Indirect effects of overfishing on Caribbean reefs: sponges overgrow reef-building corals

Effects of ocean acidification on growth and photophysiology of two tropical reef macroalgae

Macroalgae can modify coral reef community structure and ecosystem function through a variety of mechanisms, including mediation of biogeochemistry through photosynthesis and the associated production of dissolved organic carbon (DOC). Ocean acidification has the potential to fuel macroalgal growth and photosynthesis and alter DOC production, but responses across taxa and regions are widely varied and difficult to predict. Focusing on algal taxa from two different functional groups on Caribbean coral reefs, we exposed fleshy (Dictyota spp.) and calcifying (Halimeda tuna) macroalgae to ambient and low seawater pH for 25 days in an outdoor experimental system in the Florida Keys. We quantified algal growth, calcification, photophysiology, and DOC production across pH treatments. We observed no significant differences in the growth or photophysiology of either species between treatments, except for lower chlorophyll b concentrations in Dictyota spp. in response to low pH. We were unable to quantify changes in DOC production. The tolerance of Dictyota and Halimeda to near-future seawater carbonate chemistry and stability of photophysiology, suggests that acidification alone is unlikely to change biogeochemical processes associated with algal photosynthesis in these species. Additional research is needed to fully understand how taxa from these functional groups sourced from a wide range of environmental conditions regulate photosynthesis (via carbon uptake strategies) and how this impacts their DOC production. Understanding these species-specific responses to future acidification will allow us to more accurately model and predict the indirect impacts of macroalgae on coral health and reef ecosystem processes.

Effects of sponge-to-sponge contact on the microbiomes of three spatially competing Caribbean coral reef species

Sponges perform important ecosystem functions, host diverse microbial symbiont communities (microbiomes), and have been increasing in density on Caribbean coral reefs over the last decade. Sponges compete for space in coral reef communities through both morphological and allelopathic strategies, but no studies of microbiome impacts during these interactions have been conducted. Microbiome alterations mediate spatial competition in other coral reef invertebrates and may similarly impact competitive outcomes for sponges. In this study, we characterized the microbiomes of three common Caribbean sponges (Agelas tubulata, Iotrochota birotulata, and Xestospongia muta) observed to naturally interact spatially in Key Largo, Florida (USA). For each species, replicate samples were collected from sponges in contact with neighbors at the site of contact (contact) and distant from the site of contact (no contact), and from sponges spatially isolated from neighbors (control). Next-generation amplicon sequencing (V4 region of 16S rRNA) revealed significant differences in microbial community structure and diversity among sponge species, but no significant effects were observed within sponge species across all contact states and competitor pairings, indicating no large community shifts in response to direct contact. At a finer scale, particular symbiont taxa (operational taxonomic units at 97% sequence identity, OTUs) were shown to decrease significantly in some interaction pairings, suggesting localized effects for specific sponge competitors. Overall, these results revealed that direct contact during spatial competition does not significantly alter microbial community composition or structure of interacting sponges, suggesting that allelopathic interactions and competitive outcomes are not mediated by microbiome damage or destabilization.

Sea urchin harvest inside marine protected areas: an opportunity to investigate the effects of exploitation where trophic upgrading is achieved

Background

Marine protected areas (MPAs) usually have both positive effects of protection for the fisheries' target species and indirect negative effects for sea urchins. Moreover, often in MPAs sea urchin human harvest is restricted, but allowed. This study is aimed at estimating the effect of human harvest of the sea urchin Paracentrotus lividus within MPAs, where fish exploitation is restricted and its density is already controlled by a higher natural predation risk. The prediction we formulated was that the lowest densities of commercial sea urchins would be found where human harvest is allowed and where the harvest is restricted, compared to where the harvest is forbidden.

Methods

At this aim, a collaborative database gained across five MPAs in Sardinia (Western Mediterranean, Italy) and areas outside was gathered collecting sea urchin abundance and size data in a total of 106 sites at different degrees of sea urchin exploitation: no, restricted and unrestricted harvest sites (NH, RH and UH, respectively). Furthermore, as estimates made in past monitoring efforts (since 2005) were available for 75 of the sampled sites, for each of the different levels of exploitation, the rate of variation in the total sea urchin density was also estimated.

Results

Results have highlighted that the lowest sea urchin total and commercial density was found in RH sites, likely for the cumulative effects of human harvest and natural predation. The overall rate of change in sea urchin density over time indicates that only NH conditions promoted the increase of sea urchin abundance and that current local management of the MPAs has driven towards an important regression of populations, by allowing the harvest. Overall, results suggest that complex mechanisms, including synergistic effects between natural biotic interactions and human pressures, may occur on sea urchin populations and the assessment of MPA effects on P. lividus populations would be crucial to guide management decisions on regulating harvest permits. Overall, the need to ban sea urchin harvest in the MPAs to avoid extreme reductions is encouraged, as inside the MPAs sea urchin populations are likely under natural predation pressures for the trophic upgrading.

Coral reef benthic community changes in the Anthropocene: Biogeographic heterogeneity, overlooked configurations, and methodology

Non-random community changes are becoming more frequent in many ecosystems. In coral reefs, changes towards communities dominated by other than hard corals are increasing in frequency, with severe impacts on ecosystem functioning and provision of ecosystem services. Although new research suggests that a variety of alternative communities (i.e. not dominated by hard corals) exist, knowledge on the global diversity and functioning of alternative coral reef benthic communities, especially those not dominated by algae, remains scattered. In this systematic review and meta-analysis of 523 articles, we analyse the different coral reef benthic community changes reported to date and discuss the advantages and limitations of the methods used to study these changes. Furthermore, we used field cover data (1116 reefs from the ReefCheck database) to explore the biogeographic and latitudinal patterns in dominant benthic organisms. We found a mismatch between literature focus on coral-algal changes (over half of the studies analysed) and observed global natural patterns. We identified strong biogeographic patterns, with the largest and most biodiverse biogeographic regions (Western and Central Indo-Pacific) presenting previously overlooked soft-coral-dominated communities as the most abundant alternative community. Finally, we discuss the potential biases associated with methods that overlook ecologically important cryptobenthic communities and the potential of new technological advances in improving monitoring efforts. As coral reef communities inevitably and swiftly change under changing ocean conditions, there is an urgent need to better understand the distribution, dynamics as well as the ecological and societal impacts of these new communities.

Detrimental conditions affecting Xestospongia muta across shallow and mesophotic coral reefs off the southwest coast of Puerto Rico

Sponges are fundamental components of coral reef communities and, unfortunately, like other major benthic members, they too have been impacted by epizootic and panzootic events. We report on the prevalence of disease-like conditions affecting populations of the giant barrel sponge Xestospongia muta across shallow and mesophotic coral reefs off La Parguera Natural Reserve (LPNR) and Mona Island Marine Reserve (MIMR) in Puerto Rico. Four different conditions affecting X. muta were observed during our surveys, of which 3 have been previously reported: cyclic spotted bleaching (CSB; apparently non-lethal), Xestospongia-tissue wasting disease (X-TWD; apparently lethal), and sponge orange band disease (SOB; sparsely associated with X-TWD infected individuals). Additionally, we describe a fourth condition, Xestospongia-tissue hardening condition (X-THC), a previously unreported disease recently observed along the insular shelf margin off LPNR and MIMR. Within LPNR, a total of 764 specimens of X. muta were inspected and measured. Of these, 590 sponges (72.2%) had CSB, 25 (3.27%) had signs of X-TWD, 7 (0.92%) had SOB, and the remaining 142 (18.6%) were apparently healthy. Three colonies inhabiting upper mesophotic depths on the LPNR insular shelf showed signs of CSB and X-TWD. At MIMR, video-transect surveys revealed a total of 514 colonies, of which 40 (7.78%) had signs of CSB and/or XTWD, 14 (2.72%) were affected by X-THC, while the remaining 460 (89.5%) showed no external signs of disease and appeared healthy. The presence of 4 concomitant disease-like conditions in barrel sponges of Puerto Rico is alarming, and indicative of the deteriorating status of Caribbean coral reefs.

‘Taking Fishers’ Knowledge to the Lab’: An Interdisciplinary Approach to Understand Fish Trophic Relationships in the Brazilian Amazon

Trophic levels can be applied to describe the ecological role of organisms in food webs and assess changes in ecosystems. Stable isotopes analysis can assist in the understanding of trophic interactions and use of food resources by aquatic organisms. The local ecological knowledge (LEK) of fishers can be an alternative to advance understanding about fish trophic interactions and to construct aquatic food webs, especially in regions lacking research capacity. The objectives of this study are: to calculate the trophic levels of six fish species important to fishing by combining data from stable isotopes analysis and fishers’ LEK in two clear water rivers (Tapajós and Tocantins) in the Brazilian Amazon; to compare the trophic levels of these fish between the two methods (stable isotopes analysis and LEK) and the two rivers; and to develop diagrams representing the trophic webs of the main fish prey and predators based on fisher’s LEK. The fish species studied were Pescada (Plagioscion squamosissimus), Tucunaré (Cichla pinima), Piranha (Serrasalmus rhombeus), Aracu (Leporinus fasciatus), Charuto (Hemiodus unimaculatus), and Jaraqui (Semaprochilodus spp.). A total of 98 interviews and 63 samples for stable isotopes analysis were carried out in both rivers. The average fish trophic levels did not differ between the stable isotopes analysis and the LEK in the Tapajós, nor in the Tocantins Rivers. The overall trophic level of the studied fish species obtained through the LEK did not differ from data obtained through the stable isotopes analysis in both rivers, except for the Aracu in the Tapajós River. The main food items consumed by the fish according to fishers’ LEK did agree with fish diets as described in the biological literature. Fishers provided useful information on fish predators and feeding habits of endangered species, such as river dolphin and river otter. Collaboration with fishers through LEK studies can be a viable approach to produce reliable data on fish trophic ecology to improve fisheries management and species conservation in tropical freshwater environments and other regions with data limitations.

High taxonomic resolution surveys and trait-based analyses reveal multiple benthic regimes in North Sulawesi (Indonesia)

As coral reef communities change and reorganise in response to increasing disturbances, there is a growing need for understanding species regimes and their contribution to ecosystem processes. Using a case study on coral reefs at the epicentre of tropical marine biodiversity (North Sulawesi, Indonesia), we explored how application of different biodiversity approaches (i.e., use of major taxonomic categories, high taxonomic resolution categories and trait-based approaches) affects the detection of distinct fish and benthic communities. Our results show that using major categories fails to identify distinct coral reef regimes. We also show that monitoring of only scleractinian coral communities is insufficient to detect different benthic regimes, especially communities dominated by non-coral organisms, and that all types of benthic organisms need to be considered. We have implemented the use of a trait-based approach to study the functional diversity of whole coral reef benthic assemblages, which allowed us to detect five different community regimes, only one of which was dominated by scleractinian corals. Furthermore, by the parallel study of benthic and fish communities we provide new insights into key processes and functions that might dominate or be compromised in the different community regimes.

A centuries-old manmade reef in the Caribbean does not substitute natural reefs in terms of species assemblages and interspecific competition

With increasing maritime activities in the proximity of coral reefs, a growing number of manmade structures are becoming available for coral colonisation. Yet, little is known about the sessile community composition of such artificial reefs in comparison with that of natural coral reefs. Here, we compared the diversity of corals and their competitors for substrate space between a centuries-old manmade structure and the nearest natural reef at St. Eustatius, eastern Caribbean. The artificial reef had a significantly lower species richness and fewer competitive interactions than the natural reef. The artificial reef was dominated by a cover of crustose coralline algae and zoantharians, instead of turf algae and fire corals on the natural reef. Significant differences in species composition were also found between exposed and sheltered sites on both reefs. Our study indicates that even a centuries-old manmade reef cannot serve as a surrogate for natural reefs.

Ocean Acidification and Direct Interactions Affect Coral, Macroalga, and Sponge Growth in the Florida Keys

Coral reef community composition, function, and resilience have been altered by natural and anthropogenic stressors. Future anthropogenic ocean and coastal acidification (together termed “acidification”) may exacerbate this reef degradation. Accurately predicting reef resilience requires an understanding of not only direct impacts of acidification on marine organisms but also indirect effects on species interactions that influence community composition and reef ecosystem functions. In this 28-day experiment, we assessed the effect of acidification on coral–algal, coral–sponge, and algal–sponge interactions. We quantified growth of corals (Siderastrea radians), fleshy macroalgae (Dictyota spp.), and sponges (Pione lampa) that were exposed to local summer ambient (603 μatm) or elevated (1105 μatm) pCO2 seawater. These species are common to hard-bottom communities, including shallow reefs, in the Florida Keys. Each individual was maintained in isolation or paired with another organism. Coral growth (net calcification) was similar across seawater pCO2 and interaction treatments. Fleshy macroalgae had increased biomass when paired with a sponge but lost biomass when growing in isolation or paired with coral. Sponges grew more volumetrically in the elevated seawater pCO2 treatment (i.e., under acidification conditions). Although these results are limited in temporal and spatial scales due to the experimental design, they do lend support to the hypothesis that acidification may facilitate a shift towards increased sponge and macroalgae abundance by directly benefiting sponge growth which in turn may provide more dissolved inorganic nitrogen to macroalgae in the Florida Keys.

Rapid relative increase of crustose coralline algae following herbivore exclusion in a reef of El Salvador

The Eastern Tropical Pacific (ETP) is one of the most isolated and least studied regions in the world. This particularly applies to the coast of El Salvador, where the only reef between Guatemala and Nicaragua, called Los Cóbanos reef, is located. There is very little published information about the reef’s biodiversity, and to our knowledge, no research on its ecology and responses to anthropogenic impacts, such as overfishing, has been conducted. The present study, therefore, described the benthic community of Los Cóbanos reef, El Salvador, using the Line-Point-Intercept-Transect method and investigated changes in the benthic community following the exclusion of piscine macroherbivores over a period of seven weeks. Results showed high benthic algae cover (up to 98%), dominated by turf and green algae, and low coral cover (0–4%). Porites lobata was the only hermatypic coral species found during the surveys. Surprisingly, crustose coralline algae (CCA) showed a remarkable total cover increase by 58%, while turf algae cover decreased by 82%, in experimental plots after seven weeks of piscine macroherbivore exclusion. These findings apparently contradict the results of most previous similar studies. While it was not possible to ascertain the exact mechanisms leading to these drastic community changes, the most likely explanation is grazing on turf by small grazing macroherbivores that had access to the cages during the experiment and clearing of CCA initially covered by epiphytes and sediments. A higher CCA cover would promote the succesful settlement by corals and prevent further erosion of the reef framework. Therefore it is crucial to better understand algal dynamics, herbivory, and implications of overfishing at Los Cóbanos to avoid further reef deterioration. This could be achieved through video surveys of the fish community, night-time observations of the macroinvertebrate community, exclusion experiments that also keep out herbivorous macroinvertebrates, and/or experimental assessments of turf algae/CCA interactions.

Coupled beta diversity patterns among coral reef benthic taxa

Unraveling the processes that drive diversity patterns remains a central challenge for ecology, and an increased understanding is especially urgent to address and mitigate escalating diversity loss. Studies have primarily focused on singular taxonomic groups, but recent research has begun evaluating spatial diversity patterns across multiple taxonomic groups and suggests taxa may have congruence in their diversity patterns. Here, we use surveys of the coral reef benthic groups: scleractinian corals, macroalgae, sponges and gorgonians conducted in the Bahamian Archipelago across 27 sites to determine if there is congruence between taxonomic groups in their site-level diversity patterns (i.e. alpha diversity: number of species, and beta diversity: differences in species composition) while accounting for environmental predictors (i.e. depth, wave exposure, market gravity (i.e. human population size and distance to market), primary productivity, and grazing). Overall, we found that the beta diversities of these benthic groups were significant predictors of each other. The most consistent relationships existed with algae and coral, as their beta diversity was a significant predictor of every other taxa's beta diversity, potentially due to their strong biotic interactions and dominance on the reef. Conversely, we found no congruence patterns in the alpha diversity of the taxa. Market gravity and exposure showed the most prevalent correlation with both alpha and beta diversity for the taxa. Overall, our results suggest that coral reef benthic taxa can have spatial congruence in species composition, but not number of species, and that future research on biodiversity trends should consider that taxa may have non-independent patterns.

An unusual microbiome characterises a spatially-aggressive crustose alga rapidly overgrowing shallow Caribbean reefs

Several species of crustose coralline algae (CCA) and their associated microbial biofilms play important roles in determining the settlement location of scleractinian corals on tropical reefs. In recent decades, peyssonnelid algal crusts (PAC) have become spatial dominants across large areas of shallow Caribbean reefs, where they appear to deter the recruitment of scleractinians. Our genetic investigations of PAC in St. John, US Virgin Islands, amplifying the large-subunit ribosomal RNA and psbA protein D1 marker genes, revealed them to be identical to Ramicrusta textilis previously reported overgrowing corals in Jamaica. Specimens of PAC sampled from the Honduras were likewise identical, confirming that this crustose alga inhabits the easternmost and westernmost regions of the Caribbean. We also analysed 16S rDNA tag amplicon libraries of the biofilms associated with PAC and sympatric CCA, which is favoured for coral settlement. Our results show that the microbial communities on PAC (vs. CCA) are characterized by significantly lower numbers of the epibiotic bacterial genus Pseudoalteromonas, which facilitates the recruitment and settlement of marine invertebrates. From these data, we infer that PAC are therefore unlikely to be attractive as settlement sites for coral larvae. Given the significant ecological change anticipated on these reefs due to increasing cover of PAC, there is an urgent need to further investigate competitive interactions between PAC and scleractinian corals, and elucidate the role of PAC and their associated microbiomes in accentuating phase shifts from coral to algae on tropical reefs.

Testing the efficacy of lionfish traps in the northern Gulf of Mexico

Spearfishing is currently the primary approach for removing invasive lionfish (Pterois volitans/miles) to mitigate their impacts on western Atlantic marine ecosystems, but a substantial portion of lionfish spawning biomass is beyond the depth limits of SCUBA divers. Innovative technologies may offer a means to target deepwater populations and allow for the development of a lionfish trap fishery, but the removal efficiency and potential environmental impacts of lionfish traps have not been evaluated. We tested a collapsible, non-containment trap (the ‘Gittings trap’) near artificial reefs in the northern Gulf of Mexico. A total of 327 lionfish and 28 native fish (four were species protected with regulations) recruited (i.e., were observed within the trap footprint at the time of retrieval) to traps during 82 trap sets, catching 144 lionfish and 29 native fish (one more than recruited, indicating detection error). Lionfish recruitment was highest for single (versus paired) traps deployed <15 m from reefs with a 1-day soak time, for which mean lionfish and native fish recruitment per trap were approximately 5 and 0.1, respectively. Lionfish from traps were an average of 19 mm or 62 grams larger than those caught spearfishing. Community impacts from Gittings traps appeared minimal given that recruitment rates were >10X higher for lionfish than native fishes and that traps did not move on the bottom during two major storm events, although further testing will be necessary to test trap movement with surface floats. Additional research should also focus on design and operational modifications to improve Gittings trap deployment success (68% successfully opened on the seabed) and reduce lionfish escapement (56% escaped from traps upon retrieval). While removal efficiency for lionfish demonstrated by traps (12–24%) was far below that of spearfishing, Gittings traps appear suitable for future development and testing on deepwater natural reefs, which constitute >90% of the region’s reef habitat.

Interocean patterns in shallow water sponge assemblage structure and function

Sponges are a major component of benthic ecosystems across the world and fulfil a number of important functional roles. However, despite their importance, there have been few attempts to compare sponge assemblage structure and ecological functions across large spatial scales. In this review, we examine commonalities and differences between shallow water (<100 m) sponges at bioregional (15 bioregions) and macroregional (tropical, Mediterranean, temperate, and polar) scales, to provide a more comprehensive understanding of sponge ecology. Patterns of sponge abundance (based on density and area occupied) were highly variable, with an average benthic cover between ~1 and 30%. Sponges were generally found to occupy more space (percentage cover) in the Mediterranean and polar macroregions, compared to temperate and tropical macroregions, although sponge densities (sponges m^-2 ) were highest in temperate bioregions. Mean species richness standardised by sampling area was similar across all bioregions, except for a few locations that supported very high small-scale biodiversity concentrations. Encrusting growth forms were generally the dominant sponge morphology, with the exception of the Tropical West Atlantic, where upright forms dominated. Annelids and Arthropods were the most commonly reported macrofauna associated with sponges across bioregions. With respect to reproduction, there were no patterns in gametic development (hermaphroditism versus gonochorism), although temperate, tropical, and polar macroregions had an increasingly higher percentage of viviparous species, respectively, with viviparity being the sole gamete development mechanism reported for polar sponges to date. Seasonal reproductive timing was the most common in all bioregions, but continuous timing was more common in the Mediterranean and tropical bioregions compared to polar and temperate bioregions. We found little variation across bioregions in larval size, and the dominant larval type across the globe was parenchymella. No pattens among bioregions were found in the limited information available for standardised respiration and pumping rates. Many organisms were found to predate sponges, with the abundance of sponge predators being higher in tropical systems. While there is some evidence to support a higher overall proportion of phototrophic species in the Tropical Austalian bioregion compared to the Western Atlantic, both also have large numbers of heterotrophic species. Sponges are important spatial competitors across all bioregions, most commonly being reported to interact with anthozoans and algae. Even though the available information was limited for many bioregions, our analyses demonstrate some differences in sponge traits and functions among bioregions, and among macroregions. However, we also identified similarities in sponge assemblage structure and function at global scales, likely reflecting a combination of regional- and local-scale biological and physical processes affecting sponge assemblages, along with common ancestry. Finally, we used our analyses to highlight geographic bias in past sponge research, and identify gaps in our understanding of sponge ecology globally. By so doing, we identified key areas for future research on sponge ecology. We hope that our study will help sponge researchers to consider bioregion-specific features of sponge assemblages and key sponge-mediated ecological processes from a global perspective.

Widespread loss of Caribbean acroporid corals was underway before coral bleaching and disease outbreaks

The mass mortality of acroporid corals has transformed Caribbean reefs from coral- to macroalgal-dominated habitats since systematic monitoring began in the 1970s. Declines have been attributed to overfishing, pollution, sea urchin and coral disease, and climate change, but the mechanisms are unresolved due to the dearth of pre-1970s data. We used paleoecological, historical, and survey data to track Acropora presence and dominance throughout the Caribbean from the prehuman period to present. Declines in dominance from prehuman values first occurred in the 1950s for Acropora palmata and the 1960s for Acropora cervicornis, decades before outbreaks of acroporid disease or bleaching. We compared trends in Acropora dominance since 1950 to potential regional and local drivers. Human population negatively affected and consumption of fertilizer for agriculture positively affected A. palmata dominance, the latter likely due to lower human presence in agricultural areas. The earlier, local roots of Caribbean Acropora declines highlight the urgency of mitigating local human impacts.

The Emerging Ecological and Biogeochemical Importance of Sponges on Coral Reefs

With the decline of reef-building corals on tropical reefs, sponges have emerged as an important component of changing coral reef ecosystems. Seemingly simple, sponges are highly diverse taxonomically, morphologically, and in terms of their relationships with symbiotic microbes, and they are one of nature's richest sources of novel secondary metabolites. Unlike most other benthic organisms, sponges have the capacity to disrupt boundary flow as they pump large volumes of seawater into the water column. This seawater is chemically transformed as it passes through the sponge body as a consequence of sponge feeding, excretion, and the activities of microbial symbionts, with important effects on carbon and nutrient cycling and on the organisms in the water column and on the adjacent reef. In this review, we critically evaluate developments in the recently dynamic research area of sponge ecology on tropical reefs and provide a perspective for future studies.

Growth estimates of Caribbean reef sponges on a shipwreck using 3D photogrammetry

The growth rates and ages of many benthic marine organisms are poorly understood, complicating our understanding of ecosystem change. This is particularly true for sponges, which are morphologically diverse and lack indicators of annual growth. In this study, we used emerging technologies to measure volume, surface area, and approximate age of 16 sponge species on the Tibbetts shipwreck off Cayman Brac, Caribbean Sea. Photogrammetry was used to determine the volume of individual sponges on the wreck surface, and a time series of YouTube videos was amassed in order to approximate the greatest possible age of the sponges as 8.74 y. Applying the volume measurements to an existing growth equation for the Caribbean sponge Aiolochroia crassa yielded age estimates of 5.2–10.4 y for the largest individuals of the 16 species. Specific growth rates were then calculated for 7 species from the Tibbetts and 8 species from a second shipwreck (Spiegel Grove, Key Largo, FL). Subsequent growth forecasts from these 15 species corroborate a resource trade-off between growth and the production of chemical defenses. Shipwrecks and other anthropogenic structures can be an important source of demographic information for benthic organisms, provided that certain assumptions about their provenance and history can be met.

Microplastic Contamination Has Limited Effects on Coral Fertilisation and Larvae

Microplastics are ubiquitous throughout the world’s oceans and contaminate coral reef ecosystems. There is evidence of microplastic ingestion by corals and passive contact with coral tissues, causing adverse health effects that include energy expenditure for particle removal from the tissue surface, as well as reduced growth, tissue bleaching, and necrosis. Here, it was examined whether microplastic contamination impairs the success of gamete fertilisation, embryo development and larval settlement of the reef-building coral Acropora tenuis. Coral gametes and larvae were exposed to fifteen microplastic treatments using two types of plastic: (1) weathered polypropylene particles and (2) spherical polyethylene microbeads. The treatments ranged from five to 50 polypropylene pieces L−1 and 25 to 200 microbeads L−1. Fertilisation was only negatively affected by the largest weathered microplastics (2 mm2), but the effects were not dose dependent. Embryo development and larval settlement were not significantly impacted by either microplastic type. The study shows that moderate–high levels of marine microplastic contamination, specifically particles <2 mm2, will not substantially interfere with the success of critical early life coral processes.

Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges

BACKGROUND

Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO₄, NO_x, NH₄) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart).

RESULTS

Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO₄, and NO_x flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH₄ flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH₄ flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum.

CONCLUSIONS

Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.

Monitoring program design for data-limited marine biogenic habitats: A structured approach

Marine biogenic habitats-habitats created by living organisms-provide essential ecosystem functions and services, such as physical structuring, nutrient cycling, biodiversity support, and increases in primary, secondary, and tertiary production. With the growing trend toward ecosystem approaches to marine conservation and fisheries management, there is greater emphasis on rigorously designed habitat monitoring programs. However, such programs are challenging to design for data-limited habitats for which underlying ecosystem processes are poorly understood. To provide guidance in this area, we reviewed approaches to benthic assessments across well-studied marine biogenic habitats and identified common themes related to indicator selection, sampling methods, and survey design. Biogenic habitat monitoring efforts largely focus on the characteristics, distribution, and ecological function of foundation species, but may target other habitat-forming organisms, especially when community shifts are observed or expected, as well as proxies of habitat status, such as indicator species. Broad-scale methods cover large spatial areas and are typically used to examine the spatial configuration of habitats, whereas fine-scale methods tend to be laborious and thus restricted to small survey areas, but provide high-resolution data. Recent, emerging methods enhance the capabilities of surveying large areas at high spatial resolution and improve data processing efficiency, bridging the gap between broad- and fine-scale methods. Although sampling design selection may be limited by habitat characteristics and available resources, it is critically important to ensure appropriate matching of ecological, observational, and analytical scales. Drawing on these common themes, we propose a structured, iterative approach to designing monitoring programs for marine biogenic habitats that allows for rigorous data collection to inform management strategies, even when data and resource limitations are present. A practical application of this approach is illustrated using glass sponge reefs-a recently discovered and data-limited habitat type-as a case study.

The impact of fishing on a highly vulnerable ecosystem, the case of Juan Fernández Ridge ecosystem

The Juan Fernández Ridge (JFRE) is a vulnerable marine ecosystem (VME) located off the coast of central Chile formed by the Juan Fernández Archipelago and a group of seamounts. This ecosystem has unique biological and oceanographic features, characterized by: small geographical units, high degree of endemism with a high degree of connectivity within the system. Two fleets have historically operated in this system: a long term coastal artisanal fishery associated with the Islands, focused mainly on lobster, and a mainland based industrial demersal finfish fishery operating on the seamounts which is currently considered overexploited. The management of these fisheries has been based on a classical single-species approach to determine output controls (industrial fleet) and a mixed management system with formal and informal components (artisanal fleet). There has been growing interest in increasing the exploitation of fisheries, and modernization of the fishing fleet already operating in the JFRE. Under this scenario of increased levels of fishing exploitation and the high level of interrelation of species it might be necessary to understand the impact of these fisheries from a holistic perspective based on a ecosystem-based modeling approach. To address these challenges we developed an Atlantis end-to-end model was configured for this ecosystem. The implemented model has a high degree of skill in representing the observed trends and fluctuations of the JFRE. The model shows that the industrial fishing has a localized impact and the artisanal fisheries have a relatively low impact on the ecosystem, mainly via the lobster fishery. The model indicates that the depletion of large sized lobster has leads to an increase in the population of sea urchins. Although this increase is not sufficient, as yet, to cause substantial flow-on effects to other groups, caution is advised in case extra pressure leads the ecosystem towards a regime shift.

Hyperdiverse Macrofauna Communities Associated with a Common Sponge, Stylissa carteri, Shift across Ecological Gradients in the Central Red Sea

Sponges act as important microhabitats in the marine environment and promote biodiversity by harboring a wide variety of macrofauna, but little is known about the magnitude and patterns of diversity of sponge-associated communities. This study uses DNA barcoding to examine the macrofaunal communities associated with Stylissa carteri in the central Saudi Arabian Red Sea, an understudied ecosystem with high biodiversity and endemism. In total, 146 operational taxonomic units (OTUs) were distinguished from 938 successfully-sequenced macrofauna individuals from 99 sponges. A significant difference was found in the macrofaunal community composition of S. carteri along a cross-shelf gradient using OTU abundance (Bray–Curtis dissimilarity index), with more amphipods associated with offshore sponges and more brittle stars and fishes associated with inshore sponges. The abundance of S. carteri also showed a gradient, increasing with proximity to shore. However, no significant differences in macrofaunal community composition or total macrofauna abundance were observed between exposed and sheltered sides of the reefs and there was no significant change in total macrofauna abundance along the inshore–offshore gradient. As climate change and ocean acidification continue to impact coral reef ecosystems, understanding the ecology of sponges and their role as microhabitats may become more important for understanding their full ramifications for biodiversity.

Climate Change, Coral Loss, and the Curious Case of the Parrotfish Paradigm: Why Don't Marine Protected Areas Improve Reef Resilience?

Scientists have advocated for local interventions, such as creating marine protected areas and implementing fishery restrictions, as ways to mitigate local stressors to limit the effects of climate change on reef-building corals. However, in a literature review, we find little empirical support for the notion of managed resilience. We outline some reasons for why marine protected areas and the protection of herbivorous fish (especially parrotfish) have had little effect on coral resilience. One key explanation is that the impacts of local stressors (e.g., pollution and fishing) are often swamped by the much greater effect of ocean warming on corals. Another is the sheer complexity (including numerous context dependencies) of the five cascading links assumed by the managed-resilience hypothesis. If reefs cannot be saved by local actions alone, then it is time to face reef degradation head-on, by directly addressing anthropogenic climate change-the root cause of global coral decline.

Research gaps of coral ecology in a changing world

Coral reefs have long inspired marine ecologists and conservationists around the world due to their ecological and socioeconomic importance. Much knowledge on the anthropogenic impacts on coral species has been accumulated, but relevant research gaps on coral ecology remain underappreciated in human-modified seascapes. In this review we assessed 110 studies on coral responses to five major human disturbances- acidification, climate change, overfishing, pollution and non-regulated tourism -to identify geographic and theoretical gaps in coral ecology and help to guide further researches on the topic. We searched for papers in Web of Science published from 2000 to 2016 and classified them according to the ocean, ecoregion, human threat, level of biological organization, study approach, method of data collection, depth of data collected, and type of coral response. Most studies were carried out in the Indo-Pacific and Caribbean (36.3 and 31.9%, respectively) and used observational approach (60%) with scuba diving (36.3%) to assess the impact of ocean warming (55.4%) on coral communities (58.2%). Only 37 of the 141 global ecoregions that contain coral reefs were studied. All studies were restricted to shallow waters (0.5-27 m depth) and reported negative responses of corals to human disturbance. Our results reinforce the notion that corals are sensitive to anthropogenic changes. They reveal the scarcity of information on coral responses to pollution, tourism, overfishing and acidification, particularly in mesophotic ecosystems (>30 m depth) and in ecoregions outside the Indo-Pacific and Caribbean. Experimental studies at the individual and population levels should be also encouraged.

Climate change alterations to ecosystem dominance: how might sponge-dominated reefs function?

Anthropogenic stressors are impacting ecological systems across the world. Of particular concern are the recent rapid changes occurring in coral reef systems. With ongoing degradation from both local and global stressors, future reefs are likely to function differently from current coral-dominated ecosystems. Determining key attributes of future reef states is critical to reliably predict outcomes for ecosystem service provision. Here we explore the impacts of changing sponge dominance on coral reefs. Qualitative modelling of reef futures suggests that changing sponge dominance due to increased sponge abundance will have different outcomes for other trophic levels compared with increased sponge dominance as a result of declining coral abundance. By exploring uncertainty in the model outcomes we identify the need to (1) quantify changes in carbon flow through sponges, (2) determine the importance of food limitation for sponges, (3) assess the ubiquity of the recently described "sponge loop," (4) determine the competitive relationships between sponges and other benthic taxa, particularly algae, and (5) understand how changing dominance of other organisms alters trophic pathways and energy flows through ecosystems. Addressing these knowledge gaps will facilitate development of more complex models that assess functional attributes of sponge-dominated reef ecosystems.

Sponge chemical defenses are a possible mechanism for increasing sponge abundance on reefs in Zanzibar

Coral reefs are experiencing increasing anthropogenic impacts that result in substantial declines of reef-building corals and a change of community structure towards other benthic invertebrates or macroalgae. Reefs around Zanzibar are exposed to untreated sewage and runoff from the main city Stonetown. At many of these sites, sponge cover has increased over the last years. Sponges are one of the top spatial competitors on reefs worldwide. Their success is, in part, dependent on their strong chemical defenses against predators, microbial attacks and other sessile benthic competitors. This is the first study that investigates the bioactive properties of sponge species in the Western Indian Ocean region. Crude extracts of the ten most dominant sponge species were assessed for their chemical defenses against 35 bacterial strains (nine known as marine pathogens) using disc diffusion assays and general cytotoxic activities were assessed with brine shrimp lethality assays. The three chemically most active sponge species were additionally tested for their allelopathic properties against the scleractinian coral competitor Porites sp.. The antimicrobial assays revealed that all tested sponge extracts had strong antimicrobial properties and that the majority (80%) of the tested sponges were equally defended against pathogenic and environmental bacterial strains. Additionally, seven out of ten sponge species exhibited cytotoxic activities in the brine shrimp assay. Moreover, we could also show that the three most bioactive sponge species were able to decrease the photosynthetic performance of the coral symbionts and thus were likely to impair the coral physiology.

The importance of sponges and mangroves in supporting fish communities on degraded coral reefs in Caribbean Panama

Fish communities associated with coral reefs worldwide are threatened by habitat degradation and overexploitation. We assessed coral reefs, mangrove fringes, and seagrass meadows on the Caribbean coast of Panama to explore the influences of their proximity to one another, habitat cover, and environmental characteristics in sustaining biomass, species richness and trophic structure of fish communities in a degraded tropical ecosystem. We found 94% of all fish across all habitat types were of small body size (≤10 cm), with communities dominated by fishes that usually live in habitats of low complexity, such as Pomacentridae (damselfishes) and Gobiidae (gobies). Total fish biomass was very low, with the trend of small fishes from low trophic levels over-represented, and top predators under-represented, relative to coral reefs elsewhere in the Caribbean. For example, herbivorous fishes comprised 27% of total fish biomass in Panama relative to 10% in the wider Caribbean, and the small parrotfish Scarus iseri comprised 72% of the parrotfish biomass. We found evidence that non-coral biogenic habitats support reef-associated fish communities. In particular, the abundance of sponges on a given reef and proximity of mangroves were found to be important positive correlates of reef fish species richness, biomass, abundance and trophic structure. Our study indicates that a diverse fish community can persist on degraded coral reefs, and that the availability and arrangement within the seascape of other habitat-forming organisms, including sponges and mangroves, is critical to the maintenance of functional processes in such ecosystems.

Bleaching events regulate shifts from corals to excavating sponges in algae-dominated reefs

Changes in coral-sponge interactions can alter reef accretion/erosion balance and are important to predict trends on current algal-dominated Caribbean reefs. Although sponge abundance is increasing on some coral reefs, we lack information on how shifts from corals to bioeroding sponges occur, and how environmental factors such as anomalous seawater temperatures and consequent coral bleaching and mortality influence these shifts. A state transition model (Markov chain) was developed to evaluate the response of coral-excavating sponges (Cliona delitrix Pang 1973) after coral bleaching events. To understand possible outcomes of the sponge-coral interaction and build the descriptive model, sponge-corals were monitored in San Andres Island, Colombia (2004-2011) and Fort Lauderdale, Florida (2012-2013). To run the model and determine possible shifts from corals to excavating sponges, 217 coral colonies were monitored over 10 years (2000-2010) in Fort Lauderdale, Florida, and validated with data from 2011 to 2015. To compare and test its scalability, the model was also run with 271 coral colonies monitored in St. Croix, US Virgin Islands over 7 years (2004-2011), and validated with data from 2012 to 2015. Projections and sensitivity analyses confirmed coral recruitment to be key for coral persistence. Excavating sponge abundance increased in both Fort Lauderdale and St. Croix reefs after a regional mass bleaching event in 2005. The increase was more drastic in St. Croix than in Fort Lauderdale, where 25% of the healthy corals that deteriorated were overtaken by excavating sponges. Projections over 100 years suggested successive events of coral bleaching could shift algae-coral dominated reefs into algae-sponge dominated. The success of excavating sponges depended on the intensity of coral bleaching and consequent coral mortality. Thus, the proportion of C. delitrix excavating sponges is a sensitive indicator for the intensity and frequency of recent disturbance on Caribbean coral reefs.

A review of bottom-up vs. top-down control of sponges on Caribbean fore-reefs: what's old, what's new, and future directions

Interest in the ecology of sponges on coral reefs has grown in recent years with mounting evidence that sponges are becoming dominant members of reef communities, particularly in the Caribbean. New estimates of water column processing by sponge pumping activities combined with discoveries related to carbon and nutrient cycling have led to novel hypotheses about the role of sponges in reef ecosystem function. Among these developments, a debate has emerged about the relative effects of bottom-up (food availability) and top-down (predation) control on the community of sponges on Caribbean fore-reefs. In this review, we evaluate the impact of the latest findings on the debate, as well as provide new insights based on older citations. Recent studies that employed different research methods have demonstrated that dissolved organic carbon (DOC) and detritus are the principal sources of food for a growing list of sponge species, challenging the idea that the relative availability of living picoplankton is the sole proxy for sponge growth or abundance. New reports have confirmed earlier findings that reef macroalgae release labile DOC available for sponge nutrition. Evidence for top-down control of sponge community structure by fish predation is further supported by gut content studies and historical population estimates of hawksbill turtles, which likely had a much greater impact on relative sponge abundances on Caribbean reefs of the past. Implicit to investigations designed to address the bottom-up vs. top-down debate are appropriate studies of Caribbean fore-reef environments, where benthic communities are relatively homogeneous and terrestrial influences and abiotic effects are minimized. One recent study designed to test both aspects of the debate did so using experiments conducted entirely in shallow lagoonal habitats dominated by mangroves and seagrass beds. The top-down results from this study are reinterpreted as supporting past research demonstrating predator preferences for sponge species that are abundant in these lagoonal habitats, but grazed away in fore-reef habitats. We conclude that sponge communities on Caribbean fore-reefs of the past and present are largely structured by predation, and offer new directions for research, such as determining the environmental conditions under which sponges may be food-limited (e.g., deep sea, lagoonal habitats) and monitoring changes in sponge community structure as populations of hawksbill turtles rebound.

A decadal analysis of bioeroding sponge cover on the inshore Great Barrier Reef

Decreasing coral cover on the Great Barrier Reef (GBR) may provide opportunities for rapid growth and expansion of other taxa. The bioeroding sponges Cliona spp. are strong competitors for space and may take advantage of coral bleaching, damage, and mortality. Benthic surveys of the inshore GBR (2005–2014) revealed that the percent cover of the most abundant bioeroding sponge species, Cliona orientalis, has not increased. However, considerable variation in C. orientalis cover, and change in cover over time, was evident between survey locations. We assessed whether biotic or environmental characteristics were associated with variation in C. orientalis distribution and abundance. The proportion of fine particles in the sediments was negatively associated with the presence-absence and the percent cover of C. orientalis, indicating that the sponge requires exposed habitat. The cover of corals and other sponges explained little variation in C. orientalis cover or distribution. The fastest increases in C. orientalis cover coincided with the lowest macroalgal cover and chlorophyll a concentration, highlighting the importance of macroalgal competition and local environmental conditions for this bioeroding sponge. Given the observed distribution and habitat preferences of C. orientalis, bioeroding sponges likely represent site-specific – rather than regional – threats to corals and reef accretion.

Sponge symbioses between Xestospongia deweerdtae and Plakortis spp. are not motivated by shared chemical defense against predators

The recently described epizoic sponge-sponge symbioses between Xestospongia deweerdtae and two species of Plakortis present an unusual series of sponge interactions. Sponges from the genus Plakortis are fierce allelopathic competitors, rich in cytotoxic secondary metabolites, and yet X. deweerdtae flourishes as an epizoic encrustation on Plakortis deweerdtaephila and Plakortis symbiotica. Our objective in this study was to evaluate the hypothesis that X. deweerdtae grows epizoic to these two species of Plakortis due to a shared chemical defense against predators. We collected free-living individuals of X. deweerdtae and symbiotic pairs from a wide geographical range to generate crude organic extracts and a series of polarity fractions from sponge extract. We tested the deterrency of these extracts against three common coral reef predators: the bluehead wrasse, Thalassoma bifasciatum, the Caribbean sharpnose puffer, Canthigaster rostrata, and the white spotwrist hermit crab, Pagurus criniticornis. While the chemical defenses of P. deweerdtaephila and P. symbiotica are more potent than those of X. deweerdtae, all of the sponge species we tested significantly deterred feeding in all three generalist predators. The free-living form of X. deweerdtae is mostly defended across the region, with a few exceptions. The associated form of X. deweerdtae is always defended, and both species of Plakortis are very strongly defended, with puffers refusing to consume extract-treated pellets until the extract was diluted to 1/256× concentration. Using diode-array high performance liquid chromatography (HPLC) coupled with high-resolution mass spectrometry (LC-MS/IT-TOF), we found two secondary metabolites from P. deweerdtaephila, probably the cyclic endoperoxides plakinic acid I and plakinic acid K, in low concentrations in the associated—but not the free-living—form of X. deweerdtae, suggesting a possible translocation of defensive chemicals from the basibiont to the epibiont. Comparing the immense deterrency of Plakortis spp. extracts to the extracts of X. deweerdtae gives the impression that there may be some sharing of chemical defenses: one partner in the symbiosis is clearly more defended than the other and a small amount of its defensive chemistry may translocate to the partner. However, X. deweerdtae effectively deters predators with its own defensive chemistry. Multiple lines of evidence provide no support for the shared chemical defense hypothesis. Given the diversity of other potential food resources available to predators on coral reefs, it is improbable that the evolution of these specialized sponge-sponge symbioses has been driven by predation pressure.

Rapidly increasing macroalgal cover not related to herbivorous fishes on Mesoamerican reefs

Long-term phase shifts from coral to macroalgal dominated reef systems are well documented in the Caribbean. Although the impact of coral diseases, climate change and other factors is acknowledged, major herbivore loss through disease and overfishing is often assigned a primary role. However, direct evidence for the link between herbivore abundance, macroalgal and coral cover is sparse, particularly over broad spatial scales. In this study we use a database of coral reef surveys performed at 85 sites along the Mesoamerican Reef of Mexico, Belize, Guatemala and Honduras, to examine potential ecological links by tracking site trajectories over the period 2005–2014. Despite the long-term reduction of herbivory capacity reported across the Caribbean, the Mesoamerican Reef region displayed relatively low macroalgal cover at the onset of the study. Subsequently, increasing fleshy macroalgal cover was pervasive. Herbivorous fish populations were not responsible for this trend as fleshy macroalgal cover change was not correlated with initial herbivorous fish biomass or change, and the majority of sites experienced increases in macroalgae browser biomass. This contrasts the coral reef top-down herbivore control paradigm and suggests the role of external factors in making environmental conditions more favourable for algae. Increasing macroalgal cover typically suppresses ecosystem services and leads to degraded reef systems. Consequently, policy makers and local coral reef managers should reassess the focus on herbivorous fish protection and consider complementary measures such as watershed management in order to arrest this trend.

GoPros™ as an underwater photogrammetry tool for citizen science

Citizen science can increase the scope of research in the marine environment; however, it suffers from necessitating specialized training and simplified methodologies that reduce research output. This paper presents a simplified, novel survey methodology for citizen scientists, which combines GoPro imagery and structure from motion to construct an ortho-corrected 3D model of habitats for analysis. Results using a coral reef habitat were compared to surveys conducted with traditional snorkelling methods for benthic cover, holothurian counts, and coral health. Results were comparable between the two methods, and structure from motion allows the results to be analysed off-site for any chosen visual analysis. The GoPro method outlined in this study is thus an effective tool for citizen science in the marine environment, especially for comparing changes in coral cover or volume over time.

An Integrated Coral Reef Ecosystem Model to Support Resource Management under a Changing Climate

Millions of people rely on the ecosystem services provided by coral reefs, but sustaining these benefits requires an understanding of how reefs and their biotic communities are affected by local human-induced disturbances and global climate change. Ecosystem-based management that explicitly considers the indirect and cumulative effects of multiple disturbances has been recommended and adopted in policies in many places around the globe. Ecosystem models give insight into complex reef dynamics and their responses to multiple disturbances and are useful tools to support planning and implementation of ecosystem-based management. We adapted the Atlantis Ecosystem Model to incorporate key dynamics for a coral reef ecosystem around Guam in the tropical western Pacific. We used this model to quantify the effects of predicted climate and ocean changes and current levels of current land-based sources of pollution (LBSP) and fishing. We used the following six ecosystem metrics as indicators of ecosystem state, resilience and harvest potential: 1) ratio of calcifying to non-calcifying benthic groups, 2) trophic level of the community, 3) biomass of apex predators, 4) biomass of herbivorous fishes, 5) total biomass of living groups and 6) the end-to-start ratio of exploited fish groups. Simulation tests of the effects of each of the three drivers separately suggest that by mid-century climate change will have the largest overall effect on this suite of ecosystem metrics due to substantial negative effects on coral cover. The effects of fishing were also important, negatively influencing five out of the six metrics. Moreover, LBSP exacerbates this effect for all metrics but not quite as badly as would be expected under additive assumptions, although the magnitude of the effects of LBSP are sensitive to uncertainty associated with primary productivity. Over longer time spans (i.e., 65 year simulations), climate change impacts have a slight positive interaction with other drivers, generally meaning that declines in ecosystem metrics are not as steep as the sum of individual effects of the drivers. These analyses offer one way to quantify impacts and interactions of particular stressors in an ecosystem context and so provide guidance to managers. For example, the model showed that improving water quality, rather than prohibiting fishing, extended the timescales over which corals can maintain high abundance by at least 5–8 years. This result, in turn, provides more scope for corals to adapt or for resilient species to become established and for local and global management efforts to reduce or reverse stressors.