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This work assesses the effectiveness of sample preservation techniques for measurements of pHT (total scale), total dissolved inorganic carbon (DICT), and total alkalinity (AT) in organic-rich estuarine waters. Using HgCl2-treated and untreated water samples, measurements of these carbonate system parameters were examined over a period of three months. Over this duration, continued respiration of dissolved organic matter (DOM) in untreated samples created large discrepancies in DICT concentrations, while DICT was effectively constant in treated samples. Changes in AT were observed for both treated and untreated samples, with treated samples showing the greatest variation. In response to changing AT / DICT ratios, pHT changes were observed in both treated and untreated samples but were relatively small in treated samples. Improved accuracy of results in organic-rich estuarine waters that reflect the in situ carbonate system characteristics of the samples at the time of collection can be achieved when samples obtained for DICT and AT analysis are collected and stored separately. Accurate analyses of DICT can be obtained by filtration and preservation with HgCl2. Accuracy of AT analyses can be improved by filtration and storage in polypropylene bottles at 4 °C without adding HgCl2. Quality of pHT measurements can be improved by prompt analysis in the field and, if this cannot be accomplished, then samples can be preserved with HgCl2 and measured in the laboratory within one week.

The goal of the Bio-ICE Task Team, convened from July 2020 - January 2022, was to advance the integration of biological observations from local, regional, and federal sources using best practices to inform national needs and ultimately feed into GOOS data visualizations and reporting. Using the GOOS marine mammals and corals EOVs as examples, the Task Team sought to: 1. Reconcile U.S. federal collection of these variables with GOOS EOVs and the Group on Earth Observations’ EBVs, identifying synergies in spatial and temporal observing requirements and with existing observation infrastructure and delivery, including use of documented best practices and standards. 2. Identify and improve pathways for data flow for observations of these variables from the IOOS Regional Associations and federal sources into common data portals. This included a focus on identifying and implementing best practices for standardized data collection and delivery adhering to the FAIR and CARE data principles, as appropriate. The Task Team effort focused on corals and marine mammals to ensure the work of the task team was achievable within the time frame. These two EOVs were selected because of their importance to multiple stakeholders, as well as offering opportunities to tie-in to several critical U.S. priorities in ocean science. While the team chose this focus, it acknowledged that there are activities and communities working to advance the other biology and ecosystem essential variables in ways that might be similar to or synergistic with the task team, such as SCOR Working Group 158: Coordinated Global Research Assessment of Seagrass System (C-GRASS), global efforts to coordinate ocean sound monitoring and data, GOOS BioEco panel community workshops and ongoing panel activities, and other efforts worth tracking or considering for future engagement with IOOC.

Beginning in 2015, the United States Environmental Protection Agency’s (EPA’s) National Estuary Program (NEP) started a collaboration with partners in seven estuaries along the East Coast (Barnegat Bay; Casco Bay), West Coast (Santa Monica Bay; San Francisco Bay; Tillamook Bay), and the Gulf of Mexico (GOM) Coast (Tampa Bay; Mission-Aransas Estuary) of the United States to expand the use of autonomous monitoring of partial pressure of carbon dioxide (pCO2) and pH. Analysis of high-frequency (hourly to sub-hourly) coastal acidification data including pCO2, pH, temperature, salinity, and dissolved oxygen (DO) indicate that the sensors effectively captured key parameter measurements under challenging environmental conditions, allowing for an initial characterization of daily to seasonal trends in carbonate chemistry across a range of estuarine settings. Multi-year monitoring showed that across all water bodies temperature and pCO2 covaried, suggesting that pCO2 variability was governed, in part, by seasonal temperature changes with average pCO2 being lower in cooler, winter months and higher in warmer, summer months. Furthermore, the timing of seasonal shifts towards increasing (or decreasing) pCO2 varied by location and appears to be related to regional climate conditions. Specifically, pCO2 increases began earlier in the year in warmer water, lower latitude water bodies in the GOM (Tampa Bay; Mission-Aransas Estuary) as compared with cooler water, higher latitude water bodies in the northeast (Barnegat Bay; Casco Bay), and upwelling-influenced West Coast water bodies (Tillamook Bay; Santa Monica Bay; San Francisco Bay). Results suggest that both thermal and non-thermal influences are important drivers of pCO2 in Tampa Bay and Mission-Aransas Estuary. Conversely, non-thermal processes, most notably the biogeochemical structure of coastal upwelling, appear to be largely responsible for the observed pCO2 values in West Coast water bodies. The co-occurrence of high salinity, high pCO2, low DO, and low temperature water in Santa Monica Bay and San Francisco Bay characterize the coastal upwelling paradigm that is also evident in Tillamook Bay when upwelling dominates freshwater runoff and local processes. These data demonstrate that high-quality carbonate chemistry observations can be recorded from estuarine environments using autonomous sensors originally designed for open-ocean settings.

Structure-from-Motion (SfM) photogrammetry can be used with digital underwater photographs to generate high-resolution bathymetry and orthomosaics with millimeter-to-centimeter scale resolution at relatively low cost. Although these products are useful for assessing species diversity and health, they have additional utility for quantifying benthic community structure, such as coral growth and fine-scale elevation change over time, if accurate length scales and georeferencing are included. This georeferencing is commonly provided with “ground control,” such as pre-installed seafloor benchmarks or identifiable “static” features, which can be difficult and time consuming to install, survey, and maintain. To address these challenges, we developed the SfM Quantitative Underwater Imaging Device with Five Cameras (SQUID-5), a towed surface vehicle with an onboard survey-grade Global Navigation Satellite System (GNSS) and five rigidly mounted downward-looking cameras with overlapping views of the seafloor. The cameras are tightly synchronized with both the GNSS and each other to collect quintet photo sets and record the precise location of every collection event. The system was field tested in July 2019 in the U.S. Florida Keys, in water depths ranging from 3 to 9 m over a variety of bottom types. Surveying accuracy was assessed using pre-installed stations with known coordinates, machined scale bars, and two independent surveys of a site to evaluate repeatability. Under a range of sea conditions, ambient lighting, and water clarity, we were able to map living and senile coral reef habitats and sand waves at mm-scale resolution. Data were processed using best practice SfM techniques without ground control and local measurement errors of horizontal and vertical scales were consistently sub-millimeter, equivalent to 0.013% RMSE relative to water depth. Survey-to-survey repeatability RMSE was on the order of 3 cm without georeferencing but could be improved to several millimeters with the incorporation of one or more non-surveyed marker points. We demonstrate that the SQUID-5 platform can map complex coral reef and other seafloor habitats and measure mm-to-cm scale changes in the morphology and location of seafloor features over time without pre-existing ground control.

Coral reefs are degrading due to many synergistic stressors. Recently there have been a number of global reports of corals occupying mangrove habitats that provide a supportive environment or refugium for corals, sheltering them by reducing stressors such as oxidative light stress and low pH. This study used satellite imagery and manual ground-truthing surveys to search for mangrove-coral habitats in the Florida Keys National Marine Sanctuary and then collected basic environmental parameters (temperature, salinity, dissolved oxygen, pHNBS, turbidity) at identified sites using a multi-parameter water quality sonde. Two kinds of mangrove-coral habitats were found in both the Upper and Lower Florida Keys: (1) prop-root corals, where coral colonies were growing directly on (and around) mangrove prop roots, and (2) channel corals, where coral colonies were growing in mangrove channels under the shade of the mangrove canopy, at deeper depths and not in as close proximity to the mangroves. Coral species found growing on and directly adjacent to prop roots included Porites porites (multiple morphs, including P. divaricata and P. furcata), Siderastrea radians, and Favia fragum. Channel coral habitats predominantly hosted S. radians and a few S. siderea, although single colonies of Solenastrea bournoni and Stephanocoenia intersepta were observed. Although clear, low-turbidity water was a consistent feature of these mangrove-coral habitats, the specific combination of environmental factors that determine which mangrove habitats are favorable for coral recruitment remains to be defined. Circumstantial evidence suggests additional coral communities existed on mangrove shorelines of oceanside and backcountry islands until destroyed, likely by Hurricane Irma. These mangrove-coral habitats may be climate refugia for corals and could be included in ecosystem management plans and considered for their applications in coral restoration.

Ocean acidification (OA), the gradual decline in ocean pH and [ CO32−] caused by rising levels of atmospheric CO2, poses a significant threat to coral reef ecosystems, depressing rates of calcium carbonate (CaCO3) production, and enhancing rates of bioerosion and dissolution. As ocean pH and [ CO32−] decline globally, there is increasing emphasis on managing local stressors that can exacerbate the vulnerability of coral reefs to the effects of OA. We show that sustained, nutrient rich, lower pH submarine groundwater discharging onto nearshore coral reefs off west Maui lowers the pH of seawater and exposes corals to nitrate concentrations 50 times higher than ambient. Rates of coral calcification are substantially decreased, and rates of bioerosion are orders of magnitude higher than those observed in coral cores collected in the Pacific under equivalent low pH conditions but living in oligotrophic waters. Heavier coral nitrogen isotope (δ15N) values pinpoint not only site-specific eutrophication, but also a sewage nitrogen source enriched in 15N. Our results show that eutrophication of reef seawater by land-based sources of pollution can magnify the effects of OA through nutrient driven-bioerosion. These conditions could contribute to the collapse of coastal coral reef ecosystems sooner than current projections predict based only on ocean acidification.

Constraining coral reef metabolism and carbon chemistry dynamics are fundamental for understanding and predicting reef vulnerability to rising coastal CO2 concentrations and decreasing seawater pH. However, few studies exist along reefs occupying densely inhabited shorelines with known input from land-based sources of pollution. The shallow coral reefs off Kahekili, West Maui, are exposed to nutrient-enriched, low-pH submarine groundwater discharge (SGD) and are particularly vulnerable to the compounding stressors from land-based sources of pollution and lower seawater pH. To constrain the carbonate chemistry system, nutrients and carbonate chemistry were measured along the Kahekili reef flat every 4 h over a 6-day sampling period in March 2016. Abiotic process – primarily SGD fluxes – controlled the carbonate chemistry adjacent to the primary SGD vent site, with nutrient-laden freshwater decreasing pH levels and favoring undersaturated aragonite saturation (Ωarag) conditions. In contrast, diurnal variability in the carbonate chemistry at other sites along the reef flat was driven by reef community metabolism. Superimposed on the diurnal signal was a transition during the second sampling period to a surplus of total alkalinity (TA) and dissolved inorganic carbon (DIC) compared to ocean endmember TA and DIC measurements. A shift from positive net community production and positive net community calcification to negative net community production and negative net community calcification was identified. This transition occurred during a period of increased SGD-driven nutrient loading, lower wave height, and reduced current speeds. This detailed study of carbon chemistry dynamics highlights the need to incorporate local effects of nearshore oceanographic processes into predictions of coral reef vulnerability and resilience.

Future development patterns and an anticipated doubling of the population by 2050 could diminish both the economic and environmental integrity of Tampa Bay’s coastal habitat resources. Raabe et al. 2012 demonstrated that Tampa Bay emergent blue carbon ecosystems are trending toward subtropical-dominant mangrove forest habitats. Carbonate-rich sediments in Tampa Bay may provide a mechanism for enhanced blue carbon benefits from seagrass meadows. Distinct meso-oligohaline salt marsh plant communities are found predominantly in Tampa Bay tidal rivers and creeks where freshwater inflow reduces salinities year-round to between 0.5 and 20 psu. The potential for voluntary C market financing of blue carbon ecosystem restoration in Tampa Bay would be an additional resource management tool that would help sustain momentum for the Bay’s continued ecosystem recovery. Resource managers have an added tool to engage public and private landowners in potential C market financing incentives that would provide the needed space for Tampa Bay blue carbon ecosystems to thrive in the future.

Coral reefs serve as natural barriers that protect adjacent shorelines from coastal hazards such as storms, waves, and erosion. Projections indicate global degradation of coral reefs due to anthropogenic impacts and climate change will cause a transition to net erosion by mid-century. Here, we provide a comprehensive assessment of the combined effect of all of the processes affecting seafloor accretion and erosion by measuring changes in seafloor elevation and volume for five coral reef ecosystems in the Atlantic, Pacific, and Caribbean over the last several decades. Regional-scale mean elevation and volume losses were observed at all five study sites and in 77 % of the 60 individual habitats that we examined across all study sites. Mean seafloor elevation losses for whole coral reef ecosystems in our study ranged from −0.09 to −0.8 m, corresponding to net volume losses ranging from 3.4 × 106 to 80.5 × 106 m3 for all study sites. Erosion of both coral-dominated substrate and non-coral substrate suggests that the current rate of carbonate production is no longer sufficient to support net accretion of coral reefs or adjacent habitats. We show that regional-scale loss of seafloor elevation and volume has accelerated the rate of relative sea level rise in these regions. Current water depths have increased to levels not predicted until near the year 2100, placing these ecosystems and nearby communities at elevated and accelerating risk to coastal hazards. Our results set a new baseline for projecting future impacts to coastal communities resulting from degradation of coral reef systems and associated losses of natural and socioeconomic resources.

(1) Dalhousie University, Halifax, NS, Canada, (9) LDEO, Columbia University, New York, NY, United States, (2) U.S. Geological Survey, St. Petersburg, FL, United States, (3) College of Marine Science, University of South Florida, St. Petersburg, FL, United States, (4) Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, United States, (5) NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, United States, (6) Marine Sciences, The University of Trinidad and Tobago, Trinidad and Tobago, (7) National Commission for Knowledge and Use of Biodiversity (CONABIO), Mexico, (8) UAV Collaborative, Moffett Field, CA, United States

Space-based observations offer unique capabilities for studying spatial and temporal dynamics of the upper ocean inorganic carbon cycle and, in turn, supporting research tied to ocean acidification (OA). Satellite sensors measuring sea surface temperature, color, salinity, wind, waves, currents, and sea level enable a fuller understanding of a range of physical, chemical, and biological phenomena that drive regional OA dynamics as well as the potentially varied impacts of carbon cycle change on a broad range of ecosystems. Here, we update and expand on previous work that addresses the benefits of space-based assets for OA and carbonate system studies. Carbonate chemistry and the key processes controlling surface ocean OA variability are reviewed. Synthesis of present satellite data streams and their utility in this arena are discussed, as are opportunities on the horizon for using new satellite sensors with increased spectral, temporal, and/or spatial resolution. We outline applications that include the ability to track the biochemically dynamic nature of water masses, to map coral reefs at higher resolution, to discern functional phytoplankton groups and their relationships to acid perturbations, and to track processes that contribute to acid variation near the land-ocean interface.

Author(s): Yates, KK; Turley, C; Hopkinson, BM; Todgham, AE; Cross, JN; Greening, H; Williamson, P; Van Hooidonk, R; Deheyn, DD; Johnson, Z | Abstract: The global nature of ocean acidification (OA) transcends habitats, ecosystems, regions, and science disciplines. The scientific community recognizes that the biggest challenge in improving understanding of how changing OA conditions affect ecosystems, and nassociated consequences for human society, requires integration of experimental, observational, and modeling approaches from many disciplines over a wide range of temporal and spatial scales. Such transdisciplinary science is the next step in providing relevant, meaningful results and optimal guidance to policymakers and coastal managers. We discuss the challenges associated with integrating ocean acidification science across funding agencies, institutions, disciplines, topical areas, and regions, and the value of unifying science objectives and activities to deliver insights into local, regional, and global scale impacts. We identify guiding principles and strategies for developing transdisciplinary research in the ocean acidification science community.

Risk analyses indicate that more than 90% of the world's reefs will be threatened by climate change and local anthropogenic impacts by the year 2030 under "business-as-usual" climate scenarios. Increasing temperatures and solar radiation cause coral bleaching that has resulted in extensive coral mortality. Increasing carbon dioxide reduces seawater pH, slows coral growth, and may cause loss of reef structure. Management strategies include establishment of marine protected areas with environmental conditions that promote reef resiliency. However, few resilient reefs have been identified, and resiliency factors are poorly defined. Here we characterize the first natural, non-reef coral refuge from thermal stress and ocean acidification and identify resiliency factors for mangrove–coral habitats. We measured diurnal and seasonal variations in temperature, salinity, photosynthetically active radiation (PAR), and seawater chemistry; characterized substrate parameters; and examined water circulation patterns in mangrove communities where scleractinian corals are growing attached to and under mangrove prop roots in Hurricane Hole, St. John, US Virgin Islands. Additionally, we inventoried the coral species and quantified incidences of coral bleaching, mortality, and recovery for two major reef-building corals, Colpophyllia natans and Diploria labyrinthiformis, growing in mangrove-shaded and exposed (unshaded) areas. Over 30 species of scleractinian corals were growing in association with mangroves. Corals were thriving in low-light (more than 70% attenuation of incident PAR) from mangrove shading and at higher temperatures than nearby reef tract corals. A higher percentage of C. natans colonies were living shaded by mangroves, and no shaded colonies were bleached. Fewer D. labyrinthiformis colonies were shaded by mangroves, however more unshaded colonies were bleached. A combination of substrate and habitat heterogeneity, proximity of different habitat types, hydrographic conditions, and biological influences on seawater chemistry generate chemical conditions that buffer against ocean acidification. This previously undocumented refuge for corals provides evidence for adaptation of coastal organisms and ecosystem transition due to recent climate change. Identifying and protecting other natural, non-reef coral refuges is critical for sustaining corals and other reef species into the future.

Coral reefs serve as natural barriers that protect adjacent shorelines from coastal hazards such as storms, waves and erosion. Projections indicate global degradation of coral reefs due to anthropogenic impacts and climate change will cause a transition to net erosion by mid-century. Here, we provide a comprehensive assessment of the combined effect of all of the processes affecting seafloor accretion and erosion by measuring changes in seafloor elevation and volume for 5 coral reef ecosystems in the Atlantic, Pacific and Caribbean over the last several decades. Regional-scale mean elevation and volume losses were observed at all 5 study sites and in 78 % of the 59 individual habitats that we examined across all study sites. We estimate that 12 % to 65 % of seafloor elevation loss may be attributed to reduced carbonate production, bioerosion and carbonate dissolution and 35 % to 88 % may be attributed to physical erosion and export of sediment from these systems. Erosion of both coral-dominated substrate and non-coral substrate suggests that the current rate of carbonate production is no longer sufficient to support net accretion of coral reefs or adjacent habitats. We show that regional-scale loss of seafloor elevation and volume has accelerated the rate of relative sea level rise in these regions. Current water depths have increased to levels not predicted until near the year 2100, placing these ecosystems and nearby communities at elevated and accelerating risk to coastal hazards. Our results set a new baseline for projecting future impacts to coastal communities resulting from degradation of coral reef systems and associated losses of natural and socio-economic resources.

Light availability is an important factor driving primary productivity in benthic ecosystems, but in situ and remote sensing measurements of light quality are limited for coral reefs and seagrass beds. We evaluated the productivity responses of a patch reef and a seagrass site in the Lower Florida Keys to ambient light availability and spectral quality. In situ optical properties were characterized utilizing moored and water column bio-optical and hydrographic measurements. Net ecosystem productivity (NEP) was also estimated for these study sites using benthic productivity chambers. Our results show higher spectral light attenuation and absorption, and lower irradiance during low tide in the patch reef, tracking the influx of materials from shallower coastal areas. In contrast, the intrusion of clearer surface Atlantic Ocean water caused lower values of spectral attenuation and absorption, and higher irradiance in the patch reef during high tide. Storms during the studied period, with winds >10 m·s−1, caused higher spectral attenuation values. A spatial gradient of NEP was observed, from high productivity in the shallow seagrass area, to lower productivity in deeper patch reefs. The highest daytime NEP was observed in the seagrass, with values of almost 0.4 g·O2·m−2·h−1. Productivity at the patch reef area was lower in May than during October 2012 (mean = 0.137 and 0.177 g·O2·m−2·h−1, respectively). Higher photosynthetic active radiation (PAR) levels measured above water and lower light attenuation in the red region of the visible spectrum (~666 to ~699 nm) had a positive correlation with NEP. Our results indicate that changes in light availability and quality by suspended or resuspended particles limit benthic productivity in the Florida Keys.

Oxygen and carbonate system parameters were measured, in situ, over diurnal cycles in Tampa Bay and Florida Bay, Florida. All system parameters showed distinct diurnal trends in Tampa Bay with an average range of diurnal variation of 39.1 μmol kg− 1 for total alkalinity, 165.1 μmol kg− 1 for total CO2, 0.22 for pH, 0.093 mmol L− 1 for dissolved oxygen, and 218.1 μatm for pCO2. Average range of diurnal variation for system parameters in Tampa Bay was 73% to 93% of the seasonal range of variability for dissolved oxygen and pH. All system parameters measured in Florida Bay showed distinct variation over diurnal time-scales. However, clear diurnal trends were less evident. The average range of diurnal variability in Florida Bay was 62.8 μmol kg− 1 for total alkalinity, 130.4 μmol kg− 1 for total CO2, 0.13 for pH, 0.053 mmol L− 1 for dissolved oxygen, and 139.8 μatm for pCO2. The average range of diurnal variation was 14% to 102% of the seasonal ranges for these parameters. Diurnal variability in system parameters was most influenced by primary productivity and respiration of benthic communities in Tampa Bay, and by precipitation and dissolution of calcium carbonate in Florida Bay. Our data indicate that use of seasonal data sets without careful consideration of diurnal variability may impart significant error in calculations of annual carbon and oxygen budgets. These observations reinforce the need for higher temporal resolution measurements of oxygen and carbon system parameters in coastal ecosystems.

The severity of the impact of elevated atmospheric pCO2 to coral reef ecosystems depends, in part, on how seawater pCO2 affects the balance between calcification and dissolution of carbonate sediments. Presently, there are insufficient published data that relate concentrations of pCO2 and CO32− to in situ rates of reef calcification in natural settings to accurately predict the impact of elevated atmospheric pCO2 on calcification and dissolution processes. Rates of net calcification and dissolution, CO32− concentrations, and pCO2 were measured, in situ, on patch reefs, bare sand, and coral rubble on the Molokai reef flat in Hawaii. Rates of calcification ranged from 0.03 to 2.30 mmol CaCO3 m−2 h−1 and dissolution ranged from –0.05 to –3.3 mmol CaCO3 m−2 h−1. Calcification and dissolution varied diurnally with net calcification primarily occurring during the day and net dissolution occurring at night. These data were used to calculate threshold values for pCO2 and CO32− at which rates of calcification and dissolution are equivalent. Results indicate that calcification and dissolution are linearly correlated with both CO32− and pCO2. Threshold pCO2 and CO32− values for individual substrate types showed considerable variation. The average pCO2 threshold value for all substrate types was 654±195 μatm and ranged from 467 to 1003 μatm. The average CO32− threshold value was 152±24 μmol kg−1, ranging from 113 to 184 μmol kg−1. Ambient seawater measurements of pCO2 and CO32− indicate that CO32− and pCO2 threshold values for all substrate types were both exceeded, simultaneously, 13% of the time at present day atmospheric pCO2 concentrations. It is predicted that atmospheric pCO2 will exceed the average pCO2 threshold value for calcification and dissolution on the Molokai reef flat by the year 2100.

Holistic rates of excess organic carbon production (E) and calcification for a 0.5 km 2 segment of the backreef platform of the northern Florida reef tract (NFRT) were estimated by com- bining biotope mapping using remote sensing with community metabolic rates determined with a benthic incubation system. The use of ASTER multispectral satellite imaging for the spatial scaling of benthic metabolic processes resulted in errors in E and net calcification (G) of 48 and 431% respec- tively, relative to estimates obtained using AISA hyperspectral airborne scanning. At 19 and 125%, the E and G errors relative to the AISA-based estimates were less pronounced for an analysis that used IKONOS multispectral satellite imagery to spatially extrapolate the chamber process measurements. Our scaling analysis indicates that the holistic calcification rate of the backreef platform of the northern Florida reef tract is negligible at 0.07 g CaCO3 m -2 d -1 . All of the mapped biotopes in this reef zone are net heterotrophic, resulting in an estimated holistic excess production rate of -0.56 g C m -2 d -1 , and an overall gross primary production to respiration ratio of 0.85. Based on our finding of ubiquitous heterotrophy, we infer that the backreef platform of the NFRT is a sink for external inputs of suspended particulate organic matter. Further, our results suggest that the inward advection of inorganic nutrients is not a dominant forcing mechanism for benthic biogeo- chemical function in the NFRT. We suggest that the degradation of the northern Florida reef tract may parallel the community phase shifts documented within other reef systems polluted by organic detritus.

Water quality and criculation in Florida Bay (a shallow, subtropical estuary in south Florida) are highly dependent upon the development and evolution of carbonate mud banks distributed throughout the Bay. Predicting the effect of natural and anthropogenic perturbations on carbonate sedimentation requires an understanding of annual, seasonal, and daily variations in the biogenic and inorganic processes affecting carbonate sediment precipitation and dissolution. In this study, net calcification rates were measured over diurnal cycles on 27 d during summer and winter from 1999 to 2003 on mud banks and four representative substrate types located within basins between mud banks. Substrate types that were measured in basins include seagrass beds of sparse and intermediate densityThalassia sp., mud bottom, and hard bottom communities. Changes in total alkalinity were used as a proxy for calcification and dissolution. On 22 d (81%), diurnal variation in rates of net calcification was observed. The highest rates of net carbonate sediment production (or lowest rates of net dissolution) generally occurred during daylight hours and ranged from 2.900 to −0.410 g CaCO3 m−2d−1. The lowest rates of carbonate sediment production (or net sediment dissolution) occurred at night and ranged from 0.210 to −1.900 g CaCO3 m−2 night−1. During typical diurnal cycles, dissolution during the night consumed an average of 29% of sediment produced during the day on banks and 68% of sediment produced during the day in basins. Net sediment dissolution also occurred during daylight, but only when there was total cloud cover, high turbidity, or hypersalinity. Diurnal variation in calcification and dissolution in surface waters and surface sediments of Florida Bay is linked to cycling of carbon dioxide through photosynthesis and respiration. Estimation of long-term sediment accumulation rates from diurnal rates of carbonate sediment production measured in this study indicates an overall average accumulation rate for Florida Bay of 8.7 cm 1000 yr−1 and suggests that sediment dissolution plays a more important role than sediment transport in loss of sediment from Florida Bay.

Accurate measurement of coral reef community metabolism is a necessity for process monitoring and in situ experimentation on coral reef health. Traditional methodologies used for these measurements are effective but limited by location and scale constraints. We present field trial results for a new benthic chamber system called the Submersible Habitat for Analyzing Reef Quality (SHARQ). This large, portable incubation system enables in situ measurement and experimentation on community-scale metabolism. Rates of photosynthesis, respiration, and calcification were measured using the SHARQ for a variety of coral reef substrate types on the reef flat of South Molokai, Hawaii, and in Biscayne National Park, Florida. Values for daily gross production, 24-h respiration, and net calcification ranged from 0.26 to 6.45 g O2 m−2 day−1, 1.96 to 8.10 g O2 m−2 24 h−1, and 0.02 to 2.0 g CaCO3 m−2 day−1, respectively, for all substrate types. Field trials indicate that the SHARQ incubation chamber is an effective tool for in situ isolation of a water mass over a variety of benthic substrate types for process monitoring, experimentation, and other applications.

Microbial calcification significantly impacts the cycling and deposition of inorganic carbon. This research employs 45 Ca and 14 C techniques as radioisotopic tracers to examine the role of cellular cycling of Ca 2+ and inorganic carbon in CaCO 3 precipitation by the unicellular green alga Nannochloris atomus . Implications of the effects of these physiological aspects on CaCO 3 precipitation and the effects of microbial calcification on CaCO 3 δ 13 C ratios are discussed. Results from pulse/chase experiments indicate that intracellular Ca 2+ is incorporated into extracellular CaCO 3 . Intracellular inorganic carbon leaks from cells within 10 to 12 s after injection of unlabelled NaHCO 3 , providing a source of inorganic carbon for extracellular CaCO 3 . Cellular expulsion of calcium plays a key role in increasing the CaCO 3 saturation state at the site of calcification. The δ 13 C ratios of microbial carbonates may vary depending on the amount of photorespiratory CO 2 incorporated.

This study investigates the ability of the unicellular green alga Nannochloris atomusto precipitate CaCO3, quantifies mineral precipitation rates, estimates sediment production in a N. atomus bloom, and discusses the implications of microbial calcification for carbonate sediment deposition. A series of N. atomus cultures, isolated from Lake Reeve, Australia, were incubated at various pH and calcium concentrations to determine environmental parameters for calcification. Rates of calcification were calculated from initial and postincubation alkalinity, pH, and calcium measurements. Replicate experiments and controls consisting of non-calcifying cultures, uninoculated media, and dead cell cultures were performed using environmental culture parameters determined in series cultures. Average calcification rates from replicate experiments were used to predict daily sediment production rates in a small bloom of N. atomus. N. atomus precipitates 0.138 g/L of calcite in approximately 4 h when incubated at pH 8.5, 14.24 mM calcium concentration, 33 8C, 100 mE/m 2 /s light intensity, and a cell population density of 10 7 cells/mL. Assuming continuous precipitation, this corresponds to a maximum estimated sediment production rate of 1.6 3 10 6 kg of CaCO3 per 12 h day in a single bloom of 3.2 3 10 9 L. Our results suggest that microbial calcification contributes significantly to the carbonate sediment budget.

Autonomous in situ sensors are needed to document the effects of today's rapid ocean uptake of atmospheric carbon dioxide (e.g., ocean acidification). General environmental conditions (e.g., biofouling, turbidity) and carbon-specific conditions (e.g., wide diel variations) present significant challenges to acquiring long-term measurements of dissolved inorganic carbon (DIC) with satisfactory accuracy and resolution. SEAS-DIC is a new in situ instrument designed to provide calibrated, high-frequency, long-term measurements of DIC in marine and fresh waters. Sample water is first acidified to convert all DIC to carbon dioxide (CO2). The sample and a known reagent solution are then equilibrated across a gas-permeable membrane. Spectrophotometric measurement of reagent pH can thereby determine the sample DIC over a wide dynamic range, with inherent calibration provided by the pH indicator's molecular characteristics. Field trials indicate that SEAS-DIC performs well in biofouling and turbid waters, with a DIC accuracy and precision of ∼2 μmol kg(-1) and a measurement rate of approximately once per minute. The acidic reagent protects the sensor cell from biofouling, and the gas-permeable membrane excludes particulates from the optical path. This instrument, the first spectrophotometric system capable of automated in situ DIC measurements, positions DIC to become a key parameter for in situ CO2-system characterizations.

Marine surface waters are being acidified due to uptake of anthropogenic carbon dioxide, resulting in surface ocean areas of undersaturation with respect to carbonate minerals, including aragonite. In the Arctic Ocean, acidification is expected to occur at an accelerated rate with respect to the global oceans, but a paucity of baseline data has limited our understanding of the extent of Arctic undersaturation and of regional variations in rates and causes. The lack of data has also hindered refinement of models aimed at projecting future trends of ocean acidification. Here, based on more than 34,000 data records collected in 2010 and 2011, we establish a baseline of inorganic carbon data (pH, total alkalinity, dissolved inorganic carbon, partial pressure of carbon dioxide, and aragonite saturation index) for the western Arctic Ocean. This data set documents aragonite undersaturation in ≈ 20% of the surface waters of the combined Canada and Makarov basins, an area characterized by recent acceleration of sea ice loss. Conservative tracer studies using stable oxygen isotopic data from 307 sites show that while the entire surface of this area receives abundant freshwater from meteoric sources, freshwater from sea ice melt is most closely linked to the areas of carbonate mineral undersaturation. These data link the Arctic Ocean's largest area of aragonite undersaturation to sea ice melt and atmospheric CO2 absorption in areas of low buffering capacity. Some relatively supersaturated areas can be linked to localized biological activity. Collectively, these observations can be used to project trends of ocean acidification in higher latitude marine surface waters where inorganic carbon chemistry is largely influenced by sea ice meltwater.

to 13.7 mmol O2 m −2 h −1 . Productivity measurements from the enclosure method ranged from −11.0 to 12.9 mmol O2 m −2 h −1 . During the study, the mean hourly difference between the methods was 0.65 mmol O2 m −2 h −1 (r 2 =0 .92), resulting in well‐reconciled estimates of net community production between the boundary layer (−33.1 mmol m −2 d −1 ) and enclosure (−46.3 mmol m −2 d −1 ) techniques. The results of these independent approaches corroborate quantified rates of metabolism at Cayo Enrique Reef. Close agreement between methods demonstrates that boundary layer measurements can provide near real‐time assessments of coral reef health. Citation: McGillis, W. R., C. Langdon, B. Loose, K. K. Yates, and J. Corredor (2011), Productivity of a coral reef using boundary layer and enclosure methods, Geophys. Res. Lett., 38, L03611, doi:10.1029/2010GL046179.