Harmful algal blooms of Karenia brevis (Dinophyceae) are a global anomaly, occurring in one location worldwide, causing severe marine and acute human impacts via brevetoxins (BTXs). During 2025 an unprecedented mass marine mortality occurred in South Australia, across an area of ~20,000 km2, persisting for >12 months, resulting in the deaths of ~106 marine animals of >600 taxa, with human health impacts. Using custom metabarcoding, long-read sequencing and targeted qPCR, we characterized the microalgal assemblage. Karenia cristata dominated over the sampling area, in an assemblage with four other Karenia species with varied abundances spatially and temporally. High abundances of K. cristata appeared in the austral autumn, and hydrodynamic processes appear to have entrained cells coastward in the semi-enclosed seas. We isolated the species and characterized it using light and electron microscopy, liquid chromatography-mass spectrometry and toxicity assays. We show that the rare and little-known K. cristata produces substantial amounts of BTXs with a profile (BTX-2, BTX-3, BTX-B5) different from that of K. brevis, with toxicological effects. These findings reveal a BTX-producing Karenia that causes substantial detrimental marine ecosystem impacts, representing an emerging international threat with unknown consequences given changing ocean conditions.

Human-induced stressors are impacting the oceans and reducing the biodiversity of marine ecosystems. The many stressors affecting marine environments do not act in isolation. However, their cumulative impact is difficult to predict. Most of the available methods for quantifying cumulative impacts on marine ecosystems sum the impact of individual stressors to estimate cumulative impact. We demonstrate how experimental evidence from interacting stressors can be accounted for in cumulative impact assessments. We adapted a widely used additive model to incorporate nonadditive stressor interactions into a marine spatially explicit cumulative impact assessment for seagrasses. We combined experimental data on the impact of multiple stressors with spatial data on stressor intensity to test whether stressor interactions impact seagrasses in a case study region in South Australia. We also assessed how uncertainty about cumulative impacts changes when uncertainty in stressor interactions is included in the impact mapping. The results from an additive spatial cumulative impact assessment model were compared with results from the model incorporating interactions. Cumulative effects from the interaction model were more variable than those produced by the additive model. Five of the 15 stressor interactions that we tested produced impacts that significantly deviated from those predicted by an additive model. Areas of our study region that showed the largest discrepancies between the additive and interactive outputs were also associated with higher uncertainty. Our study demonstrates that the inclusion of stressor interactions changes the pattern and intensity of modeled spatial cumulative impact. Additive models have the potential to misrepresent cumulative impact intensity and do not provide the opportunity for targeted mitigation measures when managing the interactive effects of stressors. Appropriate inclusion of interacting stressor data may have implications for the identification of key stressors and the subsequent spatial planning and management of marine ecosystems and biodiversity.

The eastern Great Australian Bight (GAB) is a significant marine ecosystem, featuring a range of marine mammals and large pelagic fish including blue whales, sharks and tuna. Previous research has classified the region as generally oligotrophic, apart from late austral summer months when seasonal upwelling triggers phytoplankton blooms in the region. Based on multi-year field observations, this study analysed the interannual and interdecadal variability of the plankton community structure in this region. Pigment data indicate that nano- and pico-phytoplankton generally dominated the phytoplankton community structure with averages of 39% and 30% of the total biomass, including a relatively large proportion of nanophytoplankton (cryptophytes, haptophytes and prasinophytes) with cell sizes <5 µm, not resolved in microscopic cell counts. Nano- and pico-phytoplankton alone contributed ∼0.3 mg/m3 to the chlorophyll-a signal and therefore sustained an overall mesotrophic environment year-round. Distinct diatom blooms developed during the upwelling season within concentrated subsurface layers where chlorophyll-a concentrations increased to >1 mg/m3, characterising eutrophic conditions. The biomass of diatoms increased from <10% to ∼30% of total biomass. Diatom blooms coincided with relatively high abundances of three dominant zooplankton species (Oithona similis, Penilia avirostris and Microsetella norvegica) and/or the dinophyta Noctiluca scintillans, but events of high zooplankton abundance also occurred outside the upwelling season. The observational findings also show the occurrence of significant subsurface phytoplankton blooms in late spring, not reported before, that may also contribute to the ecosystem functioning of the region.

The eastern rock lobster (Sagmariasus verreauxi) inhabits the east coast of Australia from southern Queensland to the South Australian border including Tasmania, with the highest abundances found in New South Wales. Changes in strength, duration, and intensity of the eastern Australian current have expanded the species range southward but until recently, records of the species in western regions of south-eastern Australia were rare. Here, we report the first ever verified records of S. verreauxi in the northern zone rock lobster fishery of South Australia, which are the most westerly records ever documented in terms of overall distribution for this species. We hypothesise that two westward flowing systems, the offshore Flinders current and the inshore coastal current may be possible mechanisms for larval transport.

Understanding how phytoplankton respond to their physical environment is key to predicting shifts in bloom dynamics under a changing climate. This research investigates phytoplankton dynamics in a seasonal coastal upwelling system of the eastern Great Australian Bight (GAB), South Australia, using > 10 years of in-situ mooring and CTD observations together with > 18 years of satellite and wind data. Earlier studies concluded that upwelling in the region is driven by interactions between upwelling-favourable winds associated with synoptic weather events during austral summer months (Jan-March) and the formation of a pool of nutrient -rich shelf-bottom water on the Lincoln Shelf, known as the Kangaroo Island (KI) Pool. Surface phytoplankton blooms in the upwelling centre, which form off the southern tip of the Eyre Peninsula, are characterized by chlorophyll-a levels of-1-2 mg/m3. Our analysis of satellite chl-a data indicates the absence of surface phytoplankton blooms in the upwelling centre in more than a third of all upwelling seasons, despite the existence of statistically similar upwelling-favourable winds. The KI Pool is located-100 km upstream from the upwelling centre in a marine region that generally displays very low surface phytoplankton levels. Analysis of water-column data indicates strong interannual variability the KI Pool that is correlated with the intensity of surface phytoplankton blooms in the upwelling centre. The analysis also reveals the existence of substantial (-1 mg/m3 chl-a) subsurface phytoplankton blooms at depths between-20 and 70 m in shallower waters of the Lincoln Shelf, where nutrient-rich shelf-bottom water of the KI Pool reaches into the euphotic zone. Our data suggest that subsurface phytoplankton blooms, forming at depths that cannot be detected by satellites, represent a major driver of the upwelling ecosystem of the eastern GAB.

Biological dinitrogen (N2) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N2 fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N2 fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and 15N2 stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N2 fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N2 fixation (10–64 nmol L−1 d−1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N2 fixation (2 nmol L−1 d−1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO3/NO2 were significantly correlated with the highest N2 fixation rates, suggesting that N2 fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO4 concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N2 fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N2 fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N2 fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.

Many demersal marine fish species depend on a dispersive larval stage that connects geographically discrete sub-populations. Understanding connectivity between these sub-populations is necessary to determine stock structure, which identifies the appropriate spatial scale for fishery management. Such connectivity is poorly understood for King George whiting (Sillaginodes punctatus; Perciformes) in South Australia's gulf system, even though spawning grounds and nursery areas are adequately defined. In response to declines in commercial catches and estimated biomass, this study aimed to determine the most important spawning grounds and nursery areas to recruitment, and the connectivity between them. A biophysical model was seeded with particles according to the distribution and density of eggs throughout the spawning area in 2017 and 2018. Despite inter-annual differences in the origins of particles, dispersal pathways and predicted settlement areas remained consistent between years. Predicted settlement was generally highest to nursery areas only short distances from regional spawning grounds, consistent with previous hydrodynamic models. However, the model also predicted that spawning in one region could contribute to recruitment in an adjacent region later in the spawning season, which aligned with the breakdown of thermohaline fronts at the entrance of each gulf. The connectivity between spawning grounds and nursery areas predicted by the model is supported by spatio-temporal patterns in the otolith chemistry of pre-flexion larvae and settled juveniles. Consequently, the most parsimonious explanation is that the populations of King George whiting in South Australia's gulf system constitute a single, panmictic stock, which has implications for fishery management.

Marine aggregates formed through particle coagulation, large ones (>0.05 cm) also called marine snow, make a significant contribution to the global carbon flux by sinking from the euphotic zone, impacting the Earth’s climate. Since aggregate sinking velocity and carbon content are size-dependent, understanding the physical mechanisms controlling aggregate size distribution is fundamental to determining the biological carbon pump efficiency. Theoretical, laboratory and in-situ studies of flocculation have suggested that turbulence in the benthic boundary layer is important for aggregate formation and destruction, but the small number of field observations has limited our understanding of the role of turbulence on aggregation processes in the ocean surface layer away from energetic boundaries. Using simultaneous field observations of turbulence and aggregates, we show how aggregate formation, destruction, morphology and size distribution in the ocean surface layer (10–100 m) are mediated by interactions between turbulence and aggregate concentration. Our findings suggest that turbulence enhances aggregate formation up to a critical turbulent kinetic energy dissipation rate of 10 −6 (W kg −1 ), above which the smallest turbulent eddies limit aggregate size.

In the Australian spanner crab (Ranina ranina) fishery, management and industry are looking for improvements to the existing indicators of stock abundance. Prior research linked several oceanographic indices to the catchability of spanner crabs; however, it was unclear whether nearshore (e.g. river-runoff) or region-specific oceanographic features (e.g. eddies and the East Australian Current) are responsible for these effects on catch rates. Using satellite remote sensing and fishery-independent survey data, we analysed the influence of oceanographic and environmental indices on spanner crab catch rates in southern Queensland. Outputs from Generalised Additive Models (GAM) show that catch rates exhibit a large amount of variability between different regions of the fishery, with highest catch rates at fishing grounds within 40 km from the shelf break. Offshore oceanic waters, transported into various regions by different oceanographic processes, were linked to an increase in catch rates. Lower concentrations of surface chlorophyll a were also correlated with higher catch rates, but only in survey regions exposed to the effects of the Fraser Gyre and at the mouth of bays. Overall, results highlighted that the effects of environmental indices on catch rates were not homogeneous across the fishery. Rather, relationships were linked to region-specific (< 100 km), highly dynamic coastal and oceanographic features that dominate different survey regions. Outcomes from this work show that the spatial variability of oceanographic features should be taken into consideration before incorporating oceanographic indices in fishery stock assessment models.

During daily fishing operations, spanner crab Ranina ranina catch rates can fluctuate substantially, but the environmental drivers responsible for these fluctuations largely remain unresolved. Earlier research suggests that spanner crab catchability increases with strengthening currents, but uncertainties surround the magnitude of the measured current speeds and, consequently, their relationship with catch rates. Here, we explore the effects of bottom currents on spanner crab catch rates in South East Queensland, Australia. Using generalized additive mixed modeling, our results indicated that strengthening current speeds increased catch rates until reaching approximately 0.15 m/s, at which point the catch rates began to gradually decline. Results from a general linear regression model also showed that between fishing periods carried out on the same day, catch rates increased or decreased concurrently with current speeds. We conclude that bottom current speed should be considered in future stock assessment models. Better understanding the processes responsible for changes in bottom current speed will enable more accurate estimates of spanner crab population densities in the Australian fishery and will benefit the economic efficiency of commercial crabbing operations. Furthermore, future studies that investigate the effects of current speed on catch rates for other crab species should consider differences in locomotory characteristics and how they may impact the foraging efficiency of crabs under different flow conditions.

The size at which sexual maturity is reached is a key population parameter used to guide the setting of minimum legal size limits in fisheries. Understanding spatial and temporal variations in size at maturity is fundamental to management because the relationship between size at maturity and minimum legal size limits affects the fraction of the mature population biomass that is harvested, and resulting egg production, larval settlement and recruitment. This study measured the size at maturity of female Southern Rock Lobster (Jasus edwardsii) across South Australia between 1991 and 2015 in relation to known oceanographic characteristics, surface and subsurface temperature data, and relative changes in lobster abundance. There was pronounced north to south spatial variation in estimates of size at maturity. Larger average size at maturity was recorded in warmer north-western areas of the fishery relative to the cooler waters of the south-east. Estimates of size at maturity also differed over 25 years across the fishery. However, the nature of temporal responses varied spatially, and were more consistent with variations in surface and subsurface water temperature at local-scales than changes in lobster density. In the well-mixed waters of the north-western, western and south-eastern parts of the fishery, relatively high rates of increase in sea-surface temperature and size at maturity were recorded since 1991, indicating that size at maturity may be responding to ocean warming associated with global climate change. In more central parts of the fishery, contrasting temporal signals in sea-surface temperature (positive) and bottom temperature (negative) indicated increases in upwelling strength over the study period, and formation of a bottom cold pool below a warm surface layer, with corresponding decreases in size at maturity recorded. The spatio-temporal changes in size at maturity measured in this study highlight the need for oceanographic information to be integrated into future stock assessment models to enhance harvest strategy development, allow timely adaptive management decisions and increase the resilience of fisheries to the impacts of climate change.

Species catchability is an important parameter used to help optimise stock assessment modelling and the economic efficiency of commercial fishing operations. Previous studies have shown several physical oceanographic parameters, including ambient temperature, waves and currents, affect the catchability of spanner crabs (Ranina ranina) throughout the Indo-Pacific. Most notably in the Australian fishery, where oceanographic processes vary over space and time, a positive relationship between bottom boundary layer temperature (BBLT) and catch rates was observed. Here, we aimed to better understand how localised oceanographic processes affected this relationship in the southernmost South-East Queensland (SEQ) sector of the Australian fishery at seasonal and short temporal scales. Our results show cooler BBLT, upwelling-favourable alongshore wind stress and increased catch rates occurred during mating season in austral spring. At the end of austral summer, BBLT began warming, downwelling-favourable winds were dominant, and catch rates declined around the post-moult period. Outputs from the generalised linear models (GLMs) that separated these effects in each season show that, at shorter temporal scales, daily catch rates also increased with episodic BBLT cooling and upwelling-favourable alongshore wind stress, but only during austral autumn and winter. These new findings suggest that region-specific, short-term and seasonal variability of oceanographic processes responsible for changes in BBLT play an important role in influencing the catchability of spanner crabs. We suggest that the effects of region-specific physical oceanographic processes must be considered in future work when investigating the catchability of commercially important fisheries species fished over large spatial domains.

To assist with developing an understanding of the nutrient supply dynamics in the Great Australian Bight (GAB) the vertical turbulent nitrate flux was calculated at stations along two cross-shelf transects using direct measurements of turbulence and nitrate concentrations. Coincident hydrographic profiling conducted at the onset of the summertime upwelling season revealed upwelling onto the shelf in the eastern GAB (eGAB) and downwelling at the shelf slope in the central GAB (cGAB). Under these conditions, examination of the strength of competing vertical temperature and salinity gradients using the Turner angle suggested a high potential for double diffusive convective mixing. However, corresponding estimates of the mixing efficiency derived from microstructure profiling indicated turbulence was the main mixing process driving vertical fluxes across the region. The average upward nitrate flux between the surface mixed layer depth(MLD) and the base of the euphotic layer (92 m depth) was O(10(-6)-10(-5) ) mmol N m(-2) s(-1) in the cGAB, with the peak flux observed at the upper-slope station (similar to 400 m total water depth). In the eGAB, the magnitude of flux estimates at the shelf-slope and offshore stations were similar to those measured in the cGAB. An enhanced nitrate flux O(10(-4) ) mmol N m(-2) s(-1) was observed on the shelf in the eGAB (similar to 100 m total water depth) as the result of enhanced turbulence and an increased vertical nitrate gradient. Application of Redfield stoichiometry suggests vertical turbulent nitrate fluxes play a significant role in supporting up to 50% of the primary production in the GAB. We hypothesize that mixing processes resulting from interactions between upwelled and downwelled water masses and new water masses formed on the shelf during summer play an important role in maintaining the bands of subsurface chlorophyll a maxima observed below the MLD at the nitricline during periods of strong stratification. The snapshot provided by this study, emphasizes the need to better understand the variability and influence of mixing processes on nutrient supply and productivity across the GAB marine ecosystem.

We used a suite of physical, chemical and biological datasets to assess the influence of upwelling/downwelling on enrichment and primary productivity in shelf waters of the eastern Great Australian Bight at seasonal and event scales. Results showed that the length of an upwelling season did not dictate its intensity or productivity, and that long seasons were not necessarily the most intense or productive. At the event scale, temperature and salinity were found to be better indicators of enrichment of shelf waters than wind stress, with temperatures < 15 °C and salinities < 35.6 psu associated with elevated concentrations of NOx (> 2 µm) and bursts of primary productivity (up to ∼ 700 mg C m−2 d−1). A key finding of this study was the importance of differentiating between upwelling events and enrichment events. The former occurred in the early upwelling season (November-December) and were demonstrated by periods of positive wind stress. The latter only occurred in the late upwelling season (January – April), and saw water with temperatures < 15 °C and salinities < 35.6 psu drawn onto the shelf and into the euphotic zone where it was available for primary producers. We used this information to develop a conceptual model which describes five different meteorological/oceanographic scenarios that occur in the eastern GAB, and their potential influence on enrichment and primary productivity, and hypothesise that total ecosystem productivity depends on the combination of these scenarios that occurs in the region in a given season/year. It is our contention that the early upwelling season represents a preconditioning period that plays a critical role in characterising late season enrichment events, and drives overall seasonal productivity.

Marine aggregates are ubiquitous particles formed from the accretion of smaller biogenic and non-biogenic components. Visible aggregates, known as marine snow, are typically in the 0.5 to few mm size range. Aggregates are well recognised as hotspot of microbial and planktonic activities. Aggregates formation is an important pathway for transferring materials and carbon flux from surface to the deep ocean. Because aggregate sinking velocity and carbon mass content is size dependent, understanding the physical mechanism controlling aggregate size distribution is fundamental to determining the biological carbon pump efficiency. Turbulence is a physical mechanism in the aggregates formation and destruction. However, the relative roles of turbulence in aggregates formation and destruction have not been fully tested in observational studies. In this study, we analysed simultaneous in-situ observations of turbulence and aggregate in the various aquatic systems. A microstructure profiler, TurboMAP-L, was used to collect shear data and a digital still logger camera was used to collect images of aggregates. Digital images were subsequently used to determine aggregates abundances and size distributions. Direct comparison of turbulence intensity and aggregate size distributions show that turbulence below 𝜀=10-6[W/kg] enhances aggregation, increasing average particle size; greater turbulence causes particle breakup, limiting the average maximum aggregate size and decreasing the slopes of size distributions. This indicates the role of turbulence controlling aggregate size distributions. We also present fluorescence data collected by TurboMAP-L and focus on difference of aggregates size distributions among different aquatic systems.

Satellite remote sensing data can produce global environmental data and is easily accessible and widely used by the scientific and non-scientific community. However, to use satellite data, it is important to know its limitations and how it validates against in situ measurements for the different regions. Here, field measurements of chlorophyll-a concentration and euphotic depth within the Great Australian Bight, Gulf St Vincent and Spencer Gulf were used to validate ocean colour products derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite. The field data include in situ and in vivo chlorophyll-a concentration, which were compared against MODIS chlorophyll-a products derived from three algorithms (OC3M, Carder, and Garver-Siegel-Maritorena (GSM)), as well as euphotic depth measurements derived from photosynthetically active radiation (PAR) profiles, which were compared against two MODIS euphotic depth products (derived semi-analytically and from surface chlorophyll-a). The OC3M product performed well in open waters, with errors below the 35% NASA accepted limit, but it overestimated chlorophyll-a values in shallow (in situ euphotic depth were robust, with errors lower than 20%. MODIS products showed weaker or no significant relationships to in situ measurements in the Eastern Great Australian Bight. This is thought to be due to the summertime subsurface upwelling pool that is characteristic of the area. Based on these results, the OC3M product provides the most reliable estimates of chlorophyll-a, and is recommended for further applications of MODIS imagery, if the limitations in shallow waters are taken into account. Alternatively, the GSM product could be a better option if the algorithm were locally adjusted. Changes in the sampling methodology to improve the algorithms are discussed. Derived euphotic depth products can be used with confidence in applying MODIS products for monitoring water clarity, ecosystem health or primary productivity in the region.

Data from stock assessment surveys, published research and climate sensors were linked to model the interaction between fishing, physical-oceanographic processes and spatial patterns of larval settlement for western king prawn [Penaeus (Melicertus) latisulcatus]. This information was used to evaluate the trade-off between larval recruitment and catch during fishing periods that demand high prices but coincide with spawning. Total rates of larval settlement were maximized when tidal currents and atmospheric physical-forcing components were coupled with simulations of larval swimming behaviour under average gulf temperatures. Average gulf temperatures sustained longer larval durations and increased larval settlement rates by over 12% compared with warmer gulf conditions simulated under a scenario of global warming. Reproductive data coupled with outputs from the biophysical model identified consistent inter-annual patterns in the areas contributing to larval settlement success. Areas located in the north-east, and central-west of the fishery, consistently contributed to over 40% of all larvae reaching a settlement in each year. Harvest sensitivity analyses indicated that changes in the spatial patterns of pre-Christmas fishing could lead to improvements in overall rates of the larval settlement while maintaining or improving the levels of catch. Future studies to refine the model inputs relating to physical processes, larval behaviour and mortality rates for P.latisulcatus coupled with surveys of juvenile prawn abundance to ground truth the modelled predictions, would allow stock recruitment relationships to be more closely examined and inform adaptive management of the fishery in the future.

Spencer Gulf is a large ( ca 22 000 km 2 ), shallow (<60 m water depth) embayment with active heterozoan carbonate sedimentation. Gulf waters are metahaline (salinities 39 to 47‰) and warm‐temperate ( ca 12 to −28°C) with inverse estuarine circulation. The integrated approach of facies analysis paired with high‐resolution, monthly oceanographic data sets is used to pinpoint controls on sedimentation patterns with more confidence than heretofore possible for temperate systems. Biofragments – mainly bivalves, benthic foraminifera, bryozoans, coralline algae and echinoids – accumulate in five benthic environments: luxuriant seagrass meadows, patchy seagrass sand flats, rhodolith pavements, open gravel/sand plains and muddy seafloors. The biotic diversity of Spencer Gulf is remarkably high, considering the elevated seawater salinities. Echinoids and coralline algae (traditionally considered stenohaline organisms) are ubiquitous. Euphotic zone depth is interpreted as the primary control on environmental distribution, whereas seawater salinity, temperature, hydrodynamics and nutrient availability are viewed as secondary controls. Luxuriant seagrass meadows with carbonate muddy sands dominate brightly lit seafloors where waters have relatively low nutrient concentrations ( ca 0 to 1 mg Chl‐a m −3 ). Low‐diversity bivalve‐dominated deposits occur in meadows with highest seawater salinities and temperatures (43 to 47‰, up to 28°C). Patchy seagrass sand flats cover less‐illuminated seafloors. Open gravel/sand plains contain coarse bivalve–bryozoan sediments, interpreted as subphotic deposits, in waters with near normal marine salinities and moderate trophic resources (0·5 to 1·6 mg Chl‐a m −3 ) to support diverse suspension feeders. Rhodolith pavements (coralline algal gravels) form where seagrass growth is arrested, either because of decreased water clarity due to elevated nutrients and associated phytoplankton growth (0·6 to 2 mg Chl‐a m −3 ), or bottom waters that are too energetic for seagrasses (currents up to 2 m sec −1 ). Muddy seafloors occur in low‐energy areas below the euphotic zone. The relationships between oceanographic influences and depositional patterns outlined in Spencer Gulf are valuable for environmental interpretations of other recent and ancient (particularly Neogene) high‐salinity and temperate carbonate systems worldwide.

The ecology of microbial assemblages inhabiting classical (positive) estuaries has been well documented. However, we know relatively little about the microbial ecology of inverse (negative) estuaries; which exhibit different physical and hydrodynamic properties, including oligotrophy and hypersalinity. We investigated the dynamics of bacterioplankton communities in Spencer Gulf, an inverse estuary in temperate South Australia. We characterised patterns in the overall diversity and composition of the resident microbial assemblage, and tested the hypothesis that pelagic nitrogen-fixing bacteria (diazotrophs) could be an important functional group in the nutrient limited waters of the region. Prokaryotic and diazotrophic communities were evaluated using 16S ribosomal DNA and nifH amplicon tag pyrosequencing, respectively. Significant heterogeneity in microbial community composition and diazotrophic population structure was observed, which was driven by shifts in the relative importance of temperate vs. subtropical and oceanic vs. coastal ecotypes of Cyanobacteria throughout the inverse estuary. The globally significant unicellular cyanobacterium, UCYN-A 'Candidatus Atelocyano-bacterium thalassa', was the dominant diazotrophic phylotype. Temperature, chlorophyll a and nitrogen availability were all significant drivers of bacterioplankton dynamics within the gulf. These results demonstrate the heterogeneous microbiology of inverse estuaries, indicating that specific abiotic and biotic characteristics select for discrete microbial communities, and that pelagic nitrogen fixation may be important in this temperate oligotrophic system.