A stratified transect approach captures reef complexity with canopy-forming organisms

On the Great Barrier Reef (GBR), persistent changes to reef communities have begun to be documented, and on inshore reefs these shifts may favour the proliferation of macroalgae. Critical to understanding changes to reef community structure in response to anthropogenic impacts is developing effective methods to accurately document the abundance of different reef organisms. Effective monitoring must be time and cost efficient, replicable, and able to sufficiently and accurately detect disturbances to allow development of strategies to mitigate their impacts. Traditional techniques to document coral reef communities (i.e. photo-quadrats, benthic intercept transects) rely on planar views, which tend to either over- or under-represent canopy-forming organisms. As canopy-forming organisms are likely to be affected by anthropogenic influences (corals negatively, algae positively), it is essential for monitoring programs to implement methods sufficient to document changes to the vertical dimension of coral reefs. Here we build on previous work to document the canopy effect in coral-dominated ecosystems and propose a new survey approach suitable for implementation in algal-dominated systems. A vertically stratified transect, modified from a traditional point intercept transect, captures benthic and canopy-forming members of reef communities and provides information on three-dimensional complexity. To test the capability of the new method to detect changes in vertical reef structure, seaweed was removed from experimental quadrats and monitoring techniques were applied before and after four months of regrowth. A stratified method more accurately captured the three-dimensional change resulting from algal canopy growth, while resolving the over- and under-representation of algal biomass in two traditional techniques. We propose that a stratified transect method improves abundance estimates of canopy-forming organisms whilst maintaining data compatibility with traditional methods

Hitching a ride on Hercules:fatal epibiosis drives ecosystem change from mud banks to oyster reefs

[Excerpt] Best known as a "love them or hate them" luxury food, or for their pearls, oysters are also ecosystem engineers, forming vast oyster reefs. Oyster reefs provide habitat for a myriad of species, and support fisheries, improve water quality and provide coastal protection. These services are estimated to be worth US$5,500–$99,000 per hectare per year (Grabowski et al. 2012). Globally, oyster reefs have declined by 85% through destructive overfishing, coastal development, pollution, and introduced competitors, predators and diseases (Beck et al. 2011). Active restoration is becoming an increasingly popular tool to bring back lost oyster reefs and the ecosystem services they provide (Fitzsimons et al. 2019). However, restoration is not always successful, and knowledge about how reefs naturally form and function is vital to improve restoration success. Oyster larvae only settle on hard substrates. Reefs proliferate because oyster shells provide a settlement surface, and oysters provide chemical and sound cues that facilitate larval settlement (Lillis et al. 2013). However, these reefs often form on intertidal sand and mud banks. This raises the question, how do oyster reefs form on mud banks in the absence of hard surfaces

Coral restoration in a changing world - a global synthesis of methods and techniques

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades, due to increased nutrient outputs from agriculture, elevated levels of suspended sediment caused by deforestation and development, destructive fishing practices, over-harvesting of reef species, outbreaks of corallivorous crown-of-thorns starfish (COTS, Acanthaster planci), coral disease and tropical storms. However, in recent years climate change has emerged as the primary threat to coral reefs. While reefs have a natural capacity for recovery, recurring events like mass coral bleaching and extreme weather events is increasing in frequency, intensity and severity, and are eroding the time for recovery between catastrophic events. Marine conservation has primarily focused on passive habitat protection over active restoration, in contrast to terrestrial ecosystems where active restoration is common practice. Further, active restoration is well accepted for wetlands and shellfish reefs however coral reef restoration has remained controversial both in academia and amongst marine managers. This is despite recent research suggesting that optimal conservation outcomes include both habitat protection and restoration. Critics often argue that coral restoration detracts focus from mitigating climate change and other threats to the marine environment, while proponents of coral restoration counter that interventions can serve to protect coral biodiversity and endangered species in the short-term, while mitigation of large-scale threats such as climate change and water quality take effect. Despite this disconnect between coral restoration practitioners, coral reef managers and scientists, active coral restoration is increasingly used as a tool to attempt to restore coral populations. The field has largely developed through independent work of isolated groups, and has fallen victim to ‘growing pains’ associated with ecological restoration in many other ecosystems. Partly this is due to a reluctance to share outcomes of projects, and in some cases a lack of monitoring or appropriate reporting of project outcomes. To mitigate this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from a traditional literature search of the scientific literature, complemented with information gathered from online sources and through a survey of coral restoration practitioners. We identified 329 case studies on coral restoration, of which 195 were from the scientific literature, 79 were sourced from the grey literature (i.e. reports and online descriptions), and 55 were responses to our survey of restoration practitioners. We identified ten coral restoration intervention types: coral gardening - transplantation phase (23% of records), direct transplantation (21%), artificial reefs (19%), coral gardening - nursery phase (17%), coral gardening (both phases, 7%), substrate enhancement with electricity (4%), substrate stabilisation (4%), algae removal (2%), larval enhancement (1%) and microfragmentation (<1%). The majority of interventions involve coral fragmentation or transplantation of coral fragments (70%). While 52 countries are represented in the dataset, the majority of projects were conducted in the USA, Philippines, Thailand and Indonesia (together representing 40% of projects). Coral restoration case studies are dominated by short-term projects, with 66% of all projects reporting less than 18 months of monitoring of the restored sites. Overall, the median length of projects was 12 months. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 500 m2. A diverse range of species are represented in the dataset, with 221 different species from 89 coral genera. Overall, coral restoration projects focused primarily (65% of studies) on fast-growing branching corals. Among all the published documents, the top five species (22% of studies) were Acropora cervicornis, Pocillopora damicornis, Stylophora pistillata, Porites cylindrica and Acropora palmata. Over a quarter of projects (26%) involved the coral genus Acropora, while 9% of studies included a single species - Acropora cervicornis. Much of the focus on Acropora cervicornis and Acropora palmata is likely to have resulted from these important reef-forming species being listed as threatened on the United States Endangered Species List and as Endangered on the International Union for Conservation of Nature Red List of Endangered Species (IUCN 2018). We have dedicated a section to each intervention type covered in this review, and describe the potential and limitations of each intervention type in detail there. However, collating this information has highlighted the following main points which apply to coral restoration in general. 1. On average, survival in restored corals is relatively high. All coral genera with sufficient replication from which to draw conclusions (>10 studies listing that genus) report an average survival between 60-70%. 2. Differences in survival and growth are largely species and/or location specific, so the selection of specific methods should be tailored to the local conditions, costs, availability of materials, and to the specific objectives of each project. 3. Projects are overall small and short, however substantial scaling up is required for restoration to be a useful tool in supporting the persistence of reefs in the future. While there is ample evidence detailing how to successfully grow corals at smaller scales, few interventions demonstrate a capacity to be scaled up much beyond one hectare. Notable exceptions include methods which propagate sexually derived coral larvae. 4. To date, coral restoration has been plagued by the same common problems as ecological restoration in other ecosystems. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. a. Lack of clear objectives - There is a clear mismatch between the stated objectives of projects, and the design of projects and monitoring of outcomes. Poorly articulated or overinflated objectives risk alienating the general public and scientists, by over-promising and under-delivering. Social and economic objectives have inherent value and do not need to be disguised with ecological objectives. b. Lack of appropriate monitoring - A large proportion of projects do not monitor metrics relevant to their stated objectives, or do not continue monitoring for long enough to provide meaningful estimates of success. Further, there is a clear need for standardisation in the metrics that are used, to allow comparisons between projects. c. Lack of appropriate reporting - The outcomes of a large proportion of projects are not documented, which restricts knowledge-sharing and adaptive learning. While we attempted to access some of the unreported projects through our survey, it is clear we have only scratched the surface of existing knowledge. d. Poorly designed projects - An effect of inadequate monitoring and reporting is that projects are poorly suited to their specific area and conditions. Improved knowledge-sharing and development of best practice coral restoration guidelines aims to mitigate this problem

Best practice coral restoration for the Great Barrier Reef

As the Great Barrier Reef (GBR) continues to degrade through repeated mass bleaching events, crown-of-thorns starfish and major disease outbreaks, and the impacts of intense cyclones, pressure is growing for direct intervention to assist the recovery of reef-building corals. Decreasing coral cover on the GBR and other Australian reefs has been recognised as a serious problem relatively recently in Australia but follows a global trend, with many overseas reefs now highly degraded. Various types of coral restoration, rehabilitation and assisted recovery projects have been trialled overseas for decades and it makes sense to look at what has and hasn’t worked overseas to determine a range of options that may suit GBR conditions. Some direct interventions to assist coral recovery have been trialled in Australia such as transplanting corals, algae removal to promote coral recovery and larval enhancement promoting direct coral recruitment. In addition, after physical damage from cyclones, ship strikes or dragged anchors, local dive operators and dive clubs (permitted or unpermitted) often attempt to assist the recovery of corals by tipping over flipped tabular corals and reattaching broken branching corals or sea fans. These latter assisted recovery techniques are rarely underpinned by scientific data on coral recovery. A lack of best practice guidelines for these actions limits the chance of success and increases the health and safety risks of these activities

Habitat degradation and competition for resources in coral reef fishes

Habitat loss and degradation are among the most pressing threats to the persistence and diversity of species. They can directly lead to declining abundance through the loss of resources, or indirectly through disruption of important ecological interactions such as competition and predation. Coral reef ecosystems around the globe have experienced a decline in coral cover in the past few decades due to a suite of anthropogenic disturbances. Living corals not only provide the structural foundation in the reef ecosystem, but also critical resources such as food, shelter and suitable sites for reproduction for reef fishes. The loss of live coral often leads to a well-documented decline in reef fishes that associate with the coral reef matrix. However, our understanding of the causes of these declines is limited and the mechanisms are poorly understood. Habitat loss may directly impact on fitness parameters or population processes, or it may influence them indirectly by altering interactions such as competition for resources, successful sheltering from predators and habitat selection. The overall objective of this thesis is to explore how habitat degradation influences competition for resources in a common, habitat associated coral reef fish. Competition over resources is recognised as a fundamental process in ecology, with important consequences for species coexistence, the distribution of species and the regulation of populations. The role of competition in the ecology of reef fishes has been the topic of debate over several decades. While early research in the 1980's focused on the partition of resources between species (i.e niche partitioning) or the chance colonisation of space (i.e 'lottery hypothesis'), others focused on alternate theories to explain patterns of density dependence (e.g. disturbance, predation, recruitment limitation). Since then, a large body of work has accumulated, with field experiments greatly increasing our understanding of the prevalence and importance of competition in coral reef fish communities. Chapter 2 compiles and synthesises the results of experimental tests of competition and shows that evidence for competition is pervasive, thus confirming its important role in structuring reef fish communities. Competition was found to be important both within and between species, with 72% of intraspecific tests and 56% of interspecific tests demonstrating a demographically significant consequence of competition. Competition within species (intraspecific competition) is likely to be particularly intense, given that individuals of the same species are likely to have a high degree of overlap in their resource requirements. A majority of studies of intraspecific competition explored numerical responses (i.e. survival or abundances) to competition. 59% found a negative effect of increasing conspecifics on their overall survival, while relatively few studies investigated sub-lethal effects of competition. Considering levels of competition depend on the availability of resources, the intensity of competition is likely to increase in response to habitat loss and degradation. However, the review emphasised the paucity of studies which have considered links between competition and resources, and the extent to which habitat loss and degradation alter the effects of competitive interactions are poorly understood. A species' competitive response to habitat loss may affect multiple demographic parameters, and these effects may occur over different time scales. However, few studies have manipulated resource availability and documented the effects of habitat loss over time while measuring multiple demographic parameters. In Chapter 3 I evaluate the consequences of habitat loss on the abundance, body condition and behaviour of a common coral reef fish over four months following an experimental reduction in the availability of live coral habitat. I identified natural aggregations of Pomacentrus moluccensis sheltering in Acropora coral colonies, and experimentally reduced live coral tissue by exposing 60% of the coral colony to crown-of-thorns starfish. Throughout the four month post-disturbance period, P. moluccensis showed a strong association with the remnant live habitat on treatment colonies, and avoided the recently dead coral habitat. Densities within this live habitat increased following the disturbance, but gradually dropped until they matched those of control colonies, indicating density dependent mortality. Surprisingly, liver samples indicated that individuals on treatment colonies with 60% loss of live coral habitat had a higher body condition than those on control colonies with no habitat loss. Video analyses revealed P. moluccensis on treatment colonies opportunistically feeding on the algal matrix growing on the recently dead coral branches. These results indicate that successful competitors benefit by gaining access to a novel food source along the edge of prime shelter space within live coral. This edge effect allows species with a degree of flexibility in their resource requirements to benefit from living at a habitat boundary. Chapter 3 highlights a species complex response, both positive and negative, to habitat degradation. While Chapter 3 demonstrated the importance of live coral in promoting the survival of habitat associated fishes, it is still unclear what causes the mortality of less successful individuals. It is commonly hypothesised that fish mortality is increased as a consequence of the loss of shelter space between branches as dead corals become overgrown by algae. In Chapter 4, I tested this hypothesis by quantifying changes in sheltering behaviour of a common damselfish, Pomacentrus moluccensis, following the death of its host coral colony. Recently dead colonies of Acropora were allowed to accumulate algae and invertebrates over a period of five weeks. Groups of P. moluccensis were then placed on either live or dead coral colonies, startled using a visual stimulus, and their sheltering responses compared. Pomacentrus moluccensis stopped sheltering amongst the coral branches immediately following the death of the coral, despite very little change in shelter space. Instead, most individuals swam away from the dead coral into the surrounding water where they were more exposed to predators. I argue that live coral is a necessary cue that elicits the appropriate behavioural sheltering response to potential predators. Findings in Chapter 4 suggest that the disruption of this cue poses a great threat to coral-associated fishes on degrading reefs. Partial habitat loss clearly results in temporary crowding of reef fishes which may lead to density dependent habitat selection. Individuals are faced with the decision of either joining high density populations crowded into remnant high quality habitat or opting to move to low quality habitat. Chapter 5 investigates how habitat loss influences habitat selection, and ultimately the distribution, of P. moluccensis. In a survey of habitat use on 49 transects along the coral reef crest I found that P. moluccensis adults only chose dead coral colonies when the average density per live coral colony was higher than under natural conditions. These high densities on live coral colonies only occurred on reefs where >50% of colonies on were dead. This suggests that the loss of habitat causes crowding on remnant live coral until some fish start using less preferred dead colonies. I then conducted a choice experiment to investigate if density dependent habitat selection was the mechanism underlying this pattern. When presented with the choice of two colonies, fish were more likely to choose a near empty alternate colony when the other colony was severely crowded with conspecifics. The consequences of this behaviour are likely to be two-fold; first adult fish are forced to inhabit dead coral, and second their presence may encourage juvenile larvae to recruit to this unsuitable habitat if these recruits use conspecific presence as a cue to determine habitat quality. Chapter 5 provides the first example of how habitat loss induces density dependent habitat selection, adding to the growing body of work showing that habitat loss is impacting on critical ecological interactions on coral reefs. In summary, this thesis has investigated effects of habitat degradation on key ecological processes determining the distribution of reef fishes, competition for resources and their interaction with the coral reef habitat. It showed complex demographic responses to coral loss that include both positive and negative effects. It established that live coral is critical, not just for the structure it provides, but also for eliciting adaptive behavioural responses to the threat of predation. Moreover, this thesis provides the first demonstration of the crowding hypothesis in the marine environment and is the first to investigate how density dependent habitat selection is affected by habitat degradation. The outcomes of this research highlight the importance of living corals in the ecology and behaviour of coral reef fishes, and their complex responses to coral reef habitat loss and degradation

Controlling outbreaks of the coral-eating crown-of-thorns starfish using a single injection of common household vinegar

Outbreaks of the destructive coral-eating crown-of-thorns starfish, Acanthaster planci, present a considerable threat to coral reefs worldwide, and mitigating their impact has proven challenging. The most effective methods to control A. planci require injecting individual starfish with lethal chemicals. While some of these are highly effective, their administration often requires permits, training and access to specialised equipment. We aimed to identify a widely available and highly efficient alternative. We discovered that common household vinegar is lethal to A. planci individuals when injected at the base of one their arms. A single injection of 25 ml vinegar induced functional mortality in <24 h and 100 % mortality in <48 h. These results demonstrate that vinegar is an effective alternative to currently used chemicals. Vinegar is a viable alternative in the toolkit of methods that can control and eradicate local outbreaks of COTS on coral reefs

Strong intraspecific competition and habitat selectivity influence abundance of a coral-dwelling damselfish

Coral reef ecosystems are experiencing a global decline in coral cover, with direct effects on reef fishes. A decline in habitat may lead to crowding of live coral specialists into remnant habitat patches, intensifying intraspecific competition. Increased local densities of conspecifics are known to negatively affect key demographic processes, but the magnitude of density effects and the role of crowding in response to habitat loss are poorly understood. In this study we examined habitat use and relationships between habitat availability and population density in a coral-dwelling damselfish — Chrysiptera parasema. First, we conducted habitat use and availability surveys to establish the level of habitat selectivity. We then investigated the evidence for crowding due to habitat loss by comparing densities within juvenile aggregations on natural reefs with high and low cover of the preferred habitat. Finally, we used a manipulative patch-reef experiment to measure the potential effects of crowding on mortality of juvenile C. parasema. Surveys revealed that 97% of juvenile C. parasema were associated with Acropora corals. Furthermore, C. parasema densities were closely related to the cover of bottlebrush Acropora, the preferred growth form. Contrary to predictions, there was no evidence of crowding on natural reefs with low coral cover, but rather, reefs with abundant Acropora cover supported larger aggregations with double the density of juveniles. We hypothesized that low densities of C. parasema on natural reefs with low coral cover could be explained by intense intraspecific competition. Experimental manipulations showed that juvenile mortality was density-dependent, with mortality 20% higher on high-density experimental patch-reefs compared to low-density reefs. Behavioural observations on the patch-reefs revealed that the frequency of agonistic interactions and distance to shelter were both unrelated to conspecific densities, highlighting the need for further research into mechanisms underpinning density dependent mortality. These results suggest that intraspecific competition may play an important role in reducing reef fish abundance as a consequence of habitat loss. Given that coral reef systems are currently under threat, with a global decline in coral cover, this study adds to the growing body of knowledge of how disturbances to habitat may affect reef fish communities

Loss of live coral compromises predator-avoidance behaviour in coral reef damselfish

Tropical reefs have experienced an unprecedented loss of live coral in the past few decades and the biodiversity of coral-dependent species is under threat. Many reef fish species decline in abundance as coral cover is lost, yet the mechanisms responsible for these losses are largely unknown. A commonly hypothesised cause of fish decline is the loss of shelter space between branches as dead corals become overgrown by algae. Here we tested this hypothesis by quantifying changes in predator-avoidance behaviour of a common damselfish, Pomacentrus moluccensis, before and after the death of their coral colony. Groups of P. moluccensis were placed on either healthy or degraded coral colonies, startled using a visual stimulus and their sheltering responses compared over a 7-week period. P. moluccensis stopped sheltering amongst the coral branches immediately following the death of the coral, despite the presence of ample shelter space. Instead, most individuals swam away from the dead coral, potentially increasing their exposure to predators. It appears that the presence of live coral rather than shelter per se is the necessary cue that elicits the appropriate behavioural response to potential predators. The disruption of this link poses an immediate threat to coral-associated fishes on degrading reefs

Habitat degradation modifies the strength of interspecific competition in coral dwelling damselfishes

Habitat degradation is predicted to exacerbate competition for critical resources; however, the relationship between habitat quality and competition is poorly understood. In this study, we used a manipulative experiment to test the effects of habitat degradation on competition between two planktivorous, coral-dwelling damselfishes, Chrysiptera parasema and Dascyllus melanurus. Experimental reefs were constructed with either healthy (100% live) or degraded (10% live) Acropora longicyathus coral, stocked with varying densities of these two fish species, and monitored for two months. On healthy habitat, the mortality of C. parasema was density dependent, and increased substantially in the presence of the dominant interspecific competitor D. melanurus. In contrast, on reefs where habitat was degraded, C. parasema mortality was highly variable, density independent, and was no longer influenced by the presence of dominant competitor D. melanurus. Behavioral observations revealed that agonistic interactions for both species increased with density on degraded habitat, but not on healthy habitat. In addition, on degraded reefs, both species displayed a reduced association with reef habitat and ventured further away from shelter with increasing densities of the dominant competitor D. melanurus. These results suggest that reduced habitat quality can have such a profound effect on reef fishes, that it eliminates density-dependent mortality and competitive dominance hierarchies, thereby substantially altering the mechanisms that structure reef fish communities

An ecological assessment of Australia's first community oyster gardens

Summary: Oyster gardening is a community‐driven activity where oysters are grown in cages hanging off docks or other coastal infrastructure. Besides the provision of adult oysters for restoration programmes, oyster gardening may also support other ecosystem services such as providing habitat for fishes and invertebrates as well as encouraging community involvement and citizen science. Australia's first oyster gardening programme was undertaken in a canal estate on Bribie Island in Moreton Bay, Queensland between October 2016 and November 2017. Oyster gardens consisting of plastic mesh cages were deployed with either three species of bivalves (polyculture), or exclusively Sydney Rock Oysters (monoculture) to investigate whether the habitat value differed between the two garden types. After one year of growth, polyculture cages supported higher abundances and species richness of both invertebrates and fish compared to the monoculture gardens. Our study showed that oyster gardening can provide habitat for a range of invertebrate and fish species in the highly modified coastal environment of a canal estate. Further studies are needed to discern whether these oyster gardens would also support larger and mobile fauna, such as species with commercial and recreational importance