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Based on the increase of 16S rRNA gene sequences in databases it is possible to design improved oligonucleotide primers for this gene. Primers were designed in silico to specifically amplify fragments of the gene from the Alpha, Beta and Gamma subgroups of the Proteobacteria, as well as from Bacteroidetes, Firmicutes, Cyanobacteria and Planctomycetes and tested in silico and in vitro. The aim was to investigate bacterioplankton diversity and reveal greater fingerprint diversity within these groups than is possible using primers specific for the entire domain Bacteria, and also to reduce clone library redundancy. It was then aimed to investigate the potential impacts of increased pCO2 and ocean fertilisation with iron (Fe) and phosphorus (P), on bacterioplankton diversity. Group-specific clone libraries representing contrasting marine regions were analysed, and the usefulness and specificity of the primers validated. The clone libraries showed members of the oligotrophic marine group (OMG) to be present in an in situ coastal mesocosm supplemented with nutrients. The newly-developed group-specific primers were used in combination with an improved method of denaturing gradient gel electrophoresis (DGGE) to profile in detail bacterial communities in mesocosms, which were maintained at 750 ppm of pCO2, the level projected for the global surface ocean in the year 3000, and 380 ppm of CO2, the present level. Increased pCO2 correlated with a decrease in abundance of some members of the Gammaproteobacteria. Otherwise there was little impact on diversity due to raised pCO2. The same DGGE protocol was applied to samples from an ocean Fe and P fertilisation experiment. Diversity change due to Fe was not evident. However in seawater amended with P there was an explosive growth of some cells with 16S rRNA genes similar to those of the SAR86 clade, and others with similarity to Gammaproteobacteria with large genomes such as Oceanospirillum sp. and Psychromonas sp.

Despite the increased prominence of ecological measurement in fresh waters within recent national regulatory and legislative instruments, their assessment is still almost exclusively based on taxonomic structure. Integrated metrics of structure and function, though widely advocated, to date have not been incorporated into these bioassessment programmes. We sought to address this, by assessing community structure (macroinvertebrate assemblage composition) and ecosystem functioning (decomposition, primary production, and herbivory rates), in a series of replicated field experiments, at watercress farms on the headwaters of chalk streams, in southern England. The outfalls from watercress farms are typically of the highest chemical quality, however surveys have revealed long-term (30 years) impacts on key macroinvertebrate taxa, in particular the freshwater shrimp Gammarus pulex (L.), yet the ecosystem-level consequences remain unknown. Initial studies were at Europe’s largest watercress farm at St Mary Bourne, Hampshire, during the bioremediation of its complex wastewaters and changes to farm management practices. These widened to include larger scale spatiotemporal studies at other watercress farms. Detrimental ecological impacts at the start of the study were detected by the structural and functioning measures, but they did not respond to bioremediation. However, an increase in G. pulex abundance was detected, providing evidence of recovery in response to altered practices, which may be attributable to the cessation of chlorine use. The detrimental impacts were unique to the St Mary Bourne watercress farm and were not consistent across the other watercress farms in the study. Our results demonstrate the importance of integrated metrics of both ecosystem structure and functioning, to derive a more comprehensive view of aquatic ecosystems and highlights the difficulties associated with extrapolating from laboratory studies in response to stressors.

The linkages between the stream and its riparian zone have been well studied in many diverse systems on short (generally annual) timescales. No research has yet considered this in the context of longer (multi-decadal to centennial) timescales at which landscape and successional processes operate. Glacier Bay National Park and Preserve, in southeast Alaska, has a well-documented history of glacial retreat, which allows for the study of ecosystem development using a space-for-time chronosequence approach. This research was unique in analysing terrestrial invertebrates on floodplains of different ages in Glacier Bay, and was the first to utilise two complementary methods of dietary analysis to study the movement of resources between terrestrial and aquatic habitats at sites of different ages. A combination of gut contents dietary analysis and stable isotope analysis was used to determine the food sources of aquatic and terrestrial consumers. Physical habitat complexity, rather than substrate age alone, was an important factor in structuring reciprocal subsidies. This has clear implications for river managers seeking to restore streams to their natural state, particularly where juvenile salmonids are present, as well as underlining the importance of considering a stream in the wider context of its riparian zone.

As fundamental components of chalk stream ecosystems, aquatic macrophytes are intrinsically linked to flow regime and physicochemical stability. Assessment of the River Itchen, Hampshire, a classic lowland chalk stream faced with ecosystem degradation, indicates the significance of the discharge regime for controlling both water quality and the spatiotemporal distribution of macrophyte assemblages. Experimental studies using outdoor artificial stream mesocosms signify their effectiveness for macrophyte growth studies and in identifying causality attributed to environmental stressors. In such experiments, the keystone chalk stream macrophyte Ranunculus pseudofluitans was identified as having preferences to moderate water velocities, with morphological and physiological trait responses causing distinct morphotypes depending on development in optimal or sub-optimal conditions. Furthermore, when subjected to flow, nutrient and periphytic competitive stressors, main trait responses were categorised as developmental, functional and confounded, respectively, with most traits linked to healthy development associated with flow. In addition, significant filamentous algal growth under low-nutrient conditions, but removal in increased velocities, highlights the importance of flow as a control mechanism. Examination of ontogenetic effects suggest trait variation with age, and overall developmental stage linked to a combination of environmental and plant age effects. This study demonstrates the necessity for good, consistent flow regimes in chalk streams, which enhances macrophyte community diversity, promoting development of keystone taxa, which in turn encourage beneficial heterogeneous flow patterns.

Climate change is projected to increase the frequency and severity of extreme events, adding to the plethora of existing pressures that streams and rivers already face. Compound events such as drought may comprise numerous stressors that occur in concert to elicit ecological change. However the causal mechanisms of such impacts remain unknown, and research attempting to disentangle impacts of compound events, or link effects across levels of ecological organisation, remains in its infancy. This research investigates impacts of key drought stressors –sedimentation, dewatering and warming – across multiple ecological, hierarchical levels. At the individual level, macroinvertebrates displayed differential thermal sensitivity to warming which may explain idiosyncratic ecological responses reported elsewhere, whilst sedimentation intensified predator-prey interactions. Mesocosms were effective tools for studying drought stressors independently and in combination at the community and functional level. Dewatering main effects reduced the density of a common taxon and functional feeding group biomass, whilst all three stressors sometimes interacted together in complex ways. Stressors also had quantifiable effects at the whole-system level, e.g. stream metabolism. This study provides initial findings pertaining to drought impact causative mechanisms across multiple levels of ecological complexity, highlighting the importance of an experimental approach to predict future effects of compound events.

Quality classification of water bodies commonly hinges upon the results of biotic indices. Biotic indices should reliably detect environmental change caused by anthropogenic stress; distinguish between different levels of disturbance; and be applicable in different areas. This study assesses current methods used in the assessment of benthic ecosystem health in transitional and coastal waters. Specifically, this study considers the performance of macrozoobenthos based biotic and diversity indices. Data utilised in the assessment covered a range of sites and environmental gradients including long term monitoring sites in Scotland; sites impacted by fish farms, organic waste discharge, and chemical effluent; estuarine sites; and sites from Galway Bay, Ireland, one of which was impacted by river discharge. Currently used indices of environmental status are based mainly on structural ecosystem properties and may not encompass all aspects of ecosystem health, such as functioning. Structural and functional based assessment methods were evaluated by comparing the performance of a range of standard benthic abundance indices and approaches focussing on intrinsic biological characteristics. Indices did not perform consistently in response to different types of impact – organic, chemical and physical, indicating some indices are unsuitable for the detection of multiple stressors. Index quality classifications agreed best in the most impacted sites but performed unpredictably in moderate conditions. Variability of indices increased as disturbance increased, decreasing the statistical certainty and confidence in the index values. Structural indices were found to be more variable than functional indices but the sensitivity of functional indices to anthropogenic disturbance needs further testing to determine whether they are able to detect low level disturbance. Functional indices may not be advantageous in regular monitoring over traditional methods but may provide a more informative assessment of ecosystem health. Use of biological traits may also give an indication of the type or cause of disturbance. Classification of moderate-good conditions using benthic indices is particularly ambiguous and distinguishing natural from anthropogenic disturbance remains one of the biggest challenges. The results indicate that complementarity of approaches is important in the assessment of quality of coastal and transitional benthic aquatic systems.

1. With freshwater ecosystems worldwide at significant risk from global change, there is an urgent need to understand the processes involved and to develop adaptive responses. Riparian management might offer a means of increasing resilience to global change in headwaters, but evidence is scarce. This thesis investigates the potential effects of riparian management on the storage, processing and downstream export of resource subsidies – dominantly as terrestrial litter – that enter streams from the riparian zone. 2. In a large scale field study over four years, natural and experimental systems were used to test the hypothesis that riparian woodlands enhance stream ecosystem resilience to climatically mediated changes in flow regimes. Specific work included assessments of benthic organic matter stocks and export in contrasting catchments (broadleaf woodland, conifer plantations or sheep-grazed moorland), flow manipulations in mesocosms, and a large-scale field experiment simulating riparian broadleaved tree planting. 3. Standing stocks of particulate organic matter (POM) were influenced by flow regime, and declined following larger and longer flow-events, but event frequency had no apparent impact. Experimental data showed also that coarse fractions of POM in transport were significantly elevated in the early stages of simulated floods. 4. Despite flow effects on POM dynamics, streams bordered by broadleaves maintained consistently higher standing stocks of POM than conifer or moorland streams. Broadleaved streams also transported the highest concentrations of carbon in the form of high-quality FPOM. Leaf litter additions of stream channels did not reproduce these effects, possibly because the scale was insufficient to mimic real riparian woodlands. 5. While predicted flow changes under a warmer climate might affect the storage and flux of organic matter, riparian broadleaves are likely to mitigate these effects in stream ecosystems. This project illustrates the value of blending catchment-scale studies with field-based mesocosms to understanding complex global change processes.

Agricultural land use is a leading cause of habitat degradation and biodiversity loss in streams. Understanding the mechanisms by which land use change affects stream ecosystems is essential for their effective management. Despite this, the consequences of agricultural intensification for community composition and ecosystem functioning in streams remain poorly resolved. Using national-scale monitoring data and new field data from upland streams in South Wales, this study investigated the effects of pastoral intensification on the community composition, functional diversity and feeding interactions of stream macroinvertebrates. A combination of analytical tools were used, including propensity modelling, ecological traits, stable isotopes and Next Generation DNA sequencing to quantify diet. Taxonomic and functional diversity had non-linear relationships with pastoral intensity, declining beyond a threshold of 4 mg L-1 nitrate and 8% fine sediment cover. This decline occurred as a non-random loss of species possessing specific traits, including large body size and lack of resistance forms. Although monitoring data showed that at a UK-wide scale pastoral agriculture (cf. other land uses) had a positive effect on richness and sensitive species representation, the threshold intensity at which effects become negative is exceeded in many locations within the U.K. and globally. Invertebrates that feed by grazing algae were particularly vulnerable to agricultural stressors. Combined with changes in the availability and quality of basal resources with pastoral intensification, this decline in grazer representation resulted in invertebrate communities becoming increasingly reliant on detrital resources. Further, there was indication that methane-derived carbon contributed to the food web in high intensity sites, which has not previously been observed in upland streams. Although only relatively minor changes were observed in predator-prey interactions across the intensity gradient, there was a suggestion of simplification of the food web in high intensity sites. Together these changes could radically alter ecosystem properties such as secondary production, nutrient processing and resilience. Overall, the results highlight the management priorities of reducing fine sediment and nutrient inputs to agricultural streams. The identification of a threshold at which agricultural effects become deleterious will assist in guiding mitigation efforts. Further work is required to determine the generality of this threshold across stream ecosystems.

Freshwater environments are threatened worldwide by external stressors and biodiversity decline, with major implications for ecosystem resilience. The genetic consequences so far have been neglected, especially for freshwater invertebrates, though their abundance, diversity, ease of sampling and functional importance renders them ideal candidates for genetic appraisal. For three freshwater invertebrates (Amphinemura sulcicollis, Isoperla grammatica and Baetis rhodani) novel microsatellite markers were developed so that genetic structure, and genetic diversity could be assessed throughout upland Wales. The aim was to investigate dispersal and the genetic response to environmental stressors. Genetic diversity in these species was compared to species diversity across whole macroinvertebrate assemblages to investigate what factors might cause a correlation between these fundamental levels of biodiversity. The demographic history of each species was also investigated with the aim of assessing whether reduced genetic diversity was due to bottlenecks and more broadly, what this indicates in terms of the populations’ resilience. Species differed in their genetic structure and genetic diversity. All three species showed effective dispersal and geneflow, with each species displaying panmixa across catchments in southern and mid-Wales. However, A. sulcicollis and I. grammatica revealed genetic isolation and reduced genetic diversity at specific northern sites. Genetic and species diversity were correlated positively only in A. sulcicollis, where isolation combined with a common driver were the likely cause. There was evidence of recent bottlenecks in all three species. All these results could be explained by an underlying genetic response to post-industrial acidification: reduced genetic diversity correlated significantly with acidity for A. sulcicollis, while reduced species diversity and genetic bottleneck signatures was consistent with chronic and episodic acidification across the Welsh region. Overall, these results show how a positive correlation between species and genetic diversity can never be assumed, and illustrate how assessments of genetic health expand insights available from traditional biodiversity assessment.