A low-cost benthic incubation chamber for in-situ community metabolism measurements

Benthic incubation chambers facilitate in-situ metabolism studies in shallow water environments. They are used to isolate the water surrounding a study organism or community so that changes in water chemistry can be quantified to characterise physiological processes such as photosynthesis, respiration, and calcification. Such field measurements capture the biological processes taking place within the benthic community while incorporating the influence of environmental variables that are often difficult to recreate in ex-situ settings. Variations in benthic chamber designs have evolved for a range of applications. In this study, we built upon previous designs to create a novel chamber, which is (1) low-cost and assembled without specialised equipment, (2) easily reproducible, (3) minimally invasive, (4) adaptable to varied substrates, and (5) comparable with other available designs in performance. We tested the design in the laboratory and field and found that it achieved the outlined objectives. Using non-specialised materials, we were able to construct the chamber at a low cost (under $20 USD per unit), while maintaining similar performance and reproducibility with that of existing designs. Laboratory and field tests demonstrated minimal leakage (2.08 ± 0.78% water exchange over 4 h) and acceptable light transmission (86.9 ± 1.9%), results comparable to those reported for other chambers. In the field, chambers were deployed in a shallow coastal environment in Akumal, Mexico, to measure productivity of seagrass, and coral-, algae-, and sand-dominated reef patches. In both case studies, production rates aligned with those of comparable benthic chamber deployments in the literature and followed established trends with light, the primary driver of benthic metabolism, indicating robust performance under field conditions. We demonstrate that our low-cost benthic chamber design uses locally accessible and minimal resources, is adaptable for a variety of field settings, and can be used to collect reliable and repeatable benthic metabolism data. This chamber has the potential to broaden accessibility and applications of in-situ incubations for future studies.

Reef Metabolism Monitoring Methods and Potential Applications for Coral Restoration

Coral reef metabolism measurements have been used by scientists for decades to track reef responses to the globe's changing carbon budget and project shifts in reef function. Here, we propose that metabolism measurement tools and methods could also be used to monitor reef ecosystem change in response to coral restoration. This review paper provides a general introduction to net ecosystem metabolism and carbon chemistry for coral reef ecosystems, followed by a review of five metabolism monitoring methods with potential for application to coral reef restoration monitoring. Selected methodologies included those with measurement scales appropriate to assess outplant arrays and whole reef ecosystem outcomes associated with restoration interventions. Subsequently we discuss how water column and CO₂ chemistry could be used to address coral restoration monitoring research gaps and scale up from biological, colony-level metrics to ecosystem-scale function and performance assessments. Such function-based measurements could potentially be used to inform several goal-based monitoring objectives highlighted in the Coral Reef Restoration Monitoring Guide. Lastly, this review discusses important methodological factors, such as scale, reef type, and flow environment, that should be considered when determining which metabolism monitoring technique would be most appropriate for a reef restoration project.

Diel versus time-integrated (daily) photosynthesis and irradiance relationships of coral reef organisms and communities

The most important source of energy to tropical shallow water coral reefs is light, the transformation of which ultimately limits reef biomass and growth. Therefore, measurements of productivity (primary production, P) for benthic reef organisms and communities are critical to understand reef functioning. Short-term (minutes to hours) P measurements of reef photosynthesizers virtually always produce the classic hyperbolic tangent (or similar) P-E (irradiance) relationship, with P rapidly rising to a saturation point as E increases. Longer-term (days to weeks), larger-scale investigations of natural reef communities typically do not explore P-E relationships, but the few that do show no saturation of time-integrated P with high time-integrated E. In this paper we present a modeling study to reconcile this apparent contradiction. We used 52 published short-term (instantaneous) P-E curves of organisms (corals, algae) and communities (corals, mixed corals and algae) from different reefs in the Indo-Pacific and the Caribbean, each coupled with 928 diel light curves comprising a wide range of cloud cover scenarios. The diel light curves provided instantaneous E at 1-minute intervals, from which we calculated corresponding instantaneous P using the different published P-E relationships. We integrated both variables to calculate time-integrated E and P. Time-integrated E varied up to 18-fold due to changes in cloud cover and season. We found that, despite routine saturation of instantaneous P, day-scale P-E relationships were near linear in all cases, with slightly decreased linearity in cases where instantaneous light saturation occurred very early during the day. This indicates that the Functional Convergence Hypothesis (FCH) developed by terrestrial ecologists may also apply for reef photosynthesizers. The FCH states that despite short-term light saturation, plants on average do not absorb more light than they can use, since resource allocations are strictly coordinated and tailored towards an optimal use. Thus, there is no contradiction: At the growth time scale (≥ day), P should be expected to be a near linear function of E. One implication is that reef P can be estimated using rapid optical measurements, as opposed to traditional, laborious respirometry methods. The requirement going forward is to derive appropriate values for light-use efficiency, which is the rate at which the plant or community converts absorbed light into fixed carbon.

Comparability of slack water and Lagrangian flow respirometry methods for community metabolic measurements

Coral reef calcification is predicted to decline as a result of ocean acidification and other anthropogenic stressors. The majority of studies predicting declines based on in situ relationships between environmental parameters and net community calcification rate have been location-specific, preventing accurate predictions for coral reefs globally. In this study, net community calcification and production were measured on a coral reef flat at One Tree Island, Great Barrier Reef, using Lagrangian flow respirometry and slack water methods. Net community calcification, daytime net photosynthesis and nighttime respiration were higher under the flow respirometry method, likely due to increased water flow relative to the slack water method. The two methods also varied in the degrees to which they were influenced by potential measurement uncertainties. The difference in the results from these two commonly used methods implies that some of the location-specific differences in coral reef community metabolism may be due to differences in measurement methods.

Oceanic forcing of coral reefs

Although the oceans play a fundamental role in shaping the distribution and function of coral reefs worldwide, a modern understanding of the complex interactions between ocean and reef processes is still only emerging. These dynamics are especially challenging owing to both the broad range of spatial scales (less than a meter to hundreds of kilometers) and the complex physical and biological feedbacks involved. Here, we review recent advances in our understanding of these processes, ranging from the small-scale mechanics of flow around coral communities and their influence on nutrient exchange to larger, reef-scale patterns of wave- and tide-driven circulation and their effects on reef water quality and perceived rates of metabolism. We also examine regional-scale drivers of reefs such as coastal upwelling, internal waves, and extreme disturbances such as cyclones. Our goal is to show how a wide range of ocean-driven processes ultimately shape the growth and metabolism of coral reefs.

In situ coral reef oxygen metabolism: an eddy correlation study

Quantitative studies of coral reefs are challenged by the three-dimensional hard structure of reefs and the high spatial variability and temporal dynamics of their metabolism. We used the non-invasive eddy correlation technique to examine respiration and photosynthesis rates, through O₂ fluxes, from reef crests and reef slopes in the Florida Keys, USA. We assessed how the photosynthesis and respiration of different reef habitats is controlled by light and hydrodynamics. Numerous fluxes (over a 0.25 h period) were as high as 4500 mmol O₂ m⁻² d⁻¹, which can only be explained by efficient light utilization by the phototrophic community and the complex canopy structure of the reef, having a many-fold larger surface area than its horizontal projection. Over diel cycles, the reef crest was net autotrophic, whereas on the reef slope oxygen production and respiration were balanced. The autotrophic nature of the shallow reef crests implies that the export of organics is an important source of primary production for the larger area. Net oxygen production on the reef crest was proportional to the light intensity, up to 1750 µmol photons m⁻² s⁻¹ and decreased thereafter as respiration was stimulated by high current velocities coincident with peak light levels. Nighttime respiration rates were also stimulated by the current velocity, through enhanced ventilation of the porous framework of the reef. Respiration rates were the highest directly after sunset, and then decreased during the night suggesting that highly labile photosynthates produced during the day fueled early-night respiration. The reef framework was also important to the acquisition of nutrients as the ambient nitrogen stock in the water had sufficient capacity to support these high production rates across the entire reef width. These direct measurements of complex reefs systems yielded high metabolic rates and dynamics that can only be determined through in situ, high temporal resolution measurements.

Physical and biological controls on the carbonate chemistry of coral reef waters: effects of metabolism, wave forcing, sea level, and geomorphology

We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO(2), pH, and aragonite saturation state (Ω(ar)) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO(2), pH, and Ω(ar) are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO(2) relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO(2) in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO(2).