water properties. After floodwaters recede, limnological conditions become more heterogeneous among lakes in response to diversity of local basin influences (geology, slope, vegetation, depth, fetch, and biological communities and processes), and limnological changes occur at two distinct timescales. In the weeks to months after flooding, water clarity increases as suspended sediments and TP settle out of the water column. In the absence of flooding for many years to decades, evaporative concentration leads to an increase in most nutrients (TKN, inorganic N, and dissolved P), DOC and ions. Contrary to a prevailing paradigm, these results suggest that regular flooding is not required to maintain high nutrient concentrations. In light of anticipated declines in river discharge, limnological conditions in the southern Athabasca sector will become increasingly less dominated by the short-term effects of flooding, and resemble nutrient- and solute-rich lakes in the northern Peace sector that are infrequently flooded. To determine the roles of the Athabasca River and atmospheric transport as vectors for the deposition of PACs in the PAD, sediment cores spanning the last ~200 years were collected from three lakes within the delta. A closed-drainage basin elevated well above the floodplain (PAD 18) was selected to determine temporal patterns of change in PAC concentration due to atmospheric deposition and within-basin production of PACs. Known patterns of paleohydrological changes at the other two lakes (PAD 23 and 31) were used to assess the role of the Athabasca River in delivering PACs to the Athabasca Delta during the ~200 year. Well- dated sediment core samples were analysed for 52 alkylated and non-alkylated PACs (method EPA 3540/8270-GC/MS). Sediments deposited in the non-flood prone lake (PAD 18) contained lower concentrations of total PACs compared to sediments deposited during flood-prone periods in the other study lakes, and were dominated by PACs of a pyrogenic rather than bitumen origin. Multivariate analysis of similarity tests identified that the composition of PACs differs between sediments deposited during not flood-prone and flood-prone periods. Subsequent Similarities Percentage (SIMPER) analysis was used and identified seven PACs that are preferentially deposited during flood-prone periods. These seven PACs are bitumen-associated, river-transported and account for 51% of the total PACs found in oil-sands sediment. At PAD 31, which has been flood-prone both before and since onset of Athabasca oil sands development, identified no measureable differences in both the proportion and concentration of the river-transported indicator PACs in sediments deposited pre-1940s versus post-1982. Our findings suggest that natural erosion of exposed bitumen along the banks of the Athabasca River and its tributaries is the main process delivering PACs to the Athabasca Delta, and that the spring freshet is a key period for contaminant mobilization and transport. Such key baseline environmental information is essential for informed management of natural resources and human-health concerns by provincial and federal regulatory agencies and industry, and for designing effective long-term monitoring and surveillance programs for the lower Athabasca River watershed in the face of future oil sands development. Further monitoring activities and additional paleolimnological studies of the depositional history of PACs and other oil-sands- and non-oil-sands-related contaminants is strongly recommended. Overall, results of this research identify that river flooding exerts strong control on physical, chemical and biological conditions of lakes within the PAD. However, contrary to prevailing paradigms, the PAD is not a landscape that has been adversely and permanently affected by regulation of the Peace River and industrial development of the oil sands along the Athabasca River. Instead, data from contemporary and paleolimnological studies identify that natural processes continue to dominate the delivery of water and contaminants to the delta. Regular and frequent flooding is not essential to maintain the supply of nutrients and productivity of delta lakes, which has been a widespread paradigm that developed in the absence of objective scientific data. Instead, nutrient concentrations rise over years to decades after flooding and lake productivity increases. During the thesis research, novel approaches were developed and demonstrated to be effective. Namely, new artificial substrate samplers were designed for aquatic biomonitoring that accrue periphyton and can identify the occurrence of flood events. Also, paleolimnological methods were employed to characterize the composition and concentration of PACs supplied by natural processes prior to oil sands industrial activity, which serves as an important benchmark for assessing industrial impacts. These are effective methods that can be employed to improve monitoring programs and scientific understanding of the factors affecting this world-renowned landscape, as well as floodplains elsewhere.

Caractériser la dissémination des bio-agresseurs est un enjeu majeur pour la gestion et la prédiction des maladies en santé des plantes. Face aux limites des approches usuelles en pathologie végétale, une nouvelle vision a été proposée abordant les paradigmes d’histoire de vie des agents phytopathogènes en dehors des limites du système hôte-pathogène. Parmi ces agents phytopathogènes, les études sur P.syringae sont celles qui ont contribuées le plus à ce nouveau courant de pensée et dont on connaît le mieux l’histoire de vie en relation avec ses réservoirs « non hôtes ». L’espèce est détectée dans de nombreux compartiments du cycle de l’eau, des précipitations jusqu’aux rivières et eaux d’irrigation, en passant par les plantes sauvages et le manteau neigeux. L’ensemble de ces observations ont soulevé de nouvelles questions sur la manière dont P. syringae se dissémine au travers de ces environnements et sur les processus impactant sur la dynamique des populations à l’échelle d’un bassin versant. Ces recherches se sont donc intéressées à ses processus dans des précipitations jusqu’aux cours d’eau alpins dans l’optique d’acquérir des données pour la modélisation des flux de P. syringae. Elles ont mis en évidence les populations résidentes de la litière et la survie sa survie dans le sol, processus jamais identifiés à l’histoire de vie de P. syringae. Elles ont également caractérisé (i) les conditions propices à son transport via les précipitations, (ii) le rôle du manteau neigeux comme réservoir et protecteur des populations des prairies alpines et (iii) ont mis en évidence la chimie de l’eau comme indicateur témoin de la dynamique des populations des les rivières. Ces observations suggérant un transport de P. syringae dans le sol, nous l’avons quantifiée à travers des études de terrain et des simulations en laboratoire.Enfin, l’ensemble des données de ces recherches couplées à des outils SIG et des modèles météorologiques et hydrologiques ont permis de proposé un modèle sur les flux de P.syringae des habitats naturels vers les agro-systèmes. / The characterization of the spread of bio-agressors spread is a major issue for themanagement of plant health and the prediction of disease emergence. Given thelimitations of conventional approaches in plant pathology, a new vision has beenproposed addressing paradigms life history of plant pathogens outside the limits of thecrop host-pathogen system. Among the plant pathogens, studies on P. syringae are thosethat have contributed the most to this new way of thought for which life history inrelation to "non host" reservoirs has been highlighted. The species is found in manycompartments of the water cycle, from precipitation to rivers and irrigation water, wildplants and snowpack. All these observations have raised new questions about how P.syringae spreads through these environments and on the processes impactingpopulation dynamics at the scale of a watershed. This research was therefore interestedin these processes with the objective to acquire data for modeling the tranfer of P.syringae through the watershed. They highlighted the resident populations of litter andtheir survival in the soil, processes never identified in association with the life history ofP. syringae. They also revealed (i) the conditions for transport via precipitations, (ii) therole of snowpack as a reservoir and protector of the populations in alpine meadows and(iii) showed that water chemistry can be used as an indicator of the populationdynamics in headwaters. These observations suggested a transport of P. syringae via thesoil that we subsequently characterized through field studies and laboratorysimulations. Finally, all data from this research combined with GIS tools andmeteorological and hydrological models have permitted us to propose a model of theflux of P. syringae of natural habitats to agricultural systems.