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Diffraction-unlimited single-molecule techniques like STORM and (F)PALM enable three-dimensional (3D) fluorescence imaging at tens of nanometer resolution and are invaluable to investigate sub-cellular organization. The multitude of camera frames required to reconstruct a super-resolved image limits the typical throughput of these techniques to tens of cells per day, rendering these methods incompatible with large-scale cell biological or clinical application. STORM acquisition rates can be increased by over an order of magnitude, however the data volumes of about 40 TB a day and concomitant analysis burdens exceed the capacity of existing workflows. Here we present an integrated platform which transforms SMLM from a trick-pony technique into a work horse for cell biology. We leverage our developments in microscopy-specific data compression, distributed storage, and distributed analysis to automatically perform real-time localization analysis, which enable SMLM at throughputs of 10,000 cells a day. We implemented these advances in a fully-integrated environment that supports a highly-flexible architecture for distributed analysis, enabling quickly- and graphically-reconfigurable analyses to be automatically initiated from the microscope during acquisition, remotely executed, and even feedback and queue new acquisition tasks on the microscope. We demonstrate the utility of this framework by imaging hundreds of cells per well in multi-well sample formats. Our platform, the PYthon-Microscopy Environment (PYME), is easily configurable for hardware control on custom microscopes, and includes a plugin framework so users can readily extend all components of their imaging, visualization, and analysis pipeline. PYME is cross-platform, open source, and efficiently puts high-caliber visualization and analysis tools into the hands of both microscope developers and users.

MDFRC item.December 2011. DOI: 10.1899/11-009.1 A publication output from S. Perryman PhD Thesis see (Microbial Community Structure and Function: The response of denitrifiers on an environmental gradient – stream urbanization - M/PER/28).Urbanization is an important ecological modifier of stream catchments and significantly alters C type and concentration and heavy metal input to aquatic systems. C and heavy metals are important determinants of microbial community structure (population dynamics) and function (physiological processes). Understanding how changes at the landscape scale affect key nutrient-transformation processes (e.g., denitrification) and C metabolism (e.g., methanogenesis) at the micro scale requires simultaneous determination of the structural and functional responses of bacterial communities. We compared total bacterial (16S ribosomal ribonucleic acid [rRNA] gene) and denitrifying bacterial (nosZ gene) community structures in sediments taken from an urban and a nonurban stream before and after C and Zn additions. Microcosms containing stream sediment were supplemented with either proteinaceous or leaf-leachate C, increasing the C content by 36 and 130 mg/L, respectively. C was added in the presence and absence of Zn addition (200 mg/kg). Changes in community function were determined simultaneously with additions by measuring the rates of CO2, N2, and CH4 accumulation in the headspace of each mesocosm. Site had the greatest effect on total and denitrifying bacterial community structures. Added C caused a small but significant change in total bacterial community structure, but did not change denitrifying bacterial community structure. C enrichment caused a significant and rapid change in community function. Rates of methanogenesis were significantly higher at the nonurban than at the urban site and were significantly affected by C type (significant site × C interaction). Denitrification and CO2 production were unaffected by C additions but differed between sites. Zn addition changed total bacterial community structure but not denitrifying bacterial community structure. Zn affected the rate of methanogenesis, but the effect size was less than for C type. Community structures remained different between sites at the end of the study despite exposure to Zn concentrations that reflected conditions in urbanized streams and C sources that mimicked those from urban or nonurban streams. Our study supports previous observations that microbial community structure is strongly influenced by prior sediment history. The broader implication is that landscape-scale changes like urbanization alter other physical and chemical properties of the stream sediment that influence community structure more than the Zn or C concentrations in our study.

Our understanding of the effects of pharmaceuticals on key biogeochemical processes and biofilm assemblage composition in surface waters is limited despite the prevalence of ng/L to µg/L co...

In streams, gross primary production (GPP) and ecosystem respiration (ER) (i.e., stream metabolism) control the transport and fate of nutrients and organic carbon and vice versa. The import...

Many water scientists aim for their work to inform water policy and management, and in pursuit of this objective, they often work alongside government water agencies to ensure their research is relevant, timely and communicated effectively. A paper in this issue, examining 'Science integrity, public policy and water governance in the Murray-Darling Basin, Australia���, suggests that a large group of scientists, who work on water management in the Murray-Darling Basin (MDB) including the Basin Plan, have been subject to possible ���administrative capture'. Specifically, it is suggested that they have advocated for policies favoured by government agencies with the objective of gaining personal benefit, such as increased research funding. We examine evidence for this claim and conclude that it is not justified. The efforts of scientists working alongside government water agencies appear to have been misinterpreted as possible administrative capture. Although unsubstantiated, this claim does indicate that the science used in basin water planning is increasingly caught up in the politics of water management. We suggest actions to improve science-policy engagement in basin planning, to promote constructive debate over contested views and avoid the over-politicisation of basin science.

We derive the quantum limit for discriminating between M≥2 incoherent, diffraction-limited objects and identify a quantum-optimal measurement that can distinguish two orders of magnitude more objects than direct imaging with no additional error.

The first discrete bimetallic europium(iii)/copper(ii) complex for the fast, sensitive and selective luminescent detection of both aqueous and gaseous hydrogen sulfide has been developed. The chemosensor displayed an impressive response time of 30 seconds and a low theoretical limit of detection (100 ppb) for gaseous hydrogen sulfide.

We consider passive imaging tasks involving discrimination between known candidate objects and investigate the best possible accuracy with which the correct object can be identified. We analytically compute quantum-limited error bounds for hypothesis tests on any database of incoherent, quasi-monochromatic objects when the imaging system is dominated by optical diffraction. We further show that object-independent linear-optical spatial processing of the collected light exactly achieves these ultimate error rates, exhibiting superior scaling than spatially-resolved direct imaging as the scene becomes more severely diffraction-limited. We apply our results to example imaging scenarios and find conditions under which super-resolution object discrimination can be physically realized., 15 pages, 6 figures

In the face of mounting environmental problems, it is essential that accurate and timely scientific information is available to inform policy development and guide management. Scientists have specialised knowledge necessary for evidenced-based decision making, but despite extensive literature on the interface between science and policy, there is little guidance on achieving policy relevance while maintaining high standards of scientific integrity. Here, we provide a set of principles for environmental scientists to engage with policy makers and environmental water managers. We propose the adoption of a contemporary pluralistic approach using a diversity of modes of engagement between scientists, policy makers, and managers. We define a set of ‘roles’ for environmental scientists to engage effectively with policy and management, and discuss the advantages and pitfalls of each. We illustrate the breadth of modes of engagement at the science-policy-management interface using an example from Australia’s largest river system, the Murray-Darling Basin. We challenge the anachronistic, yet persistent concept that engaging with industry or government compromises the objectivity of involved scientists. We argue that there are multiple assurance processes in place to protect scientific integrity. Society needs scientists to be actively involved in finding solutions to the many urgent environmental issues we are facing, and if our principles are followed there are opportunities for healthy interaction between science, policy, and management.

We investigate our ability to determine the mean position, or centroid, of a linear array of equally-bright incoherent point sources of light, whose continuum limit is the problem of estimating the center of a uniformly-radiating object. We consider two receivers: an image-plane ideal direct-detection imager and a receiver that employs Hermite-Gaussian (HG) Spatial-mode Demultiplexing (SPADE) in the image plane, prior to shot-noise-limited photon detection. We compare the Fisher Information (FI) for estimating the centroid achieved by these two receivers, which quantifies the information-accrual rate per photon, and compare those with the Quantum Fisher Information (QFI): the maximum attainable FI by any choice of measurement on the collected light allowed by physics. We find that focal-plane direct imaging is strictly sub-optimal, although not by a large margin. We also find that the HG mode sorter, which is the optimal measurement for estimating the separation between point sources (or the length of a line object) is not only suboptimal, but it performs worse than direct imaging. We study the scaling behavior of the QFI and direct imaging's FI for a continuous, uniformly-bright object in terms of its length, and find that both are inversely proportional to the object's length when it is sufficiently larger than the Rayleigh length. Finally, we propose a two-stage adaptive modal receiver design that attains the QFI for centroid estimation., 20 pages, 4 figures; slightly reformatted version to appear in PRA

We derive the quantum limit on average error for hypothesis tests between any two incoherent, diffraction-limited objects and identify quantum-optimal measurements that achieve a quadratic scaling improvement over direct imaging.

We derive quantum limits and optimal measurements for arbitrary hypothesis tests between incoherent, diffraction-limited objects, enabling discrimination of an order of magnitude more objects than direct imaging.

We developed a quantum-inspired adaptive algorithm using spatial-mode-demultiplexing measurements to read incoherently illuminated barcodes at large distances. In simulations, our scheme accurately discriminates barcodes in 20x less time than direct imaging at a standoff of 1 km.

Water treatment wetlands are increasingly being used to reduce pollutant loads including nitrogen (N) in urban runoff. Processes such as denitrification (DNF) and anaerobic ammonium oxidation (anammox), which remove N, and dissimilatory nitrate reduction to ammonium (DNRA), which recycles N, play an important role in controlling NOx (NO3− + NO2−) removal versus recycling in wetlands. The relative importance of DNF, anammox and DNRA was investigated in four constructed stormwater urban wetlands in Melbourne, Australia. Rates of DNF and DNRA were variable and did not differ significantly among wetlands. However, rates of DNF and DNRA were significantly different (p

Fluoxetine, a selective serotonin reuptake inhibitor (SSRI), is frequently detected in surface waters globally, yet the effects of SSRIs on ecological processes at environmentally realistic concentrations are not currently known. We used a controlled, replicated artificial stream experiment to expose biofilm, algal and stream insect communities to two different concentrations of fluoxetine: 20 ng/L (typical concentration detected in surface waters) and 20 µg/L (concentration shown to influence insect emergence and algal productivity). We quantified a range of community and ecosystem response metrics over the course of the 21d experiment including; algal biomass (chl-a), net ecosystem production (NEP), gross primary production (GPP), ecosystem respiration (ER) and invertebrate emergence. At 20 ng/L, fluoxetine significantly suppressed algal colonization on rocks, and reduced GPP after 13 days, but by day 21 chl-a, NEP and GPP did not differ between treatments and control. Fluoxetine increased ER on leaves where invertebrates were excluded, but had no effect on leaves accessible to invertebrates. Streams receiving 20 ng/L of fluoxetine had adult insects from the order Diptera emerge sooner and at a greater rate than control streams. Our results suggest that ecosystem function, including primary production and respiration, and invertebrate population dynamics are sensitive to SSRIs and that fluoxetine may alter these key processes concentrations found in the environment.

We analyze a fiber-optic gyroscope design enhanced by the injection of quantum-optical squeezed vacuum into a fiber-based Sagnac interferometer. In the presence of fiber loss, we compute the maximum attainable enhancement over a classical, laser-driven fiber-optic gyroscope in terms of the angular velocity estimate variance from a homodyne measurement. We find a constant enhancement factor that depends on the degree of squeezing introduced into the system but has diminishing returns beyond $10$--$15$ dB of squeezing. Under a realistic constraint of fixed total fiber length, we show that segmenting the available fiber into multiple Sagnac interferometers fed with a multi-mode-entangled squeezed vacuum, thereby establishing quantum entanglement across the individual interferometers, improves the rotation estimation variance by a factor of $e\approx2.718$., 12 pages, 8 figures

Recent developments (2012 and onwards) in the design and application of luminescent lanthanide-based complexes for chemical sensing are reviewed. Sensors for a variety of metal cations, anions and neutral small molecules are highlighted, including several developed by Australian researchers. Emphasis is placed on describing the general design features and range of mechanisms by which such sensors are able to elicit a luminescent response upon exposure to an analyte.

A simple sample preparation method based on a modified liquid-phase extraction approach to extract selected pharmaceuticals and personal care products from freshwater organisms is described. Extracted samples were analysed using liquid chromatography with Q-Exactive plus hybrid quadrupole Orbitrap mass spectrometry, using 2.6 μm C18 media. A 0.1% v/v acetic acid/acetonitrile mobile phase was applied over a 20 min gradient. Method detection limits in full scan mode were ca. 0.04-2.38 ng of analyte per g of sample. Linearity ranged from 0.9750 to 0.9996 over the calibration range of 0.01-100 μg/L; MS mass accuracy was

Understanding the relationship between land use and the dynamics of nitrate (NO3-) is the key to constrain sources of NO3- export in order to aid effective management of waterways. In this study, isotopic compositions of NO3- (δ15N–NO3- and δ18O–NO3-) were used to elucidate the effects of land use (agriculture in particular) and rainfall on the major sources and sinks of NO3- within the Western Port catchment, Victoria, Australia. This study is one of the very few studies carried out in temperate regions with highly stochastic rainfall patterns, enabling a more comprehensive understanding of the applications of NO3- isotopes in catchment ecosystems with different climatic conditions. Longitudinal samples were collected from five streams with different agriculture land use intensities on five occasions – three during dry periods and two during wet periods. At the catchment scale, we observed significant positive relationships between NO3- concentrations (p δ15N–NO3- (p NO3- in our study sites. Artificial fertiliser was the dominant source of NO3- during the wet periods. In addition to artificial fertiliser, nitrified organic matter in sediment was also an apparent source of NO3- to the surface water during the dry periods. Denitrification was prevalent during the wet periods, while uptake of NO3- by plants or algae was only observed during the dry periods in two streams. The outcome of this study suggests that effective reduction of NO3- load to the streams can only be achieved by prioritising management strategies based on different rainfall conditions.

Ferrihydrite (Fh) and calcite were used as reactive capping layers for a eutrophic lake. The effectiveness of Fh and/or calcite capping for demobilizing phosphorus (P) in the sediment from the overlying water was tested, and the responses of carbon (C), nitrogen (N), and iron (Fe) to different capping treatments were analyzed as well. Twelve sediment cores were collected randomly using polycarbonate tubes from Ornamental Lake in the Royal Botanic Gardens of Melbourne, Australia. Four groups with three replicates were separated randomly and labeled as the control (no capping), calcite (capped with 1-cm-deep calcite), Fh (capped with 1-cm-deep synthesized Fh powder), and calcite + Fh (CaFh, capped with 0.5-cm-deep Fh powder first and then with 0.5-cm-deep calcite). Gentle bubbling was employed to prevent anoxic conditions in the sediments and stimulate vascular plant ventilation during a 15-day static incubation. The overlying water sample mixed by a small magnetic stirrer was withdrawn 1, 3, 7, 11, and 15 days after capping for the analyses of filterable reactive phosphorus (FRP), filterable N, and Fe species. The results showed that CaFh had a greater effect on the FRP removal in the overlying water than Fh alone. No significant Fe release was observed for Fh and CaFh compared to the control and calcite. The introduction of Fh increased the release of ammonium and total N. After incubation, no significant differences were observed among total P, total N, and organic carbon in the upper sediments, except for total Fe. Composite capping with Fh and calcite could be used as an effective, low-cost natural method to block the release of P from the sediment without a significant Fe pollution risk. The potential environmental risks need further attention.

Synthesized ferrihydrite (Fh) with the dosages of 0.3, 0.6 and 0.9 cm thickness (labeled as Fh, 2Fh and 3Fh respectively, equivalent to 248–774 g/m 2 ) were deployed to serve as the reactive capping layer covering the Ornamental Lake sediments, the Royal Botanic Garden of Melbourne. The sediments were exposed to an alternating regime of oxic/anoxic conditions using laboratory reactors for 45 days. Dynamics of dissolved oxygen (DO), pH, filterable reactive phosphorus (FRP), filterable ammonium (NH 4 + ), nitrate and nitrite (NO x ), total dissolved nitrogen (TDN) and dissolved iron (Fe) of overlying water were examined. After incubation, O 2 and H 2 S profiles across the water-sediment interface were observed with microelectrodes. The element distributions in the upper sediments were tested as well. Results showed that DO and pH kept relatively stable during oxic period, while decreased significantly during anoxic period. Fh cappings decreased both DO and pH, and inhibited the release of FRP. No significant increments of FRP in overlying waters were observedduring anoxic period. Fh cappings prompted the releases of NH 4 + and TDN, while inhibited that of NO x .NH 4 + increased while NO x decreased during anoxic period. Fe(II) and TFe increased only in 3Fh, especially during anoxic conditions. Fh cappings increased O 2 and H 2 S concentrations across the water-sediment interfaces. TP and TN in the sediments decreased after capping, while TFe increased significantly. We concluded that 0.6 cm thickness of (496 g/m 2 ) Fh capping could sequestrate P, even experiencing redox conditions.

Spatial-mode-sorting (SPADE) receivers surpass Rayleigh’s criterion for in coherent imaging but are sensitive to nuisance parameters (e.g., misalignment). Our multistage detection strategy uses preliminary physical measurement(s) to build up required prior information for near-quantum-optimal, sub-diffraction imaging.

Quantum-enhanced sensing promises to improve the performance of sensing tasks using non-classical probes and measurements that require far fewer scene-modulated photons than the best classical schemes, thereby granting previously-inaccessible information about a wide range of physical systems. We propose a generalized distributed sensing framework that uses an entangled quantum probe to estimate a scene-parameter encoded within an array of phases, with a functional dependence on that parameter determined by the physics of the actual system. The receiver uses a laser light source enhanced by quantum-entangled multi-partite squeezed-vacuum light to probe the phases and thereby estimate the desired scene-parameter. The entanglement suppresses the collective quantum vacuum noise across the phase array. We report simple analytical expressions for the Cram\'er Rao bound that depend only on the optical probes and the physical model of the measured system, and we show that our structured receiver asymptotically saturates the quantum Cram\'er-Rao bound in the lossless case. Our approach enables Heisenberg limited precision in estimating a scene-parameter with respect to total probe energy, as well as with respect to the number of modulated phases. Furthermore, we study the impact of uniform loss in our system and examine the behavior of both the quantum and the classical Cram\'er-Rao bounds. We apply our framework to examples as diverse as radio-frequency phased-array directional radar, beam-displacement tracking for atomic-force microscopy, and fiber-based temperature gradiometry., Comment: MRG and CNG contributed equally to this work; 11 pages, 5 figures

Because of their unique photochemical and photophysical properties, luminescent lanthanide-based complexes have long captivated chemists. In recent years, the number of reports of luminescent lanthanide complex-based probes for monitoring of biological and environmental processes has dramatically increased, namely, because of their selectivity for particular analytes, lower limits of detection, and the fact that they allow monitoring of analytes in real time. Lanthanide-based probes need to be paired with an appropriate antenna/sensitizer to allow maximum energy transfer, with the antenna typically covalently attached to the stable lanthanide chelate. We have recently investigated "dark" lanthanide-based probes where the sensitizer is not covalently linked to the lanthanide chelate. Herein we report the use of a luminescent lanthanide-based probe system for the detection of Zn2+ ions based on the formation of a ternary complex between a "dark" terbium complex, lumazine, and Zn2+. The terbium(III)-based probe incorporates a 1,4,7,10-tetraazacyclododecane-1,4,7,10-triacetic acid macrocyclic chelator covalently attached to a cyclen moiety, which is the Zn2+ ion binding group. In the presence of Zn2+ ions and lumazine (a strongly UV-absorbing sensitizer), a 1:1:1 ternary complex forms. The resulting complex is highly luminescent and selective for Zn2+ ions over other cations of environmental significance. Furthermore, with a limit of detection of 1.2 μM, this probe can detect the level of chronic zinc(II) concentrations denoted by the U.S. Environmental Protection Agency.

A bimetallic terbium(III)/copper(II) complex (Tb-1·Cu2+) for the time-gated luminescent detection of hydrogen sulfide in aqueous samples is reported. The probe shows excellent selectivity towards HS− over various anions and cations, including the ions common to natural waterways and waste water samples, displaying a 73-fold increase in luminescence in the presence of sulfide. The probe exhibits extremely fast reaction times and a low limit of detection (130 nM). The probe was used to quantify sulfide in an industrial “sour water” sample, with the result in excellent agreement with those from two independent assay methods (methylene blue and AzMC).

The effects of pharmaceuticals on aquatic ecosystems are the subject of increasing environmental concern. Of particular interest are a suite of drugs known as selective serotonin reuptake inhibitors (SSRIs), commonly prescribed to treat depression. SSRIs are now detected in the environment worldwide, but their effects on ecosystems are not well understood. We conducted replicated experiments testing for an ecosystem effect of SSRIs in streams. We used artificial stream mesocosms to expose natural biofilms and aquatic insect communities to concentrations (20 µg/L) of fluoxetine or citalopram or a mix of both (totaling 40 µg/L). These concentrations are the lowest found to have an effect on aquatic invertebrates in other studies. Treatments suppressed gross primary production by 29% and community respiration by ≥43% on rock biofilms but did not affect algal biomass or whole-stream metabolism. A common group of dipteran midges emerged earlier in all SSRI treated streams compared with the controls. To...

We used highly realistic temperature treatments based on down-scaled global circulation models for 1990–2000 (control) and 2100 (warming treatment) to experimentally assess the impacts of altered temperature regimes on the emerging adults of aquatic insect communities. Experiments were run for 6 weeks and emerging adults of insects were identified and measured for length. There were clear responses to the warming treatment, but responses were taxa- and gender-specific. Males of mayfly Ulmerophlebia pipinna Suter 1986 (Leptophlebiidae) emerged faster under 2100 temperatures. This resulted in a change in the sex ratio that could compromise populations. Mean body size of some insects decreased under warming conditions, which is in agreement with the general hypothesis of reduced body size in response to climate change. However, the degree to which organism size was affected by temperature varied within and between taxa. These changes show the potential for changed temperature regimes to impact ecological systems at individual, population, and community levels. Changes in body size and species composition of emerging insects are likely to impact different levels in both the aquatic and terrestrial communities, for example through disruption of interactions between emerging insects and riparian predators which rely on those resources.

Passive imaging receivers that demultiplex an incoherent optical field into a set of orthogonal spatial modes prior to detection can surpass canonical diffraction limits on spatial resolution. However, these mode-sorting receivers exhibit sensitivity to contextual nuisance parameters (e.g., the centroid of a clustered or extended object), raising questions on their viability in realistic scenarios where prior information about the scene is limited. We propose a multistage detection strategy that segments the total recording time between different physical measurements to build up the required prior information for near quantum-optimal imaging performance at sub-Rayleigh length scales. We show, via Monte Carlo simulations, that an adaptive two-stage scheme that dynamically allocates recording time between a conventional direct detection measurement and a binary mode sorter outperforms idealized direct detection alone when no prior knowledge of the object centroid is available, achieving one to two orders of magnitude improvement in mean squared error for simple estimation tasks. Our scheme can be generalized for more sophisticated tasks involving multiple parameters and/or minimal prior information.

An in-depth study of the interaction of a trinuclear terbium(III)-dizinc(II) complex with an array of nucleotides differing in the type of nucleobase and number of phosphate groups, as well as cyclic versus acyclic variants, is presented. The study examined the nature of the interaction and the efficiency at which guanine was able to sensitize terbium(III) luminescence. Competitive binding and titration studies were performed to help establish the nature/mode of the interactions. These established that (1) interaction occurs by the coordination of phosphate groups to zinc(II) (in addition to uridine in the case of uridine monophosphate), (2) acyclic nucleotides bind more strongly than cyclic counterparts because of their higher negative charge, (3) guanine-containing nucleotides are able to sensitize terbium(III) luminescence with the efficiency of sensitization following the order guanosine monophosphate (GMP) > guanosine diphosphate > guanosine triphosphate because of the mode of binding, and (4) nucleoside monophosphates bind to a single zinc(II) ion, whereas di- and triphosphates appear to bind in a bridging mode between two host molecules. Furthermore, it has been shown that guanine is a sensitizer of terbium(III) luminescence. On the basis of the ability of GMP to effectively sensitize terbium(III)-based luminescence while cyclic GMP (cGMP) does not, the complex has been utilized to monitor the catalytic conversion of cGMP to GMP by a phosphodiesterase enzyme in real time using time-gated luminescence on a benchtop fluorimeter. The complex has the potential to find broad application in monitoring the activity of enzymes that process nucleotides (co)substrates, including high-throughput drug-screening programs.

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed wetlands. An important factor that controls DNRA in an aquatic ecosystem is the electron donor, commonly organic carbon (OC) or alternatively ferrous iron and sulfide. In this study, we investigated the role of natural organic carbon (NOC) and acetate at different OC/NO3− ratios and ferrous iron on the partitioning between DNF and DNRA using the 15N-tracer method in slurries from four constructed stormwater urban wetlands in Melbourne, Australia. The carbon and nitrate experiments revealed that DNF dominated at all OC/NO3− ratios. The higher DNF and DNRA rates observed after the addition of NOC indicates that nitrate reduction was enhanced more by NOC than acetate. Moreover, addition of NOC in slurries stimulated DNRA more than DNF. Interestingly, slurries amended with Fe2+ showed that Fe2+ had significant control on the balance between DNF and DNRA. From two out of four wetlands, a significant increase in DNRA rates (p

Environmental flows are a critical tool for addressing ecological degradation of river systems brought about by increasing demand for limited water resources. The importance of basin scale management of environmental flows has long been recognized as necessary if managers are to achieve social, economic, and environmental objectives. The challenges in managing environmental flows are now emerging and include the time taken for changes to become manifest, uncertainty around large-scale responses to environmental flows and that most interventions take place at smaller scales. The purpose of this paper is to describe how conceptual models can be used to inform the development, and subsequent evaluation of ecological objectives for environmental flows at the basin scale. Objective setting is the key initial step in environmental flow planning and subsequently provides a foundation for effective adaptive management. We use the implementation of the Basin Plan in Australia's Murray-Darling Basin (MDB) as an example of the role of conceptual models in the development of environmental flow objectives and subsequent development of intervention monitoring and evaluation, key steps in the adaptive management of environmental flows. The implementation of the Basin Plan was based on the best science available at the time, however, this was focused on ecosystem responses to environmental flows. The monitoring has started to reveal that limitations in our conceptualization of the basin may reduce the likelihood of achieving of basin scale objectives. One of the strengths of the Basin Plan approach was that it included multiple conceptual models informing environmental flow management. The experience in the MDB suggests that the development of multiple conceptual models at the basin scale will help increase the likelihood that basin-scale objectives will be achieved.

The regulation and management of chemical contaminants rarely use community‐ and ecosystem‐level endpoints, partly due to a lack of suitable methods. To overcome this limitation, we propose contaminant exposure substrata (CES), an adaptation of the widely used nutrient‐diffusing substratum method, to assess responses of biofilm communities to chemical contaminants in situ. We describe methods for using CES to assess effects on biofilm biomass, community structure, process rates, biofilm–consumer interactions and biofilm chemistry. We also provide equations to calculate the flux of soluble chemicals from CES and describe an approach to compare contaminant dose in CES assays to the contaminant dose encountered by biofilms in polluted surface waters. Data from four case studies demonstrate that CES can detect impairment of biofilm structure and function. The adaptability, simplicity and cost‐effectiveness of CES make them valuable tools to assess community‐ and ecosystem‐level responses to contaminants, suggesting potential for routine use and incorporation of data generated from such assays into contaminant regulation and management.

Two new fluorescent chemosensors have been designed and synthesised through functionalisation of a common 7-aminocoumarin precursor. One sensor features a di(2-picoyl)amine metal ion-binding moiety that allows for selective detection of Zn2+ ions over other common cations in aqueous solution, with the sensor exhibiting a 5.4-fold increase in fluorescence upon Zn2+ binding (limit of detection = 26 nM). The second sensor incorporates an aminophenyl group designed to react with highly reactive oxygen species (hROS). This sensor reacts with ClO− in preference to other ROS, exhibiting a 27-fold increase in fluorescence upon the addition of 150 equivalents of ClO− (limit of detection = 2 μM).

The storage and release of phosphorus by sediments can act as an important control on the formation of noxious blooms of cyanobacteria in lakes and estuaries. Here we studied the uptake and release of phosphorus associated with iron oxides within sediments of a lagoon system affected by recurring summer blooms of the cyanobacterium Nodularia spumigena. Using an ascorbate extraction, we observed deep pools of iron oxide associated phosphorus (P) at concentrations of ∼5 μmol g−1 dry sed to a depth of ∼20 cm. This pool rapidly decreased with the onset of water column anoxia, leading to an integrated release of ∼300 mmol of phosphorus m−2 of sediment over 3.5 months. Scaling this flux over the periodically anoxic area of the lake and over the period of an N. spumigena bloom (November–December 2011) gave a broad mass balance agreement with the increase in total phosphorus within the water column and exported from the lagoon. Over this period we estimated that P release from the sediment would have allowed ∼130–187 tonnes of nitrogen to be fixed which agrees with previous estimates of nitrogen fixation. Upon reoxygenation of the water column, a regeneration of the deep iron oxide associated phosphorus pool was observed. This deep dynamic pool of phosphorus was most likely mediated by the burrowing activity of the polychaete Capitella capitata which was observed at the study site. This study underscores the potential importance of sediments colonized by deeply irrigating fauna to become a significant source of phosphorus during water column anoxia.

Pharmaceuticals and personal care products (PPCPs) are ubiquitous in freshwater ecosystems worldwide and are recognized as contaminants of concern. Currently, contaminants of concern are classified for their persistence, bioaccumulation, and toxicity (PBT criteria). PPCPs are not classified as persistent organic pollutants (POPs), although some PPCPs share characteristics similar to POPs. For example, PPCPs are known to be pseudopersistent due to constant discharge into the environment, often at low concentrations. At commonly reported environmental concentrations, PPCPs are rarely toxic, but the ability of these compounds to disrupt ecological processes and functions in freshwater ecosystems is often overlooked. Herein we briefly summarize recent studies highlighting the potential ecological effects of PPCPs, including effects on key ecological processes (e.g. primary productivity and community respiration), and we propose that appropriate screening for harmful effects of PPCPs in surface waters should be expanded to include Ecologically Disrupting Compounds (EcoDC) in addition to the established PBT criteria.