Coral reef ecosystem functions in a human-dominated world

bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-16

Abstract The metabolic processes sustaining coral reefs, from carbonate and primary production to secondary production, remain poorly integrated and rarely quantified simultaneously at global scales. This hampers our ability to predict global responses to accelerating human pressures and manage coral reef functioning. Using metabolic scaling and bioenergetic models applied to surveys from 1,100 reefs worldwide, we provide a global, standardized quantification of 14 ecosystem functions spanning benthic (corals and algae) and fish communities. Our analysis reveals a continuous functional spectrum of global coral reefs organized along four dominant axes: 1) primary production, 2) calcification and habitat structure, 3) secondary biomass production and consumption, and 4) biomass turnover. Functions mediated by fish and benthic communities show weak associations at the global scale rather than tight coupling. Climate stressors reduced calcification and local human impacts lowered secondary production. Yet these directional effects unfolded against a backdrop of substantial natural variability in reef functional configurations, such that heavily and minimally impacted reefs overlap substantially in the global functional space. Temporal analyses across three representative reef systems further revealed that functional trajectories following disturbance are context-dependent, with no universal pattern of recovery across locations. This continuous and context-dependent functional spectrum challenges the notion of universal functional benchmarks and supports locally tailored conservation strategies.

Data and code from: Goby gummies: a customizable and edible assay to quantify predation in aquatic ecosystems

DRYAD · 2026-03-17 · 1 citations

Predation is a critical ecosystem process that shapes the structure and functioning of biological communities. However, due to its intermittent nature, fast pace, and general unpredictability, predation is difficult to observe and quantify. Therefore, we commonly rely on indirect metrics or proxies of predation, which reflect the outcome of predation events but do not allow for inference about the predator’s decision-making process or predation rates. In terrestrial ecosystems, lifelike prey replicas have allowed ecologists to gain a broad understanding of predator choice, predation intensity, and their drivers. Yet in aquatic ecosystems, few scalable, interactive predation assays have been developed. We introduce Goby Gummies, a customizable, edible prey model developed for aquatic ecology. Gummies are constructed using an inert, edible medium that can be cast into any desired shape (in our case, a goby fish), dyed various colors, and be supplemented with edible material to introduce variation in nutritional profiles. As such, Goby Gummies are a cheap, sustainable, high-throughput assay that can be tailored to a variety of aquatic ecosystems. We performed two pilot studies to test Goby Gummies in a natural setting on coral reefs in Belize during which gummies were reliably consumed by a range of predatory fishes. First, we show that gummies supplemented with fish meal were preferred by predators over agar-only gummies, but the strength of this preference was dependent on their coloration, suggesting an intriguing interplay between external appearance and internal composition. Second, we compared fish-supplemented gummies to squidpops, a previously developed predation assay for marine systems. Goby gummies were consumed first more frequently and eaten at quicker rates than Squidpops and consistently attracted carnivorous predators whereas squidpops were frequently consumed by herbivorous parrotfishes. Our results highlight that Goby Gummies provide a new predation assay tool in aquatic ecosystems that permits the exploration of many exciting questions surrounding prey and predator traits and their interplay. We envision goby gummies to kindle a diverse range of impactful studies across disciplines that mirror those conducted in terrestrial ecosystems.

Weak trophic position–body mass relationships undermine simple size-spectrum models for coral reefs

Proceedings of the Royal Society B Biological Sciences · 2026-02-11

Unravelling food web dynamics across biological communities is a central goal of ecology. In size-structured ecosystems, the shape of trophic pyramids is often inferred from their size spectra-the distribution of biomass across body-mass classes. Size-spectrum analysis has become a popular tool to study ecosystem functioning in aquatic ecosystems, including coral reefs. However, the key assumption behind size spectra, that body size directly and positively correlates with trophic position, has rarely been evaluated in these systems. Here, we test this assumption by quantifying body mass, population densities and estimating trophic position from stable isotopes for 325 fish species across four Indo-Pacific locations. Consistent with prior studies, we found a positive relationship between biomass and body mass. However, weak and variable relationships between body mass and trophic position led to higher biomass in primary consumers than in predators, as expected in traditional bottom-heavy or diamond-shaped trophic structures. Our findings thus challenge previous reports of coral reef fish biomass prevalence in higher trophic levels (e.g. inverted biomass pyramids), supporting earlier suggestions that simple size-spectrum models do not adequately represent the trophic structure of reef fish communities.

Evaluating the success of coral reef restoration programs requires consideration of ecosystem functioning

Restoration Ecology · 2025-09-18 · 1 citations

In the past 20 years, there has been a sharp rise in the establishment of coral reef restoration programs, which generally aim to restore key services provided by healthy, natural reefs. However, the effect of restoration on arguably more important metrics related to ecosystem functioning is rarely considered, with most programs focusing their monitoring on static variables (e.g. coral cover) only. With crucial metrics related to ecosystem functioning left largely unmonitored, it is difficult to assess the outcomes of reef restoration through a truly ecological lens. We therefore propose that ecosystem functioning should be placed at the forefront of reef restoration, and suggest the following focus points for improvements in the field: (1) Implement a set of standardized methods to monitor key functional processes on restored reefs (and neighboring natural reefs), (2) better understand how reef restoration will support ecosystem functioning in a changing ocean, and the identity of organisms that carry most of the “functionality load” on reefs, and (3) adopt a function‐centric approach that implements techniques specifically targeted at protecting the respective species and processes of interest.

Community structure and microhabitat associations of cryptobenthic reef fishes in Veracruz, Mexico

Coral Reefs · 2025-10-14

Differential cryptofaunal responses to seabird nutrient inputs illuminate coral reef productivity pathways

2025-09-18

Nutrients moving across ecosystems can boost productivity, stability, and resilience. Their integration through food webs is often mediated by small, abundant taxa channelling subsidies from primary producers to higher trophic levels. On coral reefs, cryptobenthic fishes and invertebrates could fill these roles, yet their responses to allochthonous nutrients are poorly understood. We compared cryptofaunal communities and associated trophic dynamics across islands with or without seabird-derived nutrients in the Chagos Archipelago, Indian Ocean. Most cryptobenthic fishes and some invertebrates showed nutrient enrichment. Community patterns revealed strong asymmetries: cryptobenthic fish biomass doubled in nutrient-rich environments, with a tenfold increase in larger piscivorous fish productivity, while cryptic invertebrate biomass stagnated, with reduced invertivore productivity. Life-history traits likely enable cryptobenthic fishes to exploit subsidies more efficiently, intensifying pressure on invertebrates in nutrient-rich environments. Our findings reveal how nutrients are routed through cryptofaunal pathways, underscoring the far-reaching impacts of cross-ecosystem nutrient vectors on trophic functioning.

Seabird-derived nutrients influence feeding pathways and body size in cryptobenthic reef fishes

Proceedings of the Royal Society B Biological Sciences · 2025-07-01 · 2 citations

Cross-ecosystem nutrient transfer can enhance coral reef functioning in an otherwise oligotrophic environment. While the influence of seabird-derived nutrients on coral reef organisms is increasingly recognized, how they are integrated into reef food webs remains unclear. Cryptobenthic reef fishes are crucial for energy transfer on coral reefs, and their fast life histories imply that they respond strongly to seabird-derived nutrients. Here, we investigate how variation in nearshore seabird nutrient subsidies affects coral reef fish communities. By comparing fish communities across locations differing in seabird nutrient inputs and using stable isotope analysis, we explore nutrient integration across depth, their influence on cryptobenthic and associated larger reef fishes and investigated the relative reliance of cryptobenthic fishes on seabird-enriched benthic and non-enriched pelagic pathways. We find that, near seabird colonies, cryptobenthic fishes' diets can transition from pelagic to benthic dominance; cryptobenthic fish communities are larger; herbivores and all feeding groups comprising potential cryptobenthic fish predators have higher biomass. Collectively, our results stress the importance of seabirds in shaping energy pathways and suggest that, even in dynamic, ocean-swept reef systems, cryptobenthic fishes can mobilize seabird subsidies and potentially act as a nutritional bridge to higher trophic levels.

Consistent Unimodal Body Length Distributions in Hundreds of Reef Fishes Across Diverse Life Histories

Fish and Fisheries · 2025-03-30 · 2 citations

ABSTRACT Animal body size distributions result from interactions of growth, mortality and recruitment. In ecology and fisheries science, theoretical models of fish body size distributions are widely used but rely on life‐history parameters—growth coefficient (K) and natural mortality rate (M)—that remain unknown for most species and are challenging to estimate. Analysing data from underwater visual surveys and exhaustive sampling, representing 3068 populations across 797 species of shallow‐water, mostly unfished marine fishes, we demonstrate that post‐recruitment body length distributions exhibit a consistent unimodal shape across species and populations. When scaled to the mean body length, these distributions are strikingly similar across all teleost and elasmobranch species, with diverse life histories and maximum body sizes ranging from 1 cm to 3 m. Observed size structure can be approximated by a truncated normal distribution with a coefficient of variation of ~0.34 (SE = 0.002). Such consistent observed body size distributions could be aligned with Beverton–Holt population dynamics theory, if assuming an M/K ratio of ~1.5 and logistic observational selectivity with 50% detectability at ~40% of maximum body length. Alternatively, observed distributions could reflect deviations from theoretical expectations, and reconciling the unimodal distributions with theory may require relaxing some model assumptions, such as continuous recruitment, constant density‐independent growth or constant natural mortality. Overall, the consistency of population‐ and species‐level body length distributions means that unfished size structure could be predicted from a single body size parameter. It also suggests evolutionary convergence of diverse growth and mortality processes towards a narrow range of viable outcomes.

Prehistoric archives reveal evidence of predator loss and prey release in Caribbean reef fish communities

Proceedings of the National Academy of Sciences · 2025-06-30 · 2 citations

Understanding how humans have altered coral reef food webs remains challenging due to the absence of prehistoric baselines. Here, we use fish remains preserved in fossil and archaeological deposits from Panamá and the Dominican Republic to explore how Caribbean reef fish mortality patterns have changed over millennia. By quantifying accumulation rates of shark dermal denticles (scales) and bony fish otoliths (ear stones) in reef sediments, we assess relative fish abundance, while otolith size serves as a proxy for body size at death. Comparisons of these death assemblages suggest a 75% decline in shark-derived material and a 22% reduction in the sizes of human-targeted fishes-consistent with historical exploitation. This evidence of decline in large-bodied, higher trophic level fish remains coincided with a doubling in prey fish otolith accumulation and a 17% increase in their reconstructed body sizes. These patterns in time-averaged death assemblages align with effects of release from predation, documenting an often assumed (but rarely shown) cascading effect. In contrast, otoliths of predator-sheltered cryptobenthic fishes showed no change in either accumulation or size, suggesting that ''bottom-up"environmental factors were not responsible for the observed changes. Together, these data indicate that pre-exploitation predator communities strongly controlled exposed prey fishes, but this "top-down" effect diminishes rapidly toward the food chain base, especially in predator-resistant groups. Understanding trophic cascades on Caribbean reefs requires studying systems before predator depletion.

Author response for "Seabird-derived nutrients influence feeding pathways and body size in cryptobenthic reef fishes"

2025-05-10