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

Coral restoration - A systematic review of current methods, successes, failures and future directions.

Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the available knowledge in a comprehensive global review of coral restoration methods, incorporating data from the peer-reviewed scientific literature, complemented with grey literature and through a survey of coral restoration practitioners. We found that coral restoration case studies are dominated by short-term projects, with 60% of all projects reporting less than 18 months of monitoring of the restored sites. Similarly, most projects are relatively small in spatial scale, with a median size of restored area of 100 m2. A diverse range of species are represented in the dataset, with 229 different species from 72 coral genera. Overall, coral restoration projects focused primarily on fast-growing branching corals (59% of studies), and report survival between 60 and 70%. To date, the relatively young field of coral restoration has been plagued by similar 'growing pains' as ecological restoration in other ecosystems. These include 1) a lack of clear and achievable objectives, 2) a lack of appropriate and standardised monitoring and reporting and, 3) poorly designed projects in relation to stated objectives. Mitigating these will be crucial to successfully scale up projects, and to retain public trust in restoration as a tool for resilience based management. Finally, while it is clear that practitioners have developed effective methods to successfully grow corals at small scales, it is critical not to view restoration as a replacement for meaningful action on climate change

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

Substrate stabilisation and small structures in coral restoration: State of knowledge, and considerations for management and implementation.

Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of the intervention and impacts of potential risks, but there is a strong need to specify desired outcomes, the spatial and temporal context and indicators to be measured. With a focus on the Great Barrier Reef, we synthesise the techniques, successes and failures associated with rubble stabilisation and the use of small structures, review monitoring methods and indicators, and provide recommendations to ensure that we learn from past projects

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

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

Coral reef restoration in Indonesia:A review of policies and projects

Indonesia's coral reefs have been severely damaged by global and local stressors, and a range of active restoration techniques are now being used in attempts to rebuild degraded reefs. However, it is difficult to summarise Indonesia's restoration efforts as a whole due to a lack of consistent reporting. Here, we first discuss Indonesia's legal policy framework concerning reef restoration; this is included in the agenda of two government ministries (Marine Affairs and Fisheries, and Environment and Forestry), and comprises national laws and governmental, presidential and ministerial regulations. We then provide an extensive review of reef restoration projects in Indonesia, documenting 533 records across the country between 1990 and 2020. Most (73%) of these records come from the past ten years, and many (42%) are reported in online news articles rather than scientific reports or papers. This review identified 120,483 units of artificial reef installed across Indonesia, along with 53,640 units of coral transplantation (including both coral nurseries and direct out-planting onto reefs); in total, 965,992 fragments of hard coral have been planted across Indonesia. The most favoured restoration materials are concrete (46%) and steel structures (24%). Projects are organised by a diverse range of governmental, NGO, private and community-led organisations. This review demonstrates that Indonesia's policy has encouraged a diverse range of practitioners to implement reef restoration, but projects are often not coordinated with wider networks of restoration practitioners or scientists, and only 16% of the identified projects included a post-installation monitoring framework. Incorporating clear objectives and long-term monitoring programmes in project planning stages, while prioritising knowledge exchange and engagement with international scientific community, will substantially improve restoration outcomes in Indonesia. This will allow the country to fulfil its considerable potential as a global leader in rebuilding damaged coral reefs