Admixture mapping identifies novel Alzheimer's disease risk regions in African Americans

BACKGROUND

This study used admixture mapping to prioritize the genetic regions associated with Alzheimer's disease (AD) in African American (AA) individuals, followed by ancestry-aware regression analysis to fine-map the prioritized regions.

METHODS

We analyzed 10,271 individuals from 17 different AA datasets. We performed admixture mapping and meta-analyzed the results. We then used regression analysis, adjusting for local ancestry main effects and interactions with genotype, to refine the regions identified from admixture mapping. Finally, we leveraged in silico annotation and differential gene expression data to prioritize AD-related variants and genes.

RESULTS

Admixture mapping identified two genome-wide significant loci on chromosomes 17p13.2 (p = 2.2 × 10-5 ) and 18q21.33 (p = 1.2 × 10-5 ). Our fine mapping of the chromosome 17p13.2 and 18q21.33 regions revealed several interesting genes such as the MINK1, KIF1C, and BCL2.

DISCUSSION

Our ancestry-aware regression approach showed that AA individuals have a lower risk of AD if they inherited African ancestry admixture block at the 17p13.2 locus.

HIGHLIGHTS

We identified two genome-wide significant admixture mapping signals: on chromosomes 17p13.2 and 18q21.33, which are novel in African American (AA) populations. Our ancestry-aware regression approach showed that AA individuals have a lower risk of Alzheimer's disease (AD) if they inherited African ancestry admixture block at the 17p13.2 locus. We found that the overall proportion of African ancestry does not differ between the cases and controls that suggest African genetic ancestry alone is not likely to explain the AD prevalence difference between AA and non-Hispanic White populations.

Dissecting the role of Amerindian genetic ancestry and the ApoE ε4 allele on Alzheimer disease in an admixed Peruvian population

Alzheimer disease (AD) is the leading cause of dementia in the elderly and occurs in all ethnic and racial groups. The apolipoprotein E (ApoE) ε4 is the most significant genetic risk factor for late-onset AD and shows the strongest effect among East Asian populations followed by non-Hispanic white populations and has a relatively lower effect in African descent populations. Admixture analysis in the African American and Puerto Rican populations showed that the variation in ε4 risk is correlated with the genetic ancestral background local to the ApoE gene. Native American populations are substantially underrepresented in AD genetic studies. The Peruvian population with up to ~80 of Amerindian (AI) ancestry provides a unique opportunity to assess the role of AI ancestry in AD. In this study, we assess the effect of the ApoE ε4 allele on AD in the Peruvian population. A total of 79 AD cases and 128 unrelated cognitive healthy controls from Peruvian population were included in the study. Genome-wide genotyping was performed using the Illumina Global screening array v2.0. Global ancestry and local ancestry analyses were assessed. The effect of the ApoE ε4 allele on AD was tested using a logistic regression model by adjusting for age, gender, and population substructure (first 3 principal components). Results showed that the genetic ancestry surrounding the ApoE gene is predominantly AI (60.6%) and the ε4 allele is significantly associated with increased risk of AD in the Peruvian population (odds ratio = 5.02, confidence interval: 2.3-12.5, p-value = 2e-4). Our results showed that the risk for AD from ApoE ε4 in Peruvians is higher than we have observed in non-Hispanic white populations. Given the high admixture of AI ancestry in the Peruvian population, it suggests that the AI genetic ancestry local to the ApoE gene is contributing to a strong risk for AD in ε4 carriers. Our data also support the findings of an interaction between the genetic risk allele ApoE ε4 and the ancestral backgrounds located around the genomic region of ApoE gene.

River toxicity assessment using molecular biosensors: Heavy metal contamination in the Turag-Balu-Buriganga river systems, Dhaka, Bangladesh

Pollution in rapidly urbanising cities and in delta systems is a serious problem that blights the lives and livelihoods of millions of people, damaging and restricting potable water supply and supplies to industry (Whitehead et al, 2015, 2018). Employing new technology based on luminescent molecular biosensors, the toxicity in the rivers around Dhaka in Bangladesh, namely the Turag, Tongi, Balu and Buriganga, has been assessed. Samples taken at 36 sites during medium and low flow conditions and during the Bishwa Ijtema Festival revealed high levels of cell toxicity, as well as high concentrations of metals, particularly aluminium, cadmium, chromium, iron, zinc, lithium, selenium and nickel. Chemical analysis also revealed low dissolved oxygen levels and anoxic conditions in the rivers at certain sites. The bacterial molecular biosensors were demonstrated to be fast, with results in 30 min, robust and a highly sensitive method for the assessment of water toxicity in the field. Furthermore, the biosensor toxicity analysis correlated with the metals data, and a multivariate regression relationship was developed relating toxicity to key metals, such a selenium, zinc and chromium. The resulting model has been validated against split samples and the Bishwa Ijtema Festival data. The combination of modelling and the molecular biosensor technology provides a new approach to detecting and managing pollution in urban river systems.

Modelling heavy metals in the Buriganga River System, Dhaka, Bangladesh: Impacts of tannery pollution control

Heavy metal pollution from tanneries is a global problem in many rapidly developing economies. Effluent discharges into rivers cause serious problems for water quality, damaging ecology and threatening the livelihoods of people, especially in developing urban centres which often have a high concentration of factories. The industry intensive capital area of Bangladesh is impacted with high levels of metals pollution in rivers in the Greater Dhaka Watershed. Sampling and modelling studies have been undertaken to assess pollution in the Buriganga River System in Dhaka. The process based, dynamic model INCA (Integrated Catchments) model has been used to simulate metals along the Buriganga River System in Central Dhaka. Observed and simulated metals concentrations are high, and the model shows that the proposed transfer of the tannery industry upstream helps to reduce the pollution significantly downstream. However, moving the industry upstream may be counterproductive as it is discharged into the upper reaches of the river. This will create pollution upstream unless the newly constructed effluent treatment system can operate at a high level.

Water quality modelling of the Mekong River basin: Climate change and socioeconomics drive flow and nutrient flux changes to the Mekong Delta

The Mekong delta is recognised as one of the world's most vulnerable mega-deltas, being subject to a range of environmental pressures including sea level rise, increasing population, and changes in flows and nutrients from its upland catchment. With changing climate and socioeconomics there is a need to assess how the Mekong catchment will be affected in terms of the delivery of water and nutrients into the delta system. Here we apply the Integrated Catchment model (INCA) to the whole Mekong River Basin to simulate flow and water quality, including nitrate, ammonia, total phosphorus and soluble reactive phosphorus. The impacts of climate change on all these variables have been assessed across 24 river reaches ranging from the Himalayas down to the delta in Vietnam. We used the UK Met Office PRECIS regionally coupled climate model to downscale precipitation and temperature to the Mekong catchment. This was accomplished using the Global Circulation Model GFDL-CM to provide the boundary conditions under two carbon control strategies, namely representative concentration pathways (RCP) 4.5 and a RCP 8.5 scenario. The RCP 4.5 scenario represents the carbon strategy required to meet the Paris Accord, which aims to limit peak global temperatures to below a 2 °C rise whilst seeking to pursue options that limit temperature rise to 1.5 °C. The RCP 8.5 scenario is associated with a larger 3-4 °C rise. In addition, we also constructed a range of socio-economic scenarios to investigate the potential impacts of changing population, atmospheric pollution, economic growth and land use change up to the 2050s. Results of INCA simulations indicate increases in mean flows of up to 24%, with flood flows in the monsoon period increasing by up to 27%, but with increasing periods of drought up to 2050. A shift in the timing of the monsoon is also simulated, with a 4 week advance in the onset of monsoon flows on average. Decreases in nitrogen and phosphorus concentrations occur primarily due to flow dilution, but fluxes of these nutrients also increase by 5%, which reflects the changing flow, land use change and population changes.

Optimizing land management strategies for maximum improvements in lake dissolved oxygen concentrations

Eutrophication and anoxia are unresolved issues in many large waterbodies. Globally, management success has been inconsistent, highlighting the need to identify approaches which reliably improve water quality. We used a process-based model chain to quantify effectiveness of terrestrial nutrient control measures on in-lake nitrogen, phosphorus, chlorophyll and dissolved oxygen (DO) concentrations in Lake Simcoe, Canada. Across a baseline period of 2010-2016 hydrochemical outputs from catchment models INCA-N and INCA-P were used to drive the lake model PROTECH, which simulated water quality in the three main basins of the lake. Five terrestrial nutrient control strategies were evaluated. Effectiveness differed between catchments, and water quality responses to nutrient load reductions varied between deep and shallow lake basins. Nutrient load reductions were a significant driver of increased DO concentrations, however strategies which reduced tributary inflow had a greater impact on lake restoration, associated with changes in water temperature and chemistry. Importantly, when multiple strategies were implemented simultaneously, resultant large flow reductions induced warming throughout the water column. Negative impacts of lake warming on DO overwhelmed the positive effects of nutrient reduction, and limited the effectiveness of lake restoration strategies. This study indicates that rates of lake recovery may be accelerated through a coordinated management approach, which considers strategy interactions, and the potential for temperature change-induced physical and biological feedbacks. Identified impacts of flow and temperature on rates of lake recovery have implications for management sustainability under a changing climate.

Modelling metaldehyde in catchments: a River Thames case-study

The application of metaldehyde to agricultural catchment areas to control slugs and snails has caused severe problems for drinking water supply in recent years. In the River Thames catchment, metaldehyde has been detected at levels well above the EU and UK drinking water standards of 0.1 μg l^-1 at many sites across the catchment between 2008 and 2015. Metaldehyde is applied in autumn and winter, leading to its increased concentrations in surface waters. It is shown that a process-based hydro-biogeochemical transport model (INCA-contaminants) can be used to simulate metaldehyde transport in catchments from areas of application to the aquatic environment. Simulations indicate that high concentrations in the river system are a direct consequence of excessive application rates. A simple application control strategy for metaldehyde in the Thames catchment based on model results is presented.

Fate and transport of polychlorinated biphenyls (PCBs) in the River Thames catchment - Insights from a coupled multimedia fate and hydrobiogeochemical transport model

The fate of persistent organic pollutants (POPs) in riverine environments is strongly influenced by hydrology (including flooding) and fluxes of sediments and organic carbon. Coupling multimedia fate models (MMFMs) and hydrobiogeochemical transport models offers unique opportunities for understanding the environmental behaviour of POPs. While MMFMs are widely used for simulating the fate and transport of legacy and emerging pollutants, they use greatly simplified representations of climate, hydrology and biogeochemical processes. Using additional information about weather, river flows and water chemistry in hydrobiogeochemical transport models can lead to new insights about POP behaviour in rivers. As most riverine POPs are associated with suspended sediments (SS) or dissolved organic carbon (DOC), coupled models simulating SS and DOC can provide additional insights about POPs behaviour. Coupled simulations of river flow, DOC, SS and POP dynamics offer the possibility of improved predictions of contaminant fate and fluxes by leveraging the additional information in routine water quality time series. Here, we present an application of a daily time step dynamic coupled multimedia fate and hydrobiogeochemical transport model (The Integrated Catchment (INCA) Contaminants model) to simulate the behaviour of selected PCB congeners in the River Thames (UK). This is a follow-up to an earlier study where a Level III fugacity model was used to simulate PCB behaviour in the Thames. While coupled models are more complex to apply, we show that they can lead to much better representation of POPs dynamics. The present study shows the importance of accurate sediment and organic carbon simulations to successfully predict riverine PCB transport. Furthermore, it demonstrates the important impact of short-term weather variation on PCB movement through the environment. Specifically, it shows the consequences of the severe flooding, which occurred in early 2014 on sediment PCB concentrations in the River Thames.

An INCA model for pathogens in rivers and catchments: Model structure, sensitivity analysis and application to the River Thames catchment, UK

Pathogens are an ongoing issue for catchment water management and quantifying their transport, loss and potential impacts at key locations, such as water abstractions for public supply and bathing sites, is an important aspect of catchment and coastal management. The Integrated Catchment Model (INCA) has been adapted to model the sources and sinks of pathogens and to capture the dominant dynamics and processes controlling pathogens in catchments. The model simulates the stores of pathogens in soils, sediments, rivers and groundwaters and can account for diffuse inputs of pathogens from agriculture, urban areas or atmospheric deposition. The model also allows for point source discharges from intensive livestock units or from sewage treatment works or any industrial input to river systems. Model equations are presented and the new pathogens model has been applied to the River Thames in order to assess total coliform (TC) responses under current and projected future land use. A Monte Carlo sensitivity analysis indicates that the input coliform estimates from agricultural sources and decay rates are the crucial parameters controlling pathogen behaviour. Whilst there are a number of uncertainties associated with the model that should be accounted for, INCA-Pathogens potentially provides a useful tool to inform policy decisions and manage pathogen loading in river systems.

Impacts of climate change and socio-economic scenarios on flow and water quality of the Ganges, Brahmaputra and Meghna (GBM) river systems: low flow and flood statistics

The potential impacts of climate change and socio-economic change on flow and water quality in rivers worldwide is a key area of interest. The Ganges-Brahmaputra-Meghna (GBM) is one of the largest river basins in the world serving a population of over 650 million, and is of vital concern to India and Bangladesh as it provides fresh water for people, agriculture, industry, conservation and for the delta system downstream. This paper seeks to assess future changes in flow and water quality utilising a modelling approach as a means of assessment in a very complex system. The INCA-N model has been applied to the Ganges, Brahmaputra and Meghna river systems to simulate flow and water quality along the rivers under a range of future climate conditions. Three model realisations of the Met Office Hadley Centre global and regional climate models were selected from 17 perturbed model runs to evaluate a range of potential futures in climate. In addition, the models have also been evaluated using socio-economic scenarios, comprising (1) a business as usual future, (2) a more sustainable future, and (3) a less sustainable future. Model results for the 2050s and the 2090s indicate a significant increase in monsoon flows under the future climates, with enhanced flood potential. Low flows are predicted to fall with extended drought periods, which could have impacts on water and sediment supply, irrigated agriculture and saline intrusion. In contrast, the socio-economic changes had relatively little impact on flows, except under the low flow regimes where increased irrigation could further reduce water availability. However, should large scale water transfers upstream of Bangladesh be constructed, these have the potential to reduce flows and divert water away from the delta region depending on the volume and timing of the transfers. This could have significant implications for the delta in terms of saline intrusion, water supply, agriculture and maintaining crucial ecosystems such as the mangrove forests, with serious implications for people's livelihoods in the area. The socio-economic scenarios have a significant impact on water quality, altering nutrient fluxes being transported into the delta region.

Dynamic modeling of the Ganga river system: impacts of future climate and socio-economic change on flows and nitrogen fluxes in India and Bangladesh

This study investigates the potential impacts of future climate and socio-economic change on the flow and nitrogen fluxes of the Ganga river system. This is the first basin scale water quality study for the Ganga considering climate change at 25 km resolution together with socio-economic scenarios. The revised dynamic, process-based INCA model was used to simulate hydrology and water quality within the complex multi-branched river basins. All climate realizations utilized in the study predict increases in temperature and rainfall by the 2050s with significant increase by the 2090s. These changes generate associated increases in monsoon flows and increased availability of water for groundwater recharge and irrigation, but also more frequent flooding. Decreased concentrations of nitrate and ammonia are expected due to increased dilution. Different future socio-economic scenarios were found to have a significant impact on water quality at the downstream end of the Ganga. A less sustainable future resulted in a deterioration of water quality due to the pressures from higher population growth, land use change, increased sewage treatment discharges, enhanced atmospheric nitrogen deposition, and water abstraction. However, water quality was found to improve under a more sustainable strategy as envisaged in the Ganga clean-up plan.

Assessing the impacts of climate change and socio-economic changes on flow and phosphorus flux in the Ganga river system

Anthropogenic climate change has impacted and will continue to impact the natural environment and people around the world. Increasing temperatures and altered rainfall patterns combined with socio-economic factors such as population changes, land use changes and water transfers will affect flows and nutrient fluxes in river systems. The Ganga river, one of the largest river systems in the world, supports approximately 10% global population and more than 700 cities. Changes in the Ganga river system are likely to have a significant impact on water availability, water quality, aquatic habitats and people. In order to investigate these potential changes on the flow and water quality of the Ganga river, a multi-branch version of INCA Phosphorus (INCA-P) model has been applied to the entire river system. The model is used to quantify the impacts from a changing climate, population growth, additional agricultural land, pollution control and water transfers for 2041-2060 and 2080-2099. The results provide valuable information about potential effects of different management strategies on catchment water quality.

A review of arsenic and its impacts in groundwater of the Ganges-Brahmaputra-Meghna delta, Bangladesh

Arsenic in drinking water is the single most important environmental issue facing Bangladesh; between 35 and 77 million of its 156 million inhabitants are considered to be at risk from drinking As-contaminated water. This dominates the list of stress factors affecting health, livelihoods and the ecosystem of the delta region. There is a vast literature on the subject so this review provides a filter of the more important information available on the topic. The arsenic problem arises from the move in the 1980s and 1990s by international agencies to construct tube wells as a source of water free of pathogens, groundwater usually considered a safe source. Since arsenic was not measured during routine chemical analysis and also is difficult to measure at low concentrations it was not until the late 1990s that the widespread natural anomaly of high arsenic was discovered and confirmed. The problem was exacerbated by the fact that the medical evidence of arsenicosis only appears slowly. The problem arises in delta regions because of the young age of the sediments deposited by the GBM river system. The sediments contain minerals such as biotite which undergo slow "diagenetic" reactions as the sediments become compacted, and which, under the reducing conditions of the groundwater, release in the form of toxic As(3+). The problem is restricted to sediments of Holocene age and groundwater of a certain depth (mainly 30-150 m), coinciding with the optimum well depth. The problem is most serious in a belt across southern Bangladesh, but within 50 m of the coast the problem is only minor because of use of deep groundwater; salinity in shallow groundwater here is the main issue for drinking water. The Government of Bangladesh adopted a National Arsenic Policy and Mitigation Action Plan in 2004 for providing arsenic safe water to all the exposed population, to provide medical care for those who have visible symptoms of arsenicosis. There is as yet no national monitoring program in place. Various mitigation strategies have been tested, but generally the numerous small scale technological remedies have proved unworkable at village level. The current statistics show that use of deep groundwater (below 150 m) is the main source of arsenic mitigation over most of the arsenic affected areas as well as rainwater harvesting in certain location.

Rainfall runoff modelling of the Upper Ganga and Brahmaputra basins using PERSiST

There are ongoing discussions about the appropriate level of complexity and sources of uncertainty in rainfall runoff models. Simulations for operational hydrology, flood forecasting or nutrient transport all warrant different levels of complexity in the modelling approach. More complex model structures are appropriate for simulations of land-cover dependent nutrient transport while more parsimonious model structures may be adequate for runoff simulation. The appropriate level of complexity is also dependent on data availability. Here, we use PERSiST; a simple, semi-distributed dynamic rainfall-runoff modelling toolkit to simulate flows in the Upper Ganges and Brahmaputra rivers. We present two sets of simulations driven by single time series of daily precipitation and temperature using simple (A) and complex (B) model structures based on uniform and hydrochemically relevant land covers respectively. Models were compared based on ensembles of Bayesian Information Criterion (BIC) statistics. Equifinality was observed for parameters but not for model structures. Model performance was better for the more complex (B) structural representations than for parsimonious model structures. The results show that structural uncertainty is more important than parameter uncertainty. The ensembles of BIC statistics suggested that neither structural representation was preferable in a statistical sense. Simulations presented here confirm that relatively simple models with limited data requirements can be used to credibly simulate flows and water balance components needed for nutrient flux modelling in large, data-poor basins.

Distributed and dynamic modelling of hydrology, phosphorus and ecology in the Hampshire Avon and Blashford Lakes: evaluating alternative strategies to meet WFD standards

The issues of diffuse and point source phosphorus (P) pollution in the Hampshire Avon and Blashford Lakes are explored using a catchment model of the river system. A multibranch, process based, dynamic water quality model (INCA-P) has been applied to the whole river system to simulate water fluxes, total phosphorus (TP) and soluble reactive phosphorus (SRP) concentrations and ecology. The model has been used to assess impacts of both agricultural runoff and point sources from waste water treatment plants (WWTPs) on water quality. The results show that agriculture contributes approximately 40% of the phosphorus load and point sources the other 60% of the load in this catchment. A set of scenarios have been investigated to assess the impacts of alternative phosphorus reduction strategies and it is shown that a combined strategy of agricultural phosphorus reduction through either fertiliser reductions or better phosphorus management together with improved treatment at WWTPs would reduce the SRP concentrations in the river to acceptable levels to meet the EU Water Framework Directive (WFD) requirements. A seasonal strategy for WWTP phosphorus reductions would achieve significant benefits at reduced cost.

A cost-effectiveness analysis of water security and water quality: impacts of climate and land-use change on the River Thames system

The catchment of the River Thames, the principal river system in southern England, provides the main water supply for London but is highly vulnerable to changes in climate, land use and population. The river is eutrophic with significant algal blooms with phosphorus assumed to be the primary chemical indicator of ecosystem health. In the Thames Basin, phosphorus is available from point sources such as wastewater treatment plants and from diffuse sources such as agriculture. In order to predict vulnerability to future change, the integrated catchments model for phosphorus (INCA-P) has been applied to the river basin and used to assess the cost-effectiveness of a range of mitigation and adaptation strategies. It is shown that scenarios of future climate and land-use change will exacerbate the water quality problems, but a range of mitigation measures can improve the situation. A cost-effectiveness study has been undertaken to compare the economic benefits of each mitigation measure and to assess the phosphorus reductions achieved. The most effective strategy is to reduce fertilizer use by 20% together with the treatment of effluent to a high standard. Such measures will reduce the instream phosphorus concentrations to close to the EU Water Framework Directive target for the Thames.

The interactive responses of water quality and hydrology to changes in multiple stressors, and implications for the long-term effective management of phosphorus

Soluble reactive phosphorus (SRP) plays a key role in eutrophication, a global problem decreasing habitat quality and in-stream biodiversity. Mitigation strategies are required to prevent SRP fluxes from exceeding critical levels, and must be robust in the face of potential changes in climate, land use and a myriad of other influences. To establish the longevity of these strategies it is therefore crucial to consider the sensitivity of catchments to multiple future stressors. This study evaluates how the water quality and hydrology of a major river system in the UK (the River Thames) respond to alterations in climate, land use and water resource allocations, and investigates how these changes impact the relative performance of management strategies over an 80-year period. In the River Thames, the relative contributions of SRP from diffuse and point sources vary seasonally. Diffuse sources of SRP from agriculture dominate during periods of high runoff, and point sources during low flow periods. SRP concentrations rose under any future scenario which either increased a) surface runoff or b) the area of cultivated land. Under these conditions, SRP was sourced from agriculture, and the most effective single mitigation measures were those which addressed diffuse SRP sources. Conversely, where future scenarios reduced flow e.g. during winters of reservoir construction, the significance of point source inputs increased, and mitigation measures addressing these issues became more effective. In catchments with multiple point and diffuse sources of SRP, an all-encompassing effective mitigation approach is difficult to achieve with a single strategy. In order to attain maximum efficiency, multiple strategies might therefore be employed at different times and locations, to target the variable nature of dominant SRP sources and pathways.

Macronutrient cycles and climate change: key science areas and an international perspective

Human activities have doubled global cycles of Nitrogen (N) and Phosphorus (P) and elevated N and P have compromised ecosystem services through the degradation of natural resources of soils, freshwaters and marine waters with a subsequent loss of biodiversity. Elevated Carbon (C) levels in the atmosphere have been linked to global warming, with positive feedback mechanisms accelerating the warming process. In order to initiate nutrient control, both national and international mitigation measures have been implemented. However, many of these initiatives focus upon a single nutrient without considering cycle interactions. A sound understanding of processes and transformations involved in the interactions of macronutrient cycles is required to avoid inadvertently enhancing effects of one nutrient, during mitigation for impacts of another. Emerging research initiatives are addressing these research gaps, with programmes in the US (USGCRP) and the UK (Macronutrient Cycles) advocating integration between scientists and stakeholders, in order to deliver results directly to policy makers. Through these programmes the scales of nitrogen and phosphorus fluxes will be quantified, and a determination made of the nature of nutrient transformations in catchments under a changing climate and perturbed carbon cycle. The consideration of connectivity between multiple macronutrient cycles will help to minimise the threats to biodiversity, ecosystem dynamics, public water supplies and human health by improved management and better focused policy.

Using the INCA-Hg model of mercury cycling to simulate total and methyl mercury concentrations in forest streams and catchments

We present a new, catchment-scale, process-based dynamic model for simulating mercury (Hg) in soils and surface waters. The Integrated Catchments Model for Mercury (INCA-Hg) simulates transport of gaseous, dissolved and solid Hg and transformations between elemental (Hg(0)), ionic (Hg(II)) and methyl (MeHg) Hg in natural and semi-natural landscapes. The mathematical description represents the model as a series of linked, first-order differential equations describing chemical and hydrological processes in catchment soils and waters which we believe control surface water Hg dynamics. The model simulates daily time series between one and 100 years long and can be applied to catchments ranging in size from <1 to ~10,000 km(2). Here we present applications of the model to two boreal forest headwater catchments in central Canada where we were able to reproduce observed patterns of stream water total mercury (THg) and MeHg fluxes and concentrations. Model performance was assessed using Monte Carlo techniques. Simulated in-stream THg and MeHg concentrations were sensitive to hydrologic controls and terrestrial and aquatic process rates.

Modelling phosphorus dynamics in multi-branch river systems: a study of the Black River, Lake Simcoe, Ontario, Canada

High rates of nutrient loading from agricultural and urban development have resulted in surface water eutrophication and groundwater contamination in regions of Ontario. In Lake Simcoe (Ontario, Canada), anthropogenic nutrient contributions have contributed to increased algal growth, low hypolimnetic oxygen concentrations, and impaired fish reproduction. An ambitious programme has been initiated to reduce phosphorus loads to the lake, aiming to achieve at least a 40% reduction in phosphorus loads by 2045. Achievement of this target necessitates effective remediation strategies, which will rely upon an improved understanding of controls on nutrient export from tributaries of Lake Simcoe as well as improved understanding of the importance of phosphorus cycling within the lake. In this paper, we describe a new model structure for the integrated dynamic and process-based model INCA-P, which allows fully-distributed applications, suited to branched river networks. We demonstrate application of this model to the Black River, a tributary of Lake Simcoe, and use INCA-P to simulate the fluxes of P entering the lake system, apportion phosphorus among different sources in the catchment, and explore future scenarios of land-use change and nutrient management to identify high priority sites for implementation of watershed best management practises.

Estimating uncertainty in terrestrial critical loads and their exceedances at four sites in the UK

Critical loads are the basis for policies controlling emissions of acidic substances in Europe and elsewhere. They are assessed by several elaborate and ingenious models, each of which requires many parameters, and have to be applied on a spatially-distributed basis. Often the values of the input parameters are poorly known, calling into question the validity of the calculated critical loads. This paper attempts to quantify the uncertainty in the critical loads due to this "parameter uncertainty", using examples from the UK. Models used for calculating critical loads for deposition of acidity and nitrogen in forest and heathland ecosystems were tested at four contrasting sites. Uncertainty was assessed by Monte Carlo methods. Each input parameter or variable was assigned a value, range and distribution in an objective a fashion as possible. Each model was run 5000 times at each site using parameters sampled from these input distributions. Output distributions of various critical load parameters were calculated. The results were surprising. Confidence limits of the calculated critical loads were typically considerably narrower than those of most of the input parameters. This may be due to a "compensation of errors" mechanism. The range of possible critical load values at a given site is however rather wide, and the tails of the distributions are typically long. The deposition reductions required for a high level of confidence that the critical load is not exceeded are thus likely to be large. The implication for pollutant regulation is that requiring a high probability of non-exceedance is likely to carry high costs. The relative contribution of the input variables to critical load uncertainty varied from site to site: any input variable could be important, and thus it was not possible to identify variables as likely targets for research into narrowing uncertainties. Sites where a number of good measurements of input parameters were available had lower uncertainties, so use of in situ measurement could be a valuable way of reducing critical load uncertainty at particularly valuable or disputed sites. From a restricted number of samples, uncertainties in heathland critical loads appear comparable to those of coniferous forest, and nutrient nitrogen critical loads to those of acidity. It was important to include correlations between input variables in the Monte Carlo analysis, but choice of statistical distribution type was of lesser importance. Overall, the analysis provided objective support for the continued use of critical loads in policy development.

Impacts of climate change on in-stream nitrogen in a lowland chalk stream: an appraisal of adaptation strategies

The impacts of climate change on nitrogen (N) in a lowland chalk stream are investigated using a dynamic modelling approach. The INCA-N model is used to simulate transient daily hydrology and water quality in the River Kennet using temperature and precipitation scenarios downscaled from the General Circulation Model (GCM) output for the period 1961-2100. The three GCMs (CGCM2, CSIRO and HadCM3) yield very different river flow regimes with the latter projecting significant periods of drought in the second half of the 21st century. Stream-water N concentrations increase over time as higher temperatures enhance N release from the soil, and lower river flows reduce the dilution capacity of the river. Particular problems are shown to occur following severe droughts when N mineralization is high and the subsequent breaking of the drought releases high nitrate loads into the river system. Possible strategies for reducing climate-driven N loads are explored using INCA-N. The measures include land use change or fertiliser reduction, reduction in atmospheric nitrate and ammonium deposition, and the introduction of water meadows or connected wetlands adjacent to the river. The most effective strategy is to change land use or reduce fertiliser use, followed by water meadow creation, and atmospheric pollution controls. Finally, a combined approach involving all three strategies is investigated and shown to reduce in-stream nitrate concentrations to those pre-1950s even under climate change.

Bioremediation of acid mine drainage: an introduction to the Wheal Jane wetlands project

Acid mine drainage (AMD) is a widespread environmental problem associated with both working and abandoned mining operations. As part of an overall strategy to determine a long-term treatment option for AMD, a pilot passive treatment plant was constructed in 1994 at Wheal Jane Mine in Cornwall, UK. The plant consists of three separate systems; each containing aerobic reed beds, anaerobic cell and rock filters, and represents the largest European experimental facility of its kind. The systems only differ by the type of pre-treatment utilised to increase the pH of the influent minewater (pH<4): lime-dosed (LD), anoxic limestone drain (ALD) and lime free (LF), which receives no form of pre-treatment. The Wheal Jane pilot plant offered a unique facility and a major research project was established to evaluate the pilot plant and study in detail the biological mechanisms and the geochemical and physical processes that control passive treatment systems. The project has led to data, knowledge, models and design criteria for the future design, planning and sustainable management of passive treatment systems. A multidisciplinary team of scientists and managers from the U.K. universities, the Environment Agency and the Mining Industry has been put together to obtain the maximum advantage from the excellent facilities facility at Wheal Jane.

Chemical behaviour of the Wheal Jane bioremediation system

The effectiveness of remediation of the highly acidic and transition metal polluted mine water discharge from the Wheal Jane Mine by the Wheal Jane Passive Treatment Plant is described. The success of the remediation required that all the system components work as predicted. The study shows considerable success in the removal of key toxic metals and clearly demonstrates the potential for natural attenuation of acid mine drainage, particularly iron oxidation, by microbial populations. The Wheal Jane Passive Treatment Plant provides the only experimental facility of its kind.

The Wheal Jane wetlands model for bioremediation of acid mine drainage

Acid mine drainage (AMD) is a widespread environmental problem associated with both working and abandoned mining operations. As part of an overall strategy to determine a long-term treatment option for AMD, a pilot passive treatment plant was constructed in 1994 at Wheal Jane Mine in Cornwall, UK. The plant consists of three separate systems, each containing aerobic reed beds, anaerobic cell and rock filters, and represents the largest European experimental facility of its kind. The systems only differ by the type of pretreatment utilised to increase the pH of the influent minewater (pH <4): lime dosed (LD), anoxic limestone drain (ALD) and lime free (LF), which receives no form of pretreatment. Historical data (1994-1997) indicate median Fe reduction between 55% and 92%, sulphate removal in the range of 3-38% and removal of target metals (cadmium, copper and zinc) below detection limits, depending on pretreatment and flow rates through the system. A new model to simulate the processes and dynamics of the wetlands systems is described, as well as the application of the model to experimental data collected at the pilot plant. The model is process based, and utilises reaction kinetic approaches based on experimental microbial techniques rather than an equilibrium approach to metal precipitation. The model is dynamic and utilises numerical integration routines to solve a set of differential equations that describe the behaviour of 20 variables over the 17 pilot plant cells on a daily basis. The model outputs at each cell boundary are evaluated and compared with the measured data, and the model is demonstrated to provide a good representation of the complex behaviour of the wetland system for a wide range of variables.

On modelling the flow controls on macrophyte and epiphyte dynamics in a lowland permeable catchment: the River Kennet, southern England

A new in-stream model of phosphorus (P) and macrophyte dynamics, the Kennet Model, was applied to a reach of the River Kennet to investigate the impacts of changing flow conditions on macrophyte growth. The investigation was based on the assessment of two flow change scenarios, which both included the simulation of decreasing total phosphorus concentrations from a sewage treatment works due to improved effluent treatment. In the first scenario, the precipitation and potential evaporation outputs from a climate change model (HadCM2 GGx) where input into the catchment model INCA to predict the mean daily flows in the reach. In the second scenario, the mean daily flows observed in a historically dry year were repeated as input to the in-stream model to simulate an extended low flow period over 2 years. The simulation results suggest that changes in the seasonal distribution of flow were not detrimental to macrophyte growth. However, the simulation of extended periods of low flow suggests that a proliferation of epiphytic algae occurs, even when the in-stream phosphorus concentrations are reduced due to effluent treatment. This epiphytic growth was predicted to reduce the macrophyte peak biomass within the reach by approximately 80%. Thus, the model simulations suggest that flow was more important in controlling the macrophyte biomass in the River Kennet, than the in-stream phosphorus concentrations, which are elevated due to agricultural diffuse sources.

Recovery from acidification in the Tillingbourne catchment, southern England: catchment description and preliminary results

Measurements of acid deposition and streamwater chemistry made in 1979-1982 and 1999-2000 are compared for a small, acid-sensitive catchment in Southeast England. The location, geology, soils, vegetation and hydrology of the catchment are described. The catchment is located on an acidic cretaceous sandstone with a low permeability clay sub-stratum. Soils are predominantly podzol and gley, with some mesotrophic peat. The catchment is forested. Mean volume-weighted concentrations in precipitation have changed approximately in proportion to emission changes. SO4(2-) has declined by 61%, H+ by 75%, both NO- and NH4+ by 37% and Cl- by 26%. Changes in wet deposition are greater, sulfate deposition declined by 69%, non-marine SO4(2-) by 73%, H+ deposition by 75%, NO3- and NH4+ by 50% and Cl- by 41%. Sulfate deposition in throughfall, a surrogate for total deposition measurement, has declined by 82% and non-marine SO4(2-) by 86%. Some of these changes are due to alterations in the tree cover and location of the collectors. In 1979-1982, the flux of NO3- and NH4+ in throughfall was less than in rainfall, 7.5 compared with 11.3 kg N ha(-1) year(-1), showing that N uptake by the canopy was greater than dry deposition of these species. However, in 1999-2000, the throughfall flux of N was greater than rainfall, 19.6 compared to 5.7 kg N ha year(-1), indicating that canopy uptake is not occurring to the same extent. Surface water was sampled at the same locations in the catchment during the two periods. At the catchment exit, mean pH increased, from 3.93 to 4.21 mg l(-1), and SO4(2-) declined from 20.2 to 16.7 mg l(-1) (18%). The decrease in SO4(2-) is much less than the reduction in deposition, suggesting that the predicted recovery is being delayed by release of sulfur from the soil. In contrast, NO3- concentrations in the catchment waters increased from 0.22 to 0.52 mg N l(-1) (133%) despite the reduction in N deposition. NH4+ concentrations were low during both study periods. It is concluded that recovery from acidification is probably occurring, but is possibly being delayed by desorption of soil S. The catchment is also showing signs of increasing N saturation, despite a reduction in N inputs.

Steady state and dynamic modelling of nitrogen in the River Kennet: impacts of land use change since the 1930s

Steady state and dynamic models have been developed and applied to the River Kennet system. Annual nitrogen exports from the land surface to the river have been estimated based on land use from the 1930s and the 1990s. Long term modelled trends indicate that there has been a large increase in nitrogen transport into the river system driven by increased fertiliser application associated with increased cereal production, increased population and increased livestock levels. The dynamic model INCA (Integrated Nitrogen in Catchments) has been applied to simulate the day-to-day transport of N from the terrestrial ecosystem to the riverine environment. This process-based model generates spatial and temporal data and reproduces the observed instream concentrations. Applying the model to current land use and 1930s land use indicates that there has been a major shift in the short term dynamics since the 1930s, with increased river and groundwater concentrations caused by both non-point source pollution from agriculture and point source discharges.

On modelling the impacts of phosphorus stripping at sewage works on in-stream phosphorus and macrophyte/epiphyte dynamics: a case study for the River Kennet

A new model of in-stream phosphorus and macrophyte dynamics, 'The Kennet model', was applied to a reach of the River Kennet, southern England. The reach, which is 1.5 km long, is immediately downstream of Marlborough sewage treatment works, where phosphorus reduction by tertiary effluent treatment began in September 1997. The model is used to simulate the flow, water chemistry and macrophyte biomass within the reach, both before and after phosphorus removal from the effluent. Monte Carlo experiments coupled with a general sensitivity analysis indicate that the model offers a feasible explanation for the salient aspects of the system behaviour. Model simulations indicate that epiphyte smothering is an important limitation to macrophyte growth, and that higher stream and pore water soluble reactive phosphorus (SRP) concentrations allow the earlier onset of growth for the epiphytes and macrophytes, respectively. Higher flow conditions are shown to reduce the simulated peak epiphyte biomass; though at present, the effect of flow on the macrophyte biomass is unclear. Another simulation result suggests that phosphorus will not be released from the bed sediments in this reach following phosphorus removal from the effluent.

Modelling instream nitrogen variability in the Dee catchment, NE Scotland

The Integrated Nitrogen in CAtchments model (INCA) was applied to the River Dee, Aberdeenshire, NE Scotland. To a first approximation the model was able to simulate the annual mean streamwater NO3-N concentrations observed along the length of the main channel. This provided the basis for using INCA to subsequently explore the effects of N deposition and land use management on streamwater NO3-N concentrations and loads. On an annual timescale, the model predictions suggest that NO3-N concentrations will decrease by 5% following a 20% reduction in fertiliser application. Furthermore, model results also suggest that a 50% increase in N deposition will cause a 15% increase in the streamwater NO3-N concentrations. The utility of INCA as a tool for catchment management is discussed, current limitations are highlighted and possible improvements are suggested.

The water quality of the River Kennet: initial observations on a lowland chalk stream impacted by sewage inputs and phosphorus remediation

The water quality of seven sites on the upper reaches of the River Kennet round the market town of Marlborough is described and related to the introduction of phosphorus treatment of effluent from Marlborough sewage treatment works (STW). The River Kennet is mainly groundwater-fed from a Cretaceous chalk aquifer and hence the river water is calcium- and bicarbonate-bearing and has a relatively constant composition of many major water quality determinants. In-stream biological activity gives rise to marked diurnal fluctuations in pH (of approx. 0.8 units). Dissolved carbon dioxide and dissolved oxygen also show marked diurnal fluctuations. Dissolved carbon dioxide varies from approximately 10 to 70 times atmospheric pressure, indicating net release of carbon dioxide and the dominance of heterotrophic (respiratory) processes over autotrophic processes (photosynthesis). Much of the excess carbon dioxide is probably associated with carbon dioxide laden groundwater inputs and the relatively short within-stream residence times ensures only limited degassing to the atmosphere. Diurnal fluctuations in dissolved oxygen vary from approximately 20% to 200% saturation. For both dissolved carbon dioxide and dissolved oxygen, the amplitude of fluctuations is much lower during the winter period, when biological activity is at its lowest. The concentrations of soluble reactive phosphorus (SRP), total phosphorus (TP) and boron increase markedly just downstream of the sewage works as a result of this point source input. These concentrations slowly decline further downstream as additional groundwater inputs dilute the effluent further. The introduction of chemical treatment of sewage effluent for phosphorus reduction at Marlborough STW resulted in a marked decrease in within-river SRP and TP concentrations to levels approximately the same as those upstream of the STW. A comparison of SRP and boron concentrations reveals a reduction in in-stream SRP concentrations by approximately 75% following effluent treatment. In terms of within-river processes controlling in-stream phosphorus concentrations, previous studies have indicated that one potentially important mechanism within calcium bicarbonate bearing rivers may be related to co-precipitation of phosphorus with calcium carbonate (calcite). The present study shows that the waters are oversaturated with respect to calcium carbonate, that no equilibrium conditions exist and that phosphorus removal has led to undetectable changes in calcium carbonate oversaturation. Hence, it is concluded that the primary changes in phosphorus levels within the river is directly associated with changing point source contributions from the STW and physical dilution within the river. However (1) the results relate to only the first year of study and subsequent differences may become apparent and (2) reactions between the water column and plant and bottom sediment interfaces may be important in regulating phosphorus fluxes within the river. The results presented in this paper mark a pilot phase of a longer-term initiative and this paper provides a background setting. The paper discusses the longer-term objectives and important gaps in knowledge of the system that requires further address.

Assessing the potential impacts of various climate change scenarios on the hydrological regime of the River Kennet at Theale, Berkshire, south-central England, UK: an application and evaluation of the new semi-distributed model, INCA

A new semi-distributed integrated nitrogen in catchments (INCA) model was used to attempt to assess the potential impacts of several recent Hadley Centre climate change scenarios on the hydrological flow regime of the entire River Kennet catchment to Theale, south-central England, UK. The climatically and hydrologically anomalous period 1985-1995 was used for baseline data in an attempt to: (1) represent any possible future climatic or hydrological variability not available from scenario use alone; and (2) attain maximum possible model calibration validity under future climates by simulating extremes of within-year hydrological variability. Substantial reductions in total annual runoff occurred, with an average reduction of 18.97%. Summer and late autumn soil moisture deficits (SMDs) increased in intensity, and were also found to persist for longer periods into autumn and (occasionally) winter. A generally enhanced hydrological regime of the River Kennet was simulated, with increased seasonality overall. A greater percentage of flow was observed to occur in spring and (occasionally) winter. Month-to-month variability of flow was discovered to be greater than annual changes. An average reduction in minimum annual flows of 46.03% occurred. Implications for catchment ecology and water resource requirements are briefly discussed. An evaluation of the new INCA model's performance as a tool for climate change impacts assessment is made.

Hydrological studies of schistosomiasis transport in Sichuan Province, China

Schistosomiasis is a water-bourne parasitic disease endemic to Sichuan Province of China. Long-term studies of infection and disease ecology in catchments in Sichuan have been supplemented by detailed hydrometric measurements to produce a model of water velocity and flow in an irrigation system. The model provides a means of estimating travel times of two infectious stages of the parasite from source sites to water contact exposure sites for individuals of both the human population and the intermediate vector snail populations. The hydrological transport model will be part of an overall model of schistosomiasis transmission in the catchments. A GIS system is used to manage spatial data of the drainage network, land use, infection sources and population centres. The development of the Three Gorges Dam in China will increase marshlands and irrigation in areas currently free of schistosomiasis. The potential for the spread of schistosomiasis into these new areas is a major concern. Hydrological models can be of particular importance in assessing future environmental risk.

Modelling acidification at Beacon Hill-a low rainfall, high pollutant deposition site in Central England

The model MAGIC (Model of Acidification of Groundwater In Catchments) has been applied to the Beacon Hill site, near Loughborough in Central England. This site is heavily impacted by wet and dry deposition of oxides of sulphur and nitrogen. The high acid inputs have caused soil acidification and acid stream waters. Long term simulations suggest that there has been a major decline in alkalinity and pH over the past 50 years. Despite recent reductions in deposition levels, soils and streams are predicted to continue to acidify in the future. For this heavily impacted site, deposition must be reduced by 80-90% to reverse the acidification trend and allow recovery of soil and stream waters.

Restoring acidified streams in upland Wales: a modelling comparison of the chemical and biological effects of liming and reduced sulphate deposition

Increasing emphasis is being placed on the restoration of surface waters which have been affected by acidification. Amongst the possible strategies are management of the causes, by reducing acidic deposition, and management of the symptoms, by treating affected areas with basic material such as limestone. In few cases have there been comparisons of the likely effect of these two strategies on surface water chemistry and ecology, although there is widespread belief that the two are similar in outcome. At present, only a modelling approach permits such a comparison. This paper describes chemical and biological responses of three Welsh streams whose catchments were limed experimentally in 1987-1988 as part of the Llyn Brianne project. Actual changes are compared with simulated changes which occur following reduced acid deposition according to the hydrochemical model, MAGIC (Model of Acidification of Groundwaters in Catchments). The results indicate that liming and 90% reduction in sulphate deposition reduce concentrations of toxic aluminium to similar levels. However, calcium concentrations and pH were increased by liming to values which were high by comparison with conditions simulated at low acid deposition, either in the past or future. Trout density increased in two of the streams following liming to levels similar to those simulated under low acid deposition. By contrast, the aquatic invertebrate fauna changed after liming so that streams acquired species typical of higher calcium concentrations than those simulated under low acid deposition. Species characteristic of 'soft water' communities were apparently lost, although more data are required to separate treatment effects from random change in the longer term. The 'soft water' community also declined in the model as a result of acidification, indicating that both liming and acid deposition resulted in a different faunal community from that prior to acidification. The results support those who conclude that liming is suitable for the restoration or protection of a fishery, but indicate that there may be other ramifications, for example to conservation, which must be considered when liming is implemented. However, the simulation of biological conditions under low acid deposition involves extrapolation from the initial data base. Further data are now required to assess empirically the likely biological character of British streams which have low base cation concentrations unaffected by acid deposition.