Stony coral tissue loss disease indirectly alters reef communities

Many Caribbean coral reefs are near collapse due to various threats. An emerging threat, stony coral tissue loss disease (SCTLD), is spreading across the Western Atlantic and Caribbean. Data from the U.S. Virgin Islands reveal how SCTLD spread has reduced the abundance of susceptible coral and crustose coralline algae and increased cyanobacteria, fire coral, and macroalgae. A Caribbean-wide structural equation model demonstrates versatility in reef fish and associations with rugosity independent of live coral. Model projections suggest that some reef fishes will decline due to SCTLD, with the largest changes on reefs that lose the most susceptible corals and rugosity. Mapping these projected declines in space indicates how the indirect effects of SCTLD range from undetectable to devastating.

Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

Towards a scientific community consensus on designating Vulnerable Marine Ecosystems from imagery

Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species' co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs.

Habitat configurations shape the trophic and energetic dynamics of reef fishes in a tropical-temperate transition zone: implications under a warming future

Understanding the extent to which species' traits mediate patterns of community assembly is key to predict the effect of natural and anthropogenic disturbances on ecosystem functioning. Here, we apply a trait-based community assembly framework to understand how four different habitat configurations (kelp forests, Sargassum spp. beds, hard corals, and turfs) shape the trophic and energetic dynamics of reef fish assemblages in a tropical-temperate transition zone. Specifically, we tested (i) the degree of trait divergence and convergence in each habitat, (ii) which traits explained variation in species' abundances, and (iii) differences in standing biomass (kg ha-1), secondary productivity (kg ha-1 day-1) and turnover (% day-1). Fish assemblages in coral and kelp habitats displayed greater evidence of trait convergence, while turf and Sargassum spp. habitats displayed a higher degree of trait divergence, a pattern that was mostly driven by traits related to resource use and thermal affinity. This filtering effect had an imprint on the trophic and energetic dynamics of reef fishes, with turf habitats supporting higher fish biomass and productivity. However, these gains were strongly dependent on trophic guild, with herbivores/detritivores disproportionately contributing to among-habitat differences. Despite these perceived overall gains, turnover was decoupled for fishes that act as conduit of energy to higher trophic levels (i.e. microinvertivores), with coral habitats displaying higher rates of fish biomass replenishment than turf despite their lower productivity. This has important implications for biodiversity conservation and fisheries management, questioning the long-term sustainability of ecological processes and fisheries yields in increasingly altered marine habitats.

Functional and phylogenetic responses of motile cryptofauna to habitat degradation

Biodiversity of terrestrial and marine ecosystems, including coral reefs, is dominated by small, often cryptic, invertebrate taxa that play important roles in ecosystem structure and functioning. While cryptofauna community structure is determined by strong small-scale microhabitat associations, the extent to which ecological and environmental factors shape these communities are largely unknown, as is the relative importance of particular microhabitats in supporting reef trophodynamics from the bottom up. The goal of this study was to address these knowledge gaps, provided coral reefs are increasingly exposed to multiple disturbances and environmental gradients that influence habitat complexity, condition and ecosystem functioning. We compared the density, biomass, size range, phylogenetic diversity and functional roles of motile cryptofauna in Palau, Western Micronesia, among four coral-derived microhabitats representing various states of degradation (live coral [Acropora and Pocillopora], dead coral and coral rubble) from reefs along a gradient of effluent exposure. In total, 122 families across ten phyla were identified, dominated by the Arthropoda (Crustacea) and Mollusca. Cryptofauna biomass was greatest in live Pocillopora, while coral rubble contained the greatest density and diversity. Size ranges were broader in live corals than both dead coral and rubble. From a bottom-up perspective, effluent exposure had mixed effects on cryptic communities including a decline in total biomass in rubble. From a top-down perspective, cryptofauna were generally unaffected by predator biomass. Our data show that, as coral reef ecosystems continue to decline in response to more frequent and severe disturbances, habitats other than live coral may become increasingly important in supporting coral reef biodiversity and food webs.

Community size structure varies with predator-prey size relationships and temperature across Australian reefs

Climate change and fisheries exploitation are dramatically changing the abundances, species composition, and size spectra of fish communities. We explore whether variation in 'abundance size spectra', a widely studied ecosystem feature, is influenced by a parameter theorized to govern the shape of size-structured ecosystems-the relationship between the sizes of predators and their prey (predator-prey mass ratios, or PPMRs). PPMR estimates are lacking for avast number of fish species, including at the scale of trophic guilds. Using measurements of 8128 prey items in gut contents of 97 reef fish species, we established predator-prey mass ratios (PPMRs) for four major trophic guilds (piscivores, invertivores, planktivores, and herbivores) using linear mixed effects models. To assess the theoretical predictions that higher community-level PPMRs leads to shallower size spectrum slopes, we compared observations of both ecosystem metrics for ~15,000 coastal reef sites distributed around Australia. PPMRs of individual fishes were remarkably high (median ~71,000), with significant variation between different trophic guilds (~890 for piscivores; ~83,000 for planktivores), and ~8700 for whole communities. Community-level PPMRs were positively related to size spectrum slopes, broadly consistent with theory, however, this pattern was also influenced by the latitudinal temperature gradient. Tropical reefs showed a stronger relationship between community-level PPMRs and community size spectrum slopes than temperate reefs. The extent that these patterns apply outside Australia and consequences for community structure and dynamics are key areas for future investigation.

Emerging insights on effects of sharks and other top predators on coral reefs

Predation is ubiquitous on coral reefs. Among the most charismatic group of reef predators are the top predatory fishes, including sharks and large-bodied bony fishes. Despite the threat presented by top predators, data describing their realized effects on reef community structure and functioning are challenging to produce. Many innovative studies have capitalized on natural experimental conditions to explore predator effects on reefs. Gradients in predator density have been created by spatial patterning of fisheries management. Evidence of prey release has been observed across some reefs, namely that potential prey increase in density when predator density is reduced. While such studies search for evidence of prey release among broad groups or guilds of potential prey, a subset of studies have sought evidence of release at finer population levels. We find that some groups of fishes are particularly vulnerable to the effects of predators and more able to capitalize demographically when predator density is reduced. For example, territorial damselfish appear to realize reliable population expansion with the reduction in predator density, likely because their aggressive, defensive behavior makes them distinctly vulnerable to predation. Relatedly, individual fishes that suffer from debilitating conditions, such as heavy parasite loads, appear to realize relatively stronger levels of prey release with reduced predator density. Studying the effects of predators on coral reefs remains a timely pursuit, and we argue that efforts to focus on the specifics of vulnerability to predation among potential prey and other context-specific dimensions of mortality hold promise to expand our knowledge.

Interactions between coral restoration and fish assemblages: implications for reef management

Corals create complex reef structures that provide both habitat and food for many fish species. Because of numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. Although restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically validated research. This study reviews the limited data on reef restoration and fish assemblages, and complements this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. It also discusses which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, the study aims to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. Although alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature.

Human exploitation shapes productivity-biomass relationships on coral reefs

Coral reef fisheries support the livelihoods of millions of people in tropical countries, despite large-scale depletion of fish biomass. While human adaptability can help to explain the resistance of fisheries to biomass depletion, compensatory ecological mechanisms may also be involved. If this is the case, high productivity should coexist with low biomass under relatively high exploitation. Here we integrate large spatial scale empirical data analysis and a theory-driven modelling approach to unveil the effects of human exploitation on reef fish productivity-biomass relationships. We show that differences in how productivity and biomass respond to overexploitation can decouple their relationship. As size-selective exploitation depletes fish biomass, it triggers increased production per unit biomass, averting immediate productivity collapse in both the modelling and the empirical systems. This 'buffering productivity' exposes the danger of assuming resource production-biomass equivalence, but may help to explain why some biomass-depleted fish assemblages still provide ecosystem goods under continued global fishing exploitation.

Mangroves reduce the vulnerability of coral reef fisheries to habitat degradation

Despite general and wide-ranging negative effects of coral reef degradation on reef communities, hope might exist for reef-associated predators that use nursery habitats. When reef structural complexity is lost, refuge density declines and prey vulnerability increases. Here, we explore whether the presence of nursery habitats can promote high predator productivity on degraded reefs by mitigating the costs of increased vulnerability in early life, whilst allowing for the benefits of increased food availability in adulthood. We apply size-based ecosystem models of coral reefs with high and low structural complexity to predict fish biomass and productivity in the presence and absence of mangrove nurseries. Our scenarios allow us to elucidate the interacting effects of refuge availability and ontogenetic habitat shifts for fisheries productivity. We find that low complexity, degraded reefs with nurseries can support fisheries productivity that is equal to or greater than that in complex reefs that lack nurseries. We compare and validate model predictions with field data from Belize. Our results should inform reef fisheries management strategies and protected areas now and into the future.

Despite wide-ranging negative effects of coral reef degradation on reef communities, hope might exist for reef-associated predators that use nursery habitats. This study uses size-based ecosystem models of coral reefs to assess the effects of the presence and absence of mangrove nurseries.