Eco-Physiology of Shallow Benthic Communities

The eco-physiology of shallow benthic marine communities examines how physiological traits (e.g., metabolism, osmoregulation, photosynthesis, and stress responses) are shaped by, and respond to, environmental variables such as salinity, temperature, irradiance, and nutrient availability, and specifically how organisms acclimate to environmental gradients that fluctuate on diurnal, seasonal, annual, and even inter-annual timescales [1,2,3,4]. This acclimation response results from interlinked physiological traits: from the osmoregulation that allows microbial communities and benthic diatoms to persist across the salinity swings of tidal zones [3,5], to the photosynthetic acclimation of microphytobenthos and coral reef algae, to shifting irradiance, temperature, and nutrient regimes [3,6], the plasticity on the tolerance thresholds that lets marine invertebrates withstand hyposalinity, hypoxia, and wide thermal regimens [4,7], and the bioenergetic balance that benthic macrofauna and suspension feeders must maintain during synergic stress periods [4,8]. Therefore, ecophysiology may be used as a predictive tool to understand a single species or a whole ecosystem’s response to normal or abnormal fluctuations in environmental conditions or changes (and even introductions) in the biotic components, making this discipline essential for predicting how climate change, eutrophication, and other anthropogenic stressors will reshape shallow benthic communities and their ecosystem functions [4,6,8].

Particularly shallow benthic coastal marine communities constitute functional ecosystems whose composition of passive substrates and biological components creates highly productive communities such as coral reefs, kelp forests, and rocky reefs, among others. Their functional role goes from active nutrient cycling, mediating the exchange of carbon, nitrogen, and other elements through processes such as bioturbation, filtration, and microbially mediated remineralization [6,9,10]. The activity of assemblages of infaunal and epifaunal invertebrates, algae, and associated microbial communities provides most of the primary production and helps buffer coastal biogeochemical fluxes [10]. At the same time, the physical and biogenic structures created by benthic organisms provide the three-dimensional complexity that shelters and sustains the associated fauna, from conspicuous and cryptic species to commercially important fisheries resources [11]. Despite similar functions, each shallow benthic community differs in its structural basis (e.g., rock and sand), its primary producers such as macroalgae, seagrasses, crustose coralline algae, and zooxanthellate scleractian corals, and the associated organism assemblage, creating differences in habitat complexity and functional redundancy, which results in high-biodiversity and productivity systems [12,13].

However, this same complexity increases their vulnerability to environmental fluctuations, as their structure and function are shaped by natural gradients in light, depth, hydrodynamic disturbance, grazing pressure, and nutrient availability [5,7]. In addition to the natural variability, the anthropogenic pressures, from contaminants, overfishing, poorly regulated tourism, and coastal urbanization [14,15], interact with the effects of climate change, including ocean warming, marine heatwaves, and acidification [16], to diminish their resilience. The cumulative footprint of these stressors is now so widespread that few shallow marine habitats remain unaffected by at least one form of human disturbance [17], and global assessments have documented parallel large-scale declines in coral cover, seagrass extent, and the condition of temperate rocky reefs over the last four decades [18]. Due to their relevance, it is imperative to support science-based tools to understand the present and future dynamics of shallow benthic communities.

This Special Issue, titled “Eco-Physiology of Shallow Benthic Marine Communities”, sought original contributions on the community and functional ecology of these systems, the physiological mechanisms that determine organismal and ecosystem responses to local, regional, and global stressors, and the management and policy tools that can support their conservation and rehabilitation. These studies respond to that call from complementary angles: thermal stress and coral mortality; reproductive failure in a keystone species; taxonomic resolution of a foundational macroalga; decadal coral growth records from a remote atoll; and the functional structure of reef fish assemblages across an oceanic-to-coastal gradient [19,20,21,22,23]. Read together, they sketch a single, coherent story about how shallow benthic systems in the Eastern Tropical Pacific and the Caribbean region are coping with or declining under the synergistic stress of ocean warming and local human pressure.

Alvarado et al. [19] documented the devastating impact of the 2023–2024 El Niño event on Costa Rica’s Gulf of Papagayo, where record-breaking heat stress caused over 90% coral loss in inner-bay reefs, while outer-bay reefs partially recovered thanks to upwelling and greater genetic diversity, demonstrating that resilience emerges from the holobiont acclimatization rather than being a fixed species trait; more importantly, this benthic collapse created a cascade effect on reducing populations of invertebrate-feeding fish. This disturbance also affected the Caribbean, where global stressors have not only affected the survival of Acropora palmata coral colonies but also their reproduction, which, in synergy with chronic local stressors, can eventually cause a population collapse [20]. In a long-term study, Ochoa-Serena et al. [21] analyzed coral skeletal growth records from the remote Clipperton Atoll and found that even this thermally stable, human-disturbance-free system exhibited reduced growth and calcification compared with other Pacific reefs, as Porites shifts their maintenance strategy, prioritizing structural extension or density in response to non-anthropogenic stressors such as storm exposure and coastal distance, not just normal or abnormal temperature regimes as usually observed in the coastal areas, and reinforcing that isolation does not equal to protection. A coral reef or community is shaped not only by the coral assemblage but also by other key groups, such as fishes; Cáceres et al. [22] present a trait-based comparison of fish communities across oceanic, coastal-influenced, and coastal reefs. Finally, a foundational gap was addressed by Viales-Cubillo et al. [23], resolving long-standing taxonomic confusion in Sargassum seaweed forests along the Central American Pacific coast, using genetic and morphological evidence to identify two distinct species and correct prior misidentifications, providing the scientific basis for future ecological studies of these ecologically important, nursery-providing macroalgal habitats. These studies demonstrate that climate-driven and locally driven stressors have negative effects on distinct yet interacting timescales and mechanisms, and that resilience across these ecosystems depends on the interplay of connectivity, disturbance patterns, and human pressure.

These works addressed a set of common and important insights. First, thermal stress associated with ENSO events is intensifying and can now produce mortality and reproductive failure that exceed historical benchmarks [19,20]. Second, resilience to this stress is highly heterogeneous and contingent on local oceanography, genetic diversity, symbiont identity, and connectivity, rather than being an intrinsic property of species or reefs [19,21]. Third, chronic local stressors—artificial light, trampling, fishing pressure, fragmentation—can erode the reproductive and functional capacity of benthic communities even in the absence of acute thermal events, and these pressures interact with, rather than substitute for, climate-driven stress [20,22]. Fourth, accurate taxonomic and functional baselines remain indispensable tools for detecting and interpreting these changes [23]. Finally, remoteness and protection from direct anthropogenic contact do not guarantee resilience; isolated systems can exhibit distinct vulnerabilities of their own, whether expressed as depressed coral growth potential or elevated functional vulnerability in fish assemblages [21,22].

In conclusion, this collection reinforces the framing set out in the call for this Special Issue: shallow benthic communities are shaped simultaneously by global and local drivers and require a long-term, multi-taxon, and physiologically informed monitoring approach. More importantly, the eco-physiological and functional frameworks applied in these five studies are the base for future work in the region, and the management implications they raise—such as protecting climate refugia shaped by upwelling, reducing chronic local stressors at reproductively critical sites, maintaining colony density and connectivity for restoration efforts, and incorporating functional vulnerability into conservation prioritization—will inform conservation practice as shallow benthic ecosystems continue to face an increasingly variable climate.