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Bottom trawling and eutrophication are large stressors that are critically coupled. Here we show, using a before‐after control‐effect design, the significant reduction in denitrification as a result of experimental bottom trawling in a shallow coastal system. Trawl disturbance destroys the complex three‐dimensional redox structures in surface sediments that maximize denitrification potential, resulting in up to a 50% reduction in net denitrification. The decrease in net denitrification also increased after each trawling event suggesting a declining resilience to trawling and eutrophication. Bottom trawling occurs at such a large scale that it could result in significant amounts of nitrogen being retained on the continental shelf. As such, impacts on the global ocean nitrogen cycle and associated eutrophication should be counted among the many negative consequences of extensive seafloor trawling.

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.

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.

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.

Jellyfish often form blooms that persist for weeks to months before they collapse en masse, resulting in the sudden release of large amounts of organic matter to the environment. This study investigated the biogeochemical and ecological effects of the decomposition of jellyfish in a shallow coastal lagoon in New South Wales, Australia. Catostylus mosaicus carrion was added to the surface of shallow sub-tidal sediments and biogeochemical parameters and macrofaunal abundance immediately below the jellyfish carrion were measured over three days. Sediment plots without jellyfish served as controls. Sediment oxygen demand and carbon and nitrogen efflux increased by up to 60-fold in the jellyfish plots, compared to control plots, and dissolved organic nutrient fluxes were more sustained than in previous studies due to the use of fresh rather than frozen biomass. The decomposing jellyfish progressively altered sediment redox conditions, indicated by an increase in porewater iron (II) and sulfide concentrations measured by high-resolution in situ diffusive samplers. Abundance of some macrofaunal taxa in the jellyfish plots decreased relative to controls, however, the abundance of a carnivorous gastropod, which was presumably feeding on the carrion, increased in the jellyfish plots. While jellyfish carrion may be a food source for some macrofauna, low oxygen conditions coupled with the accumulation of toxic dissolved sulfides in the near-surface sediments may explain the overall change in the macroinfaunal community. Refereed/Peer-reviewed

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.

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.

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.

Seagrass habitat is strongly constrained by light availability. Decline in benthic light due to anthropogenic activities (e.g. eutrophication, dredging and catchment modification) is a major threat to seagrass ecosystems, both within Australia and internationally. Even in pristine conditions, light available to seagrasses can be highly variable on timescales ranging from seconds to years. This chapter outlines the three primary mechanisms which enable seagrass to adapt to and/or resist temporary light deprivation: (1) consumption of accumulated carbon; (2) reduction in rates of growth and carbon loss; and (3) increased efficiency of radiation capture and usage. The capacity to withstand severe light deprivation ranges from only two weeks for small, colonising seagrass species such as Halophila ovalis , to beyond two years for large, persistent species such as Posidonia sinuosa. This “tolerance time” depends on the magnitude and timing of the light deprivation, current environmental conditions (e.g. temperature and sediment sulphides) as well as preceding conditions. This chapter proposes a simple conceptual model for seagrass resilience to temporary light reduction , combining both resistance (the capacity of seagrass to survive the light deprivation event), and the capacity to recover once the disturbance ends. Data is synthesized for several potential indicators of seagrass resistance to light reduction.

Oxygen flux between aquatic ecosystems and the water column is a measure of ecosystem metabolism. However, the oxygen flux varies during the day in a “hysteretic” pattern: there is higher net oxygen production at a given irradiance in the morning than in the afternoon. In this study, we investigated the mechanism responsible for the hysteresis in oxygen flux by measuring the daily pattern of oxygen flux, light, and temperature in a seagrass ecosystem (Zostera muelleri in Swansea Shoals, Australia) at three depths. We hypothesised that the oxygen flux pattern could be due to diel variations in either gross primary production or respiration in response to light history or temperature. Hysteresis in oxygen flux was clearly observed at all three depths. We compared this data to mathematical models, and found that the modification of ecosystem respiration by light history is the best explanation for the hysteresis in oxygen flux. Light history-dependent respiration might be due to diel variations in seagrass respiration or the dependence of bacterial production on dissolved organic carbon exudates. Our results indicate that the daily variation in respiration rate may be as important as the daily changes of photosynthetic characteristics in determining the metabolic status of aquatic ecosystems.

In this study we quantified nitrate (NO3−) reduction (denitrification, anammox and DNRA) and N2O production in sediments and epibiont communities associated with Sydney Rock Oyster (Saccostrea glomerata) farming. In sediments beneath an active suspended oyster farm, DNRA accounted for 98% of NO3− reduction with rates of up to 169 ± 45 μmol N m−2 h−1. Much of this DNRA was fuelled by NO3− derived from nitrification. Reference sediments had significantly lower DNRA rates of 83.8 ± 28.2 μmol N m−2 h−1, however this constituted 96% of the sites total NO3− reduction. Fatty acid analysis showed that sediment organic matter was more labile in the oyster impacted sediments, facilitating subtle shifts in sediment oxygen demand which increased the Fe2+ availability with respect to the reference sediments. The difference in DNRA rate between the sites was attributed to autotrophic oxidation of soluble Fe2+ in sediments underlying the oyster cultures. DNRA was absent in the oyster shell epibiont communities and rates of anammox and denitrification were lower than in the sediments. Production of NH4+ from the oysters and their associated epibionts was larger than DNRA and reached a rate of 206.2 μmol N m−2 h−1. Nitrous oxide production rates were generally low compared to other aquaculture systems and the net flux of N2O for the combined oyster cultivation system (i.e. sediments plus epibionts) was negative, i.e. there was N2O consumption in the sediments beneath the oysters. Overall, subtropical suspended oyster farming systems favour inorganic N retention over N loss.

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.

Benthic biogeochemistry and macrofauna were investigated six times over 1 year in a shallow sub-tropical embayment. Benthic fluxes of oxygen (annual mean −918 μmol O2 m−2 h−1), ammonium (NH4 +), nitrate (NO3 −), dissolved organic nitrogen, dinitrogen gas (N2), and dissolved inorganic phosphorus were positively related to OM supply (N mineralisation) and inversely related to benthic light (N assimilation). Ammonium (NH4 +), NO3 − and N2 fluxes (annual means +14.6, +15.9 and 44.6 μmol N m−2 h−1) accounted for 14, 16 and 53 % of the annual benthic N remineralisation respectively. Denitrification was dominated by coupled nitrification–denitrification throughout the study. Potential assimilation of nitrogen by benthic microalgae (BMA) accounted for between 1 and 30 % of remineralised N, and was greatest during winter when bottom light was higher. Macrofauna biomass tended to be highest at intermediate benthic respiration rates (−1,000 μmol O2 m−2 h−1), and appeared to become limited as respiration increased above this point. While bioturbation did not significantly affect net fluxes, macrofauna biomass was correlated with increased light rates of NH4 + flux which may have masked reductions in NH4 + flux associated with BMA assimilation during the light. Peaks in net N2 fluxes at intermediate respiration rates are suggested to be associated with the stimulation of potential denitrification sites due to bioturbation by burrowing macrofauna. NO3 − fluxes suggest that nitrification was not significantly limited within respiration range measured during this study, however comparisons with other parts of Moreton Bay suggest that limitation of coupled nitrification–denitrification may occur in sub-tropical systems at respiration rates exceeding −1,500 μmol O2 m−2 h−1.

Climatic variables, water quality, benthic fluxes, sediment properties, and infauna were measured six times over an annual cycle in a shallow sub-tropical embayment to characterize carbon and nutrient cycling, and elucidate the role of pelagic–benthic coupling. Organic carbon (OC) inputs to the bay are dominated by phytoplankton (mean 74%), followed by catchment inputs (15%), and benthic microalgae (BMA; 9%). The importance of catchment inputs was highly variable and dependent on antecedent rainfall, with significant storage of allochthonous OC in sediments following high flow events and remineralization of this material supporting productivity during the subsequent period. Outputs were dominated by benthic mineralization (mean 59% of total inputs), followed by pelagic mineralization (16%), burial (1%), and assimilation in macrofaunal biomass (2%). The net ecosystem metabolism (NEM = production minus respiration) varied between −4 and 33% (mean 9%) of total primary production, whereas the productivity/respiration (p/r) ranged between 0.96 and 1.5 (mean 1.13). Up to 100% of the NEM is potentially removed via the demersal detritivore pathway. Dissolved inorganic nitrogen (DIN) inputs from the catchment contributed less than 1% of the total phytoplankton demand, implicating internal DIN recycling (pelagic 23% and benthic 19%) and potentially benthic dissolved organic nitrogen (DON) fluxes (27%) or N fixation (up to 47%) as important processes sustaining productivity. Although phytoplankton dominated OC inputs in this system, BMA exerted strong seasonal controls over benthic DIN fluxes, limiting pelagic productivity when mixing/photic depth approached 1.3. The results of this study suggest low DIN:TOC and net autotrophic NEM may be a significant feature of shallow sub-tropical systems where the mixing/photic depth is consistently less than 4.

Denitrification, N-fixation, and dissolved inorganic and organic fluxes of nitrogen (N) and phosphorus (P) were measured in each of the major benthic habitat types of a shallow oligotrophic sub-tropical coastal system, and N and P budgets were constructed to quantify the importance of each habitat to N and P cycling in the whole ecosystem. The productivity/respiration (p/r) ratio (trophic status) of the habitats was an important control on the rates, direction (uptake, efflux) and composition (dissolved inorganic N (DIN), dissolved organic N (DON), N2) of N fluxes across the sediment–water interface, with an efflux below p/r = 1.5 and an uptake above p/r = 1.5. The Zostera Seagrass Community was the most important habitat for N loss via net N2 effluxes (denitrification; 48%). Denitrification rates in seagrass were higher than those previously measured in temperate regions, most likely due to greater availability of NH4 + for coupled nitrification–denitrification. Yabby Shoals (sub-tidal shoals inhabited by burrowing shrimp, Trypaea australiensis) accounted for the second largest loss of N via denitrification, the largest recycling of DIN and dissolved inorganic P (DIP; statistically significant only during the dark in summer) across the sediment–water interface and the second largest uptake of DON (statistically significant only in summer). This study highlighted that shallow subtropical coastal systems have a complex mosaic of benthic habitats and that some less ‘iconic’ habitats (i.e. non-seagrass) also make an important functional contribution that controls the flow of N and P through the whole ecosystem.

The major benthic habitats in a shallow oligotrophic sub-tropical coastal system were mapped, benthic productivity and respiration were measured seasonally (summer, winter) in each open water habitat, and an annual carbon budget was constructed using measured, modelled and literature fluxes to estimate the functional importance of each major benthic habitat to the whole ecosystem. Stable Zostera Seagrass Communities covered 16% of the open water system but made little contribution to whole system metabolism. In contrast, ephemeral Halophila Seagrass Communities covered only 8% of the open water system but contributed 46% of the net productivity (p). The less ‘iconic’ Inter- and Sub-tidal Pimpama Shoals also only had a small areal extent (10%) but accounted for 50% of the net benthic production. Similarly, Yabby Shoals only covered 27% of the open water system but accounted for 89% of the net respiration (r). Budget estimates suggest that lateral import of organic matter, most likely tidally transported phytoplankton trapped in seagrass beds, across the Broadwater boundaries was required to balance the carbon budget if any reasonable estimate of burial was invoked. However, budget errors make it difficult to distinguish this import from zero. This study demonstrated that shallow subtropical coastal systems have a complex mosaic of benthic habitats, and that some of the less ‘iconic’ habitats (i.e. non-seagrass, non-mangrove) also make an important functional contribution that controls the flow of energy and nutrients through the whole ecosystem and determines the net ecosystem metabolism and possible exchanges with adjacent systems.

Denitrification efficiency [DE; (N2 − N/(DIN + N2 − N) × 100%)] as an indicator of change associated with nutrient over-enrichment was evaluated for 22 shallow coastal ecosystems in Australia. The rate of carbon decomposition (which can be considered a proxy for carbon loading) is an important control on the efficiency with which coastal sediments in depositional mud basins with low water column nitrate concentrations recycle nitrogen as N2. The relationship between DE and carbon loading is due to changes in carbon and nitrate (NO3) supply associated with sediment biocomplexity. At the DE optimum (500–1,000 µmol m−2 h−1), there is an overlap of aerobic and anaerobic respiration zones (caused primarily by the existence of anaerobic micro-niches within the oxic zone, and oxidized burrow structures penetrating into the anaerobic zone), which enhances denitrification by improving both the organic carbon and nitrate supply to denitrifiers. On either side of the DE optimum zone, there is a reduction in denitrification sites as the sediment loses its three-dimensional complexity. At low organic carbon loadings, a thick oxic zone with low macrofauna biomass exists, resulting in limited anoxic sites for denitrification, and at high carbon loadings, there is a thick anoxic zone and a resultant lack of oxygen for nitrification and associated NO3 production. We propose a trophic scheme for defining critical (sustainable) carbon loading rates and possible thresholds for shallow coastal ecosystems based on the relationship between denitrification efficiency and carbon loading for 17 of the 22 Australian coastal ecosystems. The denitrification efficiency “optimum” occurs between carbon loadings of about 50 and 100 g C m−2 year−1. Coastal managers can use this simple trophic scheme to classify the current state of their shallow coastal ecosystems and for determining what carbon loading rate is necessary to achieve any future state.

Isotope pairing (IP) and N2:Ar techniques for measuring sediment denitrification were compared in muddy sediments in a shallow sub-tropical embayment. At a concentration of 100 µM 15 NO 3 - (our experimental conditions), IP greatly underestimated denitrification, compared to N 2:Ar, in low-respiration sediments subject to bioturbation, where denitrification produced via coupled nitrifica- tion-denitrification (Dn) dominates overall denitrification. Consistent with this underestimation was the higher N2 flux measured using N2:Ar ratios, accounting for more of the stochimetrically predicted N mineralisation. We suggest that this underestimation is primarily due to non-homogenous mixing of the added 15 NO3 - with the endogenous 14 NO3 - in the sediment, associated with differentials in the rate of diffusion of 15 NO3 - across mucus linings in burrow structures versus rates of 14 NO3 - supply from nitri- fiers in the burrow walls. Strong support for this hypothesis was provided by the relationship between the methods discrepancy and polychaete biomass (r 2 = 0.99; p = 0.001), and the almost complete removal of the methods discrepancy when the upper heterogenous sediment layer that contained the burrow structures was experimentally removed. Due to a significant increase in potential denitrifica- tion sites in association with burrow structures, this effect can potentially cause a large underestima- tion of denitrification (up to 85%) using the IP technique. Our data show no benefit in longer pre- incubation times, suggesting that this effect may represent a fundamental limitation of the IP method in the sediments of oligotrophic (low carbon loading) systems. As such, the N2:Ar flux technique rep- resents a more realistic estimation of net denitrification in sediments with low organic carbon contents and low respiration rates and significant bioturbation. Most importantly, the present study also demon- strated that methodological comparisons need to be made over a range of environmental conditions.

We examined the impact of a 1:3 year return period flood on benthic and pelagic coupling in the river-dominated sub-tropical Brunswick Estuary. The flood had a significant impact on the study site flushing it with freshwater, reducing the flushing time 0.6 days, increasing nutrient concentrations in the water column and scouring the sediment surface. In the three weeks post-flood the benthic and pelagic systems alternated between being coupled and un-coupled via dissolved, particulate and living material pathways. Immediately post-flood benthic and pelagic coupling via the deposition of phyto-detritus and viable algal cells was reduced due to the scouring of the top sediment layers, and benthic respiration and productivity and NH4+ effluxes all decreased correspondingly. In contrast, benthic and pelagic coupling was enhanced via the uptake and denitrification of NO3− due to elevated NO3− concentrations in the water column. Some of the NO3− consumed by the sediments may have also been converted to DON. Two weeks post-flood benthic and pelagic coupling was significantly enhanced via the deposition of phyto-detritus and viable algal cells associated with a phytoplankton bloom in the water column. This increased supply of phyto-detritus and viable algal cells rapidly increased benthic respiration and productivity and NH4+ efflux. The depletion of water column DIN by the phytoplankton bloom resulted in a de-coupling of the benthic and pelagic systems via the uptake and denitrification of NO3−. However, benthic and pelagic coupling was enhanced via the uptake of NH4+ by benthic microalgae. Three weeks post-flood the phytoplankton bloom had collapsed and the coupling between the benthic and pelagic systems via the deposition of phyto-detritus and living algal cells had diminished. Again benthic and pelagic coupling was enhanced via the uptake and denitrification of NO3− due to elevated NO3− concentrations in the water column associated with the recycling of bloom material. Overall the sediments became less heterotrophic (increasing benthic productivity/respiration ratio) following the flood. Floods can cause rapid and complex changes in the coupling between benthic and pelagic systems in sub-tropical estuaries.

We examined temporal variability in benthic metabolism and nitrogen (N) cycling in the subtropical Brunswick Estuary, Australia from December 2000 to December 2002. Benthic metabolism was tightly coupled to the production of labile carbon (C) in the water column (phytodetritus) and temperature, both of which increased in summer, resulting in increased rates of benthic metabolism and a shift to sulfate reduction. C : N ratios of remineralized material showed a consistently low return of N relative to ‘‘Redfield’’-type material over the 2-yr study period (up to 84 : 1 and averaging 31 : 1). The highest remineralized C : N ratios occurred at a sediment CO2 productivity/ respiration of ;0.4, which corresponds to maximum respiration and maximum productivity, and also when watercolumn dissolved inorganic nitrogen concentrations were lowest, reflecting potential N limitation. The ‘‘missing N’’ was most likely assimilated by heterotrophic bacteria and autotrophic benthic microalgae (BMA). Extracellular organic carbon extruded by the BMA and subsequently decomposed may also account for some of the high remineralized C : N ratios. Net N2 effluxes were controlled by a complex interaction between the supply of NO from 2 3 the water column and nitrification, the supply and decomposition of labile C, benthic productivity, and macrofauna abundance. A N mass balance for the sediment over the 2-yr study period showed that a significant proportion of the mineralized nitrogen may have been removed from the microbial loop and passed up to the metazoan levels of the food chain. About 22% of the remineralized N was permanently removed via denitrification. This active competition for limited N resources between heterotrophs, autotrophs, and chemoautotrophs appears to be a mechanism by which N-limited oligotrophic subtropical estuaries tightly recycle and conserve N. The metabolism of benthic communities is a central component of the nutrient cycling and overall productivity of shallow coastal ecosystems. Much of the carbon decomposition in shallow coastal ecosystems occurs in bottom sediments through heterotrophic-mediated processes (Hammond et al. 1985), and the associated release of nutrients can provide a large proportion of the nitrogen and phosphorus required by pelagic communities (Boynton and Kemp 1985; Cowan and Boynton 1996). Bottom sediments can also be a sink for nutrients through the burial of carbon (C), nitrogen (N), and phosphorus; the loss of carbon through CO2 efflux; and the loss of N through denitrification. Denitrification (the reduction of NO through NO to nitrous oxide [N2O] and 22 32

The seagrass Zostera muelleri Irmisch ex Asch. is abundant in estuaries in Australia and is under pressure from coastal developments. We studied sulfide intrusion in Z. muelleri along a gradient of anthropogenic impact at five stations in the Wallis Lake estuary, Australia. Results showed differences in sediment biogeochemical conditions, seagrass metrics as well as nutrient content and sulfide intrusion along the gradient from the lower estuary (affected) to the lagoon (unaffected). Sulfide intrusion was driven by complex interactions and related to changes in seagrass morphology and sediment biogeochemistry and was modified by the exposure to wind and wave action. The sediments in the lower estuary had high contributions from phytoplanktonic detritus, whereas the organic pools in the lagoon were dominated by seagrass detritus. Despite high concentrations of organic matter, sulfide intrusion was lower at stations dominated by seagrass detritus, probably because of lower sulfide pressure from the less labile nature of organic matter. Porewater diffusive gradients in thin-film (DGT) sulfide samplers showed efficient sulfide reoxidation in the rhizosphere, with high sulfur incorporation in the plants from sedimentary sulfides being likely due to sulfate uptake from reoxidised sulfide. This is a unique adaptation of Z. muelleri, which allows high productivity in estuarine sediments.

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.

Aquatic ecosystems are under threat from multiple stressors, which vary in distribution and intensity across temporal and spatial scales. Monitoring and assessment of these ecosystems have historically focussed on collection of physical and chemical information and increasingly include associated observations on biological condition. However, ecosystem assessment is often lacking because the scale and quality of biological observations frequently fail to match those available from physical and chemical measurements. The advent of high-performance computing, coupled with new earth observation platforms, has accelerated the adoption of molecular and remote sensing tools in ecosystem assessment. To assess how emerging science and tools can be applied to study multiple stressors on a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was held on 10–12 September 2014 at the Sydney Institute of Marine Sciences, Australia. Here we introduce a conceptual framework for assessing multiple stressors across ecosystems using emerging sources of big data and critique a range of available big-data types that could support models for multiple stressors. We define big data as any set or series of data, which is either so large or complex, it becomes difficult to analyse using traditional data analysis methods.

The process of sulfide oxidation in acid sulfate soils (ASS) is complex, involving the formation of numerous oxidation products. In this study the sulfide oxidation process was examined in 2 ASS materials over a period of 36 days using laboratory incubation experiments. Both ASS materials experienced substantial sulfide oxidation and acidification during incubation. The oxidation of pyrite was the primary cause of acidification in these ASS materials. Although a decrease in magnetic susceptibility (χ) over the initial 4 days of incubation suggested the rapid oxidation of ferromagnetic iron monosulfide greigite (Fe3S4), the total acid volatile sulfur (SAV) fraction increased in concentration by an order of magnitude over the initial 8 days of incubation. Oxygen (O2) concentration profiles indicated the presence of anoxic conditions in the centre of the incubating materials even after 16 days of exposure to the atmosphere enabling SAV formation to occur. The oxidation of the SAV fraction did not result in substantial acidification. A large proportion of the water-soluble iron released by sulfide oxidation was precipitated as iron oxides and hydroxides. Sulfate (SO42–) was the dominant sulfur species produced from sulfide oxidation in both ASS materials, although water-soluble SO42– was a poor indicator of the extent of sulfide oxidation. The sulfoxyanion intermediates, thiosulfate (S2O32–) and tetrathionate (S4O62–), were detected only in the early stages of incubation, with minimal amounts being detected after the initial 4 days. The relative abundance of these 2 intermediate sulfur species appeared to be dependent on the soil pH, with S4O62– dominating S2O32– in the more acidic ASS material (i.e. pH