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.

Based on noninvasive eddy correlation measurements at a marine and a freshwater site, this study documents the control that current flow and light have on sediment-water oxygen fluxes in permeable sediments. The marine sediment was exposed to tidal-driven current and light, and the oxygen flux varied from night to day between 229 and 78 mmol m 22 d 21 . A fitting model, assuming a linear increase in oxygen respiration with current flow, and a photosynthesis-irradiance curve for light-controlled production reproduced measured fluxes well (R 2 5 0.992) and revealed a 4-fold increase in oxygen uptake when current velocity increased from , 0 to 20 cm s 21 . Application of the model to a week-long measured record of current velocity and light showed that net ecosystem metabolism varied substantially among days, between 227 and 31 mmol m 22 d 21 , due to variations in light and current flow. This variation is likely typical of many shallow-water systems and highlights the need for long-term flux integrations to determine system metabolism accurately. At the freshwater river site, the sediment-water oxygen flux ranged from 2360 to 137 mmol m 22 d 21 . A direct comparison during nighttime with concurrent benthic chamber incubations revealed a 4.1 times larger eddy flux than that obtained with chambers. The current velocity during this comparison was 31 cm s 21 , and the large discrepancy was likely caused by poor imitation by the chambers of the natural pore-water flushing at this high current velocity. These results emphasize the need for more noninvasive oxygen flux measurements in permeable sediments to accurately assess their role in local and global carbon budgets.

Accurate light measurements are important in the analysis of photosynthetic systems. Many commercial instruments are available to determine light; however, the comparison of light estimates between studies is difficult due to the differences in sensor types and their calibrations. The measurement of underwater irradiance is also complicated by the scattering and attenuation of light due to interactions with particulates, molecules, and the bottom. Here, three sensor types are compared to evaluate the calibration of light intensity loggers to estimate photosynthetically active radiation (PAR). We present a simple calibration of light intensity loggers that agree within 3.8% to factory-calibrated scalar PAR sensors under a wide range of environmental conditions. Under the same range of conditions, two identical factory-calibrated PAR sensors showed a similar difference of 3.7%. The light intensity loggers were calibrated to a high-quality PAR sensor using an exponential fit (r 2 = 0.983) that accounts for differences in sensor types with respect to the angle of incoming light, scattering, and attenuation. The light loggers are small, robust, and simple to operate and install, and thus well-suited for typical subsurface research. They are also useful for small-scale measurements, when broad spatial coverage is needed, or in research requiring multiple sensors. Many studies have used these simple light intensity sensors to estimate PAR, yet their limitations and advantages in mimicking PAR have not been well defined previously. We present these small and user-friendly loggers as an excellent alternative to more sophisticated scalar PAR sensors.

The metabolism of seagrass ecosystems was examined at 4 sites in south Florida, USA, using the eddy covariance technique under in situ conditions. Three sites were located across a phosphorus-driven productivity gradient to examine the combined effects of dynamic variables (irradiance, flow velocity) and state variables (sediment phosphorus and organic content, seagrass biomass) on ecosystem metabolism and trophic status. Gross primary production and respiration rates varied significantly across Florida Bay in the summer of 2012 with the lowest rates (64 and −53 mmol O 2 m −2 d −1 , respectively) in low-phosphorus sediments in the northeast and the highest (287 and −212 mmol O 2 m −2 d −1 , respectively) in the southwest where sediment phosphorus, organic matter, and seagrass biomass are higher. Seagrass eco systems offshore of the Florida Keys had similar large daily production and respiration rates (397 and −217 mmol O 2 m −2 d −1 , respectively) and were influenced by flow through the permeable offshore sediments. Across all sites, net ecosystem metabolism rates indicated that the seagrass ecosystems were autotrophic in the summertime. Substantial day-today variability in metabolic rates was found due to variations in irradiance and flow velocity. At all sites the relationship between photosynthesis and irradiance was linear and did not show any sign of saturation over the entire irradiance range (up to 1400 µmol photons m −2 s −1). This was likely due to the efficient use of light by the large photosynthetic surface area of the seagrass canopy, an effect which can only be examined by in situ measurements that integrate across all autotrophs in the seagrass ecosystem.

Abstract. This study examined fluxes across the ice-water interface utilizing the eddy correlation technique. Temperature eddy correlation systems were used to determine rates of ice melting and freezing, and O 2 eddy correlation systems were used to examine O 2 exchange rates driven by biological and physical processes. The study was conducted below 0.7 m thick sea-ice in mid-March 2010 in a southwest Greenland fjord and revealed low rates of ice melt at a maximum of 0.80 mm d −1 . The O 2 flux associated with release of O 2 depleted melt water was less than 13 % of the average daily O 2 respiration rate. Ice melt and insufficient vertical turbulent mixing due to low current velocities caused periodic stratification immediately below the ice. This prevented the determination of fluxes 61 % of the deployment time. These time intervals were identified by examining the velocity and the linearity and stability of the cumulative flux. The examination of unstratified conditions through vertical velocity and O 2 spectra and their cospectra revealed characteristic fingerprints of well-developed turbulence. From the measured O 2 fluxes a photosynthesis/irradiance curve was established by least-squares fitting. This relation showed that light limitation of net photosynthesis began at 4.2 µmol photons m −2 s −1 , and that algal communities were well-adapted to low-light conditions as they were light saturated for 75 % of the day during this early spring period. However, the sea-ice associated microbial and algal community was net heterotrophic with a daily gross primary production of 0.69 mmol O 2 m −2 d −1 and a respiration rate of −2.13 mmol O 2 m −2 d −1 leading to a net ecosystem metabolism of −1.45 mmol O 2 m −2 d −1 . This application of the eddy correlation technique produced high temporal resolution O 2 fluxes and ice melt rates that were measured without disturbing the in situ environmental conditions while integrating over an area of approximately 50 m 2 which incorporated the highly variable activity and spatial distributions of sea-ice communities.

Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structurefrom-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.

Sediment-bound phosphorus (P) is a potential nutrient source for P-limited seagrasses inhabiting carbonate sediments. We explored the role of organic acid (OA) exudation by seagrasses in liberating mineral P from carbonate sediments. Organic acids can act to increase available P by dissolving carbonate sediment, competing with P for binding sites and complexing dissolution end products, and also by fueling microbial processes that change pore-water pH. We used dialysis tubing placed around individual roots in situ to quantify dissolved species immediately adjacent to roots (root zone) and compared these to bulk pore-water concentrations in vegetated and nonvegetated sediments. Total OA concentrations were highest in the root zone (29.8 6 1.8 mmol L 21 ) compared to bulk measures of 15.5 6 1.9 and 7.5 6 0.6 mmol L 21 in vegetated and nonvegetated sediments, respectively. Phosphate concentrations were also highest in the root zone and were linearly related to OA concentrations (R 2 5 0.63). Organic acid concentrations increased along a seagrass productivity gradient, and ratios of OA concentrations to productivity showed a significant response to a gradient in P-limitation of seagrasses. Organic acid concentrations found in and around roots, compared to those found in bulk sediment measures, indicate that seagrasses are a significant source of OA. Sampling at small spatial scales (mm) immediately adjacent to the roots is critical, because bulk sediment pore-water measures did not capture the observed fluctuations caused by the rapid reaction and consumption of OA in the sediment. Root-zone processes can liberate considerable quantities of P, and OA exudates likely contribute significantly to the success of T. testudinum in P-limited environments.

An aquatic eddy covariance (EC) system was developed to measure the exchange of oxygen (O 2 ) and hydrogen ions (H 1 ) across the sediment-water interface. The system uses O 2 optodes and a newly developed micro-flow cell H 1 ion selective field effect transistor; these sensors displayed sufficient precision and rapid enough response times to measure concentration changes associated with turbulent exchange. Discrete samples of total alkalinity and dissolved inorganic carbon were used to determine the background carbonate chemistry of the water column and relate the O 2 and H 1 fluxes to benthic processes. The ECHOES system was deployed in a eutrophic estuary (Waquoit Bay), and revealed that the benthos was a sink for acidity during the day and a source of acidity during the night, with H 1 and O 2 fluxes of 6 0.0001 and 6 10 mmol m 22 h 21 , respectively. H 1 and O 2 fluxes were also determined using benthic flux chambers, for comparison with the EC rates. Chamber fluxes determined in 0.25 h intervals co-varied with EC fluxes but were 4 times lower in magnitude. This difference was likely due to suppressed pore-water advection in the chambers and changes in the chemistry of the enclosed chamber overlying water. The individual H 1 and O 2 fluxes were highly correlated in each dataset (EC and chambers), and both methods yielded H 1 fluxes that could not be explained by O 2 metabolism alone. The ECHOES system provides a new tool for determining the influence of benthic biogeochemical cycling on coastal ocean acidification and carbon cycling.