Tuyet Hoang

Depauperate macroinvertebrates in a mine affected stream: Clean water may be the key to recovery

Publisher: Elsevier BV

Date: 11-2005

DOI: 10.1016/J.ENVPOL.2005.02.022

Abstract: Acid mine drainage (AMD) is frequently linked with changes in macroinvertebrate assemblages, but the relative contribution of water and sediment to toxicity is equivocal. We have shown that the macroinvertebrate fauna of Neubecks Ck, a mine impacted stream in New South Wales, Australia, was much poorer than in two reference streams. Multivariate RELATE analyses indicated that the patterns in the biological data were more strongly correlated with the concentrations of common metals in the surface water than the pore water of these streams. From this we hypothesised that the water was more toxic to the biota than the sediment and we tested this hypothesis with a sediment transplant experiment. Sediment from Neubecks Ck that was placed in reference streams retained high concentrations of metals throughout the experiment, yet supported a macroinvertebrate assemblage similar to that in the reference streams. Sediment from the reference streams that was placed in Neubecks Ck supported few, if any, animals. This indicates that water in Neubecks Ck is toxic to biota, but that sediment is able to support aquatic biota in clean water. Therefore, remediation should focus on improving water quality rather than sediment quality.

Invertebrate traits, diversity and the vulnerability of groundwater ecosystems

Publisher: Wiley

Date: 30-07-2022

DOI: 10.1111/1365-2435.14125

Abstract: Groundwater comprises the largest freshwater ecosystem on the planet. It has a distinct regime of extreme, yet stable environmental conditions that have favoured the development of similar morphological and functional traits in the resident invertebrate fauna (stygofauna). The analysis of community traits is increasingly used as an alternative to taxonomy‐based assessments of bio ersity, especially for monitoring ecosystem status and linking the functions of organisms to ecological processes, yet it has been rarely applied to stygofauna and groundwater ecosystems. In this paper, we review the variation in functional traits among the invertebrate fauna of this important ecosystem. We focus on the stygofauna and processes of alluvium and fractured rock aquifers that are typified by small voids and fissures that constrain the habitats and environmental conditions. As a first step, we compare trait variability between groundwater and surface water invertebrate communities and then examine the significance of the ranges of these traits to the vulnerability of the ecosystem to change. Fifteen potentially useful functional traits are recognised. Eight of these have narrower ranges (i.e. exhibit fewer states, or attributes, of a particular trait) in groundwater than they do in surface water. Two traits have wider ranges. Our synthesis suggests that the relative stability of groundwater environments has led to low trait variability. The low biomass and low reproductive rate of stygofauna suggest that recovery potential following disturbance is likely to be low. For the purposes of both improved understanding and effective management, further work is needed to document additional functional traits and their states in groundwater fauna, enabling a better understanding of the relationship between response and effect traits in these ecosystems. Read the free Plain Language Summary for this article on the Journal blog.

Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA

Publisher: Microbiology Society

Date: 09-2020

DOI: 10.1099/JMM.0.001238

Abstract: Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues. Aim. To establish and validate a reverse transcription loop-mediated isothermal lification (RT- LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs. Methodology. We used a commercial RT-LAMP mastermix from OptiGene in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby 1 µl of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65 °C for 30 min and measure fluorescence in the FAM channel at 1 min intervals. Results. Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87 and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical s les of 14 min ( sd ±7 min). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID 50 ml −1 ), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay. Conclusion. With a simplified workflow, The N1 gene Single Tube Optigene LAMP assay (N1-STOP-LAMP) is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.

Identifying key sedimentary indicators of geomorphic structure and function of upland swamps in the Blue Mountains for use in condition assessment and monitoring

Publisher: Elsevier BV

Date: 12-2016

DOI: 10.1016/J.CATENA.2016.08.016

Effects of River Water and Salinity on the Toxicity of Deltamethrin to Freshwater Shrimp, Cladoceran, and Fish

Publisher: Springer Science and Business Media LLC

Date: 18-03-2008

DOI: 10.1007/S00244-008-9147-0

Abstract: Deltamethrin is a pyrethroid insecticide used extensively to control invertebrate pests on cotton and other crops. It is acutely toxic to nontarget aquatic organisms, but existing toxicity data are mostly from toxicity tests using purified laboratory water that differs greatly from the turbid, high-conductivity rivers in the cotton-growing regions of Australia. The aim of this study was to determine whether the water quality variables conductivity, suspended particles, and dissolved organic matter alter the toxicity of deltamethrin to freshwater crustaceans and a fish. We tested three Australian native species: a cladoceran (Ceriodaphnia cf. dubia), a freshwater shrimp (Paratya australiensis), and larvae of the eastern rainbow fish (Melanotaenia duboulayi). Conductivity of the test solutions ranged from 200 to 750 microS/cm, but such changes did not modify the toxicity of deltamethrin to any of the test species. However, the toxicity of deltamethrin to C. cf. dubia and P. australiensis in river water was significantly decreased (1.8-fold to 6.3-fold reduction) compared to that in laboratory water. Variability in the toxicity data limited our ability to detect differences between laboratory and river water for M. duboulayi. Despite reductions in toxicity in natural waters, deltamethrin remained highly toxic [all L(E)C(50) values <0.26 microg/L] to all organisms tested thus, further investigation of the hazard of deltamethrin is warranted.

A comparison of mixture toxicity assessment: Examining the chronic toxicity of atrazine, permethrin and chlorothalonil in mixtures to Ceriodaphnia cf. dubia

Publisher: Elsevier BV

Date: 11-2011

DOI: 10.1016/J.CHEMOSPHERE.2011.07.061

Abstract: Pesticides predominantly occur in aquatic ecosystems as mixtures of varying complexity, yet relatively few studies have examined the toxicity of pesticide mixtures. Atrazine, chlorothalonil and permethrin are widely used pesticides that have different modes of action. This study examined the chronic toxicities (7-d reproductive impairment) of these pesticides in binary and ternary mixtures to the freshwater cladoceran Ceriodaphnia cf. dubia. The toxicity of the mixtures was compared to that predicted by the independent action (IA) model for mixtures, as this is the most appropriate model for chemicals with different modes of action. Following this they were compared to the toxicity predicted by the concentration addition (CA) model for mixtures. According to the IA model, the toxicity of the chlorothalonil plus atrazine mixture conformed to antagonism, while that of chlorothalonil and permethrin conformed to synergism. The toxicity of the atrazine and permethrin mixture as well as the ternary mixture conformed to IA implying there was either no interaction between the components of these mixtures and/or in the case of the ternary mixture the interactions cancelled each other out to result in IA. The synergistic and antagonistic mixtures deviated from IA by factors greater than 3 and less than 2.5, respectively. When the toxicity of the mixtures was compared to the predictions of the CA model, the binary mixture of chlorothalonil plus atrazine, permethrin plus atrazine and the ternary mixture all conformed to antagonism, while the binary mixture of chlorothalonil plus permethrin conformed to CA. Using the CA model provided estimates of mixture toxicity that did not markedly underestimate the measured toxicity, unlike the IA model, and therefore the CA model is the most suitable to use in ecological risk assessments of these pesticides.

Lessons from 10 Years of Experience with Australia’s Risk-Based Guidelines for Managed Aquifer Recharge

Publisher: MDPI AG

Date: 14-02-2020

DOI: 10.3390/W12020537

Abstract: The Australian Managed Aquifer Recharge Guidelines, published in 2009, were the world’s first Managed Aquifer Recharge (MAR) Guidelines based on risk-management principles that also underpin the World Health Organisation’s Water Safety Plans. In 2015, a survey of Australian MAR project proponents, consultants and regulators revealed that in those states advancing MAR, the Guidelines were lauded for giving certainty on approval processes. They were also considered to be pragmatic to use, but there was feedback on onerous data requirements. The rate of uptake of MAR has varied widely among Australian state jurisdictions, for reasons that are not explained by the drivers for and feasibility of MAR. The states where MAR has progressed are those that have adopted the Guidelines into state regulations or policy. It was originally intended that these Guidelines would be revised after five to ten years, informed by experience of any hazards not considered in the guidelines, and by new scientific developments including advances in monitoring and control methods for risk management. As such revision has not yet occurred, this paper was prepared to give a precis of these Guidelines and review ten years of experience in their application and to identify issues and suggest improvements for consideration in their revision by Australian water regulators. This paper also discusses the factors affecting their potential international applicability, including the capabilities required for implementation, and we use India as an ex le for which an intermediate level water quality guideline for MAR was developed. This paper is intended to be useful information for regulators in other countries considering adopting or developing their own guidelines. Note that the purpose of these Guidelines is to protect human health and the environment. It is not a guide to how to site, design, build and operate a managed aquifer recharge project, for which there are many other sources of information.

Reproducibility of AUSRIVAS rapid bioassessments using macroinvertebrates

Publisher: University of Chicago Press

Date: 2004

DOI: 10.1899/0887-3593(2004)023<0126:ROARBU>2.0.CO;2

Short-term colonisation by macroinvertebrates of cobbles in main channel and inundated stream bank habitats

Publisher: Springer Science and Business Media LLC

Date: 06-07-2007

DOI: 10.1007/S10750-007-0791-6

Stygofaunal diversity and ecological sustainability of coastal groundwater ecosystems in a changing climate: The Australian paradigm

Publisher: Wiley

Date: 10-09-2022

DOI: 10.1111/FWB.13987

Abstract: Coastal aquifers are vital water sources for humanity. Their quality and the ecosystem services they provide depend on the integrity of their subterranean biota. However, current anthropogenic impacts such as climate change effects and coastal population growth place enormous pressure on the sustainability of these environments. Despite the significance of subterranean biota to ecosystem function and the delivery of ecosystem services, stygofauna—groundwater‐dwelling aquatic animals—have until recently been largely ignored in aquifer monitoring and management. This issue is of importance in both coastal and inland zones. Common threats in inland and coastal areas are water extraction, reduced recharge caused by aridification, and pollution, while, in coastal zones, additional complications arise from sea‐level change and salt water ingress. This review examines stygofaunal ersity, impacts, and future conservation challenges in coastal aquifers. Focussing on Australia, we provide a summary of the available data on stygofaunal communities and distributions identify and describe potential threats to these communities across the erse coastal regions of the continent and propose future research priorities with the goal of facilitating the long‐term preservation of these ecosystems on the Australian continent. While we focus this review on Australia, the threats and management issues discussed are relevant globally. Recent subterranean studies in Australia have been primarily undertaken in inland areas, and while coastal data exist, ecological assessment of coastal subterranean ecosystems is incomplete, compromising the efficacy of conservation plans. This review indicates that the Australian continent hosts five major coastal stygofaunal bio ersity areas characterised by heterogeneous community assemblages, involving a total of 17 taxonomic groups spanning microscopic aquatic invertebrates to vertebrates. The most relevant impacts and threats identified were aquifer size reduction, intrusion of seawater, land clearing, contamination, and mining. Given the projections of increasing coastal development and subsequent loss or degradation of habitat during coming decades, it is important to improve our limited understanding of the ecology of coastal aquifers. Future research should include the refinement of biological assessment tools for coastal systems, functional and ecotoxicological studies, and faunal surveys of urban coastal aquifers. The recommendations and guidelines outlined in this review are applicable globally and provide a further step toward the sustainable use of coastal groundwater resources and the maintenance of healthy groundwater ecosystems.

3D conservation planning: Including aquifer protection in freshwater plans refines priorities without much additional effort

Publisher: Wiley

Date: 14-06-2019

DOI: 10.1002/AQC.3129

Water Sources of Upland Swamps in Eastern Australia: Implications for System Integrity with Aquifer Interference and a Changing Climate

Publisher: MDPI AG

Date: 09-01-2019

DOI: 10.3390/W11010102

Abstract: Temperate Highland Peat Sw s on Sandstone (THPSS) in Eastern Australia are Groundwater Dependent Terrestrial Ecosystems that occur in the headwaters of streams on low relief plateaus. Like upland sw s and peatlands globally, they provide base flow to downstream catchments. However, these sw s are subject to aquifer interference from mining and groundwater extraction and are threatened by urbanization and climate change. We collected winter and summer water s les from sw s in two highland regions of Eastern Australia. Water from the sw s was analyzed for hydrogen (δ2H) and oxygen (δ18O) isotopes and compared with rainwater, surface water and groundwater s les from the surrounding bedrock aquifers to identify likely sw water sources. Radon (222Rn) was used as an environmental tracer to determine whether the sw s were predominantly groundwater or rainwater fed. Four out of five sw s s led in the Blue Mountains had greater than 30% of water derived from the surrounding bedrock aquifer, whereas sw s in the Southern Highlands received less than 15% of water from the surrounding aquifer. The water sources for sw s in both regions are controlled by catchment morphology, e.g., valley shape. Understanding water sources of these systems is critical for the determination of likely impacts on THPSS from aquifer interference activities and a changing climate.

A weight-of-evidence approach for identifying potential sources of untreated sewage inputs into a complex urbanized catchment

Publisher: Elsevier BV

Date: 04-2021

DOI: 10.1016/J.ENVPOL.2021.116575

Prevalence and Molecular Identification of Nematode and Dipteran Parasites in an Australian Alpine Grasshopper (Kosciuscola tristis)

Publisher: Public Library of Science (PLoS)

Date: 28-04-2015

DOI: 10.1371/JOURNAL.PONE.0121685

The hydrological function of upland swamps in eastern Australia: The role of geomorphic condition in regulating water storage and discharge

Publisher: Elsevier BV

Date: 06-2018

DOI: 10.1016/J.GEOMORPH.2018.03.004

What do qualitative rapid assessment collections of macroinvertebrates represent? A comparison with extensive quantitative sampling

Publisher: Springer Science and Business Media LLC

Date: 27-02-2009

DOI: 10.1007/S10661-008-0186-9

Abstract: It is a fundamental tenet of Rapid Biological Assessments (RBA) that the s les collected reflect the community from which they are drawn. As with any biological s ling, RBA collections are subject to s ling error resulting in the omission of some taxa. The aim of this study is to compare the composition of RBA s les with an estimate of community structure based on extensive quantitative s ling. We used logistic regression to explore the relationships between the frequency of a taxon being collected in an RBA s le and its biological and ecological traits, namely its abundance, distribution, body size and habit. RBA s les and quantitative estimates of community structure were made in riffles in the Kangaroo and Nepean Rivers, New South Wales, Australia. Single RBA s les may collect up to 63% of the taxa that are collected by extensive quantitative s ling at a site. The frequency of a taxon being recorded in an RBA s le was significantly and positively related to all traits tested indicating a bias in the collection methods towards large, abundant and widely distributed taxa. Accordingly, taxa missed by RBA s ling were generally small, narrowly distributed or rare. These findings enhance our understanding of what RBA s les represent, and the bias and source of errors associated with RBA s ling. This study also quantifies the utility of RBA methods for bio ersity assessment.

Urban impacts across realms: Making the case for inter-realm monitoring and management

Publisher: Elsevier BV

Date: 2019

DOI: 10.1016/J.SCITOTENV.2018.08.134

Abstract: Burgeoning populations and the increasing concentration of humans in urban areas have resulted in extensive and increasing degradation and destruction of natural ecosystems. The multitude of impacts and their drivers in urban areas across realms are often studied at local scales, but there is regularly a mismatch between the spatial extent of the impacts and that of the pressures driving those impacts. For ex le, most human activities occur on land and therefore disturb terrestrial habitats (intrinsic impacts), but their impacts can also extend to the atmosphere and aquatic realms (extrinsic impacts). Management of urban impacts is often designed at local scales and aims to control local pressures, mostly overlooking pressures originating outside the 'managed' area. This is often due to jurisdictional barriers but can also result from the lack of knowledge and recognition among scientists and managers of larger scale pressures. With the aim to highlight the importance of ameliorating extrinsic impacts for holistic management of urban areas, this paper discusses the range and extent of extrinsic impacts produced by the most common pressures in urban environments. We discuss that the terrestrial realm is a 'net-donor' of impacts, as most human activities occur on land and the resulting impacts are transferred to aquatic and atmospheric realms. However, activities in aquatic realms can result in impacts on land. We conclude that, to achieve effective management strategies, greater collaboration is needed between scientists and managers focussing on different realms and regions and we present suggestions for approaches to achieve this.

Intrinsic and extrinsic controls on the geomorphic condition of upland swamps in Eastern NSW

Publisher: Elsevier BV

Date: 02-2016

DOI: 10.1016/J.CATENA.2015.09.002

Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance

Publisher: Cold Spring Harbor Laboratory

Date: 02-02-2023

DOI: 10.1101/2023.02.01.526694

Abstract: The capacity to undertake whole genome sequencing (WGS) in public health laboratories (PHLs) has grown rapidly in response to COVID-19, and SARS-CoV-2 genomic data has been invaluable for managing the pandemic. The public health response has been further supported by the rapid upgrade and implementation of laboratory and bioinformatic resources. However, there remains a high degree of variability in methods and capabilities between laboratories. In addition to evolving methodology and improved understanding of SARS-CoV-2, public health laboratories have become strained during surges in case numbers, adding to the difficulty of ensuring the highest data accuracy. Here, we formed a national working group comprised of laboratory scientists and bioinformaticians from Australia and New Zealand to improve data concordance across PHLs. Through investigating discordant sequence data from Australia’s first external SARS-CoV-2 WGS proficiency testing program (PTP), we show that most discrepancies in genome assessment arose from intrahost variation. While others could be remedied using reasonable, parsimonious bioinformatic quality control. Furthermore, we demonstrate how multidisciplinary national working groups can inform guidelines in real time for bioinformatic quality acceptance criteria. Provision of technical feedback allows laboratory improvement during a pandemic in real time, enhancing public health responses. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. The COVID-19 pandemic has brought the utility of genomics to the forefront of microbial surveillance in public health. Our findings provide recommendations for monitoring bioinformatic quality controls in a pandemic context and how multidisciplinary national working groups can provide technical feedback for actionable improvement towards sequence data concordance.

Assessing the Chronic Toxicity of Atrazine, Permethrin, and Chlorothalonil to the Cladoceran Ceriodaphnia cf. dubia in Laboratory and Natural River Water

Publisher: Springer Science and Business Media LLC

Date: 29-11-2012

DOI: 10.1007/S00244-012-9837-5

Abstract: The majority of ecotoxicological data are generated from standard laboratory-based experiments with organisms exposed in nonflowing systems using highly purified water, which contains very low amounts of dissolved organic matter and suspended particulates. However, such experimental conditions are not ecologically relevant. Thus, there is a need to develop more realistic approaches to determining toxicity, including both lethal and sublethal effects. This research provides information on the effect of natural water constituents, such as suspended particulates and dissolved organic matter, in river water (RW) on the chronic toxicity (7-day reproductive impairment) of the pesticides atrazine, chlorothalonil, and permethrin to the freshwater cladoceran Ceriodaphnia cf. dubia. Standard bioassays were conducted under standard laboratory and more environmentally realistic conditions (using RW). The 7-day IC25 (reproduction impairment) values of atrazine, chlorothalonil, and permethrin to C. cf. dubia ranged from 862.4 to >1000, 51.3 to 66.4, and 0.19 to 0.23 μg/L, respectively. Using the Globally Harmonized System of Classification and Labelling of Chemicals, atrazine is classified as moderately to highly toxic, whereas permethrin and chlorothalonil were both highly toxic. The presence of dissolved organic matter and suspended particles in natural RW did not significantly (p > 0.05) change the toxicity of any of the pesticides to C. cf. dubia compared with that tested in laboratory water (LW). For the tested pesticides, toxicity testing in LW provided an adequate estimate of the hazard posed.

Macquarie University

Location: Australia

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University Of Melbourne

Location: Australia

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University Of Technology Sydney

Location: Australia

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Macquarie University Department Of Biological Sciences

Location: Australia

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Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989680

Start Date: 2009

End Date: 12-2009

Amount: $300,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP1095200

Start Date: 07-2010

End Date: 06-2015

Amount: $169,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100120

Start Date: 11-2013

End Date: 12-2018

Amount: $179,945.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP190100927

Start Date: 05-2021

End Date: 05-2024

Amount: $366,244.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP160100686

Start Date: 11-2016

End Date: 06-2021

Amount: $410,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP110200105

Start Date: 12-2011

End Date: 12-2015

Amount: $296,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP130100508

Start Date: 07-2013

End Date: 06-2016

Amount: $447,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0775468

Start Date: 01-2007

End Date: 12-2009

Amount: $174,100.00

Funder: Australian Research Council

Special Research Initiatives - Grant ID: SR0354817

Start Date: 2004

End Date: 12-2004

Amount: $10,000.00

Funder: Australian Research Council