Multivariate and multiway analysis of hyperspectral and fluorescence landscape data

University of Technology, Sydney. Faculty of Science.The majority of the methods that have been used for the analysis of hyperspectral images have focussed on classification of spectra within an image, and there have been few examples of using whole hyperspectral images (one image per sample) for classification purposes. In this project, feature vectors were created to capture the heterogeneity present in each hyperspectral image for subsequent classification. All of the feature vectors methods were compared to single-point spectra and literature methods. The MIQ (the median- interquartile superspectrum) achieved the best classification of a set of heterogeneous powder mixtures, classifying 100% of the external test set. Mid-infrared (MIR) hyperspectral images and LA-ICP-MS elemental maps were collected of 'real-world' samples of soil collected from various locations around Sydney. For both the MIR and LA-ICP-MS data, the MIQ feature vector achieved superior classification compared to the averages alone (used to represent single-point spectra). For the Sydney soil samples, the classification performance of the LA-ICP-MS elemental maps was superior to MIR reflection hyperspectral images. For the LA-ICP-MS data, using elemental ratios for calibration proved to be a more suitable strategy than using silicon as an internal standard. A major application of PARAFAC has been the analysis of fluorescent landscapes. In the other main area of this project, novel applications of PARAFAC were investigated. The first application explored was the use of PARAFAC and fluorescent landscapes for the characterisation of phytoplankton. Algal species were placed under different wavelengths of light and monitored over time to determine their response to these environments. PARAFAC was able to isolate components that were identified as p-carotene, chlorophyll a and b, and chlorophyll a degradation products. The advantage of using PARAFAC for the characterisation of phytoplankton is that it can simultaneously determine all pigment concentrations without the need for prior separation or extraction. Background interference due to highly coloured / patterned and fluorescence remains an issue with many techniques of fingerprint visualisation. The second application of PARAFAC in this project was to analyse fluorescent landscapes constructed by collecting series of images of fluorescent fingerprints on these traditionally difficult backgrounds. Whilst PARAFAC successfully isolated the fluorescence due to the fingerprint, there was typically only a small reduction in background interference. However, it is expected that PARAFAC would be more successful for samples where the background is also fluorescent, such as DFO- developed prints on fluorescent yellow paper

Isotopic and chromatographic fingerprinting of the sources of dissolved organic carbon in a shallow coastal aquifer

The terrestrial subsurface is the largest source of freshwater globally. The organic carbon contained within it and processes controlling its concentration remain largely unknown. The global median concentration of dissolved organic carbon (DOC) in groundwater is low compared to surface waters, suggesting significant processing in the subsurface. Yet the processes that remove this DOC in groundwater are not fully understood. The purpose of this study was to investigate the different sources and processes influencing DOC in a shallow anoxic coastal aquifer. Uniquely, this study combines liquid chromatography organic carbon detection with organic (δ13CDOC) carbon isotope geochemical analyses to fingerprint the various DOC sources that influence the concentration, carbon isotopic composition, and character with respect to distance from surface water sources, depth below surface, and inferred groundwater residence time (using 3H activities) in groundwater. It was found that the average groundwater DOC concentration was 5 times higher (5 mg L−1) than the global median concentration and that the concentration doubled with depth at our site, but the chromatographic character did not change significantly. The anoxic saturated conditions of the aquifer limited the rate of organic matter processing, leading to enhanced preservation and storage of the DOC sources from peats and palaeosols contained within the aquifer. All groundwater samples were more aromatic for their molecular weight in comparison to other lakes, rivers and surface marine samples studied. The destabilization or changes in hydrology, whether by anthropogenic or natural processes, could lead to the flux of up to 10 times more unreacted organic carbon from this coastal aquifer compared to deeper inland aquifers

Coupling of flow and biogeochemical processes controlling the environmental conditions in the hyporheic zone: Implications for the streambed habitat

The hyporheic zone of streams not only connects groundwater and surface water, but is essential for nutrient and carbon cycling and provides crucial habitat for organisms (termed hyporheos). Here we demonstrate how flow (groundwater discharge and hyporheic exchange) and biogeochemical processes interact to form environmental conditions and habitat for hyporheos. This provides the understanding to assess how hyporheic conditions may be altered by changing flow paths caused by flow perturbations such as groundwater pumping. The studied reaches in the Maules Creek Catchment in New South Wales, Australia, comprise intermittent losing, perennial gaining and perennial losing sections, and are therefore well-suited to study how different flow paths affect water quality. Surface water, hyporheic zone pore water (at depths between 0.4 and 0.8 m), and groundwater from monitoring bores, was sampled and analysed for water quality and hyporheos. For each hyporheic site the hydraulic potential for upwelling or down-welling was measured by the vertical hydraulic head difference. Upwelling regional groundwater was generally oxic with detectable nitrate and low DOC (dissolved organic carbon). On the other hand, hyporheic water in down-welling zones became anoxic at shallow depths (< 1 m), with dissolved reduced species such as Fe2+, Mn2+ and NH4+ and no O2, forming a steep vertical redox gradient from the streambed into the sediment. Upwelling hyporheic water (originating from the stream) was found to have a similar hydrochemical signature. These zones did not support habitat for hyporheic invertebrates because metazoan organisms cannot permanently inhabit anoxic environments. No invertebrates were found for Fe2+ concentrations above 2 mg/L. The hyporheos in these zones appeared to be dominated by anaerobic microbes including Fe-reducing bacteria. Our results show that flow conditions affect water quality, which in turn regulates the habitat of hyporheic invertebrates as they will not exist under anoxic conditions. The results have implications for understanding the ecological responses of the hyporheic zone to perturbations which affect flow and biogeochemical processes

Out of sight, out of mind: the hyporheic zone is an under-recognised ecosystem service provider

The hyporheic zone is an important ecotone where hydrological, biogeochemical and ecological processes interact and influence stream ecosystem functions including the breakdown of organic carbon, nutrient cycling and primary productivity. The objective of this study was to understand how changes in flow regime, hyporheic exchange and biogeochemical conditions affect the ecological conditions for hyporheic fauna and stream ecosystem function. The Maules Creek catchment in northern NSW supports a rich hyporheic fauna (hyporheos) including numerous species of stygofauna. The streams exhibit flow regimes ranging from intermittent to perennial, and interactions with groundwater that include stream ‘gaining’ and stream ‘losing’ conditions. As hypothesised, losing stream conditions supported few stygofauna and rapidly became hypoxic / anoxic as down-welling organic matter (OM) was oxidised in the hyporheic zone. In contrast, gaining stream conditions supported a rich hyporheos where upwelling oxygenated groundwater low in OM mixed with stream hyporheic water high in OM and nutrients. The stream with a highly intermittent flow regime supported a rich hyporheos indicating that non-perenniality cannot be used as an argument to diminish the ecosystem services potential of intermittent streams which are typical of many Australian catchments. Small changes in aquifer pressure or groundwater levels may switch conditions from gaining to losing and thus change the ecological conditions for hyporheic fauna and stream ecosystem function. This is relevant in many regions where groundwater drawdown from activities such as mine dewatering, coal seam gas extraction and irrigation for agriculture, potentially threaten stream ecosystem processes and services

Investigation of the kinetics of water uptake into partially saturated shales

Several processes have been proposed to describe the low recovery of hydraulic fracturing fluid in unconventional shale reservoirs which has caused both technical and environmental concerns. This study describes novel hydraulic experiments to quantitatively investigate the kinetics of water uptake into partially saturated shale through investigating the pressure response of injecting fluids (NaCl, KCl, MgCl2, and CaCl2 with different ionic concentrations) into crushed and sieved shale fragments. The results of the study indicate that the cumulative water uptake under pressure is likely to be controlled by three processes: surface hydration, capillary hydration including advective flow, and osmotic hydration. Each of these processes is a function of the differences between the in situ pore fluid and the injection fluid (solution chemistry and concentration) and the shale physicochemical properties, in particular the contact surface area, pore diameter, and the Cation Exchange Capacity (CEC). The uptake is not instantaneous, but is diffusion limited, with the rate governed by a number of kinetic processes. Uptake proceeds in three stages, each associated with a different process: (1) predominantly surface hydration, (2) predominantly capillary hydration and finally, (3) predominantly osmotic hydration. It was also shown that shale can take up a significant amount of water compared to its available solid volume. However, contrary to the conventional understanding, the increase in salinity of the injection fluid does not necessarily lead to reduced water uptake into shales, but is dependent on the type and concentration of cations within the shale and injecting fluid

Biogeochemical processes in the hyporheic zone: the role of flow regime in controlling habitat.

Flow of water is essential to provide food (organic matter - OM), nutrients (e.g. N and P) and electron acceptors (e.g. oxygen, nitrate, etc.) for groundwater-dependent ecosystems. In the hyporheic zone, subsurface flows may have multiple sources, i.e. regional groundwater or surface water via hyporheic exchange. These water sources may have very different chemical composition in terms of nutrients, electron acceptors and OM and its quality (i.e. reactivity). Regional groundwater tends to be geochemically evolved and has low concentrations of labile OM. In contrast, surface water has higher concentrations of labile OM. Hence down-welling surface water leads to steep redox-gradients along hyporheic flow paths caused by rapid degradation of OM. As a consequence contrasting subsurface environmental conditions can be formed depending on the source of water, with a range of redox-conditions from oxic to anoxic. Up-welling oxic groundwater will support ecosystems with higher trophic levels (i.e. invertebrates) whereas anoxic conditions will lead to an anaerobic microbe-dominated ecosystem. Altering the flow regime in hyporheic systems will change the hydrogeochemical conditions, OM degradation and microbial processes, and the habitat for invertebrates. For instance depriving streams of their groundwater contribution (e.g. due to groundwater abstraction) could decrease amount and duration of surface flow, enhance down-welling of surface water and alter water quality towards more anoxic conditions. This has significant implications for ecohydrological processes and ecosystem functioning in the hyporheic zone. This presentation will explore these processes by theoretical considerations and field studies undertaken at Maules Creek, NSW

Dripwater organic matter and trace element geochemistry in a semi-arid karst environment: Implications for speleothem paleoclimatology

A series of four short-term infiltration experiments which revealed hydrochemical responses relevant to semi-arid karst environments were carried out above Cathedral Cave, Wellington, New South Wales (NSW), Australia. Dripwater samples were collected at two sites for trace element and organic matter analysis. Organic matter was characterised using fluorescence and interpreted using a PARAFAC model. Three components were isolated that represented unprocessed, soil-derived humic-like and fulvic-like material, processed humic/fulvic-like material and tryptophan-like fluorescence. Principal Component Analysis (PCA) performed on the entire dataset comprising trace element concentrations and PARAFAC scores revealed two dominant components that were identified as soil and limestone bedrock. The soil component was assigned based on significant contributions from the PARAFAC scores and additionally included Ba, Cu, Ni and Mg. The bedrock component included the expected elements of Ca, Mg and Sr as well as Si. The same elemental behaviour was observed in recent stalagmite growth collected from the site. Our experiments demonstrate that existing paleoclimate interpretations of speleothem Mg and Sr, developed in regions of positive water balance, are not readily applicable to water limited environments. We provide a new interpretation of trace element signatures unique to speleothems from water limited karst environments. © 2014, Elsevier Ltd

Ecohydrological Impacts of Groundwater Drawdown : Effects on Microbial Activity in the Hyporheic Zone

Our current understanding of ecohydrological processes in the ecotone between surface water and groundwater - the hyporheic zone - is limited. Groundwater drawdown is a key stressor for many groundwater dependent ecosystems, as groundwater levels are declining globally. It is caused by different perturbations, including agriculture, mine dewatering and climate change. Therefore, there is a pressing need to examine how different ecohydrological systems work under different types of stress. This research aims to investigate the impacts of groundwater drawdown on hyporheic zone microbial activity. For two six week sampling campaigns (winter and summer) at Maules Creek, Namoi, New South Wales, Australia, microbial activity was measured using the cotton strip degradation method. Unprimed cotton canvas was affixed to rulers which were then placed for six weeks in different habitats (dry bar, hyporheic zone and surface waters) at three different water regimes found at different sections of the creek (perennial, ephemeral, and losing). The microbial activity was related to the loss of cotton strip tensile strength. The water regimes were used as proxies for different stages of groundwater drawdown. Key physico-chemical variables were also measured. The preliminary results show that there is a positive correlation between moisture status (i.e. the degree of habitat saturation over six weeks) and microbial activity.This suggests that groundwater drawdown and desaturation of streambed sediments may lead to a decrease in microbial activity and therefore, the recycling of organic carbon and nutrients. This research has local implications for environmental impact assessments and global implications for the assessment and management of ecological impacts of declining shallow groundwater levels

The effect of microbial activity and adsorption processes on groundwater dissolved organic carbon character and concentration

Balancing the terrestrial global carbon budget has proven to be a significant challenge. Whilst the movement of carbon in the atmosphere, rivers and oceans has been extensively studied, the potential for groundwater to act as a carbon source or sink through both microbial activity and sorption to and from mineral surfaces, is poorly understood.To investigate the biodegradable component of groundwater dissolved organic carbon (DOC), groundwater samples were collected from multiple coastal and inland sites. Water quality parameters such as pH, electrical conductivity, temperature, dissolved oxygen were measured in the field. Samples were analysed and characterised for their biodegradable DOC content using spectrofluorometric and Liquid Chromatography-Organic Carbon Detection (LC-OCD) techniques at set intervals within a 28 day period.Further to this, we performed laboratory sorption experiments on our groundwater samples using different minerals to examine the effect of adsorption processes on DOC character and concentration. Calcium carbonate, quartz and iron coated quartz were heated to 400ºC to remove potential carbon contamination, and then added at various known masses (0 mg to 10 g) to 50 mL of groundwater. Samples were then rotated for two hours, filtered at 0.2 μm and analysed by LC-OCD.This research forms part of an ongoing project which will assist in identifying the factors affecting the mobilisation, transport and removal of DOC in uncontaminated groundwater. By quantifying the relative importance of these processes, we can then determine whether the groundwater is a carbon source or sink. Importantly, this information will help guide policy and identify the need to include groundwater resources as part of the carbon economy