Mangrove habitats provide refuge from climate change for reef-building corals

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Introduction
Evidence that repeated coral bleaching events (Baker et al., 2008;Eakin et al., 2009;Fitt et al., 2001;Hoegh-Guldberg et al., 2007;Hoegh-Guldberg, 2011;Lesser, 2011) and ocean acidification (Fabricius et al., 2011;Kleypas and Yates, 2009;Kroeker et al., 2013;Silverman et al., 2009) will severely impede coral growth within the next few decades (Burke et al., 2011;Hooidonk et al., 2014) has prompted an urgent search for coral reef systems that provide natural refuges from climate threats and efforts to identify mechanisms that could help reef organisms acclimatize to changing climate.The complex interplay among climate, oceanographic, and biological factors that influences susceptibility and resilience of reefs has made identification and characterization of refuges challenging.Focus has been placed on identifying reefs with low exposure to or potential for adaptation to climate threats, and reduced local anthropogenic impacts (Keller et al., 2009;McClanahan et al., 2011;Mumby and Steneck, 2008;Salm et al., 2006;West and Salm, 2003).Recent studies have identified only a few reef systems in the Western Indian Ocean (McClanahan et al., 2011), on the Great Barrier Reef (Berkelmans, 2002), and in shallow bays of Palau (van Woesik et al., 2012) that show resistance to elevated temperatures and less coral bleaching.Only one reef, in the Florida Keys, has been identified as a potential refuge from ocean acidification (Manzello et al., 2012).To our knowledge, no alternative (non-reef) natural habitats have ever been identified as potential climate change refuges for corals.
Mangrove communities, while often near coral reef ecosystems, are not thought of as having suitable conditions for coral recruitment and growth due to high sedimentation rates, lack of suitable substrate, and inadequate water quality.Therefore, no prior focus has been placed on identifying mangrove-coral habitats, the scientific literature Introduction

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Full contains few references to scleractinian corals growing in mangroves (e.g.Macintyre et al., 2000;Rützler et al., 2000), and no comprehensive surveys or multidisciplinary studies of these habitats have been performed.In St. John, US Virgin Islands, over 30 species of scleractinian corals are growing on and under mangrove prop roots in bays in Hurricane Hole within Virgin Islands Coral Reef National Monument (Table 1).Many are reef-building corals that survived a 2005 to 2006 bleaching and disease event that caused major losses of coral throughout the northeastern Caribbean (Miller et al., 2009).Qualitative surveys conducted in one bay in 1984 suggest that there has been an increase in the abundance and diversity of corals in mangrove communities since that time (Beets et al., 1986), possibly a response to climate change.This ecosystem is an example of how some mangrove habitats could provide alternative refuges for corals from climate threats, particularly increasing seawater temperature, high levels of solar radiation, and decreasing pH.We identified and quantified physical, chemical, and biological resiliency factors in mangrove communities with corals in Hurricane Hole, St. John, US Virgin Islands.We present a baseline list of resiliency factors to help guide identification of other alternative refuges for reef-building corals.

Methods
Physical, chemical, and biological attributes were characterized in three small, adjacent bays in Hurricane Hole including Water Creek, Otter Creek, and Princess Bay from November 2010 to July 2012 (Fig. 1).In each bay, we measured diurnal and seasonal variations in temperature, salinity, photosynthetically active radiation (PAR), and seawater chemistry (total alkalinity (A T ), dissolved inorganic carbon (C T ), pH T (pH on the total H + scale), dissolved oxygen (DO), and nutrients).We characterized substrate parameters and examined water circulation patterns associated with inner bay mangrove communities with no corals (MNC sites), nearby mid-to outer-bay mangrove communities with corals growing on and under prop roots (MC sites), and rock outcrops Introduction

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Full with unshaded corals (ROC sites) in all three bays.Additionally, we inventoried coral species in all three bays, 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 in the bay with the highest coral diversity (Otter Creek).November 2010 and July 2011.In November 2010, nutrient samples were collected in transects spanning from the innermost reaches to the mouth of all three bays (58 samples).During July 2011, water samples were collected every 4 h throughout 24 h time periods at every sample site in all three bays.Water samples (20 mL) were filtered through 0.22 µm pore size Millepore Sterivex filters rinsed with 2 volumes of sample water.Samples were stored in 20 mL acid-washed polypropylene scintillation vials at 0 • C until time of analysis.Nutrient samples were analyzed at the NOAA Atlantic Oceanographic and Meteorological Laboratory in Miami, FL.Carbonate system parameters including aragonite mineral saturation state (Ω A ) and pCO 2 were calculated from A T , pH T , temperature and salinity measurements using the carbonate speciation program CO2sys (Pierrot et al., 2006) with dissociation constants K1 and K2 from Merbach et al. (1973) refit by Dickson and Millero (1987), KSO 4 from Dickson (1990), and using the total pH scale (pH T ).

Sediment samples
Bulk surface sediment samples (approximately 2 kg wet weight) were collected via grab-sampling from the seafloor (approximately 1.2 m water depth) at each study site in each bay (Fig. 1).Wet samples were dehydrated to remove water and salts within 6 h of collection by rinsing with 70 % isopropyl alcohol, allowing samples to settle, decanting the alcohol, and repeating this process two additional times.Dehydrated samples were then allowed to air dry prior to analysis for grain size and composition.Grain-size was measured via settling-tube for sand-sized fractions (Gibbs, 1974), and pipette for mud-sized fractions (Folk, 1965).Calcium carbonate content was determined by the acid leaching method (Milliman, 1974).Total organic matter (TOM) was measured by loss on ignition (LOI) at 550 • C for > 2.5 h (Dean, 1974).Mineralogic composition was measured by XRD on a Bruker D-8 advanced system using cobalt radiation at the University of Georgia, Department of Geology.Introduction

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Temperature and PAR measurements
Temperature measurements were collected every 2 h during 2010 and 2011 using HOBO Pendant data loggers at 18 locations in Hurricane Hole (Table 2).Loggers were (15 min averages) at study sites in Otter Creek and Water Creek approximately 20 cm above the seafloor using LI-COR 4π sensors and approximately 3 m above sea level and the mangrove canopy using LI-COR 2π sensors coupled with LI-COR 1000 or LI-COR 1400 data loggers.PAR sensors were placed on the seafloor under the mangrove canopy and outside of the mangrove canopy at MNC and MC sites, on the seafloor at unshaded ROC sites, and above the mangrove canopy at MC and MNC sites.

Heterogeneity of the physical environment
Heterogeneity in the physical environment provides for semi-isolation of coastal water masses from open ocean water enabling local differentiation of physical, chemical, and biological attributes of coastal ecosystems.The potential for a refuge to sustain characteristics that promote climate change resiliency is, in part, dependant upon the ability of the system to remain out of equilibrium with open ocean chemical conditions.The bays in Hurricane Hole range in area from 0.06 to 0.11 km 2 , have small watersheds ranging in area from 0.11 km 2 to 0.43 km 2 , are surrounded by steeply sloped, rocky hillsides, and have a narrow (up to approximately 10 m) fringe of red mangroves (Rhizophora mangle).There is no permanent source of freshwater inflow to any of the bays, nutrient concentrations are low, water clarity is generally high, and tidal range is low (< 0.25 m).The inner areas of the bays are very shallow, less than 2 m, and well protected from high winds and seas.The mangrove fringe is thickest in the inner bays.Prop roots support abundant communities of reef and mangrove organisms including crustose coralline algae, and are near communities of intermediate density seagrass (Thalassia testudinum), and calcareous algae including Halimeda spp.and Penicillus spp.Very few corals are growing near inner bay mangroves.Grain size analyses showed that sediments in the inner bays are primarily fine-grained ranging from 16 to 65 % mud-sized fractions (Table 3).Introduction

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Full Mid-to outer-bay areas are characterized by the narrowest mangrove fringe and shallow (< 1 m) water depths immediately adjacent to the shoreline that slopes steeply to 5 to 10 m just beyond the mangrove canopy.The mangrove prop roots support sponges, crustose coralline algae, numerous scleractinian corals and other organisms (Fig. 2).The outer bays are infrequently exposed to storm waves that remove finegrained sediments, and sediments consist primarily of 69 to 96 % sand and gravel with occasional occurrences of large boulders (Table 3).Corals are growing attached directly to prop roots and to hard substrates under roots.Near the entrance to the bays, there are rock outcrops with few or no mangroves nearby.These sites have primarily hard bottom substrate with small pockets of coarse-grained sediments, corals growing directly on hard bottom, very sparse occurrences of calcareous algae, and little seagrass growing nearby.

Chemical heterogeneity
Heterogeneity in the physical environment and benthic community structure creates chemical micro-climates that can affect localized, adjacent habitats.Variations in chemical parameter trends were observed at sub-kilometer scale in each bay and in association with specific habitat types (Fig. 3).Inner bay sites where mangroves grow without corals (MNC sites) showed the lowest dissolved oxygen levels (with the exception of Otter Creek in November 2010), highest pCO 2 , A T , and C T levels, and lowest pH T and aragonite mineral saturation states (Ω A ).A T and salinity showed the greatest range in variation during passage of Tropical Storm Tomás in November 2010 in Water Creek and Princess Bay, both of which have a larger watershed than Otter Creek and are more heavily influenced by terrestrial run-off during rain events.No consistent differences in chemical parameters were observed between mangrove-coral (MC) sites and rock outcrop coral (ROC) sites.MC and ROC sites showed higher DO, lower pCO 2 , A T , and C T levels, and higher pH T and aragonite saturation states than MNC sites indicating that seawater chemical characteristics of MC sites are more similar to ROC sites than to MNC sites.Introduction

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Full Average total nitrate and phosphate values for all samples in November 2010 were 0.999 ± 2.626 and 0.072 ± 0.094, respectively.Average total nitrate and phosphate values for all samples collected in July 2011 were 0.238 ± 0.359 µmol L −1 and 0.066 ± 0.069 µmol L −1 , respectively.The values of nutrient measurements distributed both temporally and spatially were near the range of analytical precision and accuracy for A T measurements and, therefore, were not included in calculation of carbonate system parameters from A T and pH T measurements.Nutrient data are available at http://doi.pangaea.de/10.1594/PANGAEA.825752.X-ray diffraction analyses of surface sediment samples indicate sediments at all three of the inner bay MNC sites have the lowest percentages of carbonate sediments (12 to 55 %) and no high-magnesium calcite (high-Mg calcite, the most soluble phase of calcium carbonate) in two of the three bays (Princess Bay and Water Creek) (Tables 3  and 4).Percent total organic matter (TOM) is less than 12 % throughout the bays, but higher at inner-and mid-bay sites than outer-bay sites.Low pH T and high pCO 2 conditions generated by respiration and oxidation of organic matter in inner bays generate a chemical environment that is conducive to dissolution of the fine-grained sediments produced by the calcareous green algae and coralline algae associated with these mangrove communities.Highest percentages of carbonate sediments (approximately 70 to 97 %) are found in MC and ROC sites in the middle and outer bays, and high-Mg calcite is present at all locations.The only MNC site with high-Mg calcite in sediments was in Otter Creek.Highest pH T of all MNC sites was in Otter Creek while the lowest was in Water Creek.The lowest pH T observed at the MNC site in Otter Creek was 7.90, however no median pH T dropped below 7.95.The lowest pH T at the MNC site in Princess Bay (where no Mg-calcite was observed) was above 7.90; however median pH T at this site fell to 7.93 during July 2011.The lowest median and minimum pH at a coral site was 7.97 and 7.93, respectively, and occurred at the MC site in Water Creek during July 2011.These findings suggest that dissolution of fine-grained carbonate sediments occurs in areas with frequent exposure to pH T below 7.93 to 7.95, and coral growth is limited to areas with minimum pH T above 7.93.Introduction

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Full Calcification/dissolution thresholds are the levels of aragonite saturation state below which (and pCO 2 levels above which) net dissolution of carbonate sediments exceeds calcification rates as determined by in situ, mesocosm, and modeling studies of coral reef ecosystems.Aragonite saturation states fell considerably lower than calcification/dissolution threshold ranges of 3.0 to 3.2 and/or pCO 2 exceeded thresholds of 504 to 584 µatm (Langdon et al., 2003;Silverman et al., 2009;Yamamoto et al., 2012;Yates and Halley, 2006) at all MNC study sites during both November and July, except in Otter Creek where thresholds were exceeded only during July 2011.Maximum pCO 2 values at MC sites and ROC sites exceeded the dissolution threshold during only 4 of 9 measurement periods and 2 of 9 measurement periods, respectively.Minimum aragonite saturation states at MC and ROC sites fell below dissolution thresholds during only 2 of 9 and 3 of 9 measurement periods, respectively.Maximum pCO 2 and minimum Ω A observed at a coral site was 550 µatm (Water Creek MC site, July 2011) and 2.82 (Princess Bay ROC site, November 2010), respectively (Fig. 3g and h).

Process heterogeneity
Process heterogeneity resulting from spatial variations in community structure and hydrographic conditions is a key factor in maintaining disequilibrium between coastal and open ocean water masses.Correlation of salinity-normalized total alkalinity (nA T ) and dissolved inorganic carbon (nC T ) can be used to indicate the potential influence of calcification, carbonate sediment dissolution, photosynthesis, and respiration on seawater carbonate chemistry (Suzuki and Kawahata, 2003).A linear regression slope approaching 2 indicates calcification and dissolution are dominant processes, and the slope can be used to calculate the ratio of net ecosystem calcification (NEC) to net community production (NCP).Eighteen of 27 site measurements showed a correlation between nA T and nC T with a r 2 value of greater than 0.5 (Fig. 4).MNC sites showed the greatest range of nA T and nC T and the greatest potential/tendency toward carbonate sediment dissolution.This result is consistent with the low pH T , high pCO 2 , low mineral saturation state, and lower percentages of carbonate sediments characteristic of MNC 5063 Introduction

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Full sites.MC and ROC sites showed similar ranges and values of nA T and nC T .Ratios of NEC : NCP were calculated for the 18 site measurements with r 2 values greater than 0.5 (Table 5).NEC : NCP for all sites ranged from 0.14 to 12.1.Average values were lowest at MC sites (0.5±0.6), highest at ROC sites (3.1±5.0), with intermediate values at MNC sites (0.9 ± 1.1).Standard deviations were large among study sites (Table 5).
However, generally lower NEC : NCP ratios at MC sites and low TOM in sediments may help maintain higher pH T at MC sites relative to MNC sites.Intermediate NEC : NCP ratios at MNC sites likely reflect the dominance of calcareous algae and seagrass, while highest NEC : NCP ratios at ROC sites reflect the dominance of corals and lack of seagrass and calcareous algae in close proximity.
Lagrangian drifter studies were conducted in Water Creek, Otter Creek, and Princess Bay during August 2011, and indicated that surface currents within the bays move primarily from inner to outer bay due to prevailing easterly winds (McKenzie, 2012).Additionally, estimated water mass residence times in each of these bays are long, on the time scale of days (McKenzie, 2012), which, combined with shallow water depths, can increase the impact of NEC and NCP on seawater chemistry (Anthony et al., 2011).Carbonate sediment dissolution (a process that consumes CO 2 and generates HCO − 3 and Ca 2+ ) at upstream, inner bay MNC sites may provide a source of alkalinity to downstream coral sites that helps to maintain mineral saturation states and support coral calcification.The collocation of corals with mangroves in areas of relatively high NCP, and low TOM in sediments also helps maintain pH T and saturation states at MC sites that are similar to ROC sites.This combined effect of heterogeneity in community structure, hydrography, and biologically driven changes in seawater has been demonstrated as an effective means to buffer decreases in mineral saturation state and increase calcification in downstream communities in experimental coral/macroalgal assemblages (Anthony et al., 2011) and in seagrass/coralline algae and coral/seagrass assemblages on coral reefs in Tanzania and Moorea (Kleypas et al., 2011;Semesi et al., 2009a and b).This same combination of spatial and temporal variations in community structure and processes in mangrove/coral habitats may help buffer against ocean acidification.Introduction

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Biological responses
The presence of decades-old coral colonies in these mangrove-lined bays suggests adaptation to higher water temperatures and more resistance to and rapid recovery from bleaching events such as the one in 2005 that was followed by severe mortality from disease on the island's coral reefs.PAR measurements made above the sea surface and at the seafloor at MC sites and ROC sites of similar depth during November 2010 and July 2011 and 2012 indicate that PAR was attenuated during peak daylight hours of 10 a.m. to 2 p.m. by 88.6 ± 5.3 %, 70.7 ± 4.8 %, and 72.0 ± 1.7 %, respectively (Fig. 5) where corals grow shaded by the mangroves at MC sites.Re-examination of a subset of Otter Creek colonies in spring 2011 showed general recovery from bleaching but some mortality.Different proportions of C. natans (72.5 % shaded, 27.5 % unshaded) and D. labyrinthiformis (18.2 % shaded, 81.8 % unshaded) were found in shaded vs. unshaded conditions (p < 0.0001) and had different levels of initial bleaching (p < 0.0001, C. natans: no shaded colonies bleached, 10.5 % of unshaded colonies bleached; D. labyrinthiformis: 34.2 % of shaded colonies bleached, 66.1 % of unshaded colonies bleached).Different mortality outcomes were also observed combining partial and total mortality (p = 0.0327) (Fig. 6, Table 6).There was no mortality of shaded C. natans colonies and 10.5 % mortality in unshaded colonies.D. labyrinthiformis showed 10.5 % mortality in shaded and 12.3 % mortality in unshaded colonies, respectively.More C. natans colonies grew in the shade than D. labyrinthiformis colonies.Although more unshaded D. labyrinthiformis colonies Introduction

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Full bleached and bleaching of these was more severe, shaded colonies were not more likely to recover normal pigmentation.For this species, shading affected the proportion of colonies that initially bleached (p < 0.0001), but not the outcome (p = 0.7582).Although more unshaded colonies of D. labyrinthiformis bleached, the mortality outcome for shaded and unshaded colonies was similar (p = 0.7508).Overall, recovery from bleaching was high, with little mortality.Only two C. natans colonies bleached.Both had partial mortality and none of the initially unbleached corals showed any mortality (p < 0.0001).
Comparison of temperature records in the shallow waters of Hurricane Hole to those from coral reefs around St. John (Miller et al., 2009;National Park Service, 2012) indicate that corals growing in Hurricane Hole are exposed to higher (0.5 ± 0.5 • C on average) and more variable temperatures than coral reefs around the island (Fig. 7).Low bleaching and mortality have been observed for corals growing on nearshore reefs of Palau that have constant exposure to high temperatures, more variable temperatures, and high vertical attenuation of light caused by suspended particulate matter (van Woesik et al., 2012).Similarly, the resilience of mangrove corals following elevated temperatures likely results from relief from solar radiation stress provided by shading of corals by mangroves.

Alternative refuges and resiliency factors
There is an urgent need to identify the characteristics of corals and other reef organisms that could enable them to adapt to the variety of stressors associated with climate change and ocean acidification.Research is needed on how these factors interact and how they will affect the overall biodiversity, function, and transition of these ecosystems.The high diversity of coral reefs (among species and within species) and variable responses of organisms to climate change increase the likelihood that at least some reef species will be able to persist in locations with particular environmental conditions in the face of changing climate (Rogers, 2013).The presence and increase in abundance Introduction

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Full and diversity of corals in the mangrove habitats of St. John could be a recent phenomenon (within the past several decades).Evidence of shoreward migrations of coral in response to past changes in sea level rise is well documented in the geologic record (e.g.Hopley et al., 1983;Neumann and Macintyre, 1985).However, evidence for colocation of live corals and mangroves is not.Mangrove-coral habitats provide evidence of ecosystem transition that may be a response to pressures from unprecedented rates of recent climate change.These habitats may serve as an example of a novel coastal ecosystem (Graham et al., 2014) resulting from differential species responses, and provide insights into future evolution of tropical coastal ecosystems with increasing sea level rise, thermal stress, and ocean acidification.
As reefs decline worldwide and sea level continues to rise, alternative (non-reef) shallow-water refuges like mangrove-coral habitats are critical for ensuring the survival of coral species.Identification and protection of other natural, alternative, shallow-water refuges is essential as one of the few viable management strategies for sustaining coral and other reef species, and provides one of the only direct actions that can be taken locally to manage climate change impacts (Salm et al., 2006).The unlikely association of corals with mangroves in many coastal ecosystems due to unsuitable growth conditions has dissuaded previous consideration of these habitats as potential coral refuges.However, numerous small tropical islands worldwide have physical characteristics similar to the US Virgin Islands and the potential for suitable mangrove-coral refuge conditions.Our findings identify the first naturally existing, alternative (non-reef) refuge from climate change for reef-building corals and provide baseline resiliency factors to assist in identifying mangrove-coral and other alternative refuges around the world.Key resiliency factors for mangrove-coral habitats include: (1) high diversity and variable responses of coral species to climate change stressors, (2) heterogeneity of benthic community composition, processes, and proximity of different habitat types, (3) hydrographic conditions that amplify biogeochemical effects on seawater chemistry and promote chemical characteristics that support coral growth, ( 4) exposure to variable water temperatures and physical shading of corals from solar radiation (Table 7).Introduction

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Full The appropriate combination of all of these factors for creating refuge conditions is not generally characteristic of most coral reef environments.Thus, only a few reef systems that protect against increased temperatures, solar radiation or ocean acidification have been identified, and none have been identified that protect from all three stressors like the mangrove-coral habitats of St. John.

BGD Introduction Conclusions References
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Full  1. Species list of corals living in mangroves.

Coral Species
Princess Bay Otter Creek Water Creek  Full  Full  Full    Full Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | A T , C T , and pH T analyses from each site every 4 h (n = 7) throughout 24 h periods in November 2010, July 2011, and July 2012.Measurements were made every 4 h for 3 consecutive days (n = 19) in Otter Creek during July 2012.No DO data was collected in Water Creek during July 2012 due to DO sensor failure.Twenty percent of pH measurements (47 of 225) were calculated from A T and C T .A peristaltic pump was used to pump seawater from approximately 1 m below the water surface through a 0.45 µm filter into 500 mL borosilicate glass bottles.Samples for A T and C T were preserved by adding 100 µL saturated HgCl 2 solution.Bottles were positive-pressure sealed with ground glass stoppers coated with Apiezon grease.Seawater samples for pH T were collected from the same peristaltic pump and filtered into 30 mL glass optical cells, and were analyzed within 1 h of collection.Samples were analyzed for A T (±1 µmol kg −1 ) using spectrophotometric methods of Yao and Byrne (1998) with an Ocean Optics USB2000 spectrometer and bromo-cresol purple indicator dye, for C T (±3 µmol kg −1 ) using a UIC carbon coulometer model CM5014 and CM5130 acidification module using methods of Dickson et al. (2007) and for pH T (±0.005) via spectrophotometric methods of Zhang and Byrne (1996) with an Ocean Optics USB2000 spectrometer and thymol blue indicator dye.Dissolved oxygen (±0.1 mg L −1 ), temperature (±0.01 • C), and salinity (±0.01) were measured using a YSI multimeter calibrated daily.Certified reference materials (CRM) for A T and C T analyses were from the Marine Physical Laboratory of Scripps Institution of Oceanography (A.Dickson).Duplicate or triplicate analyses were performed on at least 10 % of samples.Seawater samples were also collected for measurement of total nitrogen and phosphate in 5057 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | placed near mangrove and coral habitats at inner-, mid-, and outer-bay locations.Daily averages were generated from all loggers.Temperature data from long-term monitoring transects were collected every 2 h from loggers at reef depth on the forereef slope area of 6 reefs around St. John during 2005 by Miller et al. (2009), and during 2010 by the National Park Service (2012).These data were used to calculate daily means at each site and averaged among sites to generate daily averages for the long-term reef transects.Photosynthetically Active Radiation (PAR) was measured every 15 min Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | West, J. M. and Salm, R. V.: Resistance and resilience to coral bleaching: implications for coral reef conservation and management,Cons.Biol., 17, 956-967, 2003.van Hooidonk, R., Maynard, J. A., Manzello, D., and  Planes, S.: Opposite latitudinal gradients in projected ocean acidification and bleaching impacts on coral reefs, Glob.Change Biol., 20, 103-112, doi:10.1111/gcb.12394,2014.van Woesik, R., Houk, P., Isechal, A. L., Idechong, J. W., Victor, S., and Golbuu, Y.: Climatechange refugia in the sheltered bays of Palau: analogs of future reefs, Ecol.Evol., 2, 1-11, doi:10.1002/ece3.363,2012.Yamamoto, S., Kayanne, H., Terai, M., Watanabe, A., Kato, K., Negishi, A., and Nozaki, K.: Threshold of carbonate saturation state determined by CO 2 control experiment, Biogeosciences, 9, 1441-1450, doi:10.5194/bg-9-1441-2012,2012.Yao, W. and Byrne, R. H. Simplified seawater alkalinity analysis: use of linear array spectrometers, Deep-Sea Res.Part 1, 45, 1383-1392, 1998.Rixen, T., Goyet, C., and Ittekkot, V.: Diatoms and their influence on the biologically mediated uptake of atmospheric CO 2 in the Arabian Sea upwelling system, Biogeosciences, 3, 1-13, doi:10.5194/bg-3-1-2006,2006.Zhang, H. and Byrne, R. H.: Spectrophotometric pH measurements of surface seawater at insitu conditions: absorbance and protonation behavior of thymol blue, Mar.Chem., 52, 17Discussion Paper | Discussion Paper | Discussion Paper | Table Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Ratios of net ecosystem calcification to net community production (NEC : NCP) were calculated from the slopes of best-fit linear regression lines for 18 of 27 site measurements showing a correlation between nA T and nC T with r 2 > 0.5.NEC : NCP was calculated using the equation Discussion Paper | Discussion Paper | Discussion Paper |

Figure 1 . 7 Fig. 1 .Figure 2 . 4 5Fig. 2 .
Figure 1.Study sites (STJ#s) in Hurricane Hole, St. John, USVI.MC = mangroves with 3 corals growing on and near mangrove prop roots and shaded by the mangrove canopy, MNC 4 = mangrove with no corals growing in association with them, ROC = rock outcrops with live 5 corals and no shading from mangroves.6 7

Fig. 3 .
Fig. 3.Chemical and physical parameters.Median and range for chemical and physical parameters in Hurricane Hole bays during November 2010, and July 2011 and 2012.Measurements were made every 4 h throughout a diurnal cycle (n = 7) at each study site during November 2010 and July 2011 and 2012, and for 3 consecutive days (n = 19) in Otter Creek during July 2012.No DO data was collected in Water Creek during July 2012 due to DO sensor failure.Red shaded areas (3g and 3h) show reported ranges for pCO 2 and Ω A thresholds for carbonate sediment calcification and dissolution.Data available at http://doi.pangaea.de/10.1594/PANGAEA.825752.

Figure 3 .FigFigure 4 .
Figure 3.Chemical and physical parameters.Median and range for chemical and physical parameters in Hurricane Hole bays during November 2010, and July 2011 and 2012.Measurements were made every 4-hours throughout a diurnal cycle (n=7) at each study site

Fig. 4 .Fig. 5 .
Fig. 4. Salinity normalized total alkalinity (nA T ) and total carbon (nC T ) plots with best fit linear regressions (see Table5for equations and r 2 values) for November 2010, July 2011, and July 2012 in Otter Creek, Water Creek, and Princess Bay.Average nA T and nC T for each time period was calculated from all data collected from each site within each bay.Gray lines represent the theoretical impact of calcification (G), carbonate sediment dissolution (D), photosynthesis (P), respiration (R), CO 2 uptake (CU), and CO 2 release (CR) on A T and C T .

2.3 Coral surveys
Coral surveys indicate at least 33 species of scleractinian corals are growing in Hurricane Hole Bays (Table 1).Many coral colonies are growing directly on or close to mangrove prop roots, and others grow on rocks or hard substrate close to shore to a depth of approximately 6 m.Initial surveys of bleached and unbleached corals from November 2010 to January 2011 indicate that only 4.5 % and 1.7 % of C. natans colonies were bleached in Otter Creek and Water Creek, respectively, while 58.9 % and 17.4 % of D. labyrinthiformis colonies were bleached in Otter and Water Creeks, respectively.

Table 2 .
Location of HOBO temperature loggers in Hurricane Hole, St. John, USVI.

Table 3 .
Grain size of surface sediments.

Table 4 .
Carbonate mineralogical composition of surface sediments.

Table 5 .
NEC : NEP ratios for study sites with nA T vs. nC T r 2 > 0.5.