Neutrophilic, microaerophilic Fe(II)-oxidizing bacteria are ubiquitous in aquatic habitats of a subtropical Australian coastal catchment (ubiquitous FeOB in catchment aquatic habitats)

We examined the abundance and distribution of neutrophilic, microaerophilic Fe(II)-oxidizing bacteria (FeOB) in aquatic habitats of a highly weathered, subtropical coastal catchment where Fe biogeochemistry is of environmental significance. Laboratory cultivation and microscopy indicated that stalked Gallionella and sheathed Leptothrix-like FeOB were present in microbial mats associated with a circumneutral-pH, groundwater seep and streambank surface sediment,whereas unicellular FeOB werewidespread in surface and subsurface waters, including a seep, shallow stream and estuary-adjacent groundwater. Direct Gallionella-specificPCR detected dominant bacterial members related to Sideroxydans paludicola (95% sequence identity, SI) and Gallionella capsiferriformans (96% SI) in the seep microbialmat. TGGE analysis indicated that themost common FeOB in water enrichment cultures were related to S. lithotrophicus (96% SI). The ubiquity of FeOB in Poona catchment aquatic habitats suggests bacterial Fe(II) oxidation is integral to catchment Fe biogeochemistry.

Determination of coastal ground and surface water processes and character by use of hydrochemistry and stable isotopes, Fraser Coast, Queensland

This study was part of an integrated project developed in response to concerns regarding current and future land practices affecting water quality within coastal catchments and adjacent marine environments. Two forested coastal catchments on the Fraser Coast, Australia, were chosen as examples of low-modification areas with similar geomorphological and land-use characteristics to many other coastal zones in southeast Queensland. For this component of the overall project, organic , physico-chemical (Eh, pH and DO), ionic (Fe2+, Fe3+), and isotopic (ä13CDIC, ä15NDIN ä34SSO4) data were used to characterise waters and identify sources and processes contributing to concentrations and form of dissolved Fe, C, N and S within the ground and surface waters of these coastal catchments. Three sites with elevated Fe concentrations are discussed in detail. These included a shallow pool with intermittent interaction with the surface water drainage system, a monitoring well within a semi-confined alluvial aquifer, and a monitoring well within the fresh/saline water mixing zone adjacent to an estuary. Conceptual models of processes occurring in these environments are presented. The primary factors influencing Fe transport were; microbial reduction of Fe3+ oxyhydroxides in groundwaters and in the hyporheic zone of surface drainage systems, organic input available for microbial reduction and Fe3+ complexation, bacterial activity for reduction and oxidation, iron curtain effects where saline/fresh water mixing occurs, and variation in redox conditions with depth in ground and surface water columns. Data indicated that groundwater seepage appears a more likely source of Fe to coastal waters (during periods of low rainfall) via tidal flux. The drainage system is ephemeral and contributes little discharge to marine waters. However, data collected during a high rainfall event indicated considerable Fe loads can be transported to the estuary mouth from the catchment.

A catchment modelling approach integrating surface and groundwater processes, land use and distribution of nutrients : Elimbah Creek, southeast Queensland

As the world’s population is growing, so is the demand for agricultural products. However, natural nitrogen (N) fixation and phosphorus (P) availability cannot sustain the rising agricultural production, thus, the application of N and P fertilisers as additional nutrient sources is common. It is those anthropogenic activities that can contribute high amounts of organic and inorganic nutrients to both surface and groundwaters resulting in degradation of water quality and a possible reduction of aquatic life. In addition, runoff and sewage from urban and residential areas can contain high amounts of inorganic and organic nutrients which may also affect water quality. For example, blooms of the cyanobacterium Lyngbya majuscula along the coastline of southeast Queensland are an indicator of at least short term decreases of water quality. Although Australian catchments, including those with intensive forms of land use, show in general a low export of nutrients compared to North American and European catchments, certain land use practices may still have a detrimental effect on the coastal environment. Numerous studies are reported on nutrient cycling and associated processes on a catchment scale in the Northern Hemisphere. Comparable studies in Australia, in particular in subtropical regions are, however, limited and there is a paucity in the data, in particular for inorganic and organic forms of nitrogen and phosphorus; these nutrients are important limiting factors in surface waters to promote algal blooms. Therefore, the monitoring of N and P and understanding the sources and pathways of these nutrients within a catchment is important in coastal zone management. Although Australia is the driest continent, in subtropical regions such as southeast Queensland, rainfall patterns have a significant effect on runoff and thus the nutrient cycle at a catchment scale. Increasingly, these rainfall patterns are becoming variable. The monitoring of these climatic conditions and the hydrological response of agricultural catchments is therefore also important to reduce the anthropogenic effects on surface and groundwater quality. This study consists of an integrated hydrological–hydrochemical approach that assesses N and P in an environment with multiple land uses. The main aim is to determine the nutrient cycle within a representative coastal catchment in southeast Queensland, the Elimbah Creek catchment. In particular, the investigation confirms the influence associated with forestry and agriculture on N and P forms, sources, distribution and fate in the surface and groundwaters of this subtropical setting. In addition, the study determines whether N and P are subject to transport into the adjacent estuary and thus into the marine environment; also considered is the effect of local topography, soils and geology on N and P sources and distribution. The thesis is structured on four components individually reported. The first paper determines the controls of catchment settings and processes on stream water, riverbank sediment, and shallow groundwater N and P concentrations, in particular during the extended dry conditions that were encountered during the study. Temporal and spatial factors such as seasonal changes, soil character, land use and catchment morphology are considered as well as their effect on controls over distributions of N and P in surface waters and associated groundwater. A total number of 30 surface and 13 shallow groundwater sampling sites were established throughout the catchment to represent dominant soil types and the land use upstream of each sampling location. Sampling comprises five rounds and was conducted over one year between October 2008 and November 2009. Surface water and groundwater samples were analysed for all major dissolved inorganic forms of N and for total N. Phosphorus was determined in the form of dissolved reactive P (predominantly orthophosphate) and total P. In addition, extracts of stream bank sediments and soil grab samples were analysed for these N and P species. Findings show that major storm events, in particular after long periods of drought conditions, are the driving force of N cycling. This is expressed by higher inorganic N concentrations in the agricultural subcatchment compared to the forested subcatchment. Nitrate N is the dominant inorganic form of N in both the surface and groundwaters and values are significantly higher in the groundwaters. Concentrations in the surface water range from 0.03 to 0.34 mg N L..1; organic N concentrations are considerably higher (average range: 0.33 to 0.85 mg N L..1), in particular in the forested subcatchment. Average NO3-N in the groundwater has a range of 0.39 to 2.08 mg N L..1, and organic N averages between 0.07 and 0.3 mg N L..1. The stream bank sediments are dominated by organic N (range: 0.53 to 0.65 mg N L..1), and the dominant inorganic form of N is NH4-N with values ranging between 0.38 and 0.41 mg N L..1. Topography and soils, however, were not to have a significant effect on N and P concentrations in waters. Detectable phosphorus in the surface and groundwaters of the catchment is limited to several locations typically in the proximity of areas with intensive animal use; in soil and sediments, P is negligible. In the second paper, the stable isotopes of N (14N/15N) and H2O (16O/18O and 2H/H) in surface and groundwaters are used to identify sources of dissolved inorganic and organic N in these waters, and to determine their pathways within the catchment; specific emphasis is placed on the relation of forestry and agriculture. Forestry is predominantly concentrated in the northern subcatchment (Beerburrum Creek) while agriculture is mainly found in the southern subcatchment (Six Mile Creek). Results show that agriculture (horticulture, crops, grazing) is the main source of inorganic N in the surface waters of the agricultural subcatchment, and their isotopic signature shows a close link to evaporation processes that may occur during water storage in farm dams that are used for irrigation. Groundwaters are subject to denitrification processes that may result in reduced dissolved inorganic N concentrations. Soil organic matter delivers most of the inorganic N to the surface water in the forested subcatchment. Here, precipitation and subsequently runoff is the main source of the surface waters. Groundwater in this area is affected by agricultural processes. The findings also show that the catchment can attenuate the effects of anthropogenic land use on surface water quality. Riparian strips of natural remnant vegetation, commonly 50 to 100 m in width, act as buffer zones along the drainage lines in the catchment and remove inorganic N from the soil water before it enters the creek. These riparian buffer zones are common in most agricultural catchments of southeast Queensland and are indicated to reduce the impact of agriculture on stream water quality and subsequently on the estuary and marine environments. This reduction is expressed by a significant decrease in DIN concentrations from 1.6 mg N L..1 to 0.09 mg N L..1, and a decrease in the �15N signatures from upstream surface water locations downstream to the outlet of the agricultural subcatchment. Further testing is, however, necessary to confirm these processes. Most importantly, the amount of N that is transported to the adjacent estuary is shown to be negligible. The third and fourth components of the thesis use a hydrological catchment model approach to determine the water balance of the Elimbah Creek catchment. The model is then used to simulate the effects of land use on the water balance and nutrient loads of the study area. The tool that is used is the internationally widely applied Soil and Water Assessment Tool (SWAT). Knowledge about the water cycle of a catchment is imperative in nutrient studies as processes such as rainfall, surface runoff, soil infiltration and routing of water through the drainage system are the driving forces of the catchment nutrient cycle. Long-term information about discharge volumes of the creeks and rivers do, however, not exist for a number of agricultural catchments in southeast Queensland, and such information is necessary to calibrate and validate numerical models. Therefore, a two-step modelling approach was used to calibrate and validate parameters values from a near-by gauged reference catchment as starting values for the ungauged Elimbah Creek catchment. Transposing monthly calibrated and validated parameter values from the reference catchment to the ungauged catchment significantly improved model performance showing that the hydrological model of the catchment of interest is a strong predictor of the water water balance. The model efficiency coefficient EF shows that 94% of the simulated discharge matches the observed flow whereas only 54% of the observed streamflow was simulated by the SWAT model prior to using the validated values from the reference catchment. In addition, the hydrological model confirmed that total surface runoff contributes the majority of flow to the surface water in the catchment (65%). Only a small proportion of the water in the creek is contributed by total base-flow (35%). This finding supports the results of the stable isotopes 16O/18O and 2H/H, which show the main source of water in the creeks is either from local precipitation or irrigation waters delivered by surface runoff; a contribution from the groundwater (baseflow) to the creeks could not be identified using 16O/18O and 2H/H. In addition, the SWAT model calculated that around 68% of the rainfall occurring in the catchment is lost through evapotranspiration reflecting the prevailing long-term drought conditions that were observed prior and during the study. Stream discharge from the forested subcatchment was an order of magnitude lower than discharge from the agricultural Six Mile Creek subcatchment. A change in land use from forestry to agriculture did not significantly change the catchment water balance, however, nutrient loads increased considerably. Conversely, a simulated change from agriculture to forestry resulted in a significant decrease of nitrogen loads. The findings of the thesis and the approach used are shown to be of value to catchment water quality monitoring on a wider scale, in particular the implications of mixed land use on nutrient forms, distributions and concentrations. The study confirms that in the tropics and subtropics the water balance is affected by extended dry periods and seasonal rainfall with intensive storm events. In particular, the comprehensive data set of inorganic and organic N and P forms in the surface and groundwaters of this subtropical setting acquired during the one year sampling program may be used in similar catchment hydrological studies where these detailed information is missing. Also, the study concludes that riparian buffer zones along the catchment drainage system attenuate the transport of nitrogen from agricultural sources in the surface water. Concentrations of N decreased from upstream to downstream locations and were negligible at the outlet of the catchment.

Turbulent mixing and sediment processes in peri-urban estuariesin South-East Queensland (Australia)

An estuary is formed at the mouth of a river where the tides meet a freshwater flow and it may be classified as a function of the salinity distribution and density stratification. An overview of the broad characteristics of the estuaries of South-East Queensland(Australia) is presented herein, where the small peri-urban estuaries may provide an useful indicator of potential changes which might occur in larger systems with growing urbanisation. Small peri-urban estuaries exhibits many key hydrological features and associated with ecosystem types of larger estuaries, albeit at smaller scales, often with a greater extent of urban development as a proportion of catchment area. We explore the potential for some smaller peri-urban estuaries to be used as natural laboratories to gain some much needed information on the estuarine processes, although any dynamics similarity is presently limited by critical absence of in-depth physical investigation in larger estuarine systems. The absence of the detailed turbulence and sedimentary data hampers the understanding and modelling of the estuarine zones. The interactions between the various stake holders are likely to define the vision for the future of South-East Queensland's peri-urban estuaries. This will require a solid understanding of the bio-physical function and capacity of the peri-urban estuaries. Based upon the knowledge gap, it is recommended that an adaptive trial and error approach be adopted for the future of investigation and management strategies.

Catchment-specific element signatures in estuarine crocodiles (Crocodylus porosus) from the Alligator Rivers Region, northern Australia

The concentrations of Na, K, Ca, Mg, Ba, Sr, Fe, Al, Mn, Zn, Pb, Cu, Ni, Cr, Co, Se, U and Ti were determined in the osteoderms and/or flesh of estuarine crocodiles (Crocodylus porosus) captured in three adjacent catchments within the Alligator Rivers Region (ARR) of northern Australia. Results from multivariate analysis of variance showed that when all metals were considered simultaneously, catchment effects were significant (P≤0.05). Despite considerable within-catchment variability, linear discriminant analysis (LDA) showed that differences in elemental signatures in the osteoderms and/or flesh of C. porosus amongst the catchments were sufficient to classify individuals accurately to their catchment of occurrence. Using cross-validation, the accuracy of classifying a crocodile to its catchment of occurrence was 76% for osteoderms and 60% for flesh. These data suggest that osteoderms provide better predictive accuracy than flesh for discriminating crocodiles amongst catchments. There was no advantage in combining the osteoderm and flesh results to increase the accuracy of classification (i.e. 67%). Based on the discriminant function coefficients for the osteoderm data, Ca, Co, Mg and U were the most important elements for discriminating amongst the three catchments. For flesh data, Ca, K, Mg, Na, Ni and Pb were the most important metals for discriminating amongst the catchments. Reasons for differences in the elemental signatures of crocodiles between catchments are generally not interpretable, due to limited data on surface water and sediment chemistry of the catchments or chemical composition of dietary items of C. porosus. From a wildlife management perspective, the provenance or source catchment(s) of 'problem' crocodiles captured at settlements or recreational areas along the ARR coastline may be established using catchment-specific elemental signatures. If the incidence of problem crocodiles can be reduced in settled or recreational areas by effective management at their source, then public safety concerns about these predators may be moderated, as well as the cost of their capture and removal. Copyright © 2002 Elsevier Science B.V.

High-resolution GNSS-tracked drifter for studying surface dispersion in shallow water

The use of GNSS tracked Lagrangian drifters allows more realistic quantification of fluid motion and dispersion coefficients than Eulerian techniques because such drifters are analogues of particles that are relevant to flow field characterisation and pollutant dispersion. Using the fast growing Real Time Kinematic (RTK) positioning technique derived from Global Satellite Navigation Systems (GNSS), drifters are developed for high frequency (10 Hz) sampling with position estimates to centimetre accuracy. The drifters are designed with small size and less direct wind drag to follow the sub-surface flow which characterizes dispersion in shallow waters. An analysis of position error from stationary observation indicates that the drifter can efficiently resolve motion up to 1 Hz. The result of the field deployments of the drifter in conjunction with acoustic Eulerian devices shows higher estimate of the drifter streamwise velocities. Single particle statistical analysis of field deployments in a shallow estuarine zone yielded dispersion coefficients estimate comparable to those of dye tracer studies. The drifters capture the tidal elevation during field studies in a tidal estuary.

Automated counting of the Northern Pacific Sea Star in the Derwent using shape recognition

A novel shape recognition algorithm was developed to autonomously classify the Northern Pacific Sea Star (Asterias amurenis) from benthic images that were collected by the Starbug AUV during 6km of transects in the Derwent estuary. Despite the effects of scattering, attenuation, soft focus and motion blur within the underwater images, an optimal joint classification rate of 77.5% and misclassification rate of 13.5% was achieved. The performance of algorithm was largely attributed to its ability to recognise locally deformed sea star shapes that were created during the segmentation of the distorted images.

Estimate of Lagrangian integral scales in shallow tidal water using high resolution GPS-tracked drifters

In estuaries and natural water channels, the estimate of velocity and dispersion coefficients is critical to the knowledge of scalar transport and mixing. This estimate is rarely available experimentally at sub-tidal time scale in shallow water channels where high frequency is required to capture its spatio-temporal variation. This study estimates Lagrangian integral scales and autocorrelation curves, which are key parameters for obtaining velocity fluctuations and dispersion coefficients, and their spatio-temporal variability from deployments of Lagrangian drifters sampled at 10 Hz for a 4-hour period. The power spectral densities of the velocities between 0.0001 and 0.8 Hz were well fitted with a slope of 5/3 predicted by Kolmogorov’s similarity hypothesis within the inertial subrange, and were similar to the Eulerian power spectral previously observed within the estuary. The result showed that large velocity fluctuations determine the magnitude of the integral time scale, TL. Overlapping of short segments improved the stability of the estimate of TL by taking advantage of the redundant data included in the autocorrelation function. The integral time scales were about 20 s and varied by up to a factor of 8. These results are essential inputs for spatial binning of velocities, Lagrangian stochastic modelling and single particle analysis of the tidal estuary.

Memory of past random wave conditions in submarine groundwater discharge

Submarine groundwater discharge (SGD) is an integral part of the hydrological cycle and represents an important aspect of land-ocean interactions. We used a numerical model to simulate flow and salt transport in a nearshore groundwater aquifer under varying wave conditions based on yearlong random wave data sets, including storm surge events. The results showed significant flow asymmetry with rapid response of influxes and retarded response of effluxes across the seabed to the irregular wave conditions. While a storm surge immediately intensified seawater influx to the aquifer, the subsequent return of intruded seawater to the sea, as part of an increased SGD, was gradual. Using functional data analysis, we revealed and quantified retarded, cumulative effects of past wave conditions on SGD including the fresh groundwater and recirculating seawater discharge components. The retardation was characterized well by a gamma distribution function regardless of wave conditions. The relationships between discharge rates and wave parameters were quantifiable by a regression model in a functional form independent of the actual irregular wave conditions. This statistical model provides a useful method for analyzing and predicting SGD from nearshore unconfined aquifers affected by random waves

Size-dependent natural mortality of juvenile banana prawns Penaeus merguiensis in the Gulf of Carpentaria, Australia

Natural mortality of marine invertebrates is often very high in the early life history stages and decreases in later stages. The possible size-dependent mortality of juvenile banana prawns, P. merguiensis (2-15 mm carapace length) in the Gulf of Carpentaria was investigated. The analysis was based on the data collected at 2-weekly intervals by beam trawls at four sites over a period of six years (between September 1986 and March 1992). It was assumed that mortality was a parametric function of size, rather than a constant. Another complication in estimating mortality for juvenile banana prawns is that a significant proportion of the population emigrates from the study area each year. This effect was accounted for by incorporating the size-frequency pattern of the emigrants in the analysis. Both the extra parameter in the model required to describe the size dependence of mortality, and that used to account for emigration were found to be significantly different from zero, and the instantaneous mortality rate declined from 0.89 week(-1) for 2 mm prawns to 0.02 week(-1) for 15 mm prawns.