Benthic community composition affects O2 availability and variability in a Northern Red Sea fringing reef

Many coral reef ecosystems experience shifts in benthic community composition from scleractinian corals to algae. However, consequences of such phase shifts on O₂ availability, important for many reef organisms, are unresolved. This study therefore comparatively investigated potential in situ effects of different benthic cover by reef macroalgae and scleractinian corals on water column O₂ concentrations in a Northern Red Sea fringing reef. Findings revealed that mean daily O₂ concentrations at algae-dominated sites were significantly lower compared to coral-dominated sites. Minimum O₂ concentrations were significantly negatively correlated, while diurnal variability in O₂ concentration was significantly positively correlated, with increasing benthic cover by algae. In contrast, no correlation with coral cover was found. These results indicate that shifts from corals to benthic algae may likely affect both in situ O₂ availability and variability. This may be particularly pronounced in reef systems with low water exchange (e.g. closed lagoons) or under calm weather conditions and suggests potential O₂-mediated effects on reef organisms.     

Organic matter release by dominant hermatypic corals of the Northern Red Sea

Particulate organic matter (POM) and dissolved organic carbon (DOC) release by six dominant hermatypic coral genera (Acropora, Fungia, Goniastrea, Millepora, Pocillopora and Stylophora) were measured under undisturbed conditions by laboratory incubations during four seasonal expeditions to the Northern Red Sea. In addition, the influence of environmental factors (water temperature, light availability and ambient inorganic nutrient concentrations) was evaluated. Particulate organic carbon (POC) and particulate nitrogen (PN) release were always detectable and genus-specific, with Stylophora releasing most POM (6.5 mg POC and 0.5 mg PN m⁻² coral surface area h⁻¹) during all seasons. The fire coral Millepora released significantly less POM (0.3 mg POC and 0.04 mg PN m⁻² coral surface area h⁻¹) than all investigated anthozoan genera. The average POC:PN ratio of POM released by all coral genera was 12 ± 1, indicating high carbon/low nitrogen content of coral-derived organic matter. POM release showed little seasonal variation, but average values of POC and PN release rates correlated with water temperature, light availability and ambient nitrate concentrations. DOC net release and elevated DOC:POC ratios were detectable for Acropora, Goniastrea and Millepora, revealing maximum values for Acropora (30.7 mg DOC m⁻² coral surface area h⁻¹), whilst predominant DOC uptake was observed for Pocillopora, Fungia and Stylophora. Depth-mediated light availability influenced DOC fluxes of Acropora and Fungia, while fluctuations in water temperature and ambient inorganic nutrient concentrations showed no correlation. These comprehensive data provide an important basis for the understanding of coral reef organic matter dynamics and relevant environmental factors.     

Effects of High Dissolved Inorganic and Organic Carbon Availability on the Physiology of the Hard Coral Acropora millepora from the Great Barrier Reef

Coral reefs are facing major global and local threats due to climate change-induced increases in dissolved inorganic carbon (DIC) and because of land-derived increases in organic and inorganic nutrients. Recent research revealed that high availability of labile dissolved organic carbon (DOC) negatively affects scleractinian corals. Studies on the interplay of these factors, however, are lacking, but urgently needed to understand coral reef functioning under present and near future conditions. This experimental study investigated the individual and combined effects of ambient and high DIC (pCO₂ 403 μatm/ pH_Total 8.2 and 996 μatm/pH_Total 7.8) and DOC (added as Glucose 0 and 294 μmol L^-1, background DOC concentration of 83 μmol L^-1) availability on the physiology (net and gross photosynthesis, respiration, dark and light calcification, and growth) of the scleractinian coral Acropora millepora (Ehrenberg, 1834) from the Great Barrier Reef over a 16 day interval. High DIC availability did not affect photosynthesis, respiration and light calcification, but significantly reduced dark calcification and growth by 50 and 23%, respectively. High DOC availability reduced net and gross photosynthesis by 51% and 39%, respectively, but did not affect respiration. DOC addition did not influence calcification, but significantly increased growth by 42%. Combination of high DIC and high DOC availability did not affect photosynthesis, light calcification, respiration or growth, but significantly decreased dark calcification when compared to both controls and DIC treatments. On the ecosystem level, high DIC concentrations may lead to reduced accretion and growth of reefs dominated by Acropora that under elevated DOC concentrations will likely exhibit reduced primary production rates, ultimately leading to loss of hard substrate and reef erosion. It is therefore important to consider the potential impacts of elevated DOC and DIC simultaneously to assess real world scenarios, as multiple rather than single factors influence key physiological processes in coral reefs.     

Distribution of dissolved organic carbon and nitrogen in a coral reef

Dissolved organic matter (DOM) concentrations in a fringing coral reef were measured for both carbon and nitrogen with the analytical technique of high-temperature catalytic oxidation. Because of high precision of the analytical system, not only the concentrations of dissolved organic carbon and nitrogen (DOC and DON, respectively) but the C:N ratio was also determined from the distribution of DOC and DON concentrations. The observed concentrations of DOC and DON ranged 57–76 and 3.8–5.6 μmol l⁻¹, respectively. The C:N ratios of the DOM that was produced on the reef flat were very similar between seagrass- and coral-dominated areas; the C:N ratio was 10 on average. The C:N ratio of DOM was significantly higher than that of particulate organic matter (POM) that was produced on the reef flat. Production rates of DOC were measured on the reef flat during stagnant periods and accounted for 3–7% of the net primary production, depending on the sampling site. The production rate of DON was estimated to be 10–30% of the net uptake of dissolved inorganic N in the reef community. Considering that the DOM and POM concentrations were not correlated with each other, a major source of the reef-derived DOM may be the benthic community and not POM such as phytoplankton. It was concluded that a widely distributed benthic community in the coral reef released C-rich DOM to the overlying seawater, conserving N in the community.     

Effects of nutrient enrichment on the release of dissolved organic carbon and nitrogen by the scleractinian coral Montipora digitata

The effects of nutrient enrichment on the release of dissolved organic carbon and nitrogen (DOC and DON, respectively) from the coral Montipora digitata were investigated in the laboratory. Nitrate (NO₃ ⁻) and phosphate (PO₄ ³⁻) were supplied to the aquarium to get the final concentrations of 10 and 0.5 μmol l⁻¹, respectively, and the corals were incubated for 8 days. The release rate of DON per unit coral surface area significantly decreased after the nutrient enrichment, while the release rate of DOC was constant. Because the chlorophyll a (chl a) content of zooxanthellae per unit surface area increased, the release rate of DOC significantly decreased when normalized to unit chl a. These results suggested that the incorporation of NO₃ ⁻ and PO₄ ³⁻ stimulated the synthesis of new cellular components in the coral colonies and consequently, reduced extracellular release of DOC and DON. Actually, significant increase in N and P contents relative to C content was observed in the coral’s tissue after the nutrient enrichment. The present study has concluded that inorganic nutrient enrichment not only affects coral-algal metabolism inside the colony but also affects a microbial community around the coral because the organic matter released from corals functions as energy carrier in the coral reef ecosystem.     

Symbiodiniaceae-bacteria interactions: rethinking metabolite exchange in reef-building corals as multi-partner metabolic networks

The intimate relationship between scleractinian corals and their associated microorganisms is fundamental to healthy coral reef ecosystems. Coral-associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi and viruses) support coral health and resilience through metabolite transfer, inter-partner signalling, and genetic exchange. However, much of our understanding of the coral holobiont relationship has come from studies that have investigated either coral-Symbiodiniaceae or coral-bacteria interactions in isolation, while relatively little research has focused on other ecological and metabolic interactions potentially occurring within the coral multi-partner symbiotic network. Recent evidences of intimate coupling between phytoplankton and bacteria have demonstrated that obligate resource exchange between partners fundamentally drives their ecological success. Here, we posit that similar associations with bacterial consortia regulate Symbiodiniaceae productivity and are in turn central to the health of corals. Indeed, we propose that this bacteria-Symbiodiniaceae-coral relationship underpins the coral holobiont's nutrition, stress tolerance and potentially influences the future survival of coral reef ecosystems under changing environmental conditions. Resolving Symbiodiniaceae-bacteria associations is therefore a logical next step towards understanding the complex multi-partner interactions occurring in the coral holobiont.     

Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity

Benthic primary producers in marine ecosystems may significantly alter biogeochemical cycling and microbial processes in their surrounding environment. To examine these interactions, we studied dissolved organic matter release by dominant benthic taxa and subsequent microbial remineralization in the lagoonal reefs of Moorea, French Polynesia. Rates of photosynthesis, respiration, and dissolved organic carbon (DOC) release were assessed for several common benthic reef organisms from the backreef habitat. We assessed microbial community response to dissolved exudates of each benthic producer by measuring bacterioplankton growth, respiration, and DOC drawdown in two-day dark dilution culture incubations. Experiments were conducted for six benthic producers: three species of macroalgae (each representing a different algal phylum: Turbinaria ornata – Ochrophyta; Amansia rhodantha – Rhodophyta; Halimeda opuntia – Chlorophyta), a mixed assemblage of turf algae, a species of crustose coralline algae (Hydrolithon reinboldii) and a dominant hermatypic coral (Porites lobata). Our results show that all five types of algae, but not the coral, exuded significant amounts of labile DOC into their surrounding environment. In general, primary producers with the highest rates of photosynthesis released the most DOC and yielded the greatest bacterioplankton growth; turf algae produced nearly twice as much DOC per unit surface area than the other benthic producers (14.0±2.8 µmol h⁻¹ dm⁻²), stimulating rapid bacterioplankton growth (0.044±0.002 log10 cells h⁻¹) and concomitant oxygen drawdown (0.16±0.05 µmol L⁻¹ h⁻¹ dm⁻²). Our results demonstrate that benthic reef algae can release a significant fraction of their photosynthetically-fixed carbon as DOC, these release rates vary by species, and this DOC is available to and consumed by reef associated microbes. These data provide compelling evidence that benthic primary producers differentially influence reef microbial dynamics and biogeochemical parameters (i.e., DOC and oxygen availability, bacterial abundance and metabolism) in coral reef communities.     

Chemistry of the consumption and excretion of the bumphead parrotfish (Bolbometopon muricatum), a coral reef mega-consumer

Coral Reefs - Bolbometopon muricatum are ecologically unique mega-consumers in coral reef ecosystems. They primarily divide their dietary intake between living scleractinian corals and coral rock,...     

Symbiont diversity in scleractinian corals from tropical reefs and subtropical non-reef communities in Taiwan

We examined zooxanthellae diversity in scleractinian corals from southern Taiwan and the Penghu Archipelago, a tropical coral reef and a subtropical non-reefal community, respectively. Zooxanthellae diversity was investigated in 52 species of scleractinian corals from 26 genera and 13 families, using restriction fragment length polymorphism (RFLP), and phylogenetic analyses of the nuclear small-subunit ribosomal DNA (nssrDNA) and large-subunit ribosomal DNA (nlsrDNA). RFLP and phylogenetic analyses of nuclear-encoded ribosomal RNA genes showed that Symbiodinium clade C was the dominant zooxanthellae in scleractinian corals in the seas around Taiwan; Symbiodinium clade D was also found in some species. Both Symbiodinium clade C and D were found in colonies of seven species of scleractinian corals. Symbiodinium clade D was associated with corals that inhabit either shallow water or the reef edge in deep water, supporting the hypothesis that Symbiodinium clade D is a relatively stress-tolerant zooxanthellae found in marginal habitats.Communicated by Biological Editor H.R. Lasker     

Biogeochemical responses following coral mass spawning on the Great Barrier Reef: pelagic–benthic coupling

This study quantified how the pulse of organic matter from the release of coral gametes triggered a chain of pelagic and benthic processes during an annual mass spawning event on the Australian Great Barrier Reef. Particulate organic matter (POM) concentrations in reef waters increased by threefold to 11-fold the day after spawning and resulted in a stimulation of pelagic oxygen consumption rates that lasted for at least 1 week. Water column microbial communities degraded the organic carbon of gametes of the broadcast-spawning coral Acropora millepora at a rate of >15% h⁻¹, which is about three times faster than the degradation rate measured for larvae of the brooding coral Stylophora pistillata. Stable isotope signatures of POM in the water column reflected the fast transfer of organic matter from coral gametes into higher levels of the food chain, and the amount of POM reaching the seafloor immediately increased after coral spawning and then tailed-off in the next 2 weeks. Short-lasting phytoplankton blooms developed within a few days after the spawning event, indicating a prompt recycling of nutrients released through the degradation of spawning products. These data show the profound effects of coral mass spawning on the reef community and demonstrate the tight recycling of nutrients in this oligotrophic ecosystem.     

Instream release of dissolved organic matter from coarse and fine particulate organic matter of different origins

Dissolved organic matter (DOM), produced through leaching from particulate organic matter (POM), is an essential component of the carbon cycle in streams. The present study investigated the instream DOM release from POM, varying in size and chemical quality. We produced large and medium sized fine particulate organic matter (L-FPOM, 250–500 μm; M-FPOM, 100–250 μm) of defined quality by feeding five types of coarse particulate organic matter (CPOM) to shredding amphipods (Gammarus spp.). Microscopic observations showed that L-FPOM and M-FPOM mainly consisted of the fecal pellets of amphipods, and incompletely eaten plant fragments, respectively. DOM release experiments were conducted by exposing CPOM and M- and L-FPOM fractions in natural stream water over a two week period. For CPOM, the release of dissolved organic carbon (DOC) by leaching was highest during the first 6 h (3.64–23.9 mg C g C^?1 h^?1) and decreased rapidly afterwards. For M- and L-FPOM, the DOC release remained low during the entire study period (range: 0.008–0.15 mg C g C^?1 h^?1). Two-way ANOVA revealed that the DOC release rate significantly differed with POM source and size fraction, both at day 1 and after a week of exposure. Multiple regression analyses revealed a significant correlation of elemental contents and lignin content to DOC release rate after a week of exposure. Overall, the results indicated that DOC release rate of FPOM, on a carbon basis, is comparable to that of CPOM after leaching, while size and source of POM significantly affect DOC release rate.     

Nitrate Uptake by Reef Corals

In specimens of the hermatypic coral species Fungia scutaria and Montipora verrucosa and in the alga Ulva lactuca, nitrate uptake was measured in light and dark with a flow-through apparatus. The nitrate uptake was measurable in high-nitrate bay water of Kaneohe Bay and also in low-nitrate open ocean water. Nitrate consumption rates by the corals and the alga did not differ from light to dark. Neither the coral nor the alga showed measurable immediate nitrate uptake in open ocean water of low nitrate concentration when they had been held previously in the high-nitrate bay water. In low-nitrate open ocean water the uptake per unit time increases when the flow of the water increases. The uptake of nitrate by reef corals even from low concentrations indicates nonspecific nutrient sources for reef corals.     

Distribution,food preference,and trophic position of the corallivorous fireworm Hermodice carunculata in a Caribbean coral reef

The fireworm Hermodice carunculata is a facultative corallivore on coral reefs. It can interact with algal overgrowth to cause coral mortality. However, because of its cryptic nature, little is known about its ecology. We used micropredator attracting devices (MADs) and stable isotope analyses to provide insights into the distribution and diet of H. carunculata in a coral reef on Curaçao, southern Caribbean. MADs consisted of algal clumps inside accessible mesh nets which H. carunculata could use as refuge. To obtain indications on its distribution pattern, MADs filled with Halimeda opuntia were deployed in different reef habitats ranging from 0 to 16 m water depth. Fireworms were found inside MADs in all reef habitats, indicating that they have a widespread horizontal and vertical distribution, ranging from the shoreline to the deeper reef slope. On the reef crest, MADs were filled using different algal species and deployed on dead or live scleractinian corals. MADs hosted more fireworms when placed on live corals, regardless of algal species used, suggesting that algal-induced corallivory may be widespread. To test for food preferences, different food sources were added inside the MADs. Fireworms detected potential prey within 6 h and were significantly more attracted by decaying corals and raw fish than by live corals, hydrozoans, or gorgonians. Stable isotope analyses indicated detritus, macroalgae, and scleractinian corals as potential food sources and revealed an ontogenetic dietary shift toward enriched δ ¹³C and δ ¹⁵N values with increasing fireworm size, suggesting that large-sized individuals feed on food sources of higher trophic levels. Our findings highlight H. carunculata as a widespread, and omnivorous scavenger that has the potential to switch feeding toward weakened or stressed corals, thereby likely acting as a harmful corallivore on degraded reefs.     

First Evidence of an Important Organic Matter Trophic Pathway between Temperate Corals and Pelagic Microbial Communities

Mucus, i.e., particulate and dissolved organic matter (POM, DOM) released by corals, acts as an important energy carrier in tropical ecosystems, but little is known on its ecological role in temperate environments. This study assessed POM and DOM production by the temperate coral Cladocora caespitosa under different environmental conditions. The subsequent enzymatic degradation, growth of prokaryotes and virus-like particles (VLPs) as well as changes in the structure of the prokaryotic communities were also monitored. C. caespitosa produced an important quantity of mucus, which varied according to the environmental conditions (from 37.8 to 67.75 nmol carbon h^-1 cm^-2), but remained higher or comparable to productions observed in tropical corals. It has an important nutritional value, as highlighted by the high content in dissolved nitrogen (50% to 90% of the organic matter released). Organic matter was rapidly degraded by prokaryotes’ enzymatic activities, and due to its nitrogen content, aminopeptidase activity was 500 fold higher than the α-glucosidase activity. Prokaryotes, as well as VLPs, presented a rapid growth in the mucus, with prokaryote production rates as high as 0.31 μg h^-1 L^-1. Changes in bacterial and archaeal communities were observed in the ageing mucus and between mucus and the water column, suggesting a clear impact of mucus on microorganism diversity. Overall, our results show that the organic matter released by temperate corals, such as C. caespitosa, which can form reef structures in the Mediterranean Sea, stimulates microbial activity and thereby functions as a significant carbon and nitrogen supplier to the microbial loop.     

Specificity is rarely absolute in coral-algal symbiosis: implications for coral response to climate change

Some reef-building corals have been shown to respond to environmental change by shifting the composition of their algal symbiont (genus Symbiodinium) communities. These shifts have been proposed as a potential mechanism by which corals might survive climate stressors, such as increased temperatures. Conventional molecular methods suggest this adaptive capacity may not be widespread because few (～25%) coral species have been found to associate with multiple Symbiodinium clades. However, these methods can fail to detect low abundance symbionts (typically less than 10-20% of the total algal symbiont community). To determine whether additional Symbiodinium clades are present, but are not detected using conventional techniques, we applied a high-resolution, real-time PCR assay to survey Symbiodinium (in clades A-D) from 39 species of phylogenetically and geographically diverse scleractinian corals. This survey included 26 coral species thought to be restricted to hosting a single Symbiodinium clade ('symbiotic specialists'). We detected at least two Symbiodinium clades (C and D) in at least one sample of all 39 coral species tested; all four Symbiodinium clades were detected in over half (54%) of the 26 symbiotic specialist coral species. Furthermore, on average, 68 per cent of all sampled colonies within a given coral species hosted two or more symbiont clades. We conclude that the ability to associate with multiple symbiont clades is common in scleractinian (stony) corals, and that, in coral-algal symbiosis, 'specificity' and 'flexibility' are relative terms: specificity is rarely absolute. The potential for reef corals to adapt or acclimatize to environmental change via symbiont community shifts may therefore be more phylogenetically widespread than has previously been assumed.     

Environmental Records from Great Barrier Reef Corals: Inshore versus Offshore Drivers

The biogenic structures of stationary organisms can be effective recorders of environmental fluctuations. These proxy records of environmental change are preserved as geochemical signals in the carbonate skeletons of scleractinian corals and are useful for reconstructions of temporal and spatial fluctuations in the physical and chemical environments of coral reef ecosystems, including The Great Barrier Reef (GBR). We compared multi-year monitoring of water temperature and dissolved elements with analyses of chemical proxies recorded in Porites coral skeletons to identify the divergent mechanisms driving environmental variation at inshore versus offshore reefs. At inshore reefs, water Ba/Ca increased with the onset of monsoonal rains each year, indicating a dominant control of flooding on inshore ambient chemistry. Inshore multi-decadal records of coral Ba/Ca were also highly periodic in response to flood-driven pulses of terrigenous material. In contrast, an offshore reef at the edge of the continental shelf was subject to annual upwelling of waters that were presumed to be richer in Ba during summer months. Regular pulses of deep cold water were delivered to the reef as indicated by in situ temperature loggers and coral Ba/Ca. Our results indicate that although much of the GBR is subject to periodic environmental fluctuations, the mechanisms driving variation depend on proximity to the coast. Inshore reefs are primarily influenced by variable freshwater delivery and terrigenous erosion of catchments, while offshore reefs are dominated by seasonal and inter-annual variations in oceanographic conditions that influence the propensity for upwelling. The careful choice of sites can help distinguish between the various factors that promote Ba uptake in corals and therefore increase the utility of corals as monitors of spatial and temporal variation in environmental conditions.     

海洋酸化对珊瑚礁生态系统的影响研究进展

目前,大气CO2浓度的升高已导致海水pH值比工业革命前下降了约0.1,海水碳酸盐平衡体系随之变化,进而影响珊瑚礁生态系统的健康。近年来的研究表明海洋酸化导致造礁石珊瑚幼体补充和群落恢复更加困难,造礁石珊瑚和其它造礁生物(Reef-building organisms)钙化率降低甚至溶解,乃至影响珊瑚礁鱼类的生命活动。虽然海洋酸化对造礁石珊瑚光合作用的影响不显著,但珊瑚-虫黄藻共生体系会受到一定影响。建议选择典型海区进行长期系统监测,结合室内与原位模拟试验,从个体、种群、群落到系统不同层面,运用生理学和分子生物学技术,结合生态学研究手段,综合研究珊瑚的相应响应,以期深入认识海洋酸化对珊瑚礁生态系统健康(例如珊瑚白化)的影响及其效应。     

Benthic Primary Production Budget of a Caribbean Reef Lagoon (Puerto Morelos,Mexico)

High photosynthetic benthic primary production (P) represents a key ecosystem service provided by tropical coral reef systems. However, benthic P budgets of specific ecosystem compartments such as macrophyte-dominated reef lagoons are still scarce. To address this, we quantified individual and lagoon-wide net (P_n) and gross (P_g) primary production by all dominant functional groups of benthic primary producers in a typical macrophyte-dominated Caribbean reef lagoon near Puerto Morelos (Mexico) via measurement of O₂ fluxes in incubation experiments. The photosynthetically active 3D lagoon surface area was quantified using conversion factors to allow extrapolation to lagoon-wide P budgets. Findings revealed that lagoon 2D benthic cover was primarily composed of sand-associated microphytobenthos (40%), seagrasses (29%) and macroalgae (27%), while seagrasses dominated the lagoon 3D surface area (84%). Individual P_g was highest for macroalgae and scleractinian corals (87 and 86 mmol O₂ m⁻² specimen area d⁻¹, respectively), however seagrasses contributed highest (59%) to the lagoon-wide P_g. Macroalgae exhibited highest individual P_n rates, but seagrasses generated the largest fraction (51%) of lagoon-wide P_n. Individual R was highest for scleractinian corals and macroalgae, whereas seagrasses again provided the major lagoon-wide share (68%). These findings characterise the investigated lagoon as a net autotrophic coral reef ecosystem compartment revealing similar P compared to other macrophyte-dominated coastal environments such as seagrass meadows and macroalgae beds. Further, high lagoon-wide P (P_g: 488 and P_n: 181 mmol O₂ m⁻² lagoon area d⁻¹) and overall P_g:R (1.6) indicate substantial benthic excess production within the Puerto Morelos reef lagoon and suggest the export of newly synthesised organic matter to surrounding ecosystems.     

Three-dimensional species distribution modelling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs

The three-dimensional structure of habitats is a critical component of species' niches driving coexistence in species-rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine-scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates.     

Calcifying coral abundance near low-pH springs: implications for future ocean acidification

Rising atmospheric CO₂ and its equilibration with surface ocean seawater is lowering both the pH and carbonate saturation state (Ω) of the oceans. Numerous calcifying organisms, including reef-building corals, may be severely impacted by declining aragonite and calcite saturation, but the fate of coral reef ecosystems in response to ocean acidification remains largely unexplored. Naturally low saturation (Ω ~ 0.5) low pH (6.70–7.30) groundwater has been discharging for millennia at localized submarine springs (called “ojos”) at Puerto Morelos, México near the Mesoamerican Reef. This ecosystem provides insights into potential long term responses of coral ecosystems to low saturation conditions. In-situ chemical and biological data indicate that both coral species richness and coral colony size decline with increasing proximity to low-saturation, low-pH waters at the ojo centers. Only three scleractinian coral species (Porites astreoides, Porites divaricata, and Siderastrea radians) occur in undersaturated waters at all ojos examined. Because these three species are rarely major contributors to Caribbean reef framework, these data may indicate that today’s more complex frame-building species may be replaced by smaller, possibly patchy, colonies of only a few species along the Mesoamerican Barrier Reef. The growth of these scleractinian coral species at undersaturated conditions illustrates that the response to ocean acidification is likely to vary across species and environments; thus, our data emphasize the need to better understand the mechanisms of calcification to more accurately predict future impacts of ocean acidification.