Shortened food chain length in a fished versus unfished coral reef

Direct exploitation through fishing is driving dramatic declines of wildlife populations in ocean environments, particularly for predatory and large-bodied taxa. Despite wide recognition of this pattern and well-established consequences of such trophic downgrading on ecosystem function, there have been few empirical studies examining the effects of fishing on whole system trophic architecture. Understanding these kinds of structural impacts is especially important in coral reef ecosystems-often heavily fished and facing multiple stressors. Given the often high dietary flexibility and numerous functional redundancies in diverse ecosystems such as coral reefs, it is important to establish whether web architecture is strongly impacted by fishing pressure or whether it might be resilient, at least to moderate-intensity pressure. To examine this question, we used a combination of bulk and compound-specific stable isotope analyses measured across a range of predatory and low-trophic-level consumers between two coral reef ecosystems that differed with respect to fishing pressure but otherwise remained largely similar. We found that even in a high-diversity system with relatively modest fishing pressure, there were strong reductions in the trophic position (TP) of the three highest TP consumers examined in the fished system but no effects on the TP of lower-level consumers. We saw no evidence that this shortening of the affected food webs was being driven by changes in basal resource consumption, for example, through changes in the spatial location of foraging by consumers. Instead, this likely reflected internal changes in food web architecture, suggesting that even in diverse systems and with relatively modest pressure, human harvest causes significant compressions in food chain length. This observed shortening of these food webs may have many important emergent ecological consequences for the functioning of ecosystems impacted by fishing or hunting. Such important structural shifts may be widespread but unnoticed by traditional surveys. This insight may also be useful for applied ecosystem managers grappling with choices about the relative importance of protection for remote and pristine areas and the value of strict no-take areas to protect not just the raw constituents of systems affected by fishing and hunting but also the health and functionality of whole systems.

Quantifying energy and nutrient fluxes in coral reef food webs

The movement of energy and nutrients through ecological communities represents the biological 'pulse' underpinning ecosystem functioning and services. However, energy and nutrient fluxes are inherently difficult to observe, particularly in high-diversity systems such as coral reefs. We review advances in the quantification of fluxes in coral reef fishes, focusing on four key frameworks: demographic modelling, bioenergetics, micronutrients, and compound-specific stable isotope analysis (CSIA). Each framework can be integrated with underwater surveys, enabling researchers to scale organismal processes to ecosystem properties. This has revealed how small fish support biomass turnover, pelagic subsidies sustain fisheries, and fisheries benefit human health. Combining frameworks, closing data gaps, and expansion to other aquatic ecosystems can advance understanding of how fishes contribute to ecosystem functions and services.

Complexity-functioning relationships differ across different environmental conditions

Habitat complexity is widely considered an important determinant of biodiversity, and enhancing complexity can play a key role in restoring degraded habitats. However, the effects of habitat complexity on ecosystem functioning - as opposed to biodiversity and community structure - are relatively poorly understood for artificial habitats, which dominate many coastlines. With Greening of Grey Infrastructure (GGI) approaches, or eco-engineering, increasingly being applied around the globe, it is important to understand the effects that modifying habitat complexity has on both biodiversity and ecological functioning in these highly modified habitats. We assessed how manipulating physical (primary substrate) and/or biogenic habitat (bivalves) complexity on intertidal artificial substrata affected filtration rates, net and gross primary productivity (NPP and GPP, respectively) and community respiration (CR) - as well as abundance of filter feeders and macro-algae and habitat use by cryptobenthic fish across six locations in three continents. We manipulated both physical and biogenic complexity using 1) flat or ridged (2.5 cm or 5 cm) settlement tiles that were either 2) unseeded or seeded with oysters or mussels. Across all locations, increasing physical and biogenic complexity (5 cm seeded tiles) had a significant effect on most ecological functioning variables, increasing overall filtration rates and community respiration of the assemblages on tiles but decreasing productivity (both GPP and NPP) across all locations. There were no overall effects of increasing either type of habitat complexity on cryptobenthic fish MaxN, total time in frame or macro-algal cover. Within each location, there were marked differences in the effects of habitat complexity. In Hobart, we found higher filtration, filter feeder biomass and community respiration on 5 cm tiles compared to flat tiles. However, at this location, both macro-algae cover and GPP decreased with increasing physical complexity. Similarly in Dublin, filtration, filter feeder biomass and community respiration were higher on 5 cm tiles compared to less complex tiles. In Sydney, filtration and filter feeder biomass were higher on seeded than unseeded tiles, and fish MaxN was higher on 5 cm tiles compared to flat tiles. On unseeded tiles in Sydney, filter feeder biomass also increased with increasing physical complexity. Our findings suggest that GGI solutions via increased habitat complexity are likely to have trade-offs among potentially desired functions, such as productivity and filtration rates, and variable effects on cryptobenthic fish communities. Importantly, our results show that the effects of GGI practices can vary markedly according to the environmental context and therefore should not be blindly and uniformly applied across the globe.

Habitat-specific impacts of climate change on the trophic demand of a marine predator

Metabolic ecology predicts that ectotherm metabolic rates, and thus consumption rates, will increase with body size and temperature. Predicted climatic increases in temperature are likely to increase the consumption rates of ectothermic predators; however, the ecological impact of these increases will partly depend on whether prey productivity changes with temperature at a similar rate. Furthermore, total predator consumption and prey productivity will depend on species abundances that vary across habitat types. Here we combine energetics and biotelemetry to measure consumption rates in a critically endangered coral reef predator, the Nassau grouper (Epinephelus striatus), in The Bahamas. We estimate that, at present, the Nassau grouper needs to consume 2.2% ± 1.0% body weight day-1 , but this could increase up to 24% with a predicted 3.1°C increase in ocean temperature by the end of the century. We then used surveys of prey communities in two major reef habitat types (Orbicella reef and Gorgonian plain), to predict the proportion of prey productivity consumed by grouper and how this varied by habitat with changing climates. We found that at present, the predicted proportion of prey productivity consumed by Nassau grouper decreased with increasing prey productivity and averaged 1.2% across all habitats, with a greater proportion of prey productivity consumed (maximum of 5%) in Gorgonian plain habitats. However, because temperature increases consumption rates faster than prey productivity, the proportion of prey productivity consumed in a Gorgonian plain habitat could increase up to 24% under future climate change scenarios. Our results suggest that increasing ocean temperatures will lead to significant energetic challenges for the Nassau grouper because of differential impacts within reef food webs, but the magnitude of these impacts will probably vary across prey productivity gradients.

Reduced small-scale structural complexity on sponge-dominated areas of Indo-Pacific coral reefs

Corals provide a complex 3D framework that offers habitat to diverse coral reef fauna. However, future reefs are likely to experience reduced coral abundance. Sponges have been proposed as one potential winner on future coral reefs, but little is known of how they contribute to reef 3D structure. Given the ecological importance of structural complexity, it is critical to understand how changes in the abundance of structure-building organisms will affect the three-dimensional properties of coral reefs. To investigate the potentially important functional role of coral reef sponges as providers of structural complexity, we compared the structural complexity of coral- and sponge-dominated areas of an Indonesian coral reef, using 3D photogrammetry at a 4 m2 spatial scale. Structural complexity of 31 4 m2 quadrats was expressed as rugosity indicating reef contour complexity (R), vector dispersion indicating heterogeneity of angles between reef surfaces (1/k), and fractal dimension indicating geometrical complexity at five different spatial scales between 1 and 120 cm (D1-5). Quadrats were identified as high- or low-complexity using hierarchical clustering based on the complexity metrics. At high structural complexity, coral- and sponge-dominated quadrats were similar in terms of R and 1/k. However, smallest-scale refuge spaces (1-5 cm) were more abundant in coral-dominated quadrats, whereas larger scale refuge spaces (30-60 cm) were more abundant in sponge-dominated quadrats. Branching and massive corals contributed the most to structural complexity in coral-dominated quadrats, and barrel sponges in sponge-dominated quadrats. We show that smaller-scale refugia (1-5 cm) are reduced on sponge-dominated reefs at the spatial scale considered here (4 m2), with potential negative implications for smaller reef fauna.

Similar functional composition of fish assemblages despite contrasting levels of habitat degradation on shallow Caribbean coral reefs

Functional trait-based approaches provide an opportunity to assess how changes in habitat affect the structure of associated communities. Global analyses have found a similarity in the composition of reef fish functional traits despite differences in species richness, environmental regimes, and habitat components. These large-scale patterns raised the question of whether this same stability can be observed at smaller spatial scales. Here, we compared the fish trait composition and their functional diversity in two Caribbean shallow coral reefs with contrasting levels of habitat degradation: Limones (>30% cover), constituted mainly by colonies of Acropora palmata and Bonanza, a reef with extensive areas of dead Acropora structures, dominated by algae. To characterize the functional structure of fishes on each reef, we calculated the community-weighted mean trait values (CWM), functional richness, functional evenness, functional dispersion, and functional originality. Despite the differences in habitat quality, reefs exhibited a similar proportion and common structure on fish functional traits. Functional richness and functional evenness differed significantly, but functional dispersion and functional originality did not show differences between reefs. The greater niche complexity driven by the high availability of microhabitats provided by A. palmata may explain the higher functional richness in Limones, whereas the reef degradation in Bonanza may contribute to a higher functional evenness because of a similar distribution of abundance per fish trait combinations. Our results suggest that widespread degradation on Caribbean reefs has limited the type, variety, and range of traits, which could lead to a functional homogenization of fish communities even at local scales.

Factors influencing the biomass of large-bodied parrotfish species in the absence of fishing on coral reefs in Florida, USA

Parrotfishes are a functionally critical component of Caribbean reef fish assemblages, with large-bodied parrotfish species exerting particularly important top-down control on macroalgae. Despite their importance, low biomasses of large-bodied parrotfishes on many reefs hamper our ability to study and understand their ecology. Florida reefs, where most parrotfish fishing has been illegal since 1992, present a unique opportunity to explore covariates of their distribution. Using boosted regression tree models and 23 covariates, this study identified the major predictors of four species of Atlantic large-bodied parrotfishes. Maximum hard substrate relief, the area of the surrounding reef, and the availability of seagrass habitat were each positively related to parrotfish presence. Strong positive relationships between parrotfish presence and biomass and the biomass of other parrotfishes on a reef suggest that all four species responded to a similar subset of environmental conditions. However, relationships between parrotfish presence and biomass and depth, habitat type, coral cover, and the proximity of a reef to deepwater habitats differed among species, highlighting distinct habitat preferences. These results can improve managers' ability to target important biophysical correlates of large-bodied parrotfishes with appropriate management interventions and identify areas for protection.

Blood meal identification reveals extremely broad host range and host-bias in a temporary ectoparasite of coral reef fishes

Appreciation for the role of cryptofauna in ecological systems has increased dramatically over the past decade. The impacts blood-feeding arthropods, such as ticks and mosquitos, have on terrestrial communities are the subject of hundreds of papers annually. However, blood-feeding arthropods have been largely ignored in marine environments. Gnathiid isopods, often referred to as "ticks of the sea", are temporary external parasites of fishes. They are found in all marine environments and have many consequential impacts on host fitness. Because they are highly mobile and only associated with their hosts while obtaining a blood meal, their broader trophic connections are difficult to discern. Conventional methods rely heavily on detecting gnathiids on wild-caught fishes. However, this approach typically yields few gnathiids and does not account for hosts that avoid capture. To overcome this limitation, we sequenced blood meals of free-living gnathiids collected in light traps to assess the host range and community-dependent exploitation of Caribbean gnathiid isopods. Using fish-specific COI (cox1) primers, sequencing individual blood meals from 1060 gnathiids resulted in the identification of 70 host fish species from 27 families. Comparisons of fish assemblages to blood meal identification frequencies at four collection sites indicated that fishes within the families Haemulidae (grunts) and Lutjanidae (snappers) were exploited more frequently than expected based on their biomass, and Labrid parrotfishes were exploited less frequently than expected. The broad host range along with the biased exploitation of diel-migratory species has important implications for the role gnathiid isopods play in Caribbean coral reef communities.

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.

Trophic distribution of nutrient production in coral reef fisheries

Coral reef fisheries supply nutritious catch to tropical coastal communities, where the quality of reef seafood is determined by both the rate of biomass production and nutritional value of reef fishes. Yet our understanding of reef fisheries typically uses targets of total reef fish biomass rather than individual growth (i.e. biomass production) and nutrient content (i.e. nutritional value of reef fish), limiting the ability of management to sustain the productivity of nutritious catches. Here, we use modelled growth coefficients and nutrient concentrations to develop a new metric of nutrient productivity of coral reef fishes. We then evaluate this metric with underwater visual surveys of reef fish assemblages from four tropical countries to examine nutrient productivity of reef fish food webs. Species' growth coefficients were associated with nutrients that vary with body size (calcium, iron, selenium and zinc), but not total nutrient density. When integrated with fish abundance data, we find that herbivorous species typically dominate standing biomass, biomass turnover and nutrient production on coral reefs. Such bottom-heavy trophic distributions of nutrients were consistent across gradients of fishing pressure and benthic composition. We conclude that management restrictions that promote sustainability of herbivores and other low trophic-level species can sustain biomass and nutrient production from reef fisheries that is critical to the food security of over 500 million people in the tropics.

Two new species of Varicus from Caribbean deep reefs, with comments on the related genus Pinnichthys (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup)

Tropical deep reefs (~40-300 m) are diverse ecosystems that serve as habitats for diverse communities of reef-associated fishes. Deep-reef fish communities are taxonomically and ecologically distinct from those on shallow reefs, but like those on shallow reefs, they are home to a species-rich assemblage of small, cryptobenthic reef fishes, including many species from the family Gobiidae (gobies). Here we describe two new species of deep-reef gobies, Varicusprometheussp. nov. and V.roatanensissp. nov., that were collected using the submersible Idabel from rariphotic reefs off the island of Roatan (Honduras) in the Caribbean. The new species are the 11th and 12th species of the genus Varicus, and their placement in the genus is supported by morphological data and molecular phylogenetic analyses. Additionally, we also collected new specimens of the closely-related genus and species Pinnichthysaimoriensis during submersible collections off the islands of Bonaire and St. Eustatius (Netherland Antilles) and included them in this study to expand the current description of that species and document its range extension from Brazil into the Caribbean. Collectively, the two new species of Varicus and new records of P.aimoriensis add to our growing knowledge of cryptobenthic fish diversity on deep reefs of the Caribbean.

Links between the timing of life-history transitions and dietary and morphological variation during early life history in the sand goby, Pomatoschistus minutus

Bipartite life histories involve a suite of morphological changes that support the pelagic to demersal transition and an expanded range of prey options and microhabitats. Pelagic individuals are thought to shift (settle) to their preferred benthic habitat at the earliest opportunity once they have attained a minimum level of morphological competency to access their new environment. In theory, early changes in larval morphology (collectively termed 'metamorphosis'), habitat and diet-a measure of habitat-use-ought to be synchronous. Yet relationships may be decoupled by factors linked to behaviour, prey availability or morphological complexity, and few descriptions exist to allow such synchrony to be assessed. The sand goby, Pomatoschistus minutus, is a common coastal fish across north-western Europe, with a size at larval metamorphosis and settlement of around 10 and 16-18 mm standard length (SL), respectively. We sampled shoreline larval and juvenile populations to examine relationships between morphology, diet and life stage. Prey diversity increased with body length; however, dietary change was clearest at 16-18 mm SL, with a reduction in calanoid copepods and shift to larger prey such as Nereis polychaetes and mysid and amphipod crustacea. Early growth in five prey capture and processing morphologies was rapid. Four of these showed a subsequent marked shift to slower growth, but none of these changes were aligned with size at metamorphosis and only that of mouth width coincided with body size at settlement. Early life history in P. minutus appears geared towards a protracted morphological reorganization prior to demersal life and an alternative suite of prey resources. Larval metamorphosis seems to be of limited consequence in this regard. Comparable studies of other Baltic Sea fishes would confirm whether these dynamics relate to shared environmental pressures or to factors intrinsic to P. minutus biology.

The evolution of fast-growing coral reef fishes

Individual growth is a fundamental life history trait^1-4, yet its macroevolutionary trajectories have rarely been investigated for entire animal assemblages. Here we analyse the evolution of growth in a highly diverse vertebrate assemblage-coral reef fishes. We combine state-of-the-art extreme gradient boosted regression trees with phylogenetic comparative methods to detect the timing, number, location and magnitude of shifts in the adaptive regime of somatic growth. We also explored the evolution of the allometric relationship between body size and growth. Our results show that the evolution of fast growth trajectories in reef fishes has been considerably more common than the evolution of slow growth trajectories. Many reef fish lineages shifted towards faster growth and smaller body size evolutionary optima in the Eocene (56-33.9 million years ago), pointing to a major expansion of life history strategies in this Epoch. Of all lineages examined, the small-bodied, high-turnover cryptobenthic fishes shifted most towards extremely high growth optima, even after accounting for body size allometry. These results suggest that the high global temperatures of the Eocene⁵ and subsequent habitat reconfigurations⁶ might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems.

Viral predation pressure on coral reefs

BACKGROUND

Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health.

RESULTS

Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m^-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations.

CONCLUSIONS

The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.

Emigration patterns of motile cryptofauna and their implications for trophic functioning in coral reefs

Patterns of movement of marine species can reflect strategies of reproduction and dispersal, species' interactions, trophodynamics, and susceptibility to change, and thus critically inform how we manage populations and ecosystems. On coral reefs, the density and diversity of metazoan taxa are greatest in dead coral and rubble, which are suggested to fuel food webs from the bottom up. Yet, biomass and secondary productivity in rubble is predominantly available in some of the smallest individuals, limiting how accessible this energy is to higher trophic levels. We address the bioavailability of motile coral reef cryptofauna based on small-scale patterns of emigration in rubble. We deployed modified RUbble Biodiversity Samplers (RUBS) and emergence traps in a shallow rubble patch at Heron Island, Great Barrier Reef, to detect community-level differences in the directional influx of motile cryptofauna under five habitat accessibility regimes. The mean density (0.13-4.5 ind cm^-3) and biomass (0.14-5.2 mg cm^-3) of cryptofauna were high and varied depending on microhabitat accessibility. Emergent zooplankton represented a distinct community (dominated by the Appendicularia and Calanoida) with the lowest density and biomass, indicating constraints on nocturnal resource availability. Mean cryptofauna density and biomass were greatest when interstitial access within rubble was blocked, driven by the rapid proliferation of small harpacticoid copepods from the rubble surface, leading to trophic simplification. Individuals with high biomass (e.g., decapods, gobies, and echinoderms) were greatest when interstitial access within rubble was unrestricted. Treatments with a closed rubble surface did not differ from those completely open, suggesting that top-down predation does not diminish rubble-derived resources. Our results show that conspecific cues and species' interactions (e.g., competition and predation) within rubble are most critical in shaping ecological outcomes within the cryptobiome. These findings have implications for prey accessibility through trophic and community size structuring in rubble, which may become increasingly relevant as benthic reef complexity shifts in the Anthropocene.

New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)

Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).

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.

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.

Life-history constraints, short adult life span and reproductive strategies in coral reef gobies of the genus Trimma

Body size influences many life-history traits, with small-bodied animals tending to have short life spans, high mortality and greater reproductive effort early in life. In this study, the authors investigated the life-history traits and reproductive strategies of three small-bodied coral reef gobies of the genus Trimma: Trimma benjamini, Trimma capostriatum and Trimma yanoi. The authors found all Trimma species studied attained a small body size of <25 mm, had a short life span of <140 days and experienced high estimated daily mortality of 3.0%-6.7%. Furthermore, the pelagic larval phase accounted for 25.3%-28.5% of the maximum life span, and maturation occurred between 74.1 and 82.1 days at 15.2-15.8 mm, leaving only 35%-43% of the total life span as a reproductively viable adult. All mature individuals had gonad structures consistent with bidirectional sex change, with bisexual gonads including both ovarian and testicular portions separated by a thin wall of connective tissue. In the female and male phases, only ovaries or testes were mature, whereas gonadal tissue of the non-active sex remained. One T. benjamini individual and one T. yanoi individual had ovarian and testicular tissue active simultaneously. The results of this study highlight the life-history challenges small CRFs face on their path to reproduction and reproductive strategies that could be beneficial in fishes with high and unpredictable mortality and short reproductive life spans.

Paternal care regulates the timing, synchrony and success of hatching in a coral reef fish

In oviparous species, the timing of hatching is a crucial decision, but for developing embryos, assessing cues that indicate the optimal time to hatch is challenging. In species with pre-hatching parental care, parents can assess environmental conditions and induce their offspring to hatch. We provide the first documentation of parental hatching regulation in a coral reef fish, demonstrating that male neon gobies (Elacatinus colini) directly regulate hatching by removing embryos from the clutch and spitting hatchlings into the water column. All male gobies synchronized hatching within 2 h of sunrise, regardless of when eggs were laid. Paternally incubated embryos hatched later in development, more synchronously, and had higher hatching success than artificially incubated embryos that were shaken to provide a vibrational stimulus or not stimulated. Artificially incubated embryos displayed substantial plasticity in hatching times (range: 80-224 h post-fertilization), suggesting that males could respond to environmental heterogeneity by modifying the hatching time of their offspring. Finally, paternally incubated embryos hatched with smaller yolk sacs and larger propulsive areas than artificially incubated embryos, suggesting that paternal effects on hatchling phenotypes may influence larval dispersal and fitness. These findings highlight the complexity of fish parental care behaviour and may have important, and currently unstudied, consequences for fish population dynamics.

Ecological succession of the sponge cryptofauna in Hawaiian reefs add new insights to detritus production by pioneering species

Successional theory proposes that fast growing and well dispersed opportunistic species are the first to occupy available space. However, these pioneering species have relatively short life cycles and are eventually outcompeted by species that tend to be longer-lived and have lower dispersal capabilities. Using Autonomous Reef Monitoring Structures (ARMS) as standardized habitats, we examine the assembly and stages of ecological succession among sponge species with distinctive life history traits and physiologies found on cryptic coral reef habitats of Kāneʻohe Bay, Hawaiʻi. Sponge recruitment was monitored bimonthly over 2 years on ARMS deployed within a natural coral reef habitat resembling the surrounding climax community and on ARMS placed in unestablished mesocosms receiving unfiltered seawater directly from the natural reef deployment site. Fast growing haplosclerid and calcareous sponges initially recruited to and dominated the mesocosm ARMS. In contrast, only slow growing long-lived species initially recruited to the reef ARMS, suggesting that despite available space, the stage of ecological succession in the surrounding habitat influences sponge community development in uninhabited space. Sponge composition and diversity between early summer and winter months within mesocosm ARMS shifted significantly as the initially recruited short-lived calcareous and haplosclerid species initially recruit and then died off. The particulate organic carbon contribution of dead sponge tissue from this high degree of competition-free community turnover suggests a possible new component to the sponge loop hypothesis which remains to be tested among these pioneering species. This source of detritus could be significant in early community development of young coastal habitats but less so on established coral reefs where the community is dominated by long-lived colonial sponges.

The role of nocturnal fishes on coral reefs: A quantitative functional evaluation

The ecological functions of nocturnal coral reef fishes are poorly known. Yet, nocturnal resources for coral reef consumers are theoretically as abundant and productive, if not more so, than their diurnal counterparts. In this study, we quantify and contrast the energetic dynamics of nocturnal and diurnal fishes in a model coral reef ecosystem, evaluating whether they attain similar levels of biomass production. We integrated a detailed dataset of coral reef fish counts, comprising diurnal and nocturnal species, in sites sheltered and exposed to wave action. We combined somatic growth and mortality models to estimate rates of consumer biomass production, a key ecosystem function. We found that diurnal fish assemblages have a higher biomass than nocturnal fishes: 104% more in sheltered sites and 271% more in exposed sites. Differences in productivity were even more pronounced, with diurnal fishes contributing 163% more productivity in sheltered locations, and 558% more in exposed locations. Apogonidae dominated biomass production within the nocturnal fish assemblage, comprising 54% of total nocturnal fish productivity, which is proportionally more than any diurnal fish family. The substantially lower contributions of nocturnal fishes to biomass and biomass production likely indicate constraints on resource accessibility. Taxa that overcome these constraints may thrive, as evidenced by apogonids. This study highlights the importance of nocturnal fishes in underpinning the flow of energy and nutrients from nocturnal resources to reef communities; a process driven mainly by small, cryptic fishes.

Combining stereo‐video monitoring and physiological trials to estimate reef fish metabolic demands in the wild

Organismal metabolic rates (MRs) are the basis of energy and nutrient fluxes through ecosystems. In the marine realm, fishes are some of the most prominent consumers. However, their metabolic demand in the wild (field MR [FMR]) is poorly documented, because it is challenging to measure directly. Here, we introduce a novel approach to estimating the component of FMR associated with voluntary activity (i.e., the field active MR [AMRfield]). Our approach combines laboratory‐based respirometry, swimming speeds, and field‐based stereo‐video systems to estimate the activity of individuals. We exemplify our approach by focusing on six coral reef fish species, for which we quantified standard MR and maximum MR (SMR and MMR, respectively) in the laboratory, and body sizes and swimming speeds in the field. Based on the relationships between MR, body size, and swimming speeds, we estimate that the activity scope (i.e., the ratio between AMRfield and SMR) varies from 1.2 to 3.2 across species and body sizes. Furthermore, we illustrate that the scaling exponent for AMRfield varies across species and can substantially exceed the widely assumed value of 0.75 for SMR. Finally, by scaling organismal AMRfield estimates to the assemblage level, we show the potential effect of this variability on community metabolic demand. Our approach may improve our ability to estimate elemental fluxes mediated by a critically important group of aquatic animals through a non‐destructive, widely applicable technique.

Living on fire: Deactivating fire coral polyps for larval settlement and symbiosis in the fire coral-associated barnacle Wanella milleporae (Thoracicalcarea: Wanellinae)

Symbiosis is increasingly recognized as being an important component in marine systems, and many such relationships are initiated when free-swimming larvae of one partner settle and become sedentary on a host partner. Therefore, several crucial questions emerge such as the larva's mechanism of locating a host, selection of substratum and finally settlement on the surface of its future partner. Here, we investigated these mechanisms by studying how larvae of the fire coral-associated barnacle Wanella milleporae move, settle and establish symbiosis with their host, Millepora tenera. Cyprids of W. milleporae possess a pair of specialized antennules with bell-shaped attachment discs that enable them to explore and settle superficially on the hostile surface of the fire coral. Intriguingly, the stinging polyps of the fire coral remain in their respective pores when the cyprids explore the fire coral surface. Even when cyprids come into contact with the nematocysts on the extended stinging polyps during the exploratory phase, no immobilization effects against the cyprids were observed. The exploratory phase of Wanella cyprids can be divided into a sequence of wide searching (large step length and high walking speed), close searching (small step length and low speed) and inspection behavior, eventually resulting in permanent settlement and metamorphosis. After settlement, xenogeneic interactions occur between the fire coral and the newly metamorphosed juvenile barnacle. This involved tissue necrosis and regeneration in the fire coral host, leading to a callus ring structure around the juvenile barnacle, enhancing survival rate after settlement. The complex exploratory and settlement patterns and interactions documented here represent a breakthrough in coral reef symbiosis studies to show how invertebrates start symbiosis with fire corals.

A 3D perspective on sediment turnover and feeding selectivity in blennies

Sediments in algal turfs can modify a wide variety of key ecological processes on coral reefs. While some larger reef fishes can remove these turf-bound sediments, the role of small, yet abundant, cryptobenthic fishes is currently unclear. To address this knowledge gap, we explored the extent to which the blenny, Ecsenius stictus, can shape sediment dynamics on coral reefs by quantifying their sediment ingestion and space use. Per unit body mass, E. stictus process sediments at comparable rates to key parrotfish and surgeonfish species. However, in absolute terms, E. stictus has a negligible influence on net sediment dynamics, despite their abundance. Behavioural observations and 3D photogrammetry reveal that E. stictus preferentially feed and rest on elevated surfaces; potentially because of low sediment loads on these surfaces. Overall, E. stictus may be responding to sediment loads rather than manipulating them; it is a passenger rather than a driver in reef processes.

Biological trade-offs underpin coral reef ecosystem functioning

Human impact increasingly alters global ecosystems, often reducing biodiversity and disrupting the provision of essential ecosystem services to humanity. Therefore, preserving ecosystem functioning is a critical challenge of the twenty-first century. Coral reefs are declining worldwide due to the pervasive effects of climate change and intensive fishing, and although research on coral reef ecosystem functioning has gained momentum, most studies rely on simplified proxies, such as fish biomass. This lack of quantitative assessments of multiple process-based ecosystem functions hinders local and regional conservation efforts. Here we combine global coral reef fish community surveys and bioenergetic models to quantify five key ecosystem functions mediated by coral reef fishes. We show that functions exhibit critical trade-offs driven by varying community structures, such that no community can maximize all functions. Furthermore, functions are locally dominated by few species, but the identity of dominant species substantially varies at the global scale. In fact, half of the 1,110 species in our dataset are functionally dominant in at least one location. Our results reinforce the need for a nuanced, locally tailored approach to coral reef conservation that considers multiple ecological functions beyond the effect of standing stock biomass.

Comparative trophic ecology of microhabitat-associated guilds of reef fishes in the Adriatic Sea

Reef ecosystems are characterized by highly heterogenous habitats and functionally diverse fish communities. Few studies have examined how functional diversity differs among habitats within these communities, i.e., species associated with a specific habitat may have similar trophic ecologies meaning that the functional diversity within the community is driven by habitat diversity or, conversely, high functional diversity within each habitat would indicate that resource segregation also occurs at the habitat level. We used stable isotope ratios of carbon and nitrogen to estimate trophic position, resource use and ontogenetic niche shifts of 15 reef fishes associated with four distinct habitat types (cryptobenthic, epibenthic sand, epibenthic rock and hyperbenthic) on the Croatian coast of the Adriatic Sea. Trophic ecology was quite similar across fish assemblages, but there was strong evidence of niche segregation among fish species within each assemblage showing high functional diversity within each microhabitat. The sampled fish community contained benthic and pelagic resource users, along with multiple intermediate generalists. Consumer stable isotope ratios revealed considerable interspecific variation in resource use among fishes within each habitat type. The cryptobenthic fishes were a notable exception to this trend with the narrow range of resource use values, indicating reliance of these species on a single resource. The greatest diversity of trophic positions within a guild was observed in cryptobenthic and rock-associated epibenthic fishes. The majority of observed ontogenetic variation in studied fish species reflected an increase in benthic resource use and trophic position. However, the degree of ontogenetic variation in trophic ecology of studied species, if present, was generally low, showing no dramatic change in the ecology of any species. The size structuring among guilds was considerable, with cryptobenthic fishes the smallest on average and hyperbenthic fishes the largest, despite guilds having similar ranges of trophic positions.

A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Fish distribution and behaviour with regard to the time of day and the anthropogenic structural modification of the shallow littoral

The shallow littoral zone is under a variety of environmental drivers and anthropogenic pressures. As these factors are highly dynamic, they may affect the distribution and behaviour of littoral fish. The present study investigates the effect of the time of day and the benthic habitat type on the shallow littoral fish community. Diel variations in total fish abundance, community composition, species abundance and behaviour were studied in two neighbouring stations in the Patraikos Gulf (Greece): one with cobble seabed cover and another with anthropogenic habitat structural modifications, like large artificial blocks, rocks and other objects. Visual census revealed that community composition differed depending on both the time of day and the habitat type. Total abundance was highest in the morning, whereas both diel abundance and habitat use were found to be taxon specific, with most species showing a preference for the artificial rocky habitat. Diel differences in species behavioural patterns were also observed, with a greater percentage of fish being active during the day (morning and noon) rather than in the afternoon. Although the fish community does not change entirely within a day or between adjacent locations, it is significantly variable in even small spatial and temporal scales. Consequently, there are implications for the design and implementation of sampling designs and monitoring plans that should be consistent in time of day throughout the sampling period and include locations structurally modified by humans. Furthermore, the management of the shallow littoral zone should consider the small-scale variability and alternate anthropogenic habitat with natural unaltered patches.

Protecting connectivity promotes successful biodiversity and fisheries conservation

The global decline of coral reefs has led to calls for strategies that reconcile biodiversity conservation and fisheries benefits. Still, considerable gaps in our understanding of the spatial ecology of ecosystem services remain. We combined spatial information on larval dispersal networks and estimates of human pressure to test the importance of connectivity for ecosystem service provision. We found that reefs receiving larvae from highly connected dispersal corridors were associated with high fish species richness. Generally, larval "sinks" contained twice as much fish biomass as "sources" and exhibited greater resilience to human pressure when protected. Despite their potential to support biodiversity persistence and sustainable fisheries, up to 70% of important dispersal corridors, sinks, and source reefs remain unprotected, emphasizing the need for increased protection of networks of well-connected reefs.

Gonad morphology of Rhyacichthys aspro (Valenciennes, 1837), and the diagnostic reproductive morphology of gobioid fishes

Rhyacichthys aspro is a “basal” taxon in the Suborder Gobioidei of the teleost order Gobiiformes. We provide detailed descriptions of the reproductive morphology of adult males and females to assess the diagnostic reproductive morphological characters of this speciose clade of bony fishes. Female R. aspro are asynchronous spawners: they are able to spawn more than once in a breeding season. Oocytes are inferred to have short attachment filaments. A conspicuous feature of the external anatomy of the reproductive system (RSy) of female R. aspro is an ornate fimbriate pad upon which the urogenital papilla rests. The male reproductive system is characterized by an intralobar collection system in both the testicular and secretory lobes, termed the “sperm‐collecting canal” and “milt‐collecting canal,” respectively. These may provide additional storage for sperm and milt. The spermatogenic lobe, or testis, is that portion of the male gobioid RSy comprising seminiferous lobules and separate from other RSy components. The secretory lobe is that portion of the male gobioid reproductive system that consists of secretory lobules and is separated from other components of the male RSy. The secretory lobe has also been called, in English, the sperm‐duct gland, accessory gonadal structure, or seminal vesicle, and is endorsed as a synapomorphy of gobioid fishes.

Protection outcomes for fish trophic groups across a range of management regimes

Understanding how Marine Protected Areas (MPAs) improve conservation outcomes across anthropogenic pressures can improve the benefits derived from them. Effects of protection for coral reefs in the western and central Indian Ocean were assessed using size-spectra analysis of fish and the relationships of trophic group biomass with human population density. Length-spectra relationships quantifying the relative abundance of small and large fish (slope) and overall productivity of the system (intercept) showed inconsistent patterns with MPA protection. The results suggest that both the slopes and intercepts were significantly higher in highly and well-protected MPAs. This indicates that effective MPAs are more productive and support higher abundances of smaller fish, relative to moderately protected MPAs. Trophic group biomass spanning piscivores and herbivores, decreased with increasing human density implying restoration of fish functional structure is needed. This would require addressing fisher needs and supporting effective MPA management to secure ecosystem benefits for coastal communities.

Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification

Ocean-warming and acidification are predicted to reduce coral reef biodiversity, but the combined effects of these stressors on overall biodiversity are largely unmeasured. Here, we examined the individual and combined effects of elevated temperature (+2 °C) and reduced pH (-0.2 units) on the biodiversity of coral reef communities that developed on standardized sampling units over a 2-y mesocosm experiment. Biodiversity and species composition were measured using amplicon sequencing libraries targeting the cytochrome oxidase I (COI) barcoding gene. Ocean-warming significantly increased species richness relative to present-day control conditions, whereas acidification significantly reduced richness. Contrary to expectations, species richness in the combined future ocean treatment with both warming and acidification was not significantly different from the present-day control treatment. Rather than the predicted collapse of biodiversity under the dual stressors, we find significant changes in the relative abundance but not in the occurrence of species, resulting in a shuffling of coral reef community structure among the highly species-rich cryptobenthic community. The ultimate outcome of altered community structure for coral reef ecosystems will depend on species-specific ecological functions and community interactions. Given that most species on coral reefs are members of the understudied cryptobenthos, holistic research on reef communities is needed to accurately predict diversity-function relationships and ecosystem responses to future climate conditions.

Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra-family diversity

Habitat heterogeneity shapes biological communities, a well-known process in terrestrial ecosystems but substantially unresolved within coral reef ecosystems. We investigated the extent to which coral richness predicts intra-family fish richness, while simultaneously integrating a striking aspect of reef ecosystems-coral hue. To do so, we quantified the coral richness, coral hue diversity, and species richness within 25 fish families in 74 global ecoregions. We then expanded this to an analysis of all reef fishes (4465 species). Considering coral bleaching as a natural experiment, we subsequently examined hue's contribution to fish communities. Coral species and hue diversity significantly predict each family's fish richness, with the highest correlations (> 80%) occurring in damselfish, butterflyfish, emperors and rabbitfish, lower (60-80%) in substrate-bound and mid-water taxa such as blennies, seahorses, and parrotfish, and lowest (40-60%) in sharks, morays, grunts and triggerfish. The observed trends persisted globally. Coral bleaching's homogenization of reef colouration revealed hue's contribution to maintaining fish richness, abundance, and recruit survivorship. We propose that each additional coral species and associated hue provide added ecological opportunities (e.g. camouflage, background contrast for intraspecific display), facilitating the evolution and co-existence of diverse fish assemblages.

Trait-based vulnerability reveals hotspots of potential impact for a global marine invader

Predation from the invasive Indo-Pacific lionfish is likely to amplify declines in marine fishes observed in multiple ocean basins. As the invasion intensifies and expands, there is an urgent need to identify species that are most at risk for extirpation-and possible extinction-from this added threat. To address this gap and inform conservation plans, we develop and apply a quantitative framework for classifying the relative vulnerability of fishes based on morphological and behavioural traits known to influence susceptibility to lionfish predation (e.g. body shape, water column position and aggregation behaviour), habitat overlap with lionfish, and degree of geographic range restriction. Applying the framework to fishes across the invaded Caribbean Sea and ahead of the invasion front in the southwestern Atlantic revealed the identity of at least 77 fishes with relatively small ranges that are likely to be most affected by lionfish predation. Trait-based vulnerability scores significantly predict the probability of fishes appearing within the diets of lionfish across the invaded region. Spatial richness analyses reveal hotspots of vulnerable species in the Bahamas, Belize and Curaçao. Crucially, our framework identifies 29 vulnerable fishes endemic to Brazil, which has not yet been colonized by lionfish. Of these, we suggest reefs around offshore island groups occupied by a dozen highly vulnerable and range-restricted species as priorities for intervention should lionfish spread to the region. Observations of the rate of lionfish spread across the invaded range suggest that an average of 5 years (with a median of nearly 2 years) elapses from first sighting to maximum observed densities. This lag may allow managers to mobilize plans to suppress lionfish ahead of an invasion front in priority locations. Our framework also provides a method for assessing the relative vulnerability of cryptobenthic and/or deep-reef fishes, for which population-monitoring data are limited.

Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

This Essay argues that in order to truly understand how marine hosts benefit from the immense diversity of microbes, we need to expand towards long-term, multi-disciplinary research focussing on few areas of the world’s ocean that we refer to as “natural experiments,” where processes can be studied at scales that far exceed those captured in laboratory experiments.

Critical Review and Conceptual and Quantitative Models for the Transfer and Depuration of Ciguatoxins in Fishes

We review and develop conceptual models for the bio-transfer of ciguatoxins in food chains for Platypus Bay and the Great Barrier Reef on the east coast of Australia. Platypus Bay is unique in repeatedly producing ciguateric fishes in Australia, with ciguatoxins produced by benthic dinoflagellates (Gambierdiscus spp.) growing epiphytically on free-living, benthic macroalgae. The Gambierdiscus are consumed by invertebrates living within the macroalgae, which are preyed upon by small carnivorous fishes, which are then preyed upon by Spanish mackerel (Scomberomorus commerson). We hypothesise that Gambierdiscus and/or Fukuyoa species growing on turf algae are the main source of ciguatoxins entering marine food chains to cause ciguatera on the Great Barrier Reef. The abundance of surgeonfish that feed on turf algae may act as a feedback mechanism controlling the flow of ciguatoxins through this marine food chain. If this hypothesis is broadly applicable, then a reduction in herbivory from overharvesting of herbivores could lead to increases in ciguatera by concentrating ciguatoxins through the remaining, smaller population of herbivores. Modelling the dilution of ciguatoxins by somatic growth in Spanish mackerel and coral trout (Plectropomus leopardus) revealed that growth could not significantly reduce the toxicity of fish flesh, except in young fast-growing fishes or legal-sized fishes contaminated with low levels of ciguatoxins. If Spanish mackerel along the east coast of Australia can depurate ciguatoxins, it is most likely with a half-life of ≤1-year. Our review and conceptual models can aid management and research of ciguatera in Australia, and globally.

Collapsing ecosystem functions on an inshore coral reef

Ecosystem functions underpin productivity and key services to humans, such as food provision. However, as the severity of environmental stressors intensifies, it is becoming increasingly unclear if, and to what extent, critical functions and services can be sustained. This issue is epitomised on coral reefs, an ecosystem at the forefront of environmental transitions. We provide a functional profile of a coral reef ecosystem, linking time-series data to quantified processes. The data reveal a prolonged collapse of ecosystem functions in this previously resilient system. The results suggest that sediment accumulation in algal turfs has led to a decline in resource yields to herbivorous fishes and a decrease in fish-based ecosystem functions, including a collapse of both fish biomass and productivity. Unfortunately, at present, algal turf sediment accumulation is rarely monitored nor managed in coral reef systems. Our examination of functions through time highlights the value of directly assessing functions, their potential vulnerability, and the capacity of algal turf sediments to overwhelm productive high-diversity coral reef ecosystems.

An integrative investigation of sensory organ development and orientation behavior throughout the larval phase of a coral reef fish

The dispersal of marine larvae determines the level of connectivity among populations, influences population dynamics, and affects evolutionary processes. Patterns of dispersal are influenced by both ocean currents and larval behavior, yet the role of behavior remains poorly understood. Here we report the first integrated study of the ontogeny of multiple sensory systems and orientation behavior throughout the larval phase of a coral reef fish-the neon goby, Elacatinus lori. We document the developmental morphology of all major sensory organs (lateral line, visual, auditory, olfactory, gustatory) together with the development of larval swimming and orientation behaviors observed in a circular arena set adrift at sea. We show that all sensory organs are present at hatch and increase in size (or number) and complexity throughout the larval phase. Further, we demonstrate that most larvae can orient as early as 2 days post-hatch, and they swim faster and straighter as they develop. We conclude that sensory organs and swimming abilities are sufficiently developed to allow E. lori larvae to orient soon after hatch, suggesting that early orientation behavior may be common among coral reef fishes. Finally, we provide a framework for testing alternative hypotheses for the orientation strategies used by fish larvae, laying a foundation for a deeper understanding of the role of behavior in shaping dispersal patterns in the sea.

Juvenile corals underpin coral reef carbonate production after disturbance

Sea-level rise is predicted to cause major damage to tropical coastlines. While coral reefs can act as natural barriers for ocean waves, their protection hinges on the ability of scleractinian corals to produce enough calcium carbonate (CaCO₃ ) to keep up with rising sea levels. As a consequence of intensifying disturbances, coral communities are changing rapidly, potentially reducing community-level CaCO₃ production. By combining colony-level physiology and long-term monitoring data, we show that reefs recovering from major disturbances can produce 40% more CaCO₃ than currently estimated due to the disproportionate contribution of juvenile corals. However, the buffering effect of highly productive juvenile corals is compromised by recruitment failures, which have been more frequently observed after large-scale, repeated bleaching events. While the size structure of corals can bolster a critical ecological function on reefs, climate change impacts on recruitment may undermine this buffering effect, thus further compromising the persistence of reefs and their provision of important ecosystem services.

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

Universal rules of life: metabolic rates, biological times and the equal fitness paradigm

Here we review and extend the equal fitness paradigm (EFP) as an important step in developing and testing a synthetic theory of ecology and evolution based on energy and metabolism. The EFP states that all organisms are equally fit at steady state, because they allocate the same quantity of energy, ~ 22.4 kJ/g/generation to the production of offspring. On the one hand, the EFP may seem tautological, because equal fitness is necessary for the origin and persistence of biodiversity. On the other hand, the EFP reflects universal laws of life: how biological metabolism - the uptake, transformation and allocation of energy - links ecological and evolutionary patterns and processes across levels of organisation from: (1) structure and function of individual organisms, (2) life history and dynamics of populations, and (3) interactions and coevolution of species in ecosystems. The physics and biology of metabolism have facilitated the evolution of millions of species with idiosyncratic anatomy, physiology, behaviour and ecology but also with many shared traits and tradeoffs that reflect the single origin and universal rules of life.

Progress on Research Regarding Ecology and Biodiversity of Coastal Fisheries and Nektonic Species and Their Habitats within Coastal Landscapes

This paper aims to highlight the new research and significant advances in our understanding of links between coastal habitat quality/quantity/diversity and the diversity of fisheries species and other mobile aquatic species (hereafter nekton) that use them within coastal landscapes. This topic is quite diverse owing to the myriad of habitat types found in coastal marine waters and the variety of life history strategies fisheries species and nekton use in these environments. Thus, we focus our review on five selective but relevant topics, habitat templates, essential fish habitat, habitat mosaics/habitat connectivity, transitory/ephemeral habitat, and the emerging/maturing approaches to the study of fish-habitat systems as a roadmap to its development. We have highlighted selected important contributions in the progress made on each topic to better identify and quantify landscape scale interactions between living biota and structured habitats set within a dynamic landscape.

Drivers of reef fish assemblages in an upwelling region from the Eastern Tropical Pacific Ocean

Reef fish assemblages are exposed to a wide range of anthropogenic threats as well as chronic natural disturbances. In upwelling regions, for example, there is a seasonal influx of cool nutrient-rich waters that may shape the structure and composition of reef fish assemblages. Given that climate change may disrupt the natural oceanographic processes by altering the frequency and strength of natural disturbances, understanding how fish assemblages respond to upwelling events is essential to effectively manage reef ecosystems under changing ocean conditions. This study used the baited remote underwater video stations (BRUVS) and the traditional underwater visual census (UVC) to investigate the spatiotemporal patterns of reef fish assemblages in an upwelling region in the North Pacific of Costa Rica. A total of 183 reef fish species from 60 families were recorded, of which 166 species were detected using BRUVS and 122 using UVC. Only 66% of all species were detected using both methods. This study showed that the upwelling had an important role in shaping reef fish assemblages in this region, but there was also a significant interaction between upwelling and location. In addition, other drivers such as habitat complexity and habitat composition had an effect on reef fish abundances and species. To authors' knowledge, this is the first study in the Eastern Tropical Pacific that combines BRUVS and UVC to monitor reef fish assemblages in an upwelling region, which provides more detailed information to assess the state of reef ecosystems in response to multiple threats and changing ocean conditions.