Soil Properties of Surface Mined Lands and Their Hydrologic Impiications

Agricultural Engineerin

Fertiliser management effects on dissolved inorganic nitrogen in runoff from Australian sugarcane farms

Dissolved inorganic nitrogen (DIN) movement from Australian sugarcane farms is believed to be a major cause of crown-of-thorns starfish outbreaks which have reduced the Great Barrier Reef coral cover by ~21% (1985–2012). We develop a daily model of DIN concentration in runoff based on >200 field monitored runoff events. Runoff DIN concentrations were related to nitrogen fertiliser application rates and decreased after application with time and cumulative rainfall. Runoff after liquid fertiliser applications had higher initial DIN concentrations, though these concentrations diminished more rapidly in comparison to granular fertiliser applications. The model was validated using an independent field dataset and provided reasonable estimates of runoff DIN concentrations based on a number of modelling efficiency score results. The runoff DIN concentration model was combined with a water balance cropping model to investigate temporal aspects of sugarcane fertiliser management. Nitrogen fertiliser application in December (start of wet season) had the highest risk of DIN movement, and this was further exacerbated in years with a climate forecast for ‘wet’ seasonal conditions. The potential utility of a climate forecasting system to predict forthcoming wet months and hence DIN loss risk is demonstrated. Earlier fertiliser application or reducing fertiliser application rates in seasons with a wet climate forecast may markedly reduce runoff DIN loads; however, it is recommended that these findings be tested at a broader scale

An improved model for linking phosphorus loads in runoff to climate, soil and agricultural management

Abstract: Soil phosphorus (P) is one of the nutrients that contribute to eutrophication of waterways, algal blooms and damage to coral reefs. Reducing P movement from farm paddock to the broader environment often requires comprehensive, catchment-wide approaches to management. The substantial complexity of the physical and managerial causes of P pollution has led to a role for simulation models in evaluating the efficacy of regulations and management changes. In Queensland, the Reef Plan program (http://www.reefplan.qld.gov.au) addresses issues of sediment, nutrient and pesticide impact on the health and future of the Great Barrier Reef. Some of the associated regulations are concerned with the use of P fertilizer. The HowLeaky? model is one of few biophysical models that represent agricultural management, biophysical conditions and P exports. As reported at MODSIM07, information about P export was added to an existing model of water balance and sediment export (HowLeaky?) to create a useful model of P export from agriculture. However, the predictive power of the model was modest, especially over short periods (e.g. individual days). To improve the predictive power of the model, several changes have been made, including (i) additional empirical functions for estimating the enrichment of total P in sediment, and (ii) additional functions for estimating concentration of soluble P in runoff (mg P/L). Soil adsorption of P (P buffering), which affects the soluble P concentration in runoff, is now estimated from the widely available phosphorus buffering index test (PBI) rather than phosphorus buffering capacity (PBC). Large, high-quality datasets are used to evaluate these relationships. A case study is presented where HowLeaky? has been used to estimate P loads generated at a site in the GBR catchment. The Brigalow Catchment Study is a long-term study of the effects of land clearing and agriculture on the water balance and water quality. It is located in central Queensland, has a subcatchment that is cropped, has representative soils, and is part of the Fitzroy Catchment. HowLeaky? reproduced daily runoff amounts very well, and the revised P model in HowLeaky? was acceptably accurate at predicting daily P loads. Modelling predicted the long-term totals (6 years) of soluble and particulate P export from the field site with less than 50% error. This is a better-than-expected result with an un-calibrated model, as P exports are notoriously difficult to predict

2017 Scientific Consensus Statement: land use impacts on the Great Barrier Reef water quality and ecosystem condition. Chapter 4: management options and their effectiveness

This chapter seeks to answer the following questions: 1. What are the values of the Great Barrier Reef? 2. How effective are better agricultural practices in improving water quality? 3. How can we improve the uptake of better agricultural practices? 4. What water quality improvement can non-agricultural land uses contribute? 5. How can Great Barrier Reef water quality improvement programs be improved? Each section summarises the currently available peer reviewed literature and comments on implications for management and research gaps. This chapter has a wider scope than previous Scientific Consensus Statements, including, for the first time, the social and governance dimensions of management and the management of non-agricultural land uses. These new sections are constrained by a lack of Great Barrier Reef–specific data and information. The relevance of information from other locations must be carefully considered. In comparison, the agricultural practice change and economics sections provide an update on material compiled as part of the 2013 Scientific Consensus Statement. This report has been confined to peer reviewed literature, which is generally published in books and journals or major reports. There is additional evidence in grey literature, such as project and program reports, that has not been included here. Each section of this chapter has been compiled by a writing team and then revised following a series of review processes

Predicting the interactions between rivers and groundwater pumping

Abstract We summarise research that the eWater Cooperative Research Centre is carrying out incorporating groundwater-surface water interaction capabilities into the next generation of river management tools being developed for Australia's large river basins. We describe three simplified modelling approaches that are currently in development: (i) a reach scale 'Groundwater-Surface Water Link' model, which operates as a groundwater link to river models and accounts for interactions at the river-reach scale; (ii) a sub-reach scale 'Floodplain Processes' model, which dynamically models bank storage, evapotranspiration, and floodplain inundation. It enables more refined modelling of groundwater-surface water interactions, and can be linked to ecological response models; and (iii) a catchment scale model that estimates the surface and sub-surface flow components to streams

A Cross-Study Transcriptional Analysis of Parkinson's Disease

The study of Parkinson's disease (PD), like other complex neurodegenerative disorders, is limited by access to brain tissue from patients with a confirmed diagnosis. Alternatively the study of peripheral tissues may offer some insight into the molecular basis of disease susceptibility and progression, but this approach still relies on brain tissue to benchmark relevant molecular changes against. Several studies have reported whole-genome expression profiling in post-mortem brain but reported concordance between these analyses is lacking. Here we apply a standardised pathway analysis to seven independent case-control studies, and demonstrate increased concordance between data sets. Moreover data convergence increased when the analysis was limited to the five substantia nigra (SN) data sets; this highlighted the down regulation of dopamine receptor signaling and insulin-like growth factor 1 (IGF1) signaling pathways. We also show that case-control comparisons of affected post mortem brain tissue are more likely to reflect terminal cytoarchitectural differences rather than primary pathogenic mechanisms. The implementation of a correction factor for dopaminergic neuronal loss predictably resulted in the loss of significance of the dopamine signaling pathway while axon guidance pathways increased in significance. Interestingly the IGF1 signaling pathway was also over-represented when data from non-SN areas, unaffected or only terminally affected in PD, were considered. Our findings suggest that there is greater concordance in PD whole-genome expression profiling when standardised pathway membership rather than ranked gene list is used for comparison

NRF2 Activation Restores Disease Related Metabolic Deficiencies in Olfactory Neurosphere-Derived Cells from Patients with Sporadic Parkinson's Disease

Extent: 14p.Background: Without appropriate cellular models the etiology of idiopathic Parkinson’s disease remains unknown. We recently reported a novel patient-derived cellular model generated from biopsies of the olfactory mucosa (termed olfactory neurosphere-derived (hONS) cells) which express functional and genetic differences in a disease-specific manner. Transcriptomic analysis of Patient and Control hONS cells identified the NRF2 transcription factor signalling pathway as the most differentially expressed in Parkinson’s disease. Results: We tested the robustness of our initial findings by including additional cell lines and confirmed that hONS cells from Patients had 20% reductions in reduced glutathione levels and MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)- 2-(4-sulfophenyl)-2H-tetrazolium, inner salt] metabolism compared to cultures from healthy Control donors. We also confirmed that Patient hONS cells are in a state of oxidative stress due to higher production of H2O2 than Control cultures. siRNA-mediated ablation of NRF2 in Control donor cells decreased both total glutathione content and MTS metabolism to levels detected in cells from Parkinson’s Disease patients. Conversely, and more importantly, we showed that activation of the NRF2 pathway in Parkinson’s disease hONS cultures restored glutathione levels and MTS metabolism to Control levels. Paradoxically, transcriptomic analysis after NRF2 pathway activation revealed an increased number of differentially expressed mRNAs within the NRF2 pathway in L-SUL treated Patient-derived hONS cells compared to L-SUL treated Controls, even though their metabolism was restored to normal. We also identified differential expression of the PI3K/AKT signalling pathway, but only post-treatment. Conclusions: Our results confirmed NRF2 as a potential therapeutic target for Parkinson’s disease and provided the first demonstration that NRF2 function was inducible in Patient-derived cells from donors with uniquely varied genetic backgrounds. However, our results also demonstrated that the response of PD patient-derived cells was not co-ordinated in the same way as in Control cells. This may be an important factor when developing new therapeutics.Anthony L. Cook, Alejandra M. Vitale, Sugandha Ravishankar, Nicholas Matigian, Greg T. Sutherland, Jiangou Shan, Ratneswary Sutharsan, Chris Perry, Peter A. Silburn, George D. Mellick, Murray L. Whitelaw, Christine A. Wells, Alan Mackay-Sim and Stephen A. Woo

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

The hydrogeology of the Condamine River alluvial aquifer (Australia) – a critical review

The Condamine plain is an important agricultural zone, with ~118 thousand hectares of irrigated crops. Groundwater pumped from the shallow alluvial aquifer (40-60 GL/yr) accounts for one third of the irrigation water. Sustainable agriculture future implies, among other issues, a reliable supply of groundwater to the farmers, in terms of quality and quantity. The hydrogeology of the shallow Condamine River Alluvium Aquifer (CRAA) was studied for decades in order to provide a management framework and to determine the 'safe yield', as excessive pumping in the past has led to ongoing decline of the water table, up to ~25m in places. Not withstanding the accumulating data and knowledge, the water balance of the aquifer as well as 'safe yield' estimations are still far from being conclusive and has been substantially revised several times during the last decade. The present report, conducted at the University of Southern Queensland (USQ), collates up-to-date hydrogeological knowledge regarding the CRAA, critically evaluates the accepted hydrogeological conventions, highlights puzzling phenomena and recommends needed work, which can be implemented in a rather expeditious and inexpensive fashion, to overcome the existing knowledge gaps. Refining the hydrogeological knowledge regarding the CCRA is timely, as in the last decade there has been a rapid expansion of the CSG industry in vicinity to the Condamine plain, with the aim to extract methane from the underlying layers. The presumed hydrogeological effects of CSG production upon the shallower CRAA have been delineated but are yet to be adequately quantified. It is our view that the hydrogeological knowledge-gaps should be addressed before predictions of CSG activities effects can be made

Using stable isotopes to identify soil moisture sources of key species in drought-stressed riparian woodlands

Remnant riparian woodlands on the Upper Condamine floodplain of the northern Murray-Darling Basin are characterised by the dominant canopy species Eucalyptus camaldulensis (river red gum), a facultative phreatophyte which preferentially accesses shallow groundwater sources during drought conditions. Phyla canescens (lippia), a perennial clonal herb, is also dominant in these ecosystems. Lippia is an invasive alien species, readily dispersed by flooding, with potential to spread throughout much of the Murray-Darling system with significant economic and environmental impact. Recent research indicates that trees may facilitate the persistence of lippia, enabling it to survive and reproduce under drought conditions, and that lippia may in turn contribute to dieback severity in canopy eucalypts in these woodlands. Greater understanding of the intensity and direction of interactions between these two species will contribute to the management of both lippia and tree condition in this landscape. This research uses natural abundance stable isotopes to investigate the relative importance of water sources utilised by E. camaldulensis and P. canescens under low ambient soil moisture conditions. This approach will elucidate potentially important interactions between E. camaldulensis and P. canescens. It will also contribute to better understanding of the role of shallow groundwater resources in ecosystems subject to seasonal and long-term drought, and/or potentially at risk due to floodplain development and increasing climate variability