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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.

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.

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.