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Environmental context Knowledge of the fate of selenium in estuaries receiving inputs from coal-fired power stations is essential as these environments are important nursery habitats for marine life and selenium has been shown to cause fish and bird mortality and sublethal effects including oedema, chromosomal aberrations and reproductive success. Understanding selenium cycling allows risk assessment to be undertaken and appropriate action to protect resident organisms. Abstract The fate of selenium (Se) inputs from coal-fired power station operations in a marine dominated estuary, Lake Macquarie NSW, is explored, as well as Se toxicity, including sublethal and population effects. Selenium is rapidly adsorbed to sediments, and food webs are based on benthic food sources. Selenium is remobilised from sediments by volatilisation and diffusional processes following bioturbation. It is then transferred into food chains via benthic microalgae, deposit feeders and filter-feeding organisms processing suspended sediments. Historically, Se has been found to accumulate in fish to levels above those considered safe for human consumption. After the remediation of a major ash dam in 1995, Se inputs to Lake Macquarie have declined, and the Se concentrations of sediments have also reduced partially due to the deposition of cleaner sediment but also due to the formation of volatile dimethyl selenide. Bioturbation of oxidised surface sediments also results in the release of inorganic Se. In response to decreases in sediment Se concentrations, molluscs and fish Se concentrations have also reduced below deleterious levels, with most fish now being safe for human consumption. Selenium cycling involves the transformation of inorganic species (Se0, SeII, SeIV, SeVI) in sediments and the water column to dimethylselenide and dimethyl diselenide by bacteria with the accumulation of organic Se species in plant detritus (selenomethionine) and animals (selenomethionine and selenocysteine). Dissolved Se concentrations in Lake Macquarie, except near ash dam inputs, have always been well below those that cause toxicity. There is evidence based on Se sediment-spiking studies, however, that Se is probably causing sublethal effects. When undertaking risk assessments of Se, careful consideration should be given to understanding the fate of Se inputs and remobilisation into food webs as not all systems act in accordance with published studies that generally have high Se concentrations in the water column and phytoplankton-based food webs.

Feral horses preferentially utilise aquatic landscape elements. Damage to stream banks by feral horses potentially degrades water quality and affects aquatic ecosystems. Despite the global predominance of horse activity in or near water, there is poor understanding of in-stream impacts. Motion-sensing cameras were used near subalpine streams to quantify frequency and behaviour of horses interacting with streams. Deployed turbidity loggers were used to indicate the presence of suspended sediment from interactions and to assess long-term (3 year) seasonal suspended sediment regime at sites with very small and large amounts of horse activity. In summer, 99.9% of large grazer interactions with streams were horses and we estimate 130 horse interactions per kilometre of stream per day, resulting in stream turbidity increases up to 100 NTU. Long-term turbidity at sites with greater riparian damage from horses was significantly greater than at control sites. Turbidity in horse-affected streams peaked at 50 times the national turbidity guideline and, in summer, averaged eight times the guideline. Suspended sediment leads to a high risk of loss of aquatic diversity and impairment of ecosystem function. Linear relationships between turbidity and riparian damage suggest that any level of horse presence affects subalpine waterways.

Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following significant rainfall events.

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

The Hawkesbury-Nepean River (HNR) is the largest catchment in the Sydney region and is undergoing unprecedented population growth. The HNR system receives a mix of anthropogenic inputs such as treated sewage, stormwater and agricultural runoff. Combined, these can diminish the ecological system health and pose potential concerns to human health. Of particular concern are inputs of untreated sewage, that can occur due to a range of different reasons including illegal point source discharges, failure of the sewerage network, and overloading of wastewater treatment plants during storm events. Here, we present findings of an intensive assessment across the HNR catchment where we used a weight-of-evidence (WOE) approach to identify untreated sewage contamination in surface waters against the background of treated effluent and diffuse inputs during post high flow conditions. Total nitrogen and phosphorus concentrations were used to assess treated effluent and diffuse inputs, and microbial analysis, including both culture-based traditional methods for E. coli and enterococci and qPCR analysis of Bacteroides and Lachnospiraceae, were used to assess raw sewage contamination. Despite a background of diffuse inputs from recent high flow events and the influence of treated wastewater, we found no gradient of faecal contamination along the HNR system or its tributaries. We observed two sites with evidence of untreated sewage contamination, where the human markers Bacteroides and Lachnospiraceae qPCR copy numbers were high. The biological and chemical approaches suggested these latter two hotspots originate from an industrial runoff source and possibly from a dry weather sewage leak. Our findings demonstrate the potential of a WOE approach in the assessment of human faecal signal in an urban river that can also pinpoint small sources of contamination as a strategy that can reshape the way monitoring is performed and the chemical end-points chosen to provide pertinent information on the potential risks to aquatic system health.

Climate change is impacting ecosystems worldwide. Estuaries are diverse and important aquatic ecosystems; and yet until now we have lacked information on the response of estuaries to climate change. Here we present data from a twelve-year monitoring program, involving 6200 observations of 166 estuaries along >1100 kilometres of the Australian coastline encompassing all estuary morphologies. Estuary temperatures increased by 2.16 °C on average over 12 years, at a rate of 0.2 °C year−1, with waters acidifying at a rate of 0.09 pH units and freshening at 0.086 PSU year−1. The response of estuaries to climate change is dependent on their morphology. Lagoons and rivers are warming and acidifying at the fastest rate because of shallow average depths and limited oceanic exchange. The changes measured are an order of magnitude faster than predicted by global ocean and atmospheric models, indicating that existing global models may not be useful to predict change in estuaries., Estuaries are diverse and important aquatic ecosystems, yet we lack information on their response to climate change. Here, the authors show that east Australian estuaries are warming and acidifying faster than predicted by ocean or atmospheric models; a trend that is magnified in shallow estuaries.

Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of ‘metal’ concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.

Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.

Sustainable management and conservation of the world’s oceans requires effective monitoring, evaluation and reporting. Despite the growing political and social imperative for these activities, there are some persistent and emerging challenges that marine practitioners face in undertaking these activities. In 2015, a diverse group of marine practitioners came together to discuss the emerging challenges associated with marine monitoring, evaluation and reporting, and potential solutions to address these challenges. Three emerging challenges were identified: (1) the need to incorporate environmental, social and economic dimensions in evaluation and reporting; (2) the implications of big data, creating challenges in data management and interpretation; and, (3) dealing with uncertainty throughout monitoring, evaluation and reporting activities. We point to key solutions to address these challenges across monitoring, evaluation and reporting activities: 1) integrating models into marine management systems to help understand, interpret, and manage the environmental and socio-economic dimensions of uncertain and complex marine systems; 2) utilising big data sources and new technologies to collect, process, store, and analyse data; and 3) applying approaches to evaluate, account for, and report on the multiple sources and types of uncertainty. These solutions point towards a potential for a new wave of evidence-based marine management, through more innovative monitoring, rigorous evaluation and transparent reporting. Effective collaboration and institutional support across the science–management–policy interface will be crucial to deal with emerging challenges, and implement the tools and approaches embedded within these solutions.

The urbanisation of coastal zones is a major threat to the health of global estuaries and has been linked to increased contamination (e.g. metals) and excess organic matter. Urban stormwater networks collect and funnel contaminants into waterways at point sources (e.g. stormdrains). Under dry, low flow conditions, these stormwater contaminants can accumulate in sediments over time and result in modifications to benthic sediment biogeochemical processes. To quantify these processes, this field study measured differences in benthic metabolism (CR, GPP, NEM) and sediment-water nutrient fluxes (NH3, NOx, PO4) associated with stormdrains (0 m, 200 m and 1000 m away) and increased water-retention (embayments vs channels). Significant changes to benthic metabolism were detected with distance from stormdrains, and with differences in water-retention rates, above natural spatial and temporal variation. Oxygen consumption was ∼50% higher at stormdrains (0 m) compared to 1000 m away and >70% higher at stormdrains (0 m) located in embayments compared to channels. Oxygen production also appeared to decrease with distance from stormdrains in embayments, but patterns were variable. These changes to benthic metabolism were of a magnitude expected to influence benthic nutrient cycling, but NH3, NOx and PO4 fluxes were generally low, and highly spatially and temporally variable. Overall, metal (Cu) contamination explained most of the variation in sediment biogeochemical processes between embayments and channels, while sediment grain size explained differences in fluxes with distance from stormdrains. Importantly, although there was evidence of increased productivity associated with stormdrains, we also detected evidence of early hypoxia suggesting that systems with legacy stormwater contaminants exist on a tipping point. Future work should investigate changes to sediment processes after a major rainfall event, when large and sudden inputs of potentially toxic contaminants occur. Monitoring benthic O2 fluxes could be a sensitive measure of ecological change under these conditions.

The essential biodiversity variables (EBV) framework was developed primarily to improve the detection of significant changes in global biodiversity. Its application at national level must support county-specific policy and management needs as well as allowing comparisons of estimates of biodiversity change between countries and their aggregation for reporting at regional, continental and global scales. Here we outline a process for prioritising biodiversity variables at national scale using the EBV framework. The process involves separately identifying candidate EBVs that are useful for tracking important changes in biodiversity in each major ecological feature in each ecoregion within a country. The list is then prioritised based on the proportion of ecological feature ecoregion combinations using each variable within and across terrestrial, marine and freshwater realms. We showcased this process in Australian state of New South Wales (NSW) using terrestrial, marine and freshwater ecoregions of the world as bioregional strata; vegetation formations as terrestrial ecological features, and broad aquatic ecosystem types as marine and freshwater ecological features. There was sufficient knowledge of ecological processes to identify useful variables for 85% of the ecological feature ecoregion combinations in NSW. Eleven candidate EBVs covering all six EBV classes, were useful in all three environmental realms. Our structured, stepwise approach to variable selection provides a transparent process for identifying important elements of ecological theory underpinning biodiversity monitoring within countries. Worldwide adoption of a process for prioritising biodiversity variables such as the one we propose here would help ensure consistency of national contributions to global biodiversity assessments.

There is growing interest in the role that seagrasses play as ‘blue carbon’ stores or sinks, and their potential to offset rising CO2 levels in the atmosphere. This study measured primary aspects of the carbon balance (biomass, community metabolism, dissolved organic carbon [DOC] fluxes, seston trapping) across the depth gradient in a Zostera muelleri meadow during the seasonal biomass minimum and maximum. Over the annual estimation, the meadow was neither a sink nor source of carbon, with inputs of seston (∼58% of total inputs) balanced by exports of wrack and DOC. The carbon sink represented by wrack export depends on the nature of the environment where the wrack accumulates; if it reaches subtidal sediments it will largely be remineralised over the annual cycle, whereas between 14 and 26% of the wrack may be preserved if the material is exported to terrestrial environments. The fate of DOC exuded by seagrasses is unknown due to a lack of knowledge about its composition and lability; however, a number of lines of evidence suggest that a large fraction of DOC is mineralised. The net community metabolism (NCM) of the meadow was balanced, indicating that photosynthetic O2 production balanced community respiration and/or the reoxidation of reduced compounds (sulphur and iron) in the rhizosphere. We suggest that a balanced NCM may be the preferred state for Zostera spp. and may limit their occurrence in environments where plants cannot balance the respiratory demand exerted by seston inputs. There was a close coupling between metabolism and biomass, which in turn is forced by antecedent light over the preceding 120 days (the time integration window for antecedent light that best predicted biomass). Increased metabolism with depth and seasonal variation in light is accompanied by a decrease in the above ground:below ground biomass ratio (AGB:BGB). This trend is suggested to be a morphological adaptation that balances the competing requirements of maintaining a neutral plant carbon balance across enrichment and light gradients. Our results suggest that Zostera muelleri may be most important as a ‘blue carbon’ store (i.e. carbon stored as biomass standing stock), which is therefore vulnerable to degradation if seagrasses are lost.

In contrast to Europe, the USA and South Africa, Australia has no specific, overarching federal legislation to underpin a nationally-coordinated framework for monitoring, assessing and reporting estuarine condition. This has resulted in a complex mosaic of diverse approaches and governance structures, hindering the ability to make inter-State comparisons. In this second part of a comprehensive three-part review, we present a systematic appraisal of current and impending approaches for measuring and reporting estuarine condition in each of Australia's States and Territories. A concise summary is provided in each case, supported by extensive appendices containing detailed accounts of relevant monitoring and reporting programs. We synthesise and evaluate this output at the State/Territory level, highlighting areas of improvement and major gaps.

Biomass and morphometrics of Zostera muelleri were monitored across depth, sediment type, and nutrient gradients in 2 coastal lakes (Tuggerah Lakes and Lake Macquarie) on the east coast of Australia. Tuggerah Lakes had significantly higher nutrient, chlorophyll a, and suspended sediment concentrations in the water column and significantly higher fine sediment fraction and sediment organic matter content. Seagrass above-ground biomass (AGB) was significantly greater in the mesotrophic Tuggerah Lakes, while below-ground biomass (BGB) was significantly greater in the oligotrophic Lake Macquarie, most likely reflecting the different nutrient status of the lakes. Light gradients were the primary control over total biomass, BGB, and shoot density across the study area. Although no general trends between light and AGB were found in this study, lakeand site-specific relationships between light, AGB:BGB ratios, and leaf area index were seen to vary along gradients in nutrient status and sediment quality. These trends are thought to be driven by morphological acclimation that allows seagrass to maintain favourable plant carbon and net community metabolism balances while minimising sulphide exposure. Seagrass depth limits were best predicted by a multilinear model including Secchi depth, fine sediment fraction, and organic matter content, suggesting that negative feedbacks associated with sulphide exposure in the rhizosphere increased the minimum light requirements of this species. Our results support an emerging view that sediment quality and nutrient status are important controls over minimum light requirements in seagrasses. Morphological plasticity can moderate but not completely compensate for the negative impacts of sediment properties on minimum light requirements.

So as to assess how emerging science and new tools can be applied to study multiple stressors at a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was organised on 10–12 September 2014 at the Sydney Institute of Marine Sciences, Sydney, Australia. The present paper discusses the limitations of the current risk-assessment approaches and how multiple stressors at large scales can be better evaluated in ecological risk assessments to inform the development of more efficient and preventive management policies based on adaptive management in the future. A future risk-assessment paradigm that overcomes these limitations is presented. This paradigm includes cultural and ecological protection goals, the development of ecological scenarios, the establishment of the relevant interactions among species, potential sources of stressors, their interactions and the development of cause–effect models. It is envisaged that this will be achievable through a greater integration of approaches among different scientific disciplines and through the application of new and emerging tools such as 'big data', ecological modelling and the incorporation of ecosystem service endpoints.

Small intermittently open lagoons are the most common type of estuary in NSW but the majority of them have no seagrass despite apparently suitable physical and water quality conditions. This paper describes the consequences of a catastrophic drought on trophic structure of primary producers in two intermittently open coastal lagoons that have negligible anthropogenic stress. It examines the roles of various factors influencing primary producers and hence ecosystems in intermittently open lagoons, in both short and long timeframes. Two estuarine lagoons with undisturbed catchments (Durras Lake and Nadgee Lake) experienced decadal scale shift in production dominance from benthic to pelagic and back to benthic following a catastrophic reduction in water levels during drought conditions. Water quality deteriorated significantly (high turbidity, ammonia and chlorophyll) after loss of macrophytes and then re-established to “normal” conditions within 2–3 years. Despite this, macrophytes did not re-appear for 6–7 years. The high proportion of intermittent estuaries with no seagrass was concluded to be a consequence of recruitment limitation, and estuarine morphology shapes the ecology of these lagoons, rather than an inherent inability for seagrass and macrophytes to live in the estuaries. Recruitment of macrophytes required coincident occurrence of multiple rare stochastic events, making chance an important aspect of re-establishment of biological assemblages in disturbance driven ecosystems. Conceptual models derived for northern hemisphere, riverine, surface-water fed estuaries tend to dominate thinking about estuaries in the literature, but are clearly inappropriate for typical southern-hemisphere low-flow and groundwater-dominated intermittent estuaries. Climate change is likely to increase the frequency of occurrence of the conditions that led to the loss of seagrass and macrophytes and therefore potentially reduce the number of intermittent estuaries in NSW with macrophytes. In the systems described, maintenance of regional seagrass populations is reliant on the stochastic survival of some populations to act as source populations. Climate change is predicted to make what are currently “extreme” events more common. This could, in turn, mean that the likelihood of the sort of loss described in our two cases studies could become more common, increasing the proportion of systems with no seagrass and progressively closing the window of opportunity for external recruitment. Potentially, this could lead to localised extinction of seagrass in intermittent estuaries.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article., Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

This chapter describes the distribution of key seagrass species in the estuarine-nearshore coastal (ENC) continuum of the south-east region of Australia. We explore the potential influences of hydrodynamics (e.g. tidal currents, wave energy), estuary entrance dynamics (recruitment) and water quality, in addition to light, as primary stressors on seagrass processes and resilience. Despite primary controls exerted by light over seagrass distribution, there are significant areas of euphotic sediments in south-east region that are not colonised by seagrasses. In addition, seagrasses commonly display high degrees of inter-annual variability in coverage which cannot be explained solely by variations in light. We describe the main ecosystem types within the region, and demonstrate how the temporal and spatial gradients in hydrodynamic and water quality stressors (hence light climate), and the availability of suitable substrates for seagrass are controlled by the physical setting or geomorphology of the ecosystem. The opportunistic species Zostera muelleri is the most abundant species within the region, primarily occupying the highly dynamic estuarine niche. We provide a focus on Zostera muelleri to illustrate the direct positive/negative impacts of hydrodynamic, water quality and estuary entrance morphology stressors on seagrass metabolism and morphology across light gradients.

Historical ecology can teach us valuable lessons on the processes and drivers of environmental change that can inform future monitoring priorities and management strategies. Environmental data to study environmental history, however, is often absent or of low quality. Even when studying changes occurring during the last few decades, monitoring efforts are scarce due to logistical and cost limitations, leaving large areas unassessed. The aim of this study is to evaluate the use of estuarine water colour as an indicator of historical environmental change in catchments. Water colour change was assessed in estuaries in Australia from 1987 to 2015 using satellite remote sensing. Random points were selected for each estuary and applied to the Australian Geoscience Data Cube (based on Landsat images) to obtain reflectance data through time. We propose a framework where (i) water colour is used to detect historical changes in catchments using generalised additive models, (ii) possible stressors and pressures driving those changes are evaluated using other available historical data, and (iii) lessons learned inform appropriate monitoring and management actions. This framework represents a novel approach to generate historical data for large-scale assessments of environmental change at catchment level, even in poorly studied areas.

Microbially mediated biogeochemical processes are crucial for climate regulation and may be disrupted by anthropogenic contaminants. To better manage contaminants, we need tools that make real‐time causal links between stressors and altered microbial functions, and the potential consequences for ecosystem services such as climate regulation. In a manipulative field experiment, we used metatranscriptomics to investigate the impact of excess organic enrichment and metal contamination on the gene expression of nitrogen and sulfur metabolisms in coastal sediments. Our gene expression data suggest that excess organic enrichment results in (i) higher transcript levels of genes involved in the production of toxic ammonia and hydrogen sulfide and (ii) lower transcript levels associated with the degradation of a greenhouse gas (nitrous oxide). However, metal contamination did not have any significant impact on gene expression. We reveal the genetic mechanisms that may lead to altered productivity and greenhouse gas production in coastal sediments due to anthropogenic contaminants. Our data highlight the applicability of metatranscriptomics as a management tool that provides an immense breadth of information and can identify potentially impacted process measurements that need further investigation.

Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment.

Environmental indicators must have a predictable relationship with stressors to be of value in ecological assessments. We evaluated the information provided by commonly implemented monitoring indicators as a means of assessing of the level of ecological impact experienced by coastal lagoons in New South Wales, Australia. Existing data for environmental variables in coastal lagoons were correlated with independent estimates of catchment disturbance. There were few relationships between the monitoring variables (particularly water chemistry) and nutrient loads and catchment land use. Data from NSW catchments and lagoons were compared to analogous data from published northern hemisphere studies and it was clear that stressor variables were up to one to two orders of magnitude smaller in NSW, potentially explaining the lack of relationships with recognised indicators. Our study has highlighted the importance of using a range of indicators to assess trends in ecological condition of an estuarine ecosystem, particularly where stressor levels are not great. Using water quality as the sole means of determining lagoon condition was simply inadequate in NSW lagoons. We recommended that ecological outcome indicators such as algal abundance (macro and micro) and turbidity were most likely to show interpretable patterns at low to moderate nitrogen loadings (

Monitoring of estuary condition is essential due to the highly productive and often intensely impacted nature of these ecosystems. Assessment of the physico-chemical condition of estuaries is expensive and difficult due to naturally fluctuating water quality and biota. Assessing the vigour of ecosystem processes is an alternative method with potential to overcome much of the variability associated with physico-chemical measures. Indicators of estuary condition should have small spatial and temporal variability, have a predictable response to perturbation and be ecologically relevant. Here, we present tests of the first criterion, the spatio-temporal variability of a potential ecoassay measuring the rate of scavenging in estuaries. We hypothesised that the proposed scavenging ecoassay would not vary significantly among A) sites in an estuary, B) trips separated by weeks, or C) days in a trip. Because not all habitats are present in all estuaries, this test was undertaken in two habitats. When conducted over bare substrate there were occasional significant differences, but no discernible patterns, within levels of the experiment. When conducted over vegetated substrate, days within a trip did not vary significantly, but later trips experienced greater scavenging. This scavenging ecoassay shows potential as a tool for assessing the condition of estuarine ecosystems, and further exploration of this protocol is warranted by implementation in estuaries across a gradient of anthropogenic stress.

Environmental decision-making applies transdisciplinary knowledge to deliver optimal outcomes. Here we synthesise various aspects of seagrass ecology to aid environmental decision-making, management and policy. Managers often mediate conflicting values and opinions held by different stakeholders. Critical to this role is understanding the drivers for change, effects of management actions and societal benefits. We use the diversity of seagrass habitats in Australia to demonstrate that knowledge from numerous fields is required to understand seagrass condition and resilience. Managers are often time poor and need access to synthesised assessments, commonly referred to as narratives. However, there is no single narrative for management of seagrass habitats in Australia, due to the diversity of seagrass meadows and dominant pressures. To assist the manager, we developed a classification structure based on attributes of seagrass life history, habitat and meadow form. Seagrass communities are formed from species whose life history strategies can be described as colonising, opportunistic or persistent. They occupy habitats defined by the range and variability of their abiotic environment. This results in seagrass meadows that are either transitory or enduring. Transitory meadows may come and go and able to re-establish from complete loss through sexual reproduction. Enduring meadows may fluctuate in biomass but maintain a presence by resisting pressures across multiple scales. This contrast reflects the interaction between the spatial and temporal aspects of species life history and habitat variability. Most management and monitoring strategies in place today favour enduring seagrasses. We adopt a functional classification of seagrass habitats based on modes of resilience to inform management for all seagrass communities. These concepts have world-wide relevance as the Australian case-studies have many analogues throughout the world. Additionally, the approach used to classify primary scientific knowledge into synthesised categories to aid management has value for many other disciplines interfacing with environmental decision-making.

An attempt is made to synthesize the geological properties, water quality attributes and aspects of the ecology of south-east Australian estuaries so as to provide a framework for addressing coastal management issues. The approach is based on the underlying causal factors of geology and morphology and more immediate environmental factors (e.g. salinity and sediments) which are associated with ecological distributions, species richness and fisheries catch. This ‘ broad brush ’ approach seeks to maximize reality and generality, albeit at the expense of precision and local variability in individual circumstances. It disregards small-scale ecological patterns as noise. Unlike in the Northern Hemisphere, conditions in temperate Australia are characterized by irregular flood and fire regimes that strongly influence estuary hydrology and nutrient inputs. Three main types of estuary (tide-dominated, wave-dominated and intermittently closed) are recognized based on geological criteria and having particular entrance conditions that control tidal exchange. Four zones (marine flood-tidal delta, central mud basin, fluvial delta and riverine channel/alluvial plain) are also recognized common to each type of estuary. These zones correspond to mappable sedimentary environments in all estuaries and have characteristic water quality, nutrient cycling/primary productivity signatures and ecosystems. The ecology of a zone is modified by (a) estuary type which determines the salinity regime; (b) stage of sediment filling (evolutionary maturity) which controls the spatial distribution/size of the zones; and (c) impacts of various forms of development. By using the zones/habitats as a common currency among all estuaries, it is possible to link ecological aspects such as species richness and commercial fisheries production so as to compare different estuaries or within-estuary zones.

This paper examines concentrations of trace contaminants in oysters placed in inshore and offshore waters before and after the change to offshore disposal of sewage near Sydney, NSW, Australia. The ability to compare inshore and offshore concentrations before and after the event allows the formulation of unconfounded conclusions about the impact of sewage on the availablity of trace contaminants in the coastal environment and the effect of the change in the method of disposal of Sydney's sewage on the availability of those contaminants. The data show clearly that the diversion of sewage from nearshore to offshore areas has resulted in a significant drop in the concentrations of organochlorines in oysters deployed near sewage outfalls in the nearshore region. In offshore areas, there were no differences detected among regions prior to the commissioning of deepwater outfalls. In the post commissioning period there were a number of instances when trace metal concentrations in the regions were different from each other, but these differences were not correlated with proximity to the sewage outfalls nor was a particular metal consistently elevated, so it was concluded that the causes of difference were not related to the presence of the sewage outfalls. This study has demonstrated that oysters were useful indicators of trace metal and organochlorine contamination of marine waters; that relatively high levels of contamination of inshore waters near sewage outfalls prior to deepwater sewage disposal were reduced, to be not different from other parts of Sydney's coastline after the commencement of deepwater discharge, and that there was no concommitant increase in accumulation of contaminants in offshore waters. Further, preliminary indications are that Sydney's coastal waters are not very heavily contaminated by trace contaminants in comparison to areas of NSW with much lower levels of development. Concentrations of organochlorines are, however, high in comparison to data from similarly developed areas of the USA.

A comprehensive monitoring program (the EMP) was put in place to assess the environmental impacts of deepwater sewage discharge off Sydney (NSW, Australia). The EMP involves studies of environmental impacts on fish and macroinvertebrate community structure, on water quality in the ocean and at beaches, and of accumulation of contaminants in marine organisms and sediments. Comprehensive computer models of sewage plume behaviour were developed. The studies have shown that, since nearshore sewage discharge ceased, the extent and frequency of contamination of beaches by faecal bacteria has decreased with only small increases offshore, and there is little evidence of nutrient enrichment of offshore waters or of accumulation of contaminants in surface sediments near the outfalls. There has been a significant decrease in contamination of biota by trace metals and organochlorine compounds in nearshore areas, but no measurable increase in contaminants in organisms in offshore waters. Although no consistent pattern was observable, changes in offshore fish and invertebrate communities have occurred, manifested as increases and decreases in abundance. This intensive multidisciplinary study has allowed the accurate determination of the environmental impact of the deepwater sewage outfalls, and provides information to be used in the planning of any future discharges.

Global losses of seagrasses and mangroves, eutrophication-driven increases in ephemeral algae, and macrophyte invasions have impacted estuarine detrital resources. To understand the implications of these changes on benthic ecosystem processes, we tested the hypotheses that detrital source richness, mix identity, and biomass influence benthic primary production, metabolism, and nutrient fluxes. On an estuarine muddy sandflat, we manipulated the availability of eight detrital sources, including mangrove, seagrass, and invasive and native algal species that have undergone substantial changes in distribution. Mixes of these detrital sources were randomly assigned to one of 12 treatments and dried detrital material was added to seventy-two 0.25 m2 plots (n = 6 plots). The treatments included combinations of either two or four detrital sources and high (60 g) or low (40 g) levels of enrichments. After 2 months, the dark, light, and net uptake of NH4+, dissolved inorganic nitrogen, and the dark efflux of dissolved organic nitrogen were each significantly influenced by the identity of detrital mixes, rather than detrital source richness or biomass. However, gross and net primary productivity, average oxygen flux, and net NOX and dissolved inorganic phosphorous fluxes were significantly greater in treatments with low than with high detrital source richness. These results demonstrate that changes in detrital source richness and mix identity may be important drivers of estuarine ecosystem performance. Continued impacts to estuarine macrophytes may, therefore, further alter detritus-fueled productivity and processes in estuaries. Specific tests that address predicted future changes to detrital resources are required to determine the consequences of this significant environmental problem. © 2013 Blackwell Publishing Ltd.

An industrial accident resulted in a spillage of aldrin onto an estuarine beach at Hardys Bay, New South Wales. Samples of water and sediment were taken 3 weeks later to measure the level of contamination resulting from the spill. The abundances of some intertidal biota were also determined at the site of the spillage and in other uncontaminated areas. Three weeks after the spill, samples of water were not contaminated by aldrin but samples of sediment from the surface in the vicinity of the drain contained aldrin. In comparison to uncontaminated locations the abundances of crustacea were greatly reduced in the vicinity of the drain but abundances of polychaetes were not significantly different. The field data on the relative susceptibility of the two groups of animals agrees well with laboratory derived LC50 data for crustacea and polychaetes. The study suggests that degree of contamination of water and sediment may not always be an accurate reflection of acute impact on biota, and that different components of the biota can show different reactions to the presence of a toxic chemical.

Field experiments were done to determine the rates of uptake and depuration of chlordane, dieldrin, heptachlor epoxide, PCBs, DDT, DDD and DDE in Sydney rock oysters (Saccostrea commercialis). Oysters from a clean source were placed in a contaminated location and concentrations of organochlorines determined in samples collected at a number of times during the deployment. After 209 days (which was long enough for equilibrium to have been reached), the oysters were moved to an uncontaminated location and concentrations of the compounds were determined at various times. Mean weight of the oysters changed during the study, but not in any consistent manner. Mean content of lipids did not change significantly during the study. Detectable concentrations of all organochlorines were present after 3 days. Times to equilibrium and biological half-lives were calculated using kinetic models. Generally, rates of depuration were of the same order, but slower, than rates of uptake. There was a strong correlation between percentage lipid and organochlorine concentration, but little difference in times to equilibrium and biological half-lives derived from concentrations per wet weight and those per weight of lipid. The experiments show that times to equilibrium for each compound differ and that this should be taken into account when designing a programme to monitor these compounds.