Using a simple 2D steady-state saturated flow and reactive transport model to elucidate denitrification patterns in a hillslope aquifer

In the last 50 years, agricultural intensification has resulted in increasing nutrient losses that threaten the health of the lakes on the volcanic plateau of New Zealand’s North Island. As part of our efforts to understand the transport and transformations of nitrogen in this landscape, the 2D vertical groundwater transport model AquiferSim 2DV was used to simulate water flow, nitrate transport, denitrification, and discharge to surface waters in a hillslope adjacent to a wetland and stream discharging into Lake Taupo, Australasia’s largest lake. AquiferSim 2DV is a steady state model using the finite-difference stream function method for flow modelling and finite-volume mixing cell method for contaminant transport modelling. The ratio of horizontal to vertical hydraulic conductivity must be specified within the aquifer domain, as must effective porosity and denitrification rates. Boundary conditions consist of recharge fluxes and contaminant concentrations, as well as the assumed zone of discharge. Hydrodynamic dispersion is simulated through numerical dispersion, which depends on grid resolution. Denitrification reactions within each computational cell may include both zero-order and first-order rates. All parameters may be spatially heterogeneous. Previous applications of this model have been to essentially horizontal aquifer systems. By contrast, this hillslope system has sloping material layers and a dynamic and sloping water table. Extensions were made to AquiferSim 2DV, including representation of converging/diverging flow, which allowed a 2D steady-state model of this system to be developed. Comparison of model predictions with detailed water level and hydrochemical data from the site, however, showed that the model’s attractive simplicity in this case precluded adequate characterisation of what is essentially a 3D, transient system. While the model produced reasonable agreement with the concentration patterns under an average water table profile, predictions of oxygen and nitrate concentrations under low summer and high spring water table conditions were poor. The seasonal changes reflected an annual recharge pulse of fresh, oxidised water followed by gradual oxygen depletion till the next recharge pulse occurs in the following year, an essentially transient phenomenon which could not be represented using a steady state model. This in itself has provoked fresh thinking about the dynamic nature of flow and chemistry at the site

Pathways from land to stream: lessons from Pukemanga

Oral presentation at the New Zealand Hydrological Society Annual Conference, 20-23 November 2007, Rotorua, New Zealand.In the Pukemanga catchment, nitrate is leaching from soil under agricultural land use, and is being transported by subsurface water flow to surface waters. Groundwater is the suspected dominant transport pathway. This study proposes to determine the proportion of groundwater discharge to streamflow by partitioning of daily and hourly streamflow on the basis of groundwater dynamics

From the paddock to the stream : unravelling the nitrogen flowpaths in a New Zealand dairying catchment

The Toenepi catchment (15 km2) is dominated by dairying, and ranges in elevation from 40 to 130m above sea level (ASL). Most of the catchment is flat land, with some rolling and steep land occurring on the boundaries. Annual rainfall is 1132 mm and mean annual temperature is 13.3°C. Well-drained Allophanic soils dominate in the catchment in close association with granular soils of moderate permeability. Poorly drained Gley soils occur in the lowest areas adjacent to the stream and require artificial drainage. The average stocking rate is 3.0 cows ha–1, which graze all year. The catchment export of total nitrogen through the stream had been calculated in an earlier project as 35 kg ha–1 yr–1. The median total nitrogen concentration in the stream was 3 mg L–1 (1995/97). To better understand nitrogen flowpaths, we initially installed groundwater monitoring transects in seven subcatchments, which reflected the major site and landuse conditions. Monthly sampling indicated that the concentrations of inorganic nitrogen in the shallow groundwater were generally well below the concentrations measured in the stream. This result would not support the hypothesis that the majority of the nitrate in the stream is derived from groundwater. Monitoring of the nitrogen concentrations in drains indicated that artificial drainage may be a major conduit for nitrogen into the stream. Artificial drains bypass the deeper subsoil and riparian zones where denitrification is likely to occur. A mathematical groundwater discharge model is used to quantify the proportion of streamflow that can be explained by groundwater discharge in contrast to near-surface flowpaths (surface runoff, artificial drainage). Understanding the pathways through which nitrogen enters Toenepi Stream is considered a prerequisite for the development of the most effective and efficient measures to reduce the N contamination of the stream

Basic Atomic Physics

Contains reports on five research projects.National Science Foundation Grant PHY 96-024740National Science Foundation Grant PHY 92-21489U.S. Navy - Office of Naval Research Contract N00014-96-1-0484Joint Services Electronics Program Grant DAAHO4-95-1-0038National Science Foundation Grant PHY95-14795U.S. Army Research Office Contract DAAHO4-94-G-0170U.S. Army Research Office Contract DAAG55-97-1-0236U.S. Army Research Office Contract DAAH04-95-1-0533U.S. Navy - Office of Naval Research Contract N00014-96-1-0432National Science Foundation Contract PHY92-22768David and Lucile Packard Foundation Grant 96-5158National Science Foundation Grant PHY 95-01984U.S. Army Research OfficeU.S. Navy - Office of Naval Research Contract N00014-96-1-0485AASERT N00014-94-1-080

TBVAC2020 : advancing tuberculosis vaccines from discovery to clinical development

TBVAC2020 is a research project supported by the Horizon 2020 program of the European Commission (EC). It aims at the discovery and development of novel tuberculosis (TB) vaccines from preclinical research projects to early clinical assessment. The project builds on previous collaborations from 1998 onwards funded through the EC framework programs FP5, FP6, and FP7. It has succeeded in attracting new partners from outstanding laboratories from all over the world, now totaling 40 institutions. Next to the development of novel vaccines, TB biomarker development is also considered an important asset to facilitate rational vaccine selection and development. In addition, TBVAC2020 offers portfolio management that provides selection criteria for entry, gating, and priority settings of novel vaccines at an early developmental stage. The TBVAC2020 consortium coordinated by TBVI facilitates collaboration and early data sharing between partners with the common aim of working toward the development of an effective TB vaccine. Close links with funders and other consortia with shared interests further contribute to this goal

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

IntroductionThrough the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.MethodsThe soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.Results and DiscussionThe results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities

TBVAC2020: Advancing tuberculosis vaccines from discovery to clinical development

TBVAC2020 is a research project supported by the Horizon 2020 program of the European Commission (EC). It aims at the discovery and development of novel tuberculosis (TB) vaccines from preclinical research projects to early clinical assessment. The project builds on previous collaborations from 1998 onwards funded through the EC framework programs FP5, FP6, and FP7. It has succeeded in attracting new partners from outstanding laboratories from all over the world, now totaling 40 institutions. Next to the development of novel vaccines, TB biomarker development is also considered an important asset to facilitate rational vaccine selection and development. In addition, TBVAC2020 offers portfolio management that provides selection criteria for entry, gating, and priority settings of novel vaccines at an early developmental stage. The TBVAC2020 consortium coordinated by TBVI facilitates collaboration and early data sharing between partners with the common aim of working toward the development of an effective TB vaccine. Close links with funders and other consortia with shared interests further contribute to this goal

Complexities in interpreting chironomid-based temperature reconstructions over the Holocene from a lake in Western Ireland

Investigation of Holocene climate variability remains challenging. This is largely due to chronological uncertainties and complexities associated with proxies and their relationship with climatic drivers. Pertinent questions still exist regarding the Holocene climate in Ireland, particularly in the early Holocene. We present a mean July air temperature reconstruction based on fossil chironomidae (non-biting midge flies), along with an assessment of chironomid functional traits from five guilds (based on their feeding habits) from Lough Nakeeroge, a small glacial lake in western Ireland. These records span the early to late Holocene (c. 10,000–1500 cal yr BP). The chironomid record is supplemented with pollen data to determine landscape vegetation dynamics, and compared to climate model simulations of the same period. As reliable models are essential for robust analysis of long-term climate change, we critically assess the value of the chironomid transfer function and explore the use of chironomid functional traits to infer past climate variability. While this study demonstrates the complexities of chironomid-based temperature reconstruction in Irish lakes, it endeavours to i) disentangle a complicated Holocene climate history through the exploration of other long-term Holocene records from the island; and ii) improve our understanding of environmental responses to climate variability in Ireland. The findings of this study suggest that the interpretation of chironomid-based temperature transfer functions can be challenging. However, our results demonstrate the influence of climate on the functioning of lake ecosystems over the Holocene, with the promising performance of the collector-filterer feeding guild as a palaeothermometer

Using stream flow and chemistry data to estimate catchment scale groundwater and nitrate fluxes

Groundwater is the dominant flow path carrying land surface recharge, including dissolved contaminants, to surface waters draining a catchment. The dominance of the groundwater pathway poses a challenge to management of water quality in agricultural catchments, because groundwater quantity and quality are difficult and expensive to monitor, and groundwater assimilative capacity for nitrate is generally unknown. On the other hand, rainfall and evapotranspiration as inputs, and stream flow and nitrate concentration as outputs, can be recorded relatively easily, especially if inexpensive in-stream nitrate sensors can be developed. The eigenmodel approach has previously been used to estimate the land surface area and groundwater discharge contributing to stream flow in a small hill catchment. We extended this approach to explain seasonal patterns of nitrate and silica concentrations observed in the Toenepi Stream, which drains a lowland dairying catchment near Morrinsville, and to estimate the water and nitrate fluxes driving these observations. The resulting model (“StreamGEM”) was calibrated for the four-year period 1 April 2007 to 31 March 2011, and cross-validated using data from the period 1 April 1995 to 31 March 1997. Estimated discharge, nitrate concentration (as nitrate-N) and nitrate load from near-surface, fast groundwater, and slow groundwater flowpaths were then calculated. On an annual basis, stream flow was dominated by discharge from fast, shallow groundwater. In summer however, slow, deeper groundwater dominated both flow and chemistry. The total catchment input load (at the bottom of the root zone) was estimated to be 40 kg N ha⁻¹ y⁻¹ nitrate nitrogen (NO₃-N). Nitrate attenuation in the groundwater components accounted for 20 kg N ha⁻¹ y⁻¹ of this, with the remaining 50% being discharged to the stream. At the catchment scale, nitrate assimilation appears to occur dominantly in the shallower flow near the redox boundary, despite the strongly reduced conditions and much lower nitrate concentrations found in the deeper groundwater. The ability to estimate catchment water and nitrate fluxes from weather and in-stream data offers an inexpensive and potentially widely applicable tool for improved management of New Zealand’s land and water resources. Current research focuses on ascertaining in which type of catchments StreamGEM can be applied successfully

Using monthly stream water quality data to quantify nitrate transfer pathways in three Waikato catchments

Monthly water quality sampling at the catchment outlet is carried out at many sites across New Zealand for state of the environment monitoring. This data is used for trend analysis, but little else. We have been exploring approaches for using this data in conjunction with concurrent stream flow data to identify and quantify the principal nutrient transfer pathways within catchments. In particular, monthly data may provide sufficient information for an inverse modelling approach. Three contrasting mesoscale catchments were chosen for this study: (1) the Tahunaatara Stream (208 km²) in the Upper Waikato subregion, (2) the Puniu River (519 km²) in the Waipa subregion, and (3) the Mangatangi River (195 km²) in the Lower Waikato subregion. By considering four years of monthly water quality data from these catchments, alongside daily rainfall, potential evapotranspiration, and stream flow measurements, we were able to use the daily time step, spatially lumped catchment model “StreamGEM” with the Markov Chain Monte Carlo algorithm “DREAMZS” to predict daily stream flow and nitrate fluxes arriving at the catchment outlet via near-surface (NS), shallow fast seasonal groundwater (F), and deep slow older groundwater (S) flow paths, as well as to estimate the reliability/uncertainty of these predictions. Despite high uncertainty in some model parameters, the flow and nitrate calibration data was well reproduced across all catchments (Nash-Sutcliffe model efficiency in the range 0.70–0.83 for daily flow, and 0.17–0.88 for nitrate concentration, both on log scale). Proportions of flow attributed to near-surface, fast seasonal groundwater and slow older groundwater were well defined, and consistent with expectations based on catchment geology. Fast groundwater contributed the bulk of the annual average nitrate yield in all of these catchments (range 31–97%), although contributions from slow groundwater were also high at Tahunaatara (range 18–63%), while contributions from near-surface flow were high at Mangatangi (range 24–63%). This research highlights the potential of process based, spatially lumped modelling with commonly available monthly stream sample data, to elucidate high resolution catchment function, when appropriate calibration methods are used that correctly handle the inherent uncertainties