Daniel E. Pagendam

Conceptualisation and application of models for groundwater-surface water interactions and nitrate attenuation potential in riparian zones

Riparian zones can provide a protective buffer between streams and adjacent land-based activities, by removing nitrate from shallow groundwater flowing through them. Catchment scale water quality models are useful tools for predicting catchment behaviour under various climatic conditions and land use scenarios, but most do not account for the effect of riparian buffer zones. In this paper, we present conceptual models for surface water-groundwater interactions and formulate analytical mathematical functions that describe nitrate removal in the riparian zone. We restrict nitrate attenuation capacity to potential denitrification only and present sample calculations based on the limited field data available. The models are classed into two types according to their applicability to either ephemeral or perennial streams. In ephemeral, low-order streams with the potential to form a perched water table, a simple bucket model is used. During events, stream water flows laterally into the riparian zone and may be denitrified while residing there before discharging back to the surface water system. In perennial middle-order streams, nitrate removal may occur either as base flow intercepts the root zone or when water is temporarily stored in stream banks during flood events. We incorporate these concepts within a GIS modelling framework and investigate the potential of riparian zones to reduce nitrate delivery to streams in the Maroochy catchment located in South East Queensland, Australia. The modelling results for the Maroochy catchment show that the optimum rooting depth is about 4m and that increasing the riparian buffer width beyond 10m yields little further reduction in nitrate. The potential nitrate removal capacity per unit length of riparian buffer in each sub-catchment is an attribute that can be used to help to prioritise riparian rehabilitation activities aimed at reducing stream nitrogen loads.

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.

A bead-based suspension array for the multiplexed detection of begomoviruses and their whitefly vectors

Bead-based suspension array systems enable simultaneous fluorescence-based identification of multiple nucleic acid targets in a single reaction. This study describes the development of a novel approach to plant virus and vector diagnostics, a multiplexed 7-plex array that comprises a hierarchical set of assays for the simultaneous detection of begomoviruses and Bemisia tabaci, from both plant and whitefly samples. The multiplexed array incorporates genus, species and strain-specific assays, offering a unique approach for identifying both known and unknown viruses and B. tabaci species. When tested against a large panel of sequence-characterized begomovirus and whitefly samples, the array was shown to be 100% specific to the homologous target. Additionally, the multiplexed array was highly sensitive, efficiently and concurrently determining both virus and whitefly identity from single viruliferous whitefly samples. The detection limit for one assay within the multiplexed array that specifically detects Tomato yellow leaf curl virus-Israel (TYLCV-IL) was quantified as 200fg of TYLCV-IL DNA, directly equivalent to that of TYLCV-specific qPCR. Highly reproducible results were obtained over multiple tests. The flexible multiplexed array described in this study has great potential for use in plant quarantine, biosecurity and disease management programs worldwide.

Characterization of the banana streak virus capsid protein and mapping of the immunodominant continuous B-cell epitopes to the surface-exposed N terminus

This study identified the structural proteins of two badnavirus species, Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV), and mapped the distribution of continuous B-cell epitopes. Two different capsid protein (CP) isoforms of about 44 and 40 kDa (CP1 and CP2) and the virion-associated protein (VAP) were consistently associated with purified virions. For both viral species, the N terminus of CP2 was successfully sequenced by Edman degradation but that of CP1 was chemically blocked. De novo peptide sequencing of tryptic digests suggested that CP1 and CP2 derive from the same region of the P3 polyprotein but differ in the length of either the N or the C terminus. A three-dimensional model of the BSMYV-CP was constructed, which showed that the CP is a multi-domain structure, containing homologues of the retroviral capsid and nucleocapsid proteins, as well as a third, intrinsically disordered protein region at the N terminus, henceforth called the NID domain. Using the Pepscan approach, the immunodominant continuous epitopes were mapped to the NID domain for five different species of banana streak virus. Anti-peptide antibodies raised against these epitopes in BSMYV were successfully used for detection of native virions and denatured CPs in serological assays. Immunoelectron microscopy analysis of the virion surface using the anti-peptide antibodies confirmed that the NID domain is exposed on the surface of virions, and that the difference in mass of the two CP isoforms is due to variation in length of the NID domain.

Spatio-temporal assimilation of modelled catchment loads with monitoring data in the Great Barrier Reef

Soil erosion and sediment transport into waterways and the ocean can adversely affect water clarity, leading to the deterioration of marine ecosystems such as the iconic Great Barrier Reef (GBR) in Australia. Quantifying a sediment load and its associated uncertainty is an important task in delineating how changes in management practices can contribute to improvements in water quality, and therefore continued sustainability of the GBR. However, monitoring data are spatially (and often temporally) sparse, making load estimation complicated, particularly when there are lengthy periods between sampling or during peak flow periods of major events when samples cannot be safely taken. We develop a spatio-temporal statistical model that is mechanistically motivated by a process-based deterministic model called Dynamic SedNet. The model is developed within a Bayesian hierarchical modelling framework that uses dimension reduction to accommodate seasonal and spatial patterns to assimilate monitored sediment concentration and flow data with output from Dynamic SedNet. The approach is applied in the Upper Burdekin catchment in Queensland, Australia, where we obtain daily estimates of sediment concentrations, stream discharge volumes and sediment loads at 411 spatial locations across 20 years. Our approach provides a method for assimilating both monitoring data and modelled output, providing a statistically rigorous method for quantifying uncertainty through space and time that was previously unavailable through process-based models.

Determining the initial spatial extent of an environmental impact assessment with a probabilistic screening methodology

Abstract A crucial decision in defining the scope of an environmental impact assessment is to delineate the initial assessment area. We developed a probabilistic methodology to determine this area, which starts by identifying a key environmental variable, maximum acceptable change and acceptable probability of exceeding that threshold. The exceedance probability is determined with a limits of acceptability rejection sampling of informed prior parameter distributions. A qualitative uncertainty analysis, a formal and systematic discussion of the main assumptions and model choices, is complemented with global sensitivity analysis of the model results to identify the major sources of uncertainty and provide guidance for further research and data collection. For the case study on coal development in the Gloucester Basin (NSW, Australia), the initial assessment extent is unlikely to extend more than 5 km from the edge of the planned coal mines. The major source of uncertainty is the planned mine water production rate.

Non-stationarity of low flows and their relevance to river modelling during drought periods

Changes in groundwater storage lead to a reduction in groundwater contribution to river flow and present as non-stationarity, especially during low-flow conditions. Conventional river models typically ignore this non-stationarity, and, hence, their predictions of declines in low flows during drought periods are likely to be compromised. The present study assesses non-stationarity and highlights its implications for river modelling. A quantile regression analysis showed non-stationarity of low flows in the Namoi catchment (Australia), with statistically significant downward trends in the 10th percentile of log-transformed baseflow (10-LTB). This highlighted the usefulness of the 10-LTB metric to identify non-stationarity and, hence, alert modellers to the importance of adopting models that explicitly account for groundwater processes when modelling such river systems.

Making management decisions in the face of uncertainty: a case study using the Burdekin catchment in the Great Barrier Reef

Modelling and monitoring pollutants entering into the Great Barrier Reef (GBR) lagoon remain important priorities for the Australian and Queensland governments. Uncertainty analysis of pollutant load delivery to the GBR would: (1) inform decision makers on their ability to meet environmental targets; (2) identify whether additional measurements are required to make confident decisions; and (3) determine whether investments into remediation activities are actually making a difference to water quality and the health of the GBR. Using a case study from the Upper Burdekin catchment where sediment concentrations are the focus, herein we explore and demonstrate different ways of communicating uncertainty to a decision maker. In particular, we show how exceedance probabilities can identify hot spots for future monitoring or remediation activities and how they can be used to inform target setting activities. We provide recommendations for water quality specialists that allow them to make more informed and scientifically defensible decisions that consider uncertainty in both the monitoring and modelling data, as well as allowing the calculation of exceedances from a threshold.