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Oligotrophic marl lakes have exceptional water clarity and are rare habitats for associated species but are also susceptible to deterioration because of nutrient enrichment. This thesis aimed to determine the current status and cause of eutrophication at the Magheraveely/Kilroosky Marl Loughs SAC (Northern Ireland, UK), investigate mitigation measures, estimate groundwater influx, and assess the population status of co-designated and endangered white-clawed crayfish Austropotamobius pallipes. The surveyed nine lakes failed EU Water Framework Directive nutrient standards. During thermal stratification anoxic hypolimnia resulted in sediment Phosphorus (P) release that maintained the current trophic status. In extrapolations from measurements on sediment cores from Kilroosky Lough, sediment in hypoxia contributed 0.022 mg P L⁻¹ to the whole-lake concentration. Sediment P release decreased by 59% with aeration and by 60% after removing the upper 10 cm sediment. CaNO3 dosing supressed P release at water NO3 concentrations above 5.6 mg L⁻¹ . Groundwater discharge was measured with a RAD7 radon detector customised to process 16 L water samples. A ²²²Rn mass balance estimated annual groundwater contributions between 40% and 160% of lake volume and between 15% and 62% of total water input depending on site. Trapping surveys and mark-recapture surveys mapped crayfish presence and assessed population size. There was substantial abundance in two lakes and low-level presence in two lakes with one first record. Resampling with a Monte Carlo method investigated the relationship between survey effort and variability of catch per unit effort (CPUE). Even high trapping efforts yielded CPUE results with an excess of 20% relative standard deviation. Therefore, an assessment of conservation targets requires surveys with a measure of uncertainty. Lake restoration and survival of crayfish populations need mitigation of surface water P transfers and inhibition of sediment P release e.g., by CaNO3 dosing to stabilise marl lake self-cleaning mechanisms.

Surfactants are researched for their ability to reduce biofouling and biofilm build up in medical and industrial environments. Constant usage of these chemicals both as anti-biofilm agents and within personal care products has led to an increase in their presence environmentally. This thesis studied the effects of surfactants on marine and freshwater biofilms which are important to local aquatic biogeochemical cycling. Exposure of biofilms to the synthetic surfactant, sodium dodecyl sulphate, and biological surfactant, rhamnolipid, led to alterations in community composition, significant decreases in biodiversity, and increases in antimicrobial resistance gene retention. Overall, more sensitive taxa such as Arenimonas, decreased in favor of more resistant, and potentially pathogenic taxa, including Brevundimonas. Rhamnolipid exposed biofilms retained eight of the nine identified antimicrobial resistance genes while SDS retained five and the control retained four. Surfactant exposure also altered biofilm metabolic activity. Increases in activity of the extracellular enzymes beta glucosidase and leucine aminopeptidase occurred after rhamnolipid exposure while decreases occurred after exposure to SDS. Carbon: Nitrogen also decreased significantly when rhamnolipid and grazer exposure occurred together, disrupting a previously beneficial holobiont relationship between grazers and biofilm. Overall, both biological and synthetic surfactant exposure have direct effects on freshwater and marine biofilm structure and metabolic activity. This could lead to future biofilm loss and compositional changes, with implications for decreases in local biogeochemical cycling, and human and environmental health hazards.

To better understand the critical processes controlling where and when phosphorus (P) can be transferred to groundwater (GW) and later delivered to catchment streams, this study investigated highly mobile soil colloidal P (Pcoll) and other P fractions in the soil-groundwater-surface water continuum. Three experiments were undertaken. Firstly an investigation into soil chemical and fertilizer influences on soluble (< 450 nm) and total medium-sized colloidal P (TPcoll; 200-450 nm) at the batch scale; secondly an investigation into static and dynamic physical controls on water flow at the soil profile scale, and implications for P transfer to shallow GW; and finally, at the hillslope scale, an investigation into meteorological influences on the below-ground delivery of TPcoll and total fine, nano-particulate and truly dissolved P (TFPcoll; < 200 nm) fractions to streams. Soil Fe content and degree of P saturation increased soil TPcoll and soluble P, respectively. Synthetic fertilizer influenced TPcoll while cattle slurry did not; the latter increased soluble P. The downslope and midslope zones had similar soil hydraulic properties and subsurface water flow dynamics. Inter-annually, higher total rainfall increased water flow peaks and shallower GW level mobilised soil P which further increased GW P concentrations. The Al-rich catchment with lower soil (macro)porosity and higher bedrock hydraulic conductivity was dominated by fine reactive P (FRPcoll) in GW and in the stream. The Fe-rich catchment with higher soil (macro)porosity and lower bedrock hydraulic conductivity was dominated by coarser particulate P in GW and by FRPcoll in the stream. Rainfall event characteristics controlled the dominating hydrological flowpaths and mobilised P sources which led to contrasting contribution of TFPcoll in a receiving stream between rainfall events, even though the GW P contribution was similar. These Pcoll investigations could contribute to a better identification of the critical areas and critical times where and when TPcoll and TFPcoll can be transferred to GW and later delivered to the stream. These findings can be used to better target costeffective mitigation measures to further reduce diffuse P pollution and support sustainable food production.

The environmental dimensions of the global health problem of antibiotic resistance have remained largely uncharted, particularly in regard to biotic interactions of waterborne bacteria. This thesis studied the effect of phytoplankton and zooplankton on horizontal gene transfer (HGT) in Enterococcus faecalis strains in experimental microcosms. HGT was investigated between an E. faecalis donor strain with the plasmid borne vancomycin resistance gene vanA and rifampicin-resistant recipient strains. Gene transfer frequency (GTF) of vanA in centrifugation-induced liquid mating assays at 37 oC (10-7 ) significantly exceeded GTF at 20 oC or 30 oC (10-8). Enhanced nutrient availability increased GTF from 10-7 to 10-5 in liquid mating assays, thus documenting the importance of energy resources to conjugation in E. faecalis. Active filter feeding increased vanA GTF in Daphnia-bacteria microcosms to a range of 1.5 × 10-8 – 3.3 ×10-7, and ingested enterococci remained viable inside Daphnia for at least four days. Filter feeding zooplankton may thus facilitate the emergence of multi-resistance and disseminate transconjugants in aquatic environments. Microalgae zooplankton feeds on may further enhance HGT. Microcosm experiments documented that Palmellopsis sp. enhanced vanA GTF by an order of magnitude, indicating that the algal cell mucilage was a suitable attachment substrate and energy source for conjugation. The ciliate Tetrahymena pyriformis also facilitated HGT in E. faecalis. In the presence of live ciliates vanA GTF was 10-6 – 10-5 , an order of magnitude higher than in ciliate-free controls. GTF was higher within vesicles than in the ambient medium; it increased with time and peaked after 24 h. Overall, this thesis highlights the potential effects of interactions between eukaryotic freshwater organisms and Enterococcus faecalis as a representative of Gram positive bacteria on the emergence and spread of antibiotic resistance. It also offers a projection of gene transfer frequencies under environmentally relevant conditions in lakes and wastewater treatment plants.

Dreissena polymorpha (zebra mussel) and Margaritifera margaritifera (pearl mussel) are freshwater bivalves. Both are found within the Neagh Bann Catchment in Northern Ireland UK. This project investigated the presence and abundance of D. polymorpha in Lough Neagh, the Lower Bann and Ballinrees reservoir. Whilst D. polymorpha has extended its previously known geographic range in the Neagh Bann catchment beyond the lough, the abundance of this notoriously invasive species has remained very low in Lough Neagh. Inhibiting factors were identified and investigated. Of particular importance was substrate suitability, as 85% of the lough bed is unsuitable for D. polymorpha settlement. Due to Lough Neagh's shallow depth and large surface area wind driven currents frequently resuspend particulate matter which inhibit mussel filter feeding and potentially smother sessile mussels. Water temperature, dissolved oxygen content and electrical conductivity of Lough Neagh did not exceed the tolerance range for D. polymorpha survival and replication. The abundance of the parasitic ciliate Conchophthirus acuminatus in D. polymorpha mussels was compared across Lough Erne, Lough Neagh, the Lower River Bann and Ballinrees Reservoir. The parasite presence/absence pattern suggested that the mussels arrived in Lough Neagh as adults and spread from there as larvae throughout the Neagh Bann catchment. DNA analysis of D. polymorpha from the same four sites provided no evidence for introductions from source areas with genetically different mussel strains. Salmonid fish from the Ballinderry River (Northern Ireland) were exposed to glochidiosis by freshwater pearl mussels (Margaritifera margaritifera) under semi-natural hatchery conditions. Genetically distinct pearl mussel populations from the upper and lower regions of the Ballinderry river both displayed glochidial host preference for river trout (Salmo trutta), notably Dollaghan, thus emphasising the importance of these endemic fish for the future survival of M. margaritifera within the Ballinderry River. No Ballinderry River pearl mussel glochidia survived the parasitic life stage on Atlantic Salmon (Salmo trutta) gills showed that older fish (1+ and 2+) carried greater encysted loads, although they were less susceptible to glochidial encystment than juvenile (0+) fish. Based on other studies glochidia excyst around day 350, in this study by day 337 all glochidia had excysted from host fish during captive bred trials. Margaritifera margaritifera glochidial fish host preference in the Ballinderry River for trout differs from host preference or other pearl mussel populations in Northern Ireland. It is therefore essential that fisheries management policy change conducts risk assessments at a catchment scale, in order to make good conversation and policy choices. An increasing frequency in the occurrence of bacterial multidrug resistance against antibiotics has raised the question about the potential contribution of environmental processed to this rise. In this study's laboratory experiments filter feeding by D. polymorpha had an effect on vancomycin resistance transfer in Enterococcus faecalis. Furthermore, the presence of phytoplankton (Palmellopsis sp.) facilitated higher transfer efficiencies. Presumed conjugal transfer of antimicrobial resistance in D. polymorpha occurred at a maximal transfer efficiency of 10-6. This is evidence for the ability of benthic filter feeders such as D. polymorpha to facilitate the emergence and spread of multidrug resistance against antibiotics among faecal bacteria in aquatic environments which receive pollutant transfers from faecal sources. Careful management of the Neagh Bann Catchment is required to limit the spread of invasive zebra mussels, to encourage the survival and recovery of pear mussel populations through good habitat management and host survival and to minimise the spread of antimicrobial resistance in the natural environment by improved waste and wastewater management.

High status water-bodies (HSWs), as designated under the European Union (EU) Water Framework Directive (WFD), are rivers, lakes, transitional waters and coastal waters, that are close to natural status, representing conditions that are largely unimpacted by anthropogenic activities. These HSWs are sensitive areas that require special attention. However, in recent years large declines in the number of HSWs in Ireland have been observed, with these declines being attributed to pressures from point source pollution or unintentional discharges, along with low intensity practices potentially resulting from changes in land use and land cover. With this background, this PhD set out to present a review of HSWs and their management strategies in the European Union, and to investigate in three separate studies, the potential for HSW deteriorations to be caused by: 1) land use and land cover change; 2) hydrological (streamflow) modifications; and 3) sediment pressures. For these three studies, HSWs in Ireland were determined to have either: "Lost" their high status (e.g. gone from high to good, moderate, poor or bad); consistently "Maintained" their high status; or "Gained" in status (e.g. from good to high). The review of HSWs in Europe (Chapter 1) highlighted how it may be counter-productive for countries to focus exclusively on achieving the "good" status objective of the WFD, while ignoring deteriorations to HSWs. Additionally, using case studies from four Member States with relatively large numbers of HSWs (Sweden, Austria, Ireland, and UK (Scotland)), the review assessed variations in strategies employed to manage HSWs. Based on these case studies it was determined that lag times between implementing management strategies and seeing actual benefits make assessing the effectiveness of such measures difficult, but that countries that have developed strategies may benefit from the sharing of knowledge, for example Ireland and Scotland. The land cover change study (Chapter 2) demonstrated methods for assessing land cover change using CORINE data for three time periods: 2006-2012, 2000-2006 and 2000-2012; and found that anthropogenically influenced changes in land use and land cover types were linked to declines in water body status, with a higher level of natural/semi-natural land occurring in Maintained catchments. For example, in the period 2006-2012, land that changed from Forestry to Heterogeneous Agricultural areas was 17.5 times more likely to result in Lost status, whereas land that remained as Forestry or remained as Inland Wetlands reduced the chance of Lost status occurring by 15% and 4% respectively. However, the similarity of land cover trends between sites that have Lost and Gained status provided further research questions. In the hydrological (streamflow) modifications study (Chapter 3), despite differences being found in Lotic Index for Flow Evaluation (LIFE) scores between the Lost and Maintained status categories, all LIFE scores were generally about 7.25 and reflective of rivers hosting invertebrate communities with a preference for medium/high streamflow rates. While some hydrometric stations in the wider study area did display changing streamflow trends, which may potentially be linked to drainage and/or change in status, the overall conclusion was that for most sites, streamflow alterations are not likely to have been a major factor leading to deteriorations. However, for certain sites, and potentially in combination with other stressors, streamflow alterations may be problematic. The sediment study (Chapter 4) found that, macro-invertebrate taxa occurring in HSWs were pre-dominantly sediment sensitive taxa. However, for two sediment specific metrics, the Proportion of Sediment-sensitive Index (PSI) and the Empirically-weighted PSI (E-PSI), significant differences were observed between sites that Lost status and those that Maintained status, implying that at some sites, sedimentation is impacting on macro-invertebrates. Again, no difference between Lost and Gained sites was observed, leaving an important caveat. While weak to moderate relationships were observed between the sediment metrics and the physical sediment variables, no difference between status categories for any of the physical sediment variables was observed, although this may be related to the sampling resolution. Chapter 4 also highlighted the potential for multiple-stressors, such as the interaction between sediment, organic pollution and streamflow alterations, to contribute to deteriorations in status. However, nutrient sampling indicated little or no evidence of nutrient enrichment at the majority of sample sites, and it is suggested that nutrient analysis at HSWs may be better served by higher resolution monitoring. Finally, key recommendations were suggested based on the overall findings of the PhD, that included: investigating if measures being implemented in catchments with Gained status may be replicated and possibly used to improve conditions at Lost status sites; and potentially including "impacting on high status water-bodies" as an additional category requiring Environmental Impact Assessments (especially in relation to drainage works).

As filterfeeders, freshwater sponges encounter bacteria in streams, rivers and lakes including those from faecal sources like enterococci and coliforms, which can exhibit antibiotic resistance with potential clinical impacts through e.g. infection of humans from recreational use of these environments. Filterfeeding trials verified the potential of Irish freshwater sponges Ephydatia fluviatilis and Spongilla lacustris, which occupy wide ranges in the northern hemisphere, to reduce the abundance of Escherichia coli in ambient water. Plate counts of bacterial abundance were more reliable than monitoring methods involving turbidity or fluorescence measurements. Laboratory and field studies tested the application of the sponges for biomonitoring of microbial water quality. In the laboratory both sponge species retained Enterococcus faecalis in lower abundances than E. coli. Although gradual changes of abundance of enterococci and coliforms in sponge samples were also observed along a longitudinal river reach transect, the between river differences in retention of enterococci and coliforms were greater than within a single river. The sponges' potential for facilitating conjugal antibiotic resistance transfer was explored in microcosms with E. faecalis strains resistant to either vancomycin or rifampicin. Lack of a significant difference between transconjugant numbers on double selection plates from microcosms with live or dead sponges suggested that filtration activity had no decisive role in conjugal transfer of monitored resistance traits. Sponge gemmule surfaces were found to be associated with bacteria resistant to ampicillin, erythromycin, rifampicin, tetracycline, trimethoprim and vancomycin. Methanol extracts from freshwater sponges inhibited the growth of some nosocomial bacteria, with adult sponge extracts having a higher inhibitory effect than extracts from gemmule-grown sponges, indicating the contribution of the sponge microbiome. The antimicrobial properties of sponge samples varied with collection site, and the combination of sponge extracts from several sites caused the better inhibitor to become diluted and less effective as an antimicrobial agent.