Coral community data Heron Island Great Barrier Reef 1962-2016.

Here we describe benthic composition data derived from benthic photoquadrats collected over 41 surveys between 1962 and 2016 at four sites on Heron reef, at the southern end of Australia's Great Barrier Reef, to assess change in coral composition over time. Surveys have often been annual, in a few years sub-annual, and the longest gap is six years. A subset of the data from two sites with the most complete records has been fully processed to allow the size of all individual colonies, and changes in species composition and cover, to be tracked over time. The taxonomy in these quadrats has been carefully checked for internal consistency, and is generally at the species level. A second subset has been processed, but has not been through full quality control, while a third subset exists as images only. This is the longest, 56 years, regular photographic record of coral cover in existence, and provides a valuable temporal contrast dating back in time to more recent studies of greater geographic extent and/or resolution.

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia.

Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.

A controlled aquarium system and approach to study the role of sponge-bacteria interactions using Aplysilla rosea and Vibrio natriegens.

Sponge-bacteria interactions are very important due to their ecological and biological significance. To understand the impact of interactions between sponges and bacteria (both associated with and external to sponges) on sponge-associated microbial diversity, sponge metabolite profiles and bioactivity, we used a controlled aquarium system and designed an experimental approach that allows the study of sponge-bacteria interactions in a well-defined manner. To test the feasibility of this approach, this system was used to study the interaction between a sponge Aplysilla rosea and a marine bacterium commonly found in seawater, Vibrio natriegens. Sponge explants were exposed to V. natriegens, at 5 × 106 cfu/ml, and changes were monitored for 48 hours. Pyro-sequencing revealed significant shifts in microbial communities associated with the sponges after 24 to 48 hours. Both the control (sponge only without added bacteria) and Vibrio-exposed sponges showed a distinct shift in bacterial diversity and abundance with time. Vibrio exposure significantly increased bacterial diversity, the abundance of a number of taxa compared to control sponges. The result experimentally supports the notion of dynamic and concerted responses by the sponge when interacting with a bacterium, and demonstrates the feasibility of using this controlled aquarium system for the study of sponge-bacteria interactions.

Benthic biogeographic patterns in the southern Australian deep sea: Do historical museum records accord with recent systematic, but spatially limited, survey data?

AIM: To document biogeographic patterns in the deepwater benthic epifauna and demersal fishes of southern Australia, and determine whether museum records and systematic survey data provide matching results. LOCATION: Southern Australian (32-44oS) continental slope (200-3,000 m deep). TAXON: Marine benthic fauna (Arthropoda, Bryozoa, Cnidaria, Echinodermata, Mollusca, Porifera, Sipuncula, and fishes). METHODS: All available electronic records of fauna from the above taxa and ≥200 m depth off the southern Australian coastline, regardless of organism size, were collated from Australian museums and checked for geographic and taxonomic consistency. These records were then split into 40 geographic segments of roughly equal numbers, with each segment then treated as a sample in multivariate analyses of assemblage composition. Data from a recent (2015) systematic beam trawl survey along five north-south transects in the central Great Australian Bight were also included for comparison. MAIN CONCLUSIONS: The systematic survey data grouped with the associated geographic segments despite differences in sampling technique (single gear compared to multiple gears), with subsequent differences in taxonomic biases, and the use of a 25 mm mesh, which would undersample some smaller organisms present in the museum data. Thus, the museum data and the survey data provided the same results for the central Great Australian Bight at the level of the whole assemblage. The main biogeographic break occurred off southeastern Tasmania, with a second substantial break occurring at around the border between New South Wales and Victoria. This indicates the potential for unused museum data to describe biogeographic patterns over regional spatial scales, especially in the deep sea where the expense of collecting new data is relatively high.

Identifying knowledge gaps in seagrass research and management: An Australian perspective.

Seagrass species form important marine and estuarine habitats providing valuable ecosystem services and functions. Coastal zones that are increasingly impacted by anthropogenic development have experienced substantial declines in seagrass abundance around the world. Australia, which has some of the world's largest seagrass meadows and is home to over half of the known species, is not immune to these losses. In 1999 a review of seagrass ecosystems knowledge was conducted in Australia and strategic research priorities were developed to provide research direction for future studies and management. Subsequent rapid evolution of seagrass research and scientific methods has led to more than 70% of peer reviewed seagrass literature being produced since that time. A workshop was held as part of the Australian Marine Sciences Association conference in July 2015 in Geelong, Victoria, to update and redefine strategic priorities in seagrass research. Participants identified 40 research questions from 10 research fields (taxonomy and systematics, physiology, population biology, sediment biogeochemistry and microbiology, ecosystem function, faunal habitats, threats, rehabilitation and restoration, mapping and monitoring, management tools) as priorities for future research on Australian seagrasses. Progress in research will rely on advances in areas such as remote sensing, genomic tools, microsensors, computer modeling, and statistical analyses. A more interdisciplinary approach will be needed to facilitate greater understanding of the complex interactions among seagrasses and their environment.

The role of sponge-bacteria interactions: the sponge Aplysilla rosea challenged by its associated bacterium Streptomyces ACT-52A in a controlled aquarium system.

Sponge-associated bacteria play a critical role in sponge biology, metabolism and ecology, but how they interact with their host sponges and the role of these interactions are poorly understood. This study investigated the role of the interaction between the sponge Aplysilla rosea and its associated actinobacterium, Streptomyces ACT-52A, in modifying sponge microbial diversity, metabolite profile and bioactivity. A recently developed experimental approach that exposes sponges to bacteria of interest in a controlled aquarium system was improved by including the capture and analysis of secreted metabolites by the addition of an absorbent resin in the seawater. In a series of controlled aquaria, A. rosea was exposed to Streptomyces ACT-52A at 106 cfu/ml and monitored for up to 360 h. Shifts in microbial communities associated with the sponges occurred within 24 to 48 h after bacterial exposure and continued until 360 h, as revealed by TRFLP. The metabolite profiles of sponge tissues also changed substantially as the microbial community shifted. Control sponges (without added bacteria) and Streptomyces ACT-52A-exposed sponges released different metabolites into the seawater that was captured by the resin. The antibacterial activity of compounds collected from the seawater increased at 96 and 360 h of exposure for the treated sponges compared to the control group due to new compounds being produced and released. Increased antibacterial activity of metabolites from treated sponge tissue was observed only at 360 h, whereas that of control sponge tissue remained unchanged. The results demonstrate that the interaction between sponges and their associated bacteria plays an important role in regulating secondary metabolite production.

The influence of finfish aquaculture on benthic fish and crustacean assemblages in Fitzgerald Bay, South Australia.

The influence of sea-cage aquaculture on wildfish assemblages has received little attention outside of Europe. Sea-cage aquaculture of finfish is a major focus in South Australia, and while the main species farmed is southern bluefin tuna (Thunnus maccoyii), there is also an important yellowtail kingfish (Seriola lalandi) industry. Yellowtail kingfish aquaculture did not appear to have any local or regional effects on demersal assemblages (primarily fish, but also some crustaceans) surveyed by baited remote underwater video (BRUV) in Fitzgerald Bay. We did, however, detect small scale spatial variations in assemblages within the bay. The type of bait used strongly influenced the assemblage recorded, with significantly greater numbers of fish attracted to deployments where sardines were used as the bait to compared to those with no bait. The pelleted feed used by the aquaculture industry was just as attractive as sardines at one site, and intermediate between sardines and no bait at the other. There was significant temporal variability in assemblages at both farm sites and one control site, while the second control site was temporally stable (over the 9 weeks of the study). Overall, the results suggested that aquaculture was having little if any impact on the abundance and assemblage structure of the demersal macrofauna in Fitzgerald Bay.

An integrative method for the evaluation, monitoring, and comparison of seagrass habitat structure.

Assessing environmental condition is essential for the management of coasts and their resources, but better management decisions occur when large databases are simplified into more manageable units of information. Here we present the habitat structure index (HSI), which enables rapid assessment and direct comparison of seagrass habitat structure using scores of 0 (poor) to 100 (excellent) based on integrating five habitat variables: area, continuity, proximity, percentage cover, and species identity. Acquiring data to calculate the HSI can be done in situ or from video recordings, and requires relatively simple methodology of belt transects, estimating percentage cover, and basic taxonomy. Spatiotemporal comparisons can usefully identify locations and periods of seagrass habitat change, potentially providing an early warning indicator of habitat damage and decline in environmental quality. Overall, the integrative approach of the HSI represents a step toward simplifying the exchange of environmental information among researchers, coastal managers, and governing bodies.

Assembly rules of reef corals are flexible along a steep climatic gradient.

Coral reefs, one of the world's most complex and vulnerable ecosystems, face an uncertain future in coming decades as they continue to respond to anthropogenic climate change, overfishing, pollution, and other human impacts [1, 2]. Traditionally, marine macroecology is based on presence/absence data from taxonomic checklists or geographic ranges, providing a qualitative overview of spatial shifts in species richness that treats rare and common species equally [3, 4]. As a consequence, regional and long-term shifts in relative abundances of individual taxa are poorly understood. Here we apply a more rigorous quantitative approach to examine large-scale spatial variation in the species composition and abundance of corals on midshelf reefs along the length of Australia's Great Barrier Reef, a biogeographic region where species richness is high and relatively homogeneous [5]. We demonstrate that important functional components of coral assemblages "sample" space differently at 132 sites separated by up to 1740 km, leading to complex latitudinal shifts in patterns of absolute and relative abundance. The flexibility in community composition that we document along latitudinal environmental gradients indicates that climate change is likely to result in a reassortment of coral reef taxa rather than wholesale loss of entire reef ecosystems.

Toward routine, DNA-based detection methods for marine pests.

Marine pest incursions can cause significant ongoing damage to aquaculture, biodiversity, fisheries habitat, infrastructure and social amenity. They represent a significant and ongoing economic burden. Marine pests can be introduced by several vectors including aquaculture, aquarium trading, commercial shipping, fishing, floating debris, mining activities and recreational boating. Despite the inherent risks, there is currently relatively little routine surveillance of marine pest species conducted in the majority of countries worldwide. Accurate and rapid identification of marine pest species is central to early detection and management. Traditional techniques (e.g. physical sampling and sorting), have limitations, which has motivated some progress towards the development of molecular diagnostic tools. This review provides a brief account of the techniques traditionally used for detection and describes developments in molecular-based methods for the detection and surveillance of marine pest species. Recent advances provide a platform for the development of practical, specific, sensitive and rapid diagnosis and surveillance tools for marine pests for use in effective prevention and control strategies.

Community-level density dependence: an example from a shallow coral assemblage.

While density dependence is a popular topic of research in population ecology, it has received much less attention at the community level. Using 27 years of data from Heron Island, on Australia's Great Barrier Reef, we develop a matrix model of coral community dynamics that shows that community-level density dependence does occur and that it is fairly common, being found in 38% of the model parameters for which it was tested. In particular, colonization of free space (through either recruitment or growth of existing colonies) was nearly always density dependent. There were no consistent patterns in the results for mortality, persistence, or species interactions. Most transitions were found to be dependent on the cover of the incoming species group, with only a few dependent on that of the outgoing species group. In addition, few of the transitions representing species interactions were dependent on the amount of free space present, suggesting that the cover of other species does not influence encounters. When these results were combined into a model of community dynamics, it was found that density dependence resulted in a moderate increase in coral cover, which was spread over most species groups. The dynamics of the density-dependent assemblage were also a lot noisier than those of an assemblage without density dependence. Sensitivity analysis indicated that it was density dependence in the colonization probabilities, particularly of encrusting acroporids, bushy Acropora and staghorn Acropora, which had the main influence on the model, although persistence of free space was also important. Transitions representing mortality were only of minor importance, and those representing species interactions were of no importance.

Lotka-Volterra competition models for sessile organisms.

Markov models are widely used to describe the dynamics of communities of sessile organisms, because they are easily fitted to field data and provide a rich set of analytical tools. In typical ecological applications, at any point in time, each point in space is in one of a finite set of states (e.g., species, empty space). The models aim to describe the probabilities of transitions between states. In most Markov models for communities, these transition probabilities are assumed to be independent of state abundances. This assumption is often suspected to be false and is rarely justified explicitly. Here, we start with simple assumptions about the interactions among sessile organisms and derive a model in which transition probabilities depend on the abundance of destination states. This model is formulated in continuous time and is equivalent to a Lotka-Volterra competition model. We fit this model and a variety of alternatives in which transition probabilities do not depend on state abundances to a long-term coral reef data set. The Lotka-Volterra model describes the data much better than all models we consider other than a saturated model (a model with a separate parameter for each transition at each time interval, which by definition fits the data perfectly). Our approach provides a basis for further development of stochastic models of sessile communities, and many of the methods we use are relevant to other types of community. We discuss possible extensions to spatially explicit models.

Stochastic density dependence in population size of a benthic clonal invertebrate: the regulating role of fission.

The influence of environmental variation on the demography of clonal organisms has been poorly studied. I utilise a matrix model of the population dynamics of the intertidal zoanthid Palythoa caesia to examine how density dependence and temporal variation in demographic rates interact in regulating population size. The model produces realistic simulations of population size, with erratic fluctuations between soft lower and upper boundaries of approximately 55 and 90% cover. Cover never exceeds the maximum possible of 100%, and the population never goes to extinction. A sensitivity analysis indicates that the model's behaviour is driven by density dependence in the fission of large colonies to produce intermediate sized colonies. Importantly, there is no density-dependent mortality in the model, and density dependence in recruitment, while present, is unimportant. Thus it appears that the main demographic processes which are considered to regulate population size in aclonal organisms may not be important for clonal species.