Vertical structure of Caribbean deep-reef fishes from the altiphotic to deep-sea boundary.

While recent technical breakthroughs have enabled advances in the description of reefs down to 150 m, the structure and depth zonation of deep-reef communities below 150 m remains largely unknown. Here, we present results from over 10 years of deep-reef fish surveys using human-occupied submersibles at four locations across the Caribbean Sea, constituting one of the only continuous reef-fish surveys from 10 to 480 m (1 site) and 40 to 300 m (3 sites). We identify four vertically stratified deep-reef fish communities between 40 and 300 m bordered by an altiphotic (0-10 m) and a deep-sea (300-480 m) community. We found a strong faunal break around 150 m that separates mesophotic and rariphotic zones and secondary breaks at ~ 70 to 90 m and ~ 180 to 200 m subdividing these zones into upper and lower communities. From 300 to 480 m in Roatán, we found a single fish community dominated by deep-sea families, indicating that the lower boundary of the reef-fish realm occurs at 300 m. No differences were found between communities ranging from 20 to 60 m, suggesting that fishes from the lower altiphotic and upper mesophotic form an ecological continuum. While some variability was observed across sites, the overall depth zonation and key species characterizing depth zones were consistent. Most deep-reef species observed were depth specialists restricted to a single depth zone, but many shallow-reef species extended down to mesophotic depths. Depth segregation among species of a genus was found across ten reef-fish genera and likely constitutes one of the mechanisms driving community distinctiveness and thereby fish diversity across depths.

Host diet drives gut microbiome convergence between coral reef fishes and mammals.

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

Phospho-mimetic CD3ε variants prevent TCR and CAR signaling.

Introduction: Antigen binding to the T cell antigen receptor (TCR) leads to the phosphorylation of the immunoreceptor tyrosine-based activation motifs (ITAMs) of the CD3 complex, and thereby to T cell activation. The CD3ε subunit plays a unique role in TCR activation by recruiting the kinase LCK and the adaptor protein NCK prior to ITAM phosphorylation. Here, we aimed to investigate how phosphorylation of the individual CD3ε ITAM tyrosines impacts the CD3ε signalosome. Methods: We mimicked irreversible tyrosine phosphorylation by substituting glutamic acid for the tyrosine residues in the CD3ε ITAM. Results: Integrating CD3ε phospho-mimetic variants into the complete TCR-CD3 complex resulted in reduced TCR signal transduction, which was partially compensated by the involvement of the other TCR-CD3 ITAMs. By using novel CD3ε phospho-mimetic Chimeric Antigen Receptor (CAR) variants, we avoided any compensatory effects of other ITAMs in the TCR-CD3 complex. We demonstrated that irreversible CD3ε phosphorylation prevented signal transduction upon CAR engagement. Mechanistically, we demonstrated that glutamic acid substitution at the N-terminal tyrosine residue of the CD3ε ITAM (Y39E) significantly reduces NCK binding to the TCR. In contrast, mutation at the C-terminal tyrosine of the CD3ε ITAM (Y50E) abolished LCK recruitment to the TCR, while increasing NCK binding. Double mutation at the C- and N-terminal tyrosines (Y39/50E) allowed ZAP70 to bind, but reduced the interaction with LCK and NCK. Conclusions: The data demonstrate that the dynamic phosphorylation of the CD3ε ITAM tyrosines is essential for CD3ε to orchestrate optimal TCR and CAR signaling and highlights the key role of CD3ε signalosome to tune signal transduction.

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.

Harnessing CD3 diversity to optimize CAR T cells.

Current US Food and Drug Administration-approved chimeric antigen receptor (CAR) T cells harbor the T cell receptor (TCR)-derived ζ chain as an intracellular activation domain in addition to costimulatory domains. The functionality in a CAR format of the other chains of the TCR complex, namely CD3δ, CD3ε and CD3γ, instead of ζ, remains unknown. In the present study, we have systematically engineered new CD3 CARs, each containing only one of the CD3 intracellular domains. We found that CARs containing CD3δ, CD3ε or CD3γ cytoplasmic tails outperformed the conventional ζ CAR T cells in vivo. Transcriptomic and proteomic analysis revealed differences in activation potential, metabolism and stimulation-induced T cell dysfunctionality that mechanistically explain the enhanced anti-tumor performance. Furthermore, dimerization of the CARs improved their overall functionality. Using these CARs as minimalistic and synthetic surrogate TCRs, we have identified the phosphatase SHP-1 as a new interaction partner of CD3δ that binds the CD3δ-ITAM on phosphorylation of its C-terminal tyrosine. SHP-1 attenuates and restrains activation signals and might thus prevent exhaustion and dysfunction. These new insights into T cell activation could promote the rational redesign of synthetic antigen receptors to improve cancer immunotherapy.

Microhabitat partitioning between sympatric intertidal fish species highlights the importance of sediment composition in gravel beach conservation.

Gravel beaches in the Mediterranean ecoregion represent an economically important and unique habitat type. Yet, burgeoning tourism, intensive coastal development and artificial nourishment of beaches may jeopardize their ecological communities. To date, species that reside on gravel beaches and the consequences of beach alterations are poorly understood, which hampers the development of a sustainable coastal tourism industry along the region's shorelines. Using a simple collection method based on dredging buckets through the intertidal section of beaches, we quantified the microhabitat association of two sympatric clingfish species in the genus Gouania at seven natural and an artificial gravel beach based on sediment characteristics. We hypothesized that slender (G. pigra) and stout (G. adriatica) morphotypes would partition interstitial niche space based on sediment size, which may affect the vulnerability of the species to changes in gravel beach composition due to coastal development. We detected substantial differences in gravel composition within and among the sampled beaches which suggests scope for microhabitat partitioning in Gouania. Indeed, we found significant relationships between species identity and the presence/absence and abundance of individuals in hauls based on their positioning on PC1. Our results suggest that modifications of gravel beaches through coastal development, including beach nourishment, intensifying coastal erosion, or artificial beach creation, may have detrimental consequences for the two species if sediment types or sizes are altered. We posit that, given the simplicity and efficacy of our sampling method and the sensitivity of Gouania species to prevailing gravel composition, the genus could serve as an important indicator for gravel beach management in the Mediterranean ecoregion.

Fish feces reveal diverse nutrient sources for coral reefs.

Consumers mediate nutrient cycling through excretion and egestion across most ecosystems. In nutrient-poor tropical waters such as coral reefs, nutrient cycling is critical for maintaining productivity. While the cycling of fish-derived inorganic nutrients via excretion has been extensively investigated, the role of egestion for nutrient cycling has remained poorly explored. We sampled the fecal contents of 570 individual fishes across 40 species, representing six dominant trophic guilds of coral reef fishes in Moorea, French Polynesia. We measured fecal macro- (proteins, carbohydrates, lipids) and micro- (calcium, copper, iron, magnesium, manganese, zinc) nutrients and compared the fecal nutrient quantity and quality across trophic guilds, taxa, and body size. Macro- and micronutrient concentrations in fish feces varied markedly across species. Genera and trophic guild best predicted fecal nutrient concentrations. In addition, nutrient composition in feces was unique among species within both trophic guilds (herbivores and corallivores) and genera (Acanthurus and Chaetodon). Particularly, certain coral reef fishes (e.g., Thalassoma hardwicke, Chromis xanthura, Chaetodon pelewensis and Acanthurus pyroferus) harbored relatively high concentrations of micronutrients (e.g., Mn, Mg, Zn and Fe, respectively) that are known to contribute to ocean productivity and positively impact coral physiological performances. Given the nutrient-rich profiles across reef fish feces, conserving holistic reef fish communities ensures the availability of nutritional pools on coral reefs. We therefore suggest that better integration of consumer egestion dynamics into food web models and ecosystem-scale processes will facilitate an improved understanding of coral reef functioning.

Can metabolic traits explain animal community assembly and functioning?

All animals on Earth compete for free energy, which is acquired, assimilated, and ultimately allocated to growth and reproduction. Competition is strongest within communities of sympatric, ecologically similar animals of roughly equal size (i.e. horizontal communities), which are often the focus of traditional community ecology. The replacement of taxonomic identities with functional traits has improved our ability to decipher the ecological dynamics that govern the assembly and functioning of animal communities. Yet, the use of low-resolution and taxonomically idiosyncratic traits in animals may have hampered progress to date. An animal's metabolic rate (MR) determines the costs of basic organismal processes and activities, thus linking major aspects of the multifaceted constructs of ecological niches (where, when, and how energy is obtained) and ecological fitness (how much energy is accumulated and passed on to future generations). We review evidence from organismal physiology to large-scale analyses across the tree of life to propose that MR gives rise to a group of meaningful functional traits - resting metabolic rate (RMR), maximum metabolic rate (MMR), and aerobic scope (AS) - that may permit an improved quantification of the energetic basis of species coexistence and, ultimately, the assembly and functioning of animal communities. Specifically, metabolic traits integrate across a variety of typical trait proxies for energy acquisition and allocation in animals (e.g. body size, diet, mobility, life history, habitat use), to yield a smaller suite of continuous quantities that: (1) can be precisely measured for individuals in a standardized fashion; and (2) apply to all animals regardless of their body plan, habitat, or taxonomic affiliation. While integrating metabolic traits into animal community ecology is neither a panacea to disentangling the nuanced effects of biological differences on animal community structure and functioning, nor without challenges, a small number of studies across different taxa suggest that MR may serve as a useful proxy for the energetic basis of competition in animals. Thus, the application of MR traits for animal communities can lead to a more general understanding of community assembly and functioning, enhance our ability to trace eco-evolutionary dynamics from genotypes to phenotypes (and vice versa), and help predict the responses of animal communities to environmental change. While trait-based ecology has improved our knowledge of animal communities to date, a more explicit energetic lens via the integration of metabolic traits may further strengthen the existing framework.

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.

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 [ AM R field ] ). 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 AM R field and SMR) varies from 1.2 to 3.2 across species and body sizes. Furthermore, we illustrate that the scaling exponent for AM R field varies across species and can substantially exceed the widely assumed value of 0.75 for SMR. Finally, by scaling organismal AM R field 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.

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.

Scaling up calcification, respiration, and photosynthesis rates of six prominent coral taxa.

Coral reefs provide a range of important services to humanity, which are underpinned by community-level ecological processes such as coral calcification. Estimating these processes relies on our knowledge of individual physiological rates and species-specific abundances in the field. For colonial animals such as reef-building corals, abundance is frequently expressed as the relative surface cover of coral colonies, a metric that does not account for demographic parameters such as coral size. This may be problematic because many physiological rates are directly related to organism size, and failure to account for linear scaling patterns may skew estimates of ecosystem functioning. In the present study, we characterize the scaling of three physiological rates - calcification, respiration, and photosynthesis - considering the colony size for six prominent, reef-building coral taxa in Mo'orea, French Polynesia. After a seven-day acclimation period in the laboratory, we quantified coral physiological rates for three hours during daylight (i.e., calcification and gross photosynthesis) and one hour during night light conditions (i.e., dark respiration). Our results indicate that area-specific calcification rates are higher for smaller colonies across all taxa. However, photosynthesis and respiration rates remain constant over the colony-size gradient. Furthermore, we revealed a correlation between the demographic dynamics of coral genera and the ratio between net primary production and calcification rates. Therefore, intraspecific scaling of reef-building coral physiology not only improves our understanding of community-level coral reef functioning but it may also explain species-specific responses to disturbances.

Range expansion and complete mitochondrial genome of the highfin blenny (Lupinoblennius nicholsi).

BACKGROUND: The highfin blenny, Lupinoblennius nicholsi, is a marine fish species reported in reef and rocky inshore habitats with a disjunct distribution in the southern Gulf of Mexico. Overall, there are very few studies on this species and there is a scarcity of molecular resources for genetic comparisons. We set out to report the first mitochondrial genome for L. nicholsi and report a range expansion for the species. METHODS AND RESULTS: An individual of L. nicholsi was collected from the coast of Dauphin Island, Alabama. The mitochondrial genome was sequenced, assembled, and annotated. The fragment corresponding to cytochrome oxidase I (COI) was used to compare this sample to other cryptobenthic species of the Atlantic. Finding a mature individual in the coast of Alabama implies this species has a continuous distribution throughout the northern Gulf of Mexico. The mitochondrial genome of L. nicholsi is 16,416 bp in length and comprised of 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding D-loop. Comparisons using COI support the species is L. nicholsi and separate it from other cryptobenthic fishes found in the area. CONCLUSIONS: This study represents the first mitochondrial genome for this L. nicholsi, serving as a reference for future comparative studies with marine fishes. By reporting the range expansion of this species, this study provides insights on the fish diversity of the Gulf of Mexico.

Species richness and identity both determine the biomass of global reef fish communities.

Changing biodiversity alters ecosystem functioning in nature, but the degree to which this relationship depends on the taxonomic identities rather than the number of species remains untested at broad scales. Here, we partition the effects of declining species richness and changing community composition on fish community biomass across >3000 coral and rocky reef sites globally. We find that high biodiversity is 5.7x more important in maximizing biomass than the remaining influence of other ecological and environmental factors. Differences in fish community biomass across space are equally driven by both reductions in the total number of species and the disproportionate loss of larger-than-average species, which is exacerbated at sites impacted by humans. Our results confirm that sustaining biomass and associated ecosystem functions requires protecting diversity, most importantly of multiple large-bodied species in areas subject to strong human influences.

Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes.

Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.

Congruent trophic pathways underpin global coral reef food webs.

Ecological interactions uphold ecosystem structure and functioning. However, as species richness increases, the number of possible interactions rises exponentially. More than 6,000 species of coral reef fishes exist across the world's tropical oceans, resulting in an almost innumerable array of possible trophic interactions. Distilling general patterns in these interactions across different bioregions stands to improve our understanding of the processes that govern coral reef functioning. Here, we show that across bioregions, tropical coral reef food webs exhibit a remarkable congruence in their trophic interactions. Specifically, by compiling and investigating the structure of six coral reef food webs across distinct bioregions, we show that when accounting for consumer size and resource availability, these food webs share more trophic interactions than expected by chance. In addition, coral reef food webs are dominated by dietary specialists, which makes trophic pathways vulnerable to biodiversity loss. Prey partitioning among these specialists is geographically consistent, and this pattern intensifies when weak interactions are disregarded. Our results suggest that energy flows through coral reef communities along broadly comparable trophic pathways. Yet, these critical pathways are maintained by species with narrow, specialized diets, which threatens the existence of coral reef functioning in the face of biodiversity loss.

Functional niches of cleanerfish species are mediated by habitat use, cleaning intensity and client selectivity.

An animal's functional niche is a complex, multidimensional construct, mediated by an individual's morphology, physiology and behaviour. Behavioural aspects of the niche can be difficult to quantify, as their expression is often subtle and tailored to an infinite number of different situations that involve sophisticated mechanisms such as mutualisms, species dominance or fear effects. The extreme diversity of tropical fish assemblages has led to extensive debate over the extent to which species differ in their resource use and functional role. Ectoparasite removal by cleanerfish species is considered a behaviourally complex interspecific interaction in vertebrates, but differences in the services rendered by various species of cleanerfish, and potential consequences for the range of clients (i.e. resources) they attract, have rarely been examined. Here, we quantify differences among three coexisting species of morphologically similar cleaner wrasses (Labroides bicolor, L. dimidiatus and L. pectoralis) in the global centre of marine biodiversity, the Coral Triangle. We found no clear taxonomic partitioning of clients among cleanerfishes. However, the three cleanerfish species exhibited distinct habitat preferences, and differed in their cleaning intensity: L. bicolor serviced the fewest species and clients, while L. pectoralis serviced the most clients and spent the most time cleaning. Accordingly, L. pectoralis showed no preference for clients based on client size or abundance, while both L. bicolor and L. dimidiatus had a higher likelihood of interacting with clients based on their size (larger client species in L. bicolor, smaller client species in L. dimidiatus) and abundance (more abundant client species for both). Our results suggest that the services rendered by the three species of cleanerfishes differ in their spatial availability, quality and selectivity, thus permitting the coexistence of these species despite their ecological similarity. This, in turn, creates a complex seascape of species-specific cleaning services that underpins crucial biotic interactions in the ocean's most diverse ecosystem.

Documenting decadal disturbance dynamics reveals archipelago-specific recovery and compositional change on Polynesian reefs.

Coral reefs are declining at an unprecedented rate as a consequence of local and global stressors. Using a 26-year monitoring database, we analyzed the loss and recovery dynamics of coral communities across seven islands and three archipelagos in French Polynesia. Reefs in the Society Islands recovered relatively quickly after disturbances, which was driven by the recovery of corals in the genus Pocillopora (84% of the total recovery). In contrast, reefs in the Tuamotu and Austral archipelagos recovered poorly or not at all. Across archipelagos, predation by crown-of-thorns starfish and destruction by cyclones outweighed the effects of heat stress events on coral mortality. Despite the apparently limited effect of temperature-mediated stressors, the homogenization of coral communities towards dominance of Pocillopora in the Society Archipelago and the failure to fully recover from disturbances in the other two archipelagos concern the resilience of Polynesian coral communities in the face of intensifying climate-driven stressors.

Fine-scale foraging behavior reveals differences in the functional roles of herbivorous reef fishes.

Efforts to understand and protect ecosystem functioning have put considerable emphasis on classifying species according to the functions they perform. However, coarse classifications based on diet or feeding mode often oversimplify species' contributions to ecological processes. Behavioral variation among superficially similar species is easily missed but could indicate important differences in competitive interactions and the spatial scale at which species deliver their functions. To test the extent to which behavior can vary within existing functional classifications, we investigate the diversity of foraging movements in three herbivorous coral reef fishes across two functional groups. We find significant variation in foraging movements and spatial scales of operation between species, both within and across existing functional groups. Specifically, we show that movements and space use range from low frequency foraging bouts separated by short distances and tight turns across a small area, to high frequency, far-ranging forays separated by wide sweeping turns. Overall, we add to the burgeoning evidence that nuanced behavioral differences can underpin considerable complementarity within existing functional classifications, and that species assemblages may be considerably less redundant than previously thought.