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Can colored dissolved organic material protect coral reefs by reducing exposure to ultraviolet radiation?

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Title:
Can colored dissolved organic material protect coral reefs by reducing exposure to ultraviolet radiation?
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Ayoub, Lore Michele
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University of South Florida
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Light attenuation
Absorption coefficient
Mycosporine-like amino acids
UVR
Development
Underwater light field
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Summary:
ABSTRACT: Although mass coral bleaching events are generally triggered by high seawater temperatures, experiments have demonstrated that corals and reef-dwelling foraminifers bleach more readily when exposed to high energy, short wavelength solar radiation (blue, violet and ultraviolet UVR: Lambda ~ 280 - 490 nm). In seawater, colored dissolved organic matter (CDOM), also called gelbstoff, preferentially absorbs these shorter wavelengths, which consequently bleach and degrade the CDOM. Alteration of watersheds and destruction of coastal wetlands have reduced natural sources of CDOM to reefal waters. I tested the null hypothesis that CDOM does not differ between reefs that differ in coral health, and that water transparency to UVR is not a factor in reef health. I measured absorption of UVR and UV irradiance at various reefs in the Florida Keys that differ in distance from shore and degree of anthropogenic development of the adjacent shoreline.My results show that intact shoreline - associated reefs and inshore reefs tend to be exposed to lower intensities of UVR, and lower degrees of photic stress, than developed shoreline - associated reefs and offshore reefs. Absorption due to CDOM (ag320) was higher, and photic stress, as revealed by increased production of UV-absorbing compounds, Mycosporine - like Amino Acids (MAAs), was lower at the surface compared to the bottom. The following results support my conclusion: ag320 and UV attenuation coefficients (Kd 's) were higher at intact compared to developed shoreline - associated reefs, and at inshore compared to offshore reefs. Spectral slope, S, was higher at offshore compared to inshore reefs, indicating a higher degree of photobleaching of CDOM. Relative expression of MAAs was higher at developed compared to intact shoreline - associated reefs, at offshore reefs compared to inshore reefs, and at the surface compared to the bottom.Solar energy reaching the benthos at two inshore reefs of the same depth (6m) was approximately an order of magnitude higher at the reef near developed shoreline compared to the reef near intact shoreline, and may be due to greater degree of diffuseness of the underwater light field combined with lower ag at the developed shoreline-associated reef.
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Dissertation (Ph.D.)--University of South Florida, 2009.
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by Lore Michele Ayoub.
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Can Colored Dissolved Organic Material Protect Coral Reefs b y Reducing Exposure t o Ultraviolet Radiation? by Lore Michele Ayoub A dissertation submitted in partial fulfillment of the requirements for the degree of D octor of Philosophy College of Marine Science University of South Florida Co Major Professor: Paula G. Coble Ph.D. Co Major Professor: Pamela Hallock Muller Ph.D. Susan Bell, Ph.D. Kendall Carder, Ph.D. Gary Mitchum, Ph.D. Date of Approval: April 4, 2009 Keyword s: light attenuation, absorption coefficient, mycosporine like amino acids, UVR, development, underwater light field Copyrig ht 2009 Lore Michele Ayoub

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Acknowledgements I would like to thank Florida Institute of Oceanography/Keys Marine Laboratory, the Florida Keys National Marine Sanctuary, and Mote Tropical Research Laboratory for field s upport. Sample collection and processing was funded by NOAA NURC subcontract No. 2004 19B (PI: P. Hallock Muller); NOAA through the Florida Hurricane Alliance (PI: Thomas Mason); and the U.S. Environmental Protection Agency Gulf Ecology Division Grant No. X7 96465607 0 (PI: P. Hallock Muller). I also thank the Edmund J. and Alton S. Greenwell Foundation for funding critical instrumentation Sampling permits were issued by NOAA Florida Keys National Marine Sanctuary (KLNMS 2003 002, 2005 002, 2 007 013 I would like to thank my fellow graduate students and colleagues at the University of South Florida, especially Robyn Conmy, Jennifer Cannizarro, Chunzi Du and David English Dan Otis the Reef Indic ators Lab Kara Sedwick and Laura Fauver I would like to acknowledge my co advisors Paula G. Coble and Pamela Hallock Muller gifted scie ntists whose mentorship and dedication to marine science inspired me Their commitment, support, and guidance served well above their responsibilities as advisors. I would also like to thank my committee for providin g input i nto this manuscript, especially Gary Mitchum I would also like to thank Norm Nelson for guidance throughout my research and academic caree r. I acknowledge my family, especially Rosemarie Ayoub, my uncle, Al Ayoub, my boyfriend, Gerry Growney, and my friends, especially Erica Hudson, whose support, encouragement and love allowed me to accomplish this goal with dedication.

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Dedication This dissertation is dedicated to my father, Theodore Anthony Ayoub, DDS, and my grandmother, Sadie Ayoub.

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i T able of Contents List of Tables iii List of Figures v Abstract x 1. Introduction 1 2. Background 5 2.1. Elec tromagnetic radiation and the solar spectrum 5 2.2. Atmosphere UV interactions 7 2 .3. Annual cycle of UVR 13 2.4. UVR environment interactions 15 2.5. CDOM composition 18 2.6. CDOM optical properties 20 2.7. CDOM sources, sinks and p athways 21 2.8. Remote sensing of UVR and coral reefs: application of the spectral slope of a g 25 2.9. Photobiology of UVR and effects on aquatic ecosystems 27 2.10. Defenses against UVR: Mycosporine like amino acids (MAAs) 30 2.11. S tratospheric ozone depletion and bleaching 32 2.12. Statement of hypothesis 34 3. Introduction to the Florida Keys, Study sites, and Methodology 36 3.1. Objectives 36 3.2. Introduction 36 3.2.1. Geomorphology and water circulation patterns of the Florida Keys 36 3.2.2. Rivers and Florida Bay as sources of CDOM and other material to the Florida Keys 39 3.2.3. Annual trends in the Florida Keys 40 3.2.4. Biological Response Bleaching in the Florida Keys 43 3.3. Methods 46 3.3.1. Sites and sampling dates 46 3.3.2. In situ and incident irradiance measurements 52 3.3.3. Water samples: collection and in lab optical measurements 53 3.3.4. Calculating underwater irradiance from in lab absorption measurements 54 3.3.5. Sources of Error 55

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ii 3.3.5.1. Irradiance and absorption due to particles 55 3.3.5.2. Absorption due to colloids 59 4. Colored d issolved o rganic m aterial p rotect s c oral reefs by controlling exposure to UVR 60 4.1. Introduction 60 4.2 Material and Methods 63 4.3. Results and Discussion 66 4.4 Conclusions 78 5. Mycosporine like Amino Acids as indicators of photo oxidative stress 81 5.1. Introduction 81 5.2. Methods 85 5.3. Results and Discussion 85 5.4. Future Work 97 6. Spatial Variability of Inherent and Apparent Optical Properties on Coral Reefs 99 6.1. Background 99 6 .2 Objectives 100 6.3 Methods 100 6.3.1. Calculating underwater irradiance 101 6.3.2. The a ngular distribution of light 102 6.4. Results and Discussion 106 6.5. Conclusions 111 7. Conclusions and Future Research 116 7.1 Conclusions 116 7.2. Future Research 120 References 122 Appendices 133 Appendix A: Map of Florida Keys with waterways, cities, management areas and reefs 134 Appendix B: Important Terms and Abbreviations 135 About the Author en d page

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iii List of Tables Table 3.1. Mote Marine Laboratory / Florida Keys National Marine Sanctuary Coral Bleaching Early Warning Network, Bleachwatch. 45 Table 3.2a. Sites and parameters sampled in 2004 a nd 2005. a = absorption, R=R rs remote sensing reflectance, C = chlorophyll fluorescence (concentration), S = Spectral underwater flow through optical instrument package, P=PAR underwater, U=UV and PAR_incident, U_u = UV and PAR underwater. 47 Table 3.2b. Sites and samples for Spring/Summer 2006. 49 Table 3.2c. Sites and samples for Spring/Summer 2007 49 Table 3.3a. Tide table for sampling sites (Key Largo 6m (KL6m) Reef, Algae Reef) on dates sampled in 2004. 51 Table 3.3b. Sampling ( water collection) times for Carysfort, Algae and Key Largo 6m (KL6m) Reefs, May, July, and September 2004. 51 Table 3.4. Median a t /K d and 25 th 75 th percentile ranges for inshore and offshore reefs. 56 Table 3.5. Median a g /a t and a p /a t and 25 th 75 th percentile ranges for inshore and offshore reefs. 58 Table 4.1. Medians and 25 th 75 th percentile ranges for a g 320 at intact shoreline associated reefs compared to developed shoreline associated reefs. 69 Table 4. 2 Comparison of K d between inshore and offshore reefs 71 Table 4.3 Medians and 25 th 75 th percentile ranges for E d6m /E d0 at 305, 330, 380 nm and PAR 73 Table 4.4 Medians and 25 th 75 th percentile ranges for S

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iv (280 312 nm) for the Upper, Middl e, and Lower Keys, inshore versus offshore sites. 74 Table 4.5 Scaling gradients for % stony coral cover (%cc) and a g 320 77 Table 5.1. Medians, 25 th 75 th percentile ranges, and number of samples ( n ) for relative MAA expression at inshore ver sus offshore reefs, surface versus bottom. 89 Table 5.2. Medians, 25 th 75 th percentile ranges, and number of samples ( n ) for relative MAA expression comparing regions, Upper, Middle and Lower Keys. 91 Table 5.3 a g 320 at the surface only for the Florida Keys by region, Upper, Middle and Lower Keys 93 Table 5.4 a g 330 at the bottom and surface for the Florida Keys by region, Upper, Middle and Lower Keys 94 Table 5.5 Medians, 25 th and 75 th percentiles, and number of samples ( n ) for [ chl ] for the Lower, Middle and Upper Keys 97 Table 6.1. Meteorological data, salinity and bottom type, as well as optical parameters used as input, model bottom type, and output (modeled) for Hydrolight version 5. 0 for for Algae Reef and KL6m Reef on September 28, 2004 107 Table 6.2. Comparison of d for Algae and KL6m Reef surface and bottom at 305, 320, 330 and 380 nm. 108 Table 6.3 Inherent and Apparent Optical Properties (IOPs and AOPs) computed by Hydrolight (version 5) for Algae and KL6m Reef, surface and bottom, at 305, 320, 330 and 380 nm, based upon in situ absorption, a and scattering, b. 109 Table 6.4 Medians and 25 th 75 th percentile ranges for a g 330 at Algae and KL6m reefs, surface and bottom, for all sampling dates from 2004 2007. 111

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v List of Figures Figure 1.1 Absorption due to CDOM (also known as gelbstoff) ( a g ) is high in mangrove canals and progressively decreases with distance offshore 3 Figur e 2.1. Spectra of nonionizing solar radiation (A) and ultraviolet radiation (B) showing main radiation bands, their nomenclature, and approximate wavelength limits. 6 Figure 2.2. Interactions between ozone depletion and climate change. 8 Figure 2 .3. Solar irradiance outside the atmosphere and at sea level. 9 Figure 2.4. Example of an action spectrum for erythemal and DNA damage ( http://www.temis.nl/uvradiation /info/uvaction. html ). 10 Figure 2.5. Mean daily UV B and UVR at the Mote Marine Laboratory in the Lower Keys (latitude 24.5 o N, longitude 81.6 o W) during 2002 2003. 14 Figure 2.6a. Incident spectral irradiance (on land) measured with a LiCOR 1800 spect roradiometer at 10 minute intervals on May 25, 2005 at NURC, Key Largo, FL. 15 Figure 2.6b. Median incident spectral irradiance (above water) on May 25, 2004 (15:50 to 16:10) and on July 6, 2004 (16:00), on land (Keys Marine Lab or NURC, Key Lar go, FL). 16 Figure 2.7. Incident irradiance (E d0 350 700 nm) and spectral absorption due to CDOM ( a g ), particulate material ( a p ) and pure water ( a w ) for Key Largo 6m (KL6m) Reef in May 2004. 18 Figures 2.8. Pathways for the formation of humic substances (J. Weber in http://www.ar.wroc.pl/~weber/ powstaw2.htm#1). 20

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vi Figure 2.9. Flow chart illustrating sources, sinks and pathways of Chromophoric Dissolved Organic Matter (CDOM) in aquatic ec osystems (after Zepp 2003 and Morris et al. 1997). 22 Figure 2.10. Diagrammatic representation of the two trophic pathways in plankton communities (from Wotton 1994 based on Pomeroy and Wiebe 1988). 24 Figure 2.11. Pathways between UV radiation ex posure and cellular stress. 27 Figure 2.12. Monthly hemispheric means and growth rates of HCFCs from weighted measurements of surface air collected in flasks at remote locations (Northern Hemisphere (red) > global mean (green) > Southern Hemisphere (blue)). 33 Figure 3.1. Study sites in the Lower, Middle and Upper Florida Keys included offshore and inshore (patch) reefs that differ in degree of development of associated shoreline 37 Figure 3.2a. Temperature and precipitation at Key West (L ower Keys), 2003 2006. ( http://www.ncdc.noaa.gov/oa/ climate/research/monitoring.html#ustempprcp ). 41 Figure 3.2b. Monthly mean wind speed (WSPD), gust (GST), a ir temperature (ATMP) and water temperature (WTMP) at Key West (Lower Keys) for 2005 2007. 41 Figure 3.3. Monthly mean wind speed (WSP), gust (D GST), air temperature (ATMP) and water temperature (WTMP) at Molasses Reef (Upper Keys) for 2004 20 07. 42 Figure 3.4. Monthly mean wind speed (WSP), gust (GST), and air temperature (ATMP) at Sombrero Key (Middle Keys) for 2004 through 2007. 43 Figure 3.5 Overview of BleachWatch Observer reports submitted from August 9 August 23, 2005 ( http://isurus.mote.org/Keys/bleaching/ CC_20050823.pdf ). 46

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vii Figure 3.6. Mean percent stony coral cover in the Florida Keys by region, Upper, Middle and Lower Keys. 50 Figure 3.7. Ra tio of in lab a t to in situ K d ( a t /K d ) for inshore (x) and offshore (o) reef sites, 2005 2008. 57 Figure 4.1. Atmospheric, optical, and biological factors affecting CDOM absorptivity and related biological effects (after Morris and Hargreaves 1997 ; Zepp et al. 2008). 63 Figure 4.2. Study sites in the Lower, Middle and Upper Florida Keys included offshore reefs and inshore (patch) reefs that differ in degree of development of associated shoreline. 64 Figure 4.3. Transect of absorption due to CDOM at 320 an ( a g 320 ). 66 Figure 4.4. E d6m 320 was significantly lower at intact shoreline associated reefs compared to developed shoreline associated reefs ( p < 0.05). 67 Figure 4.5. R elative contribution of a g to a t in the UV at 305, 320, 330, 380. 68 Figure 4.6. a g 320 at intact shoreline associated reefs ( n = 10) compared to developed shoreline associated reefs ( n = 10). 69 Figure 4.7. Absorption due to CDOM at 330 nm ( a g 330 ) and the attenuation coefficient of downwelling ir radiance at 330 nm, K d 330 70 Figure 4.8a. E d6m /E d0 for 305, 330, and 380 nm for inshore versus offshore reefs sampled 2004 2007 (in = inshore, off = offshore). 72 Figure 4.8b. E d6m /E d0 for PAR for inshore versus offshore reefs sampled 2004 2 007 (in = inshore, off = offshore). 72 Figure 4.9 Spectral slope, S, (280 312 nm) for the Upper, Middle, and Lower Keys, inshore versus offshore sites. 74 Figure 4.10 The number of occurrences of different combinations of scaled % stony coral c over and

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viii a g 320 76 Figure 4.11 Percent stony coral cover versus a g 320 for the CREMP sites sampled in 2006 and 2007. 77 Figure 4.12 Relative expression of MAAs declined with increasing a g 320 for intact and developed reefs in 2004 2005. 78 Fig ure 5.1. Absorption spectra for several different MAAAs 83 Figure 5.2. Relative MAA expression is calculated from the spectral absorption due to phytoplankton, a phi or 83 Figure 5.3. Relative MAA expression versus [ chl ] for all dates sampled from 2004 2007 where data for both relative MAA expression and [ chl ] were available. 86 Figure 5.4. Relative MAA expression versus a g 320 for all sites sampled in 2004 through 2007 where data for both a g 320 and relative MAA expression were available. 87 Figure 5.5 Relative MAA expression for surface samples compared to bottom samples. 88 Figure 5.6 Relative MAA expression comparing surface and bottom samples at inshore versus offshore reefs. 89 Figure 5.7 Relative MAA expression of intact shoreline associated reefs compared to developed shoreline associated reefs. 90 Figure 5.8 Relative MAA expression by region, Lower, Middle, and Upper Keys. 91 Figure 5.9 a g 330 at only the surface for the Florida Keys by region, Lowe r, Middle and Upper Keys. 93 Figure 5.10 a g 330 at the bottom and surface for the Florida Keys by region, Lower, Middle and Upper Keys. 94 Figure 5.11 [ chl ] by region in the Lower, Middle, and Upper Keys. 97 Figure 6.1. Radiance ( L ) on a point in a surface, from a given direction, is the radiant flux in the specified direction per unit solid angle per unit projected area

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ix of the surface ( after Kirk 1994). 103 Figure 6.2. Comparison of d for Algae and KL6m Reef surface and bottom at 305, 3 20, 330 and 380 nm. 108 Figure 6.3. Although modeled E d at the surface was not very different at Algae Reef compared to KL6m, due to lower a g and lower d at the bottom, E d at the bottom was approximately an order of magnitude higher at KL6 m compared to Algae Reef (see Table 6.3). 110 Figure 6.4. a g 330 at Algae and KL6m Reefs, surface and bottom, for all sampling dates from 2004 2007. 111 Figure 6.5. Depiction of the pathways of irradiance under clear and cloudy skies, and in the oceans. 113 Figure 6.6. Spectral surface irradiance just below the sea surface (after spectral surface reflectance) for clear skies and cloudy skies. 114

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x C an C olored Dissolved Organic Material Protect Coral Reefs by Reducing Expos ure to Ultraviolet Radiation Lore Michele Ayoub Abstract Although mass coral bleaching events are generally triggered by high seawater temperatures, experiments have demonstrated that corals and reef dwelling foraminifers bleach more readily when expose d to high energy, short wavelength solar radiation (blue, violet and ultraviolet [UVR]: ~ 280 490 nm). In seawater, colored dissolved organic matter (CDOM), also called gelbstoff preferentially absorbs these shorter wavelengths, which consequently bleach and degrade the CDOM. Alteration of watersheds and destruction of coastal wetlands h ave reduced natural sources of CDOM to reefal waters. I tested the null hypothesis that CDOM does not differ between reefs that differ in coral health, and that water transparency to UVR is not a factor in reef health. I measured absorption of UVR and UV irradiance at various reefs in the Florida Keys that differ in distance from shore and degree of anthropogenic development of the adjacent shoreline. My results show that intact shoreline associated reefs and inshore reefs tend to be exposed to lower intensities of UVR, and lower degrees of photic stress, than developed shoreline associated reefs and offshore reefs Absorption due to CDOM ( a g320 ) was higher, and photic stress, as revealed by increased production of UV absorbing compounds, Mycosporine like Amino Acids (MAAs ), was lower at the s urface compared to the bottom.

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xi The following results support my conclusion: a g320 and UV attenuation coefficients ( K d s) were higher at intact compared to developed shoreline associated reefs and at inshore compared to offshore reefs. Spectral s lope, S wa s high er at offshore compared to inshore reefs indicating a higher degree of photobleaching of CDOM. R elative expression of MAAs was higher at developed compared to intact shoreline associated reefs at offshore reefs compared to inshore reefs and at the surface compared to the bottom. Solar energy reaching the benthos at two inshore reefs of the same depth (6m) was approximately an order of magnitude higher at t he reef near developed shoreline compared to the reef near intact shoreline and may be due to greater degree of diffuseness of the underwater light field combined with lower a g at the developed shoreline associated reef.

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1 1. Introduction In the last three decades of the 20th century, scientists, reef managers and the public witnessed the decline of coral reefs, first locally, then over entire reef tracts and regions. By the late 1990s, most scientists recognized that reef decline was worldwide ( e.g ., Dight and Scherl 1997, E akin et al. 1997, Risk 1999). Bryant and others (1998) estimated that more than half of the world's coral reefs were threatened by human activities such as sewage and industrial pollution, deforestation, and overfishing. Their report was released as the 1 997 98 ENSO event triggered coral mass bleaching events unprecedented in global scale and intensity ( e.g ., Hoegh Guldberg 1999, Wilkinson 2002). Subsequent prognoses on the condition of reefs have not been encouraging ( e.g. Buddemeier 2001, Birkeland 200 4, Hoegh Guldberg et al. 2007, Baker et al. 2008). For example, a decline in species richness for all habitat types from 1996 to 2001 and a general decline in stony coral cover from 1996 to 2003 have been observed in the Florida Keys National Marine Sanctu ary (Somerfield et al. 2008). As a consequence, scientists and reef managers are increasingly seeking to determine what factors can enhance resiliency of reef communities (e.g., Nystrom et al. 2000, Knowlton 2001, McClanahan et al. 2002). The relationsh ip between coral mass bleaching events and elevated sea surface temperature (SST) is well established (Goreau and Hayes 1994, Brown 1997, Hoegh Guldberg 1999). In addition, corals do not bleach in the absence of light ( e.g ., Lesser and

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2 Farrell 2004). Mas s bleaching events typically occur when sea conditions are unusually calm ( e.g. Glynn 1996, Fabricius et al. 2004) and thermal bleaching appears to be caused by photoinhibition and photodamage to photosystem II of the zooxanthellae ( e.g. Fitt et al. 200 1, Lesser 2004, Smith et al. 2005). Several reported exceptions to the correlation between mass bleaching and SST indicate that clouds or direct shading can reduce bleaching in corals (e.g., Mumby et al. 2001, Fabricius et al. 2004). In addition to supra optimal insolation and temperature, ocean acidification due to increasing CO 2 is a current and future threat to reef health, by compromising carbonate accretion and thus formation of coral skeletons (Hoegh Guldberg et al. 2007). According to the Coral Re ef Evaluation and Monitoring Project (CREMP), since 1996 inshore patch reefs have consistently exhibited lower rates of decline than offshore, clear water reefs at similar depths (NOAA 2002, Somerfield et al. 2008). Depending on degree of shoreline develo pment, inshore patch reefs tend to be closer to seagrass beds, mangroves and terrestrial sources of colored dissolved organic material (CDOM), which strongly absorbs short wavelength visible and ultraviolet (UV) radiation. While a commonly accepted hypothe sis is that inshore patch reefs are better adapted to high temperature variability than offshore reefs, my dissertation will explore another hypothesis: differences in water transparency, and the resulting differences in solar radiation reaching the bentho s, may play a role in the differences in rates of decline of coral cover between inshore patch reefs and offshore shallow reefs. The null hypothesis is thus, that differences in water transparency, and the resulting differences in solar radiation reaching the benthos, do not play a role in differences in rates of decline of coral cover between inshore patch reefs and offshore shallow reefs.

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3 The UV absorbing capacity of CDOM can potentially protect inshore patch reefs from photooxidative stress. As an illu stration, absorption due to CDOM decreases going from mangroves to inshore and offshore reefs and is lowest in offshore, open ocean blue water (Figure 1.1). The decrease in absorption results in increased Figure 1.1. Absorption due to CDOM (also known as gelbstoff) (a g ) is high in mangrove canals and progressively decreases with distance offshore. Markers: offshore blue water sites (circles), reef sites (diamonds), and sites within mangrove canals (squares). transparency to short wavelength, high energy blue and UV solar radiation at offshore sites relative to inshore sites. To examine my hypothesis, samples of whole water were collected from the surface (approximately 0.5 to 1 m) and from the depth of coral growth, and downwelling cosine irradiance prof iles of in situ ultraviolet radiation (UVR) and photosynthetically

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4 active radiation (PAR), were measured at various locations along the Florida reef tract. To address my hypothesis (see above), I measured irradiance and absorption due to CDOM at reefs vary ing in proximity to shoreline (inshore and offshore reefs) and compared these results to inshore offshore site differences in percent coral cover and rates of decline in coral cover. I compared in situ light (irradiance) measurements and CDOM absorption and at reefs that differ in type of shoreline (intact and developed). I also measured absorption due to particulates, and chlorophyll concentration ([ chl ]). The attenuation coefficient ( K d ), was calculated from in situ irradiance or total absorption (the s um of absorption due to CDOM, particulates, and pure water). Because K d is not affected by the time of day, i.e., the sun angle, this coefficient is a convenient quantitative expression for comparing water transparency and thus penetrability of UVR and PAR among sites. Mycosporine like amino acids (MAAs) are UV absorbing compounds found in photosynthetic organisms. Because they are induced by supraoptimal exposure to UV and visible radiation, MAAs can be used as an indicator of photooxidative stress. I use d relative MAA expression to compare MAA production by phytoplankton in the water column among sites. Considering the angular structure or diffuseness of the underwater light field greater diffuseness results in increased scattering, and thus increased likelihood of an object being irradiated (Kirk 1994). I used a radiative transfer model, Hydrolight to compare the diffuseness of the underwater light field between intact and deve loped shoreline associated reefs.

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5 Chapter 2. Background: aspects of in water optics 2.1. Electromagnetic radiation and the solar spectrum In this chapter, I shall introduce essential concepts and definitions relating to my study of water transpar ency and solar radiation in reef environments. For a more complete discussion, see Kirk (1994). Solar radiation is a type of electromagnetic energy which consists of a spectrum of energy characterized by different wavelengths and frequencies (Fig. 2.1) Wavelength, and frequency, v are related by the speed of light, c a constant in a given medium: "= c /# (2.1) According to (2.1), as wavelength increases, frequency decreases. Each wavelength of radiation has an associated e nergy, E which varies with frequency: E = hv = hc" (2.2) where h is Plancks constant and has the value of 6.63 x 10 34 J s. Thus, as wavelength decreases, its associated energy increases (Kirk 1994).

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6 Figure 2.1. Spectra of noni onizing solar radiation (A) and ultraviolet radiation (B) showing main radiation bands, their nomenclature, and approximate wavelength limits. Other synonyms: UV A, black light; UV B, sunburn or erythemal radiation; UV C, germicidal radiation (from Acra et al. 1990, compiled from WHO 1979, Parmeggiani 1983, and Harvey et al 1984). Nonionizing solar radiation can be categorized into visible and invisible radiation (Fig. 2.1). While some organisms, including coral, have the ability to capture UVR and fluor esce it to wavelengths useable in photosynthesis (Kawaguti 1969, Schlichter et al. 1986 ), solar radiation in the visible range (400 700 nm), commonly referred to as Photosynthetically Available Radiation (PAR), is the major source of energy for photosyn thesis. Ultraviolet radiation (UVR, 100 400 nm) occurs at wavelengths shorter than visible light, therefore the energy in a photon of UVR is higher than in a photon of visible radiation. Ultraviolet radiation is energetically differentiated into four cat egories: Vacuum UV (100 200 nm), UV C (200 280 nm), UV B (280 320 nm, or 315 nm, depending on source), and UV A (315 or 320 400 nm) (Acra et al. 1990, Kirk 1994).

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7 At the other end of the spectrum, infrared radiation (700 1400 nm), which is experi enced as heat, occurs at wavelengths longer than visible light. 2.2. Atmosphere UV interactions The components of the atmosphere that most strongly absorb UVR are sulfur dioxide (SO 2 ) and ozone (O 3 ) (Roscoe 2001). UV C does not reach the earth in app reciable intensities due to effective absorption by stratospheric ozone (Figs. 2.2, 2.3). UV B is less effectively absorbed by ozone, and thus does reach the Earth's surface in amounts inversely proportional to stratospheric ozone concentration (Acra et al 1990). Methyl halide aerosols, such as anthropogenic methyl bromide and chlorofluorocarbons, in the presence of sunlight, can break down stratospheric ozone. At the same time as it absorbs UV, sulfur dioxide promotes the formation of more reactive chloro fluorocarbons which are more effective at breaking down ozone, and thus indirectly result in increased UVR reaching the Earth's surface. The rate of ozone depletion is affected by temperature, circulation and cloud albedo (Figs. 2.2, 2.3). Explosive volcan ism contributes to atmospheric [SO 2 ] and therefore can cause increases in UVR reaching the Earth's surface (Roscoe 2001).

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8 Figure 2.2. Interactions between ozone depletion and climate change. The arrows indicate direction of influence. The effects of c limate change on ozone and UVR are discussed in the text (adapted from Clark 2001 in UNEP 2003).

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9 Figure 2.3. Solar irradiance outside the atmosphere and at sea level. Absorbing components of atmosphere and irradiance bands measured by MODIS satellite are indicated (from http://en.wikipedia.org/wiki/Solar_radiation). A general term for a continuous measure of the effects of solar radiation as a function of wavelength is the spectral weighting function (SWF). An SWF quantifies the effectiveness (or w eight') of solar radiation, for example, UVR or PAR, at causing some response in relation to wavelength. Two specific types of SWFs are action spectra and biological weighting functions. Action spectra are based on responses to narrowband (monochromatic) i rradiance and are defined for both biological and chemical effects. Biological weighting functions are determined under broadband (polychromatic) irradiance and reflect the simultaneous (and sometimes competing) effects of multiple wavelength dependent pro cesses as they occur in nature (Neale and Kieber 2000). An action spectrum illustrates the differential importance of different wavelength s of light in inducing the effects of solar exposure (Neale and Kieber 200). For example,

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10 effectiveness at producing erythemal (skin) and DNA damage (Fig. 2.4) and photoinhibition of photosynthesis in Arctic phytoplankton increase exponentially with decreasing wavele ngth in the UV range (Cullen and Neale 1997) The same effect has been found for corals. Lesser (2000) examined action spectra for the effect of UV on photosynthesis at different depths in the coral Montastrea faveolata finding a steep and rapid decrease with increasing wavelength Action spectra and biological weighting functions are used to determine biological amplification factors and have been used to assess the environmental impacts of increased surface UV irradiances resulting from stratospheric o zone depletion (Micheletti et al. 2003). Figure 2.4. Example of an action spectrum for erythemal and DNA damage ( http://www.temis.nl/uvradiation/info/uvaction.html). Changes in UVB reaching the Earth's surface due to changes in stratospheric ozone c an be expressed in terms of a radiation amplification factor ( RAF ) (Rundel and

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11 Nachtwey 1978, Rundel 1983, Smith and Cullen 1995). Since the relationship between UVB dose and ozone concentration is nonlinear, the RAF can be most generally expressed using an equation relating the change in biological effective irradiance, or dose rate, # Be( $ ) to the change in total atmospheric column ozone concentration or ozone thickness, % (Madronich and Granier 1992, Madronich 1993, Booth and Madronich 1994) : RAF = (" EBe (#))2( EBe (#))1 $ % & ( ) / "*2*1 + / 0 (2.3) Congruently, the effect of changes in ozone on UV exposures can be expressed as: RAF = ( UV("))2( UV("))1 # $ % & ( / )*2*1 + / 0 (2.4) Radiation amplification factors can in turn be used to calculate the increase of biologically effective irradiance in response to ozone depletion. Published values of RAFs for different processes have been reviewed by Madronich et al. (1998) As another example, the percent change in absorption due to CDOM, a g can be related to the proportional c hange in # Be( $ ) by a biological amplification factor, B (Smith and Cullen 1995): B = "agag # $ % & ( "EBe ())EBe ()) # $ % & ( (2.5) Combining these two factors, the percent change in ozone can be related to th e biological effect by the total amplification factor, A : A = RAF x B (2.6)

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12 The total amplification factor can be used to describe the effect of ozone depletion on a biological or chemical process such as photosynthesis. For example, Lesser (200 0) determined that RAF s for the effect of UV (290 400 nm) exposure on photosynthesis in the coral Montastrea faveolata varied from 0.15 to 0.23, while earlier estimates of RAF s for DNA damage and for the inhibition of photosynthesis in free living phytop lankton are much higher ( 2.0 and 0.5 to 0.95, respectively) (Madronich 1993). Compared to those mentioned above, modeled RAF s for the effects of changing CDOM concentrations based on in situ CDOM and UV data specifically from the Florida Keys are much h igher: at 6.0 m, RAF s were 1.65 for photosynthesis inhibition and 3.26 for DNA damage (Zepp et al. 2008). Accordingly, a 30% increase in UV transparency (as expressed by a 30% decrease in the diffuse attenuation coefficient for UV, K dUV (see section 3.2.3 .) can result in an 85% increase in photoinhibition and over 200% increase in DNA damage (Zepp et al. 2008). The RAF s were lower at shallower depths: at 3 m, 30% decrease in K dUV can result in a 30% increase in UV induced photosynthesis inhibition and a ne arly 100% increase in DNA damage (Zepp et al. 2008). Zepp et al. (2008) estimated that DNA damage decreases much more rapidly with depth than does photosynthesis inhibition due to the spectral dependence of UV dose rates on these effects. Based on CDOM pho tobleaching experiments for a water sample from the Florida Keys, Looe Key, absorption can decrease 7% per day (Zepp 2003). Osburn et al. (2001) determined spectral weighting functions for the photobleaching of CDOM in lakes. Based on their model, a 25% i ncrease in UVB radiation results in an 8% increase in photobleaching of CDOM. Generally, photobleaching increases with decreasing wavelength : the largest absolute loss of absorbance occurs at the shortest wavelengths (Kieber et al. 2007). Additionally, hi story of exposure affects photobleaching efficiency: with increasing exposure, the wavelength of

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13 maximum photobleaching may shift to lower wavelengths (Osburn et al. 2001, Akella and Uher 2006). Del Vecchio and Blough (2002) found that while the largest losses of absorption are observed at the irradiation wavelength, monochromatic irradiation (irradiation with one wavelength) results in absorption loss across the entire spectrum. 2.3. Annual cycle of UVR The annual cycle of UVR in the Lower Keys is chara cterized by maxima from May to August and minima from December to January (Fig. 2.5). Comparing equatorial regions to other geographic locations, as latitude decreases, UVA exposure increases and more nearly approximates that seen at the equator (Acra et al. 1990). In the northern hemisphere, for all UVR wavelengths from 285 to 340 nm, the solar UVR flux decreases as latitude increases for all times of year except the June solstice, when the relative irradiance is lowest at the equator (Acra et al. 1990).

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14 Figure 2.5. Mean daily UV B and UVR at the Mote Marine Laboratory in the Lower Keys (latitude 24.5 o N, longitude 81.6 o W) during 2002 2003. The data were measured by Yankee Environmental Systems UVB and UVA pyranometers at one minute intervals (from Z epp 2003). This latitude UV relationship is relevant for the Florida Keys, which lie at approximately 25 ¡ latitude: the highest measured UV irradiance in the subtropical latitudes of the Keys occurs between May and August (Fig. 2.5). Maximum insolation, without the influence of the atmosphere, occurs from May to August at the latitude of the Florida Keys (Figure 2.8 in Kirk 1994; Figure 2.5). Because of the relatively high UV irradiance at this time of year, we would expect the highest deleterious respon se to irradiance, such as bleaching, from May though August. Consequently, this is the optimal time of year to record the most acute stress associated with solar irradiance.

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15 2.4. UVR environment interactions In nature, solar radiation is scattered and r eflected as well as absorbed by particulate and dissolved material. The wavelength dependence of scattering in air, Rayleigh scattering, is 1/ 4 Due to the higher refractive index of water, the wavelength dependence of Rayleigh scattering in water devia tes from the in air value, to 1/ 4.32 T hus, shorter wavelengths, such as UVR, are more highly scattered compared to longer wavelengths such as visible light, resulting in increased UV irradiance relative to PAR (Kirk 1994). Incident spectral irradianc e typically reaches its highest intensity at 480 nm (Figs. 2.3 and 2.6). Although intensity decreases at lower wavelengths, the higher energy associated with UVR results in higher efficiency in altering the biological, chemical and physical environment (se e Fig. 2.4). Figure 2.6a. Incident spectral irradiance (on land) measured with a LiCOR 1800 spectroradiometer at 10 minute intervals on May 25, 2005 at NURC, Key Largo, FL.

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16 Figure 2.6b. Median incident spectral irradiance (above water) on May 25, 2004 (15:50 to 16:10) and on July 6, 2004 (16:00), on land (Keys Marine Lab or NURC, Key Largo, FL). Irradiance intensity at any wavelength is determined by the absorbing and scattering properties of the water column. In highly transparent, relatively sh allow waters, the reflective properties of the bottom can influence irradiance intensity in the overlying water column. The light absorbing and scattering constituents of the water column can be categorized as dissolved material, particulate material, an d water molecules. The most significant optically active components include phytoplankton, mineral particles and detritus, and CDOM (Kirk 1994). While pigment containing particles, and to a lesser extent, detrital particles, can contribute to UVR absorptio n (Ayoub et al. 1997, Vincent et al. 2001, Belzile and Vincent 2002, Frenette et al 2003, Zepp 2003), CDOM is the predominant and most consistent attenuator of UVR in most oceanic waters (Kirk 1994,

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17 Nelson et al. 1998, Siegel et al. 2002), including reefa l waters in the Florida Keys (Zepp et al. 2008). Figure 2.7 illustrates absorption and incident downwelling irradiance spectra for a coral reef site in the Florida Keys in May 2004. As mentioned above, these data illustrate that particulate matter can pl ay a significant role in UVR attenuation, with absorption increasing at decreasing wavelengths. These data also show that, even in relatively clear reefal waters, CDOM is typically the major attenuator of UVR. Pure water absorbs minimally in the visible w avelengths to 580 nm, but absorbs increasingly strongly in the red to infrared range ( Fig. 2.7 and Kirk 1994). In studies at an offshore reef, Conch Reef (30 m), in the Florida Keys, Lesser (2000) found that UVR down to 310 nm penetrates significantly t o the depth of coral growth. Thus CDOM can play a vital role in protecting reefs from UVR.

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18 Figure 2.7. Incident irradiance (E d0 350 700 nm) and spectral absorption due to CDOM ( a g ), particulate material ( a p ) and pure water ( a w ) for Key Largo 6m (KL6 m) Reef in May 2004. Note shoulder in the UVR range of a g indicative of dissolved MAAs. 2.5. CDOM composition Here, I present some essential topics relating the importance of CDOM and ocean color to water transparency. More detailed reviews of ocean col or and CDOM can be found in Del Castillo (2005) and Coble (2007), from which much of the following is summarized. Though the chemical composition, origin and dynamics of CDOM in aquatic systems are still poorly understood due to their complexity (Coble 20 07), CDOM is

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19 defined operationally by the method used to separate suspended and dissolved material. Typically the most common methods are filtration through glass fiber filters (fine, pore size 0.7 m) and polycarbonate or polysulfone membranes (0. 2 m por e size). Dissolved organic matter in seawater is composed of countless organic compounds, the majority of which are classified as humic substances, due to their original discovery and study in soil chemistry. Humic substances are typically divided into hum ic and fulvic acids, which have been separated based on their different solubilities ( McKnight and Aiken 1998 ) or molecular weights (Osburn and Morris 2003), though the chemical differences separating humic and fulvic acids are not clear cut. There are four pathways associated with the formation of fulvic and humic acids: 1) decomposition products of modified lignins, 2) microbially decomposed lignin products, 3) phenols and other plant biochemicals, and 4) polymerization products of sugars, amino aci ds, and other small particles (Fig. 2.8). In any given terrestrial ecosystem, all four pathways may occur, but not to the same extent or in the same order of importance. Lignin pathways predominate in poorly drained soils and wet sediments (swamps, etc.) ( Waksman 1932). Production from lignins can occur via microbial decomposition of lignin by aerobic pathways to directly produce humic acids (Stevenson 1982). Synthesis from lignins via polyphenols may be of considerable importance in certain forest soils. F luctuations in temperature, moisture and irradiation in terrestrial surface soils under a harsh continental climate may favor humus synthesis by sugar amine condensation (J. Weber in http://www.ar.wroc.pl/~weber/powstaw2.htm#1 )

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20 Figure 2.8. Pathwa ys for the formation of humic substances (from J. Weber in http://www.ar.wroc.pl/~weber/powstaw2.htm#1). Nonhumic pigment like components of marine CDOM such as amino acid or protein like substances may be an indicator of elevated biological activity ( Coble et al. 1998) These proteins and pigments may be truly dissolved or result from disruption of phytoplankton cells during sample preparation (filtration) (Coble 2007). 2.6. CDOM optical properties The photochemical properties of CDOM can be ascrib ed to compositional makeup. Marine and terrestrial humics differ in the amounts of aliphatic and aromatic groups, and these differences explain the differences in their optical properties. Marine humics are less aromatic, have lower C/N ratios, and contain more carboxylic groups and sugars than

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21 do terrestrial humics (Coble 2007). Both terrestrial and marine CDOM have absorbance spectra that increase exponentially toward shorter wavelengths, with no discernible peaks. This lack of features fits the explanati on that CDOM is a complex mixture of compounds that have overlapping absorption spectra, with no single compound dominating (Coble 2007). The smoothness of the absorption spectrum at wavelengths greater than 350 nm may also result from intramolecular elect ronic interactions (Del Vecchio and Blough 2004b). Terrestrial CDOM is more highly aromatic and molecularly complex than marine CDOM, resulting in higher absorption and "red shifted" fluorescence upon analysis of excitation emission spectra ("EEMS", Del Castillo 2005). In addition, most studies have found that the spectral slope is lower for higher molecular weight ("fresher") terrestrial CDOM than for marine CDOM (Del Vecchio and Blough 2004a). 2.7. CDOM sources, sinks and pathways Sources of CDOM to coral reefs include decomposed terrestrial and wetland plants, including mangroves, as well as exudates from bacteria, phytoplankton, seagrasses and coral (Fig. 2.9) (Anderson et al. 2001, Stabenau et al. 2004). Intact shorelines with coastal mangrove hamm ocks are a vital source of CDOM to fringing and other nearshore coral reefs. Comparing coral reefs with differing predominance of seagrass, Boss and Zaneveld (2003) reported that CDOM absorption of UV and PAR is higher in pore waters of coral reefs charact erized by higher densities of seagrass: grass covered sediment are found to be sources of what these authors refer to as CDM (Colored Dissolved Material = CDOM + nonalgal particles ) to the water column Seagrass roots promote the production of CDOM via ox idation of sediment POC, by injecting photosynthetically derived O 2 into the sediments (Burdige et al. 2004 ).

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22 Figure 2.9. Flow chart illustrating sources, sinks and pathways of Colored Dissolved Organic Matter (CDOM) to the Florida reef tract (after Ze pp 2003 and Morris and Hargreaves 1997). As UVR is absorbed by CDOM, the CDOM is broken down, or photobleached, producing less absorptive forms of CDOM (Morris and Hargreaves 1997, Vodacek et al. 1997, Nelson et al. 1998). In times of drought, photoblea ching can be pronounced because runoff decreases, reducing CDOM supplies. In addition, calm weather increases stratification of the water column, resulting in increased UV exposure: exponential degradation of CDOM will occur and UV transparency will increa se (Morris and Hargreaves 1997). The resultant smaller, more labile photoproducts of CDOM are available for bacterial degradation, allowing more UVR to pass through the water column

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23 (Miller and Moran 1997). At some point, CDOM can no longer be broken down and becomes recalcitrant (Aluwihare et al. 2005). While the cycle of CDOM photobleaching and increased UV transparency may continue, consistent sources of CDOM can disrupt this positive feedback loop: mangrove hammocks and seagrasses can provide regular pu lses of CDOM to reef waters (Moran et al. 1991) with each tidal cycle. Also relevant to coral reefs is the interaction of tidal cycles and CDOM sources offshore from reefs: CDOM rich plumes from the Bahama Banks may sink to depth after cooling and subseque ntly be brought onshore via tidal cyles, and thus potentially protect benthic organisms from UVR (Otis et al. 2004). CDOM is an important component of the trophic pathways of plankton communities, including the microbial loop (Fig. 2.10). CDOM is consumed by bacteria, at the same time zooplankton and phytoplankton excrete CDOM as waste or exudate (Steinberg et al. 2004). Bacteria play a dual role in the cycling of CDOM. Bacteria act as a sink by remineralizing CDOM, and as a source by exuding CDOM metaboli cally and breaking down plant material (Nelson et al. 2004). While bacteria consume as well as produce CDOM, they are in turn consumed by zooplankton (Wotton and Wotton 1994). In open ocean areas not influenced by highly colored, coastal sources of CDOM s uch as rivers and mangroves, exudates of phytoplankton and zooplankton are an important source of CDOM (Nelson et al. 2004, Steinberg et al 2004).

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24 Figure 2.10. Diagrammatic representation of the two trophic pathways in plankton communities (after Wot ton and Wotton 1994 based on Pomeroy and Wiebe 1988). Especially for coastal ecosystems, rivers are major sources of terrestrial CDOM. In Chapter 3, I will discuss riverine inputs of CDOM specifically for the Florida Keys. Land use can have a consequentia l influence on CDOM delivery to coastal waters. Water quality studies of storm waters in South Florida have shown that wetlands and pastures exhibited highest color (235 and 227 Pt Co units) subsequent to residual runoff (173 Pt Co units), while runoff fro m citrus, row crops, urban, and golf course areas were appreciably lower (Graves et al. 2004). This difference was attributed to more rapid runoff at the sites characterized by lower CDOM because grasses at these sites are more heavily managed and limit bo th production and leaching of CDOM sources such as humic and tannic acids. Thus, reduction of sources of CDOM can occur not only by

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25 replacing mangroves and coastal hammocks with buildings, but also by replacing wetlands or forests with sod and other manage d vegetation. Extensive development in the Florida Keys has displaced natural vegetation and thus decreased CDOM runoff to coastal waters. 2.8. Remote sensing of UVR and coral reefs: application of the spectral slope of a g Up to now, the application of s atellite algorithms for estimating UV irradiance has relied upon measurements made for PAR. In situ sea truthing of coral reefs is needed to formulate algorithms for estimating UVR in oceans. Coastal areas such as coral reefs possess an additional challeng e of being located in shallow waters where bottom reflectance and terrigenous inputs can complicate satellite derived estimates of irradiance. As previously mentioned, absorption due to CDOM, a g increases exponentially as wavelength decreases, beginning at approximately 490 nm. The spectral slope of a g in the UV range, and the relationship between UVR and PAR, can be elucidated by sea truthing of a g which would enable improved estimation of UV irradiance at greater spatial scales. Absorption at any wave length can be derived from spectral shape or slope scaled from absorption derived from remotely sensed a g Twardowski et al (2004) have evaluated the application and interpretation of a single exponential model describing a g as a function of wavelength, u sing 412 nm as the reference wavelength, a wavelength retrieved by satellites: ag(") = ag( 412)"412 # $ % & ( )692 (2.7)

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26 In general, the spectral slope, S is used to estimate a g at one wavelength, from another, satellite derived wavelength ( 0 ) using a non linear fit of the form: ag"( )= ag("0)eS ("0#") (2.8) (Blough and Del Vecchio 2002). The traditional usage of S is in the visible light range. Algorithms for differentiating between terrestrially and marine derived organic matter have been determ ined (Stedmon and Markager 2001). The spectral slope of a g has been shown to vary depending on location (Carder et al. 1989, Vodacek et al. 1997, Nelson et al. 1998, Twardowski et al. 2004). The estimates by Carder et al. (1989) of S for the Gulf of Mexico are 0.0141 nm 1 Lee et al (1999) reported a spectral slope of 0.01433 nm 1 for the range 400 500 nm in Florida Keys waters based on a model estimating a g from remote sensing reflectance. The spectral slope for UVR is expected to be much higher than for the 400 500 nm range (see Fig. 2.7, a g ). Kopelevich et al. (1989) estimated the spectral slope for the region 280 490 nm in the open ocean to be 0.017 0.001 nm 1 Because spectral slope increases in surface waters in summer due to increasing photo bleaching (Nelson et al. 1998; Del Vecchio and Blough 2002) it can be used to compare the degree of photobleaching between water bodies. While CDOM production by phytoplankton and zooplankton can be especially important in offshore, clear surface waters a nd the open ocean, advection and bleaching can balance net production (Nelson et al 2004, Steinberg et al 2004). For example, waters with no significant bacterial production of CDOM and high transparency typically have higher spectral slopes than more hi ghly colored waters with fresh or consistent sources of CDOM ( Blough and Del Vecchio 2002).

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27 2.9. Photobiology of UVR and effects on aquatic ecosystems Ultraviolet radiation, including UVA, has been shown to cause stress responses such as genetic damage to bacteria, phytoplankton and other organisms (Karentz et al. 1994, Huot et al. 2000), decreased growth rate, lethal effects on larvae and adult organisms (Gleason and Wellington 1995), and photoinhibition in phytoplankton (Smith and Cullen 1995), as well as bleaching (Lesser 2004, Lesser and Farrel 2004, Vincent and Neale 2004) (Fig. 2.11). Other effects of UVR include suppressed calcification and skeletal growth (Roth et al. 1982) and coral bleaching (Glynn 1996, Lesser and Farrell 2004). The increase in DNA damage to bacterioplankton that has resulted from decreases in stratospheric ozone concentration has been modeled by Huot et al. (2000). Zepp et al. (2008) estimated that DNA damage decreases much more rapidly with depth than does inhibition of photo synthesis. Figure 2.11. Pathways between UV radiation exposure and cellular stress. Damage can occur directly by photochemical degradation of biomolecules (pathway 1 or indirectly via the production of reactive oxygen species such as hydrogen peroxide a nd superoxide radicals (pathway 2a), which then cause more widespread oxidative damage within the cell (2b). The net stress is manifested in terms of: the increased energy demands of

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28 protection and repair; compositional changes (e.g., lipid content), which may affect the nutritional quality of the cells for higher trophic levels; an impairment of growth rate resulting from the photochemical damage and from the increased energy requirements; and, under severe exposures, an increased rate of mortality (from V incent and Neale in de Mora 2000). Photooxidation is the conversion of a reduced molecule to an oxidized form in the presence of molecular oxygen via a set of chemical reactions that are initiated by photolysis (Glossary of Meteorology 2000). One type of photooxidative damage to the photoautotrophic symbionts of corals, the zooxanthellae, is known as "bleaching" (Gleason and Wellington 1993). Coral bleaching is a response to environmental or biotic stress in which zooxanthellae are expelled or their photo synthetic pigments are lost (Glynn 1996). One mechanistic explanation is that bleaching is induced by excessive solar radiation, resulting in photooxidation induced photoinhibition, that is, decreased efficiency in the light harvesting capacity of the phot osynthetic apparatus of the symbionts (Lesser et al. 1990, Jones et al. 1998). Oxidative stress occurs via reactive oxygen species (ROS), resulting in damage to photosystem II, which in turn leads to bleaching of zooxanthellae, or zooxanthellae exocytosis (bleaching of coral) (Lesser 2006). ROS formation associated with exposure to elevated temperature and solar radiation is believed to be an important factor leading to coral bleaching (Lesser 2006). Thorough reviews of biological effects of UVR on coral reefs have been published by Shick et al. (1996) and, more recently, by Lesser (2004). These effects include solar and thermal stress induced coral bleaching, as well as decreased photosynthesis and growth in zooxanthellae due to damage to DNA, proteins, a nd lipids (Shick et al. 1995). Photoinhibiton of photosynthesis in zooxanthellae can be due to exposure to elevated temperature alone (Iglesias Prieto et al. 1992), UVR alone

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29 (Lesser and Shick 1989), or temperature and UVR in combination (Lesser 1996, 1997). Supraoptimal intensities and durations of exposure to visible light, particularly blue light, also have been shown to induce photoinhibition and loss of photosynthetic symbionts in corals (Jokiel and York 1982, Fitt and Warner 1995) and benthic For aminifera (Williams and Hallock 2004). Stabenau et al (2006) have shown that increases in UVR intensity on the coral surface in conjunction with the onset of high sea surface temperatures, due to stratification and resulting increased photobleaching of CD OM, correlates with decreased coral photosynthetic efficiency. E xposure to high solar irradiance leads to a lower bleaching threshold temperature and an overall shorter time to actually bleach'' compared to corals exposed to lower solar irradiances (Les ser and Farrell 2004). Production of heat shock proteins (HSPs) in coral host tissue has been observed to be upregulated in response to thermal stress (Black et al. 1995). Bioindicators of photooxidative and thermal stress such as MAAs, HSPs, and decrease in photosynthesis, present parameters for comparing reef health and environmental stressors between reefs (Fisher 2007). The effects of UVR on gene expression include pyrimidine dimer formation in DNA, which interferes with DNA replication and transcripti on, cessation of cell division, and mutations of essential genes that may cause cell death (Anderson et al. 2001, Moran and Zepp 2000). Sublethal effects include decreased growth and reproduction, permeability of membranes and transport of molecules into the cell, disruption of the electron transport chain, inactivation of membrane transport functions, and RNA damage (Moran and Zepp 2000). Ultraviolet radiation specifically has been shown to cause DNA damage, DNA mutations and cell death in marine organis ms such as corals (Banaszak and Trench 1995a,b, Shick et al. 1995, Lesser 1996). Although it is generally thought that UVR

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30 attenuates quickly, some natural water bodies, especially coral reefs, are characterized by high transparency to UVR (Gleason and Wel lington 1993, Lesser 2004). For example, the intensities of some higher wavelengths of UVR can approach the intensity of PAR at depths subsurface to 2m in Kane'ohe Bay, Hawai'i (Gleason and Wellington 1993, Gulko 1995). Other effects of UVR on aquatic bio ta on the organismal level have been summarized by Ha e der et al. (1998, 2003), Anderson et al. ( 2001), Vincent and Neale (2004), Hoogenboom et al. ( 2006), and many others. Although UVB has higher energy than UVA and blue light per unit wavelength, Osburn et al (2001) reported that UVA and low wavelength PAR are more effective in photobleaching CDOM because of their greater total energy On the other hand, Fine et al. (2002) have shown that UVR (280 400 nm) can ultimately shield corals from some bact erial infection s While overexposure to both UVR and PAR induces photoinhibition, PAR intensity must be high enough to support photosynthesis (Yentsch et al 2002). Thus there is an optimal depth range where intensity of UVR and PAR are below damaging lev els and intensity of PAR is sufficient for growth and development ( Alonso et al. 2004 ). 2.10. Defenses against UVR: Mycosporine like amino acids (MAAs) Mycosporine like amino acids (MAAs) are UV absorbing compounds with maximal absorbance at 310 360 nm (Shick et al. 1999). Because MAA production is induced by exposure to UVR (Dunlap et al. 1986, Banaszak et al. 1998, Lesser 2000),

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31 theories on MAA induction are relevant to my study of photobiology, CDOM and coral reefs. MAAs can be produced by symbiotic zooxanthellae (Schick et al. 1999) as well as by phytoplankton (Morrison and Nelson 2004). While exposing corals to UVR can induce UV protective mechanisms such as production of MAAs (Shick et al. 1996, Dunlap and Shick 1998, Morrison and Nelson 2004, Shic k 2004), and DNA repair enzymes (Banaszak and Lesser 1995, Kuffner et al. 1995, Anderson et al. 2001), prolonged overexposure to UVR can also reduce photosynthetic rates and simultaneously reduce MAA production (Lesser and Farrell 2004). In addition, prod uction of MAAs may decrease with increasing temperature, leaving zooxanthellae more susceptible to damage caused by exposure to UVR (Lesser et al. 1990). MAAs also may have an antioxidant activity (Dunlap and Yamamoto 1995, Kim et al. 2001, Suh et al. 200 3). Results from studies monitoring PAR and MAA production have been ambiguous. While increases in blue wavelengths of PAR can induce production of UV absorbing MAAs, since PAR and UVR co vary, as blue wavelengths of PAR increase, the concurrent increase in UVR may actually be responsible for MAA induction (Jokiel et al. 1997, Moisan and Mitchell 2001). Other hypotheses propose that photosynthetically usable energy (PAR) absorbed in excess of the processing capacity of cellular biochemistry may be passed on to a genetic pathway to induce MAAs (Moisan and Mitchell 2001), or that disruption of a metabolic pathway may cause MAA accumulation (Goes et al. 1995). Other coral defenses against UVR include behavioral defenses or production of mucus containing MAAs, melanin, fluorescent pigments, antioxidants such as superoxide

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32 dismutase (SOD), photoreactivation, and enzymatic photorepair (Shick et al. 1996). See Chapter 5 for a more detailed discussion of MAAs and their relevance to CDOM and UVR transparency in the F lorida Keys. 2.11. Stratospheric ozone depletion and bleaching Mass bleaching events in corals have traditionally been attributed to above normal water temperature (Atwood et al. 1992, Goreau and Hayes 1994, Glynn 1996, Lesser 1997 ). Although estimates of ozone depletion predict stabilization of the ozone layer for the coming decade, Montza et al (2009) found that the growth ( i.e. accumulation in the atmosphere) rates for certain CFCs, which destroy ozone, were approximately two times higher in 2007 than in 2004 due to lack of regulation in developing countries (Figure 2.12), and that the concentrations of ozone depleting gases did not begin to decline until 1998 (Hoffman and Montza 2009). In addition, the same study (Montza et al 2009) showed that CFCs e missions increased in 1998, concurrent with peak bleaching events for coral reefs and large benthic foraminifers ( Amphistegina sp. ) (Berkelmans et al 2004, Hallock 2006a,b). Amphistegina are particularly sensitive to the shorter (300 490 nm) wavelengths of solar radiation (Williams and Hallock 2004). Thus, the severity of the 1998 peak coral bleaching event may have been a result of the combined effects of CFC induced ozone depletion, allowing more UVR to reach coral reefs, together with supraoptimal tem peratures. From a management perspective, elucidating the roles of UVR and stratospheric ozone in reef health can support further regulations on CFCs.

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33 Figure 2.12. Monthly hemispheric means and growth rates of HCFCs from weighted measurements of surfac e air collected in flasks at remote locations (Northern Hemisphere (red) > global mean (green) > Southern Hemisphere (blue)). Tropospheric growth rates are plotted relative to the right hand axis and are derived from 12 month differences in global surface means over the previous 12 months (e.g., Jan 99 Jan 98; grey plus symbols) or from monthly differences smoothed over annual periods (black line) (from Montzka et al. 2009).

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34 2.12. Statement of hypothesis My study will investigate the distribution of CDOM on coral reefs in the Florida Keys. The basic idea is that reefs most distal from sources of CDOM experience the highest intensities of high energy blue and UV wavelengths, reefs with inconsistent CDOM sources receive variable intensities of the highest e nergy solar radiation, and reefs with consistent sources of CDOM experience lowest intensities of highest energy solar radiation compared to optimal wavelengths for photosynthesis. I further propose that (a) CDOM rich reef sites will be characterized by hi gher coral cover and lower rates of decline in coral cover than low or highly variable CDOM sites; (b) that relative MAA expression will be greater on reefs that experience consistently lower and/or more variable a g ; and (c) because absorption decreases di ffuseness (see Chapter 6) as well as increases attenuation in the underwater light field (Kirk 1994, Gregg 2002), that reefs with lower a g will be characterized by greater exposure to high energy blue and UV radiation. Spectral and qualitative difference s in photobleaching of CDOM depend on location ( Del Vecchio and Blough 2002) I further suggest that spectral slope from open ocean (blue water) sites will indicate higher degrees of CDOM photobleaching, i.e., higher spectral slopes, due to the high er exposure to low wavelength radiation; coral reefs will exhibit intermediate degrees of CDOM photobleaching, depending on location, offshore (higher degree of CDOM photobleaching) or inshore (lower rates of CDOM photobleaching); and inland waters, which are less transparent than ocean or reef water, will typically exhibit the lowest degree of CDOM photobleaching. Though spectral slope has been measured for open ocean and inland waters, my study is the first to quantify

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3 5 spectral slope for coral reefs. Man groves are one of the most significant sources of CDOM to coral reefs (Zepp et al. 2002, Zepp 2003, Jaffe et al. 2004); they also serve as a physical barrier, protecting shorelines from the destructive effects of storms, tidal waves and tsunamis (Danielsen et al. 2005). The results of my study will provide information useful to management on the importance of protecting and maintaining mangrove shorelines and elucidate the effects increased UVR and thus, of stratospheric ozone depletion, on coral reefs.

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36 3. Introduction to the Florida Keys, Study Sites, and Methodology 3.1. Objectives The goal of this chapter is to present background information on the study area and methodology used in subsequent chapters 3.2. Introduction 3.2.1. Geo morphology and water circulation patterns of the Florida Keys The general arcuate pattern of the Florida Keys is a consequence of the bathymetry of the shelf edge and the action of the Florida Current, which controls many of the environmental parameters (d epth, current, and therefore nutrient and light availability) of this area (Randazzo and Halley 1997). Hawk Channel, a n ~ 10 m deep topographic depression along the Atlantic side of the Keys, is relatively deeper than the inner shelf (0 3 m) and reef bank (0 5 m), and shallower than the seaward shelf break (30 m) (Lee and Smith 2002) (Fig. 3.1). Hawk Channel transports water from Biscayne Bay from the north, the Loop Current and Florida Bay from the west, and the Florida Current from the south and east. The s outhwest Florida Shelf and the Atlantic side of the Florida Keys coastal zone are directly connected by passages between the islands of the Middle and Lower Keys ( Fig. 3.1) CDOM rich outflows from the Everglades and other areas of South Florida sup ply CDOM to coastal reef waters in the Middle and Lower Keys via Florida Bay

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37 (Williams 2002). Movement of water between these regions depends on a combination of local wind forced currents and gravity driven transports through the passages, produced by cro ss Key sea level differences on time scales of several days to weeks (Lee and Smith 2002; Smith and Lee 2003; Johns et al. 2006), which arise because of differences in physical characteristics (shape, orientation, and depth) of the shelf on either side of the Keys. In some regions, inshore (patch) reefs may be located adjacent to or within Hawk Channel ( Lidz et al 2003, Peters et al in press), and so may receive CDOM rich waters via Hawk Channel Figure 3.1. Study sites in the Lower, Middle and Upper Fl orida Keys included offshore and inshore (patch) reefs that differ in degree of development of associated shoreline Algae Reef, near intact, mangrove shoreline, is slightly southwest of Carysfort Reef. Key Largo 6m (KL6m) Reef, offshore the city of Key La rgo, is west of Molasses Reef. Onshore to offshore transect through John Pennekamp Park, Algae Reef and Carysfort reef sampled in September 2004 is indicated by double line. Also indicated are the

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38 inshore and offshore CREMP study sites in the Lower, Middle and Upper Florida Keys sampled in 2006 and 2007. Inshore sites are circled in green. Others (uncircled) represent offshore sites. Long term mean volume transport (m 3 /s) through the Keys passages is represented as yellow arrows (from Johns et al. 2006). No t represented in the map are the following sites: Coral Gardens (Middle Keys) and Long Key (CREMP site, Middle Keys) as well as East Washerwoman ( Lower Keys) and West Washerwoman (CREMP site, Lower Keys) and White Banks (Upper Keys) (adapted from Ramirez e t al 2007, Lee and Smith 2002, Randazzo and Halley 1997). The higher mean water level of the eastern Gulf of Mexico and variations in the strength and location of the Loop Current have important influences on mean transports through the passages betwee n Keys. The long term mean volume transports through the primary channels of the Middle Keys are 55 m 3 /s each for Channels 2 and 5, 260 m 3 /s for Long Key Channel, and 370 m 3 /s for the Seven Mile Bridge Channel, where negative mean values represent outfl ows from Florida Bay (Lee and Smith 2002; Fig. 3.1a). The Seven Mile Bridge Channel accounts for about 50% of the flow, Long Key Channel for about 35%, and Channels 2 and 5 account for about 7% each. Florida Bay is rich in CDOM from the wetlands of the Eve rglades. Thus, the general region of the Middle Keys can potentially receive more CDOM than the Upper or Lower (Williams 2002). Moreover, c onstruction of causeways between islands in the Flo ri da Keys, beginning in the early 1900s, significantly altered pa tterns of exchange between Florida Bay and the Atlantic shelf (Swart et al. 1999) The Florida Current, with transport of 30 Sv (10 6 m/s), may serve as a longe range transport and/or mixing mechanism CDOM along and away from the Florida Keys (Mitchum, per s. comm.). The most important local terrestrial sources of CDOM are mangroves and coastal forests. Comparing regions of the Florida Keys, considering the extent of mangrove and coastal forests, the most occur in the Lower Keys (Lidz et al 2006), followe d by the

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39 Upper Keys, while the Middle Keys are most highly developed and have the least mangrove and intact forests. At the same time, the Middle Keys are characterized by higher turbidity than the Upper and Lower Keys, likely due to the passages bringing water from Florida Bay (Porter 2002), which can also carry CDOM. 3.2.2. Rivers and Florida Bay as sources of CDOM The closest riverine input to the Florida Keys occurs indirectly through Florida Bay and Biscayne Bay. Shark River is the major riverine in put to the Everglades and Florida Bay. To the north of the Florida Keys, the major riverine input to Biscayne Bay is Miami River (Walker et al. 1994). As a result of extreme weather conditions, other rivers sporadically influence the Florida Keys. Mississ ippi River plumes can reach the Florida Keys following episodes of extreme precipitation in the Mississippi watershed (Walker et al. 1994). Riverine input of CDOM is accompanied by nutrients, wastewater, pollutants, agricultural runoff such as pesticides, herbicides, and fertilizer, and suspended material (Coble 2007). Florida Bay nutrient concentrations and turbidity are typically high compared to the oligotrophic conditions found offshore. The intrusions of waters carrying higher nutrient concentrations a nd suspended material from Florida Bay have been hypothesized as a potential threat to the health of the Florida Reef Tract (Porter et al. 1999). In addition, land use in South Florida is dominated by citrus, pasture, urban, natural wetland, row crop, dair y and golf courses. Such activities rely on large and regular applications of pesticides and fertilizers (Graves et al. 2004). Storm water runoff increases suspended and dissolved pollutant, nutrient, and heavy metal concentrations, which in turn can decre ase dissolved oxygen concentration and productivity (Graves et al. 2004), and thus adversely affect the structure and function of biotic communities (Pait et al. 1992 and Kennish 1999 in Graves

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40 et al. 2004). Due to the lack of secondary wastewater treatmen t in much of the Florida Keys, fecal coliform bacteria and enterococci have been found to accumulate in coral surface microlayers, potentially compromising resiliency of coral reef biota (Lipp et al. 2002). 3.2.3. Annu al trends in the Florida Keys For the period 1997 2003, maximum incident UV irradiance at Everglades National Park occurred in July August (6000 6500 DUV), except in 1997 and 1998 where the maximum DUV occurred in May June ( http:// www.epa.gov/uvnet /access.html Everglades NP, FL everglade_update_may04.pdf" ). Maximum mean daily UV B and UVR at the Mote Marine Laboratory in the Lower Keys for the period of record August 2002 October 2003 occurred in May through July (Fig. 2.5). For the period sampled, in the Lower Keys (Key West), maximum water temperature occurred in July and August coincident with wind speed minima (Fig. 3.2a,b, http://www.n cdc.noaa.gov/oa/climate/research/monitoring.html#ustempprcp http://www.ndbc.noaa.gov/station_history.php?station=kywf1 ). During this time period, precipitation tended to be highe st between June and September (Fig. 3.2a) In the Upper Keys (Molasses Reef) as well as the Middle Keys (Sombrero Key), mean monthly air and wind temperature over the time period 2004 2007 occurred in August, coincident with wind speed minima (Fig. 3.3, http://www.ndbc.noaa.gov/station_history.php?station =mlrf1 ; Fig. 3.4, http://www.ndbc.noaa.gov/statio n_history.php?station =smkf1 ).

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41 Figure 3.2a. Temperature and precipitation at Key West (Lower Keys), 2003 2006 ( http://www.ncdc.noaa.gov/oa/climate/research/monitor ing.html#ustempprcp ). Figure 3.2b. Monthly mean wind speed (WSPD), gust (GST), air temperature (ATMP) and water temperature (WTMP) at Key West (Lower Keys) for 2005 2007. Wind and temperature data were not available for January and March 2005, and No vember and December 2007. Wind data not available from March through August 2005, July through December 2006 and January through June 2007; water temperature data were not available for July 2005 ( http://www.ndbc.noaa.gov/station_history.php?station=kywf1 ).

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42 Figure 3.3. Monthly mean wind speed (WSP), gust (D GST), air temperature (ATMP) and water temperature (WTMP) at Molasses Reef (Upper Keys) for 2004 2007. Water temperature d ata not available for January and March 2005 ( http://www.ndbc.noaa.gov /station_history.php?station=mlrf1 ).

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43 Figure 3.4. Monthly mean wind speed (WSP), gust (GST), and a ir temperature (ATMP) at Sombrero Key (Middle Keys) for 2004 through 2007. Temperature is in degrees Celsius. Water temperature data were not available for all of 2004 except March and January, February and March 2005 ( http://www.ndbc.noaa.gov/station_history.php? station=smkf1 ) 3.2.4. Biological Response Bleaching in the Florida Keys When the sea surface temperature is warmer than the bleaching threshold temperature, corals ex perience thermal stress. The commonly accepted cause of mass coral bleaching is thermal stress, thus NOAA's Coral Reef Watch uses sea surface temperature to monitor the threat of coral bleaching in the FKNMS. Corals are vulnerable to bleaching when the SST exceeds the temperatures they would normally experience in the hottest month. Temperature thresholds for coral bleaching are based on the amount of

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44 time a reef is subjected to supraoptimal temperatures. NOAA defines the bleaching threshold temperature (" H otSpot" value) as one degree Celsius (1 o C) above the maximum monthly mean ( Goreau et al. 2000 ). The maximum monthly mean in the Florida Keys for the sampling period 2005 2007 was typically 31 o C but reached approximately 36 o C in Key West in 2007 (Figs. 3 2 4) In addition, because normal temperature range differs depending on location, to determine the risk of coral bleaching for any given location, NOAA has devised the "degree heating week" (DHW). The DHW product accumulates any coral bleaching "HotSpo ts" greater than 1 ¡C over a 12 week window, thus showing how stressful conditions have been for corals in the last three months. It is a cumulative measurement of the intensity and duration of thermal stress, and is expressed in the unit ¡C weeks. DHWs over 4 ¡C weeks have been shown to cause significant coral bleaching, and values over 8 ¡C weeks can cause widespread bleaching and some mortality. Based on climate predictions, NOAA's Coral Reef Watch, current conditions, as well as visual field observat ions of bleaching Mote Marine Laboratory of Summerland Key determines and publishes reports on the threat for mass coral bleaching within the FKNMS ( Table 3.1, http://isurus.mote.org/K eys /current_ conditions.phtml ) For the time period of sampling ( 2005 2007), bleaching in the Florida Keys was most severe from July through the beginning of September, with maximum severity typically in mid to late August (e.g., Fig. 3.5). Widespread mass bleaching was not reported along the Florida reef tract in 2005 2007.

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45 Table 3.1. Mote Marine Laboratory / Florida Keys National Marine Sanctuary Coral Bleaching Early Warning Network, "Bleachwatch". Threat of mass coral bleaching within th e FKNMS based on current remote sensing and environmental monitoring data, field observations, and climate predictions for sampling years 2005 2007 ( http://isurus.mote.org/Keys/current_ conditions.phtml ; reports for 2004 are not available): 2007 October 30, 2007 LOW October 1, 2007 LOW September 10, 2007 HIGH August 27, 2007 MODERATE August 13, 2007 HIGH July 30, 2007 HIGH July 16, 2007 MODERATE June 29, 2007 LOW June 1 2007 LOW 2006 October 19, 2006 LOW September 19, 2006 LOW August 28, 2006 MODERATE August 14, 2006 MODERATE July 31, 2006 MODERATE June 30, 2006 LOW June 1, 2006 LOW 2005 October 18, 2005 LOW September 27, 2005 LOW September 13, 200 5 MEDIUM August 30, 2005 MEDIUM August 23, 2005 HIGH August 16, 2005 MEDIUM August 9, 2005 HIGH July 26, 2005 MEDIUM June 28, 2005 LOW June 1, 2005 LOW

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46 Figure 3.5 Overview of BleachWatch Observer reports submitted from August 9 Au gust 23, 2005 ( http://isurus.mote.org/Keys/bleaching/CC_20050823.pdf ). 3.3. Methods 3.3.1. Sites and sampling dates Water samples and in situ optical data were collected at several re efs within the Florida Keys National Marine Sanctuary (FKNMS). Samples were collected in the Upper and Middle Florida Keys in late May, early July and late September 2004, and early May and mid July 2005 (Table 3.2a, Fig. 3.1). In addition, in September 20 04 and July 2005 water samples were collected along a transect from offshore at 75m depth (50m in July 2005), shoreward at 50m and 25m depths, inshore to Carysfort Reef, and finally within a mangrove lined canal in John Pennekamp State Park, for determinat ion of absorption due to CDOM ( a g ) (Fig. 3.1). In summer 2006 and 2007, additional reefs were sampled in the

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47 Upper, Middle and Lower Keys that are annually assessed by the Coral Reef Evaluation and Monitoring Program (CREMP) (Table 3.2b,c; Fig. 3.1). Tab le 3.2a. Sites and parameters sampled in 2004 and 2005. a = absorption, R=R rs remote sensing reflectance, C= chlorophyll fluorescence (concentration), S = Spectral underwater flow through optical instrument package, P=PAR underwater, U=UV and PAR_incident U_u = UV and PAR underwater. BIC underwater spectroradiometer (BSI) was used for all measurements of underwater irradiance. Flow through optical package profile (overnight) at KL6m and Key Largo 3m, July 04. = surface absorption sample only. Only surf ace samples were collectd at open water sites (z > 27 m). Italics = intact shoreline associated reef bold case = mangrove canal regular case = impacted or developed shoreline associated reef. In July 2005, only bottom samples were collected at 27 m. The SoDoPF measures chlorophyll fluorescence, backscattering, CDOM fluorescence, transmission of red, green, and blue light, salinity, temperature and depth.

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48 Site 2004 2005 5/25 7/6 8 9/28 30 1/19 22 5/9 12 6/~18 7/21 23 Algae Reef (6 m) aRCPUS aRCPUS aRCPU S aCP aRCPS aRCP U_uS Carysfort Reef (10m) aRCPUS aRCPS aRCP U_uS offshore Carysfort (45 m) aRCPS aRCP U_uS offshore Carysfort (30 m) aRCUS aRCPS offshore Carysfort (27 m) aRCP U_uS offshore Carysfort (25,75m) aRCPUS aCP offshore Carysfort (50m) aRCPUS Pennekamp South Creek 2 sites aC aRCPS Pennekamp North Creek -2 sites aRCPU aRCP U_uS KL6m (6 m) aRCPUS aRCPUS aRCPUS aCP aCP aRCPS aRCP U_uS Molasses 10m, 25 m aRCPU aCP White Banks Reef aRC PUS aRCPUS Molasses (KL) 18 m aRCPUS aRCPUS Alinas Reef a 5/28 aP Dome Reef a 5/28 aP Molasses 12 m, 45 m aRCPS aRCP U_uS Molasses 27 m aRCPS Molasses offshore aP Key Largo 9m aRCPUS Key Largo 3m A aRCP US aRCPUS aP Long Key viaduct Post 73 aRCP U_uS Tennessee 6m aP aRCPS aRCP UuS Tennessee 10m aRCPUS aP aRCPS aRCP U_uS Tennessee 18m aRCPUS Tennessee 25m, 75 m aP Tennessee 27 m aRCPS Tennessee 45 m aRCPS aRC P U_uS Conch 10 m, 30m aRCPU Looe Key 6 10, 25, 50, 75 m aP Marquesas shallow ( 3 m ) & deep (9 m) aCP

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49 Table 3.2b. Sites and samples for Spring/Summer 2006. Measurements at all deep sites: a, C, P, U_u; all shallow sites, unless oth erwise noted: see Table 3.1a for description. = surface absorption sample only. Italics = intact shoreline associated reef regular case = impacted or developed shoreline associated reef. May 28 June 2, 2006 (Middle & Lower Keys) June 28 29, 2006 (Upper Keys) Sand Key deep (8.6 m) & shallow (4.6 m) betw. Carysfort deep & shallow (6.7 m) Rock Key deep ( 12.5 m) & shallow ( 4.3 m) blue water off Carysfort (30.5 m) Key West Offshore (blue water) (76 m) Turtle (4.6 m) (Patch) Western Head (11 m) (Patch) Al gae (4 m) Cliff Green (6 m) (Patch) Grecian Rocks (7 m) Seagrass Patch between Eastern and W. Sambo (4.3 m) Porter Patch (4 m) (Patch) W.Sambo deep (14.3 m) & shallow (6.8 m) Admiral Patch (5 m) (Patch) E. Sambo deep (15.3 m) & shallow (6.4 m) Conch De ep (15.2) offshore (blue water) (65 m) Molasses Deep (13.7 m) West Washerwoman (4.3 m) (Patch) White Banks (3.7) Jaap (ak.a. Mystery) (2.4 m) (Patch) KL6m (6.1 m) Sombrero deep (13.5 m) & shallow (4.2 m) Rodriguez Key (3.4 m) Alligator deep (12 m) & shallow (6.5 m) W. Turtle Shoal (4.1 m) (Patch) Dustan Rocks (3.6 m) (Patch) East Washerwoman (5.1 m) Looe Key deep ( 15.2 m ) & shallow (6.8 m) Blue Water off Looe Key (90 m) Coral Gardens ( 3.7 m ) Tennessee Deep ( 14 m ) Tennessee Shallow (6.1 m) (+ a, C ) Long Key Patch ( 3.7 m ) Table 3.2c. Sites and samples for Spring/Summer 2007. Measurements at all deep sites: a, C, P, U_u; all sites, unless otherwise noted: see Table 3.1a for description and Table 3.1c for depths. = surface absor ption sample only. Italics = intact shoreline associated reef regular case = impacted or developed shoreline associated reef. June 5 6, 2007 (Upper & Middle Keys) June 18 20, 2007 (Middle & Lower Keys) Tennessee Shallow Sand Key Deep Tennessee Deep no U_u Sand Key Shallow bottom no U_u Alligator Deep no U_u Rock Key Deep Conch Deep no U_u Blue Water Molasses Deep no U_u W. Head Patch Reef betw. Carysfort shallow&deep no U_u Cliff Green Patch Blue Water no U_u Sea Grass Patch Reef Turtle Reef no U_u Sombrero Deep Algae Reef no U_u W. Turtle Shoal Grecian Rocks no U_u Dustan Rocks Porter Patch no U_u E. Washerwoman Shoal Admiral Patch no U_u Blue Water off Lo oe Key Molasses Shallow no U_u Looe Key Deep White Banks no U_u W. Sambo Shallow Three Sisters (KL6m) no U_u E. Sambo Deep Blue Water off Sambo W. Washerwoman Shoal Jaap a.k.a. Mystery Reef no U_u

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50 Key Largo 6m (KL6m) Reef and Algae Reef (also 6 m depth) were selected for comparison basd on data for coral health reported by Fisher et al. (2007). Algae Reef is located offshore from the intact mangrove lined, and thus CDOM rich, coastline of John Pennekamp Park, while KL 6m Reef lies offshore from the more developed coastline of the town of Key Largo. I used this contrast in location to elucidate the influence of CDOM from terrestrial sources on coral reef resilience. Fisher (2007) found that the regenerative capacity of c orals, coral cover, and abundances of larger foraminifers were all higher at Algae Reef than KL6m Reef. In addition, studies comparing percent coral cover have revealed that corals overall are faring better at inshore reefs compared to offshore reefs (NOAA 2002, Somerfield et al. 2008). In addition, for the period 1996 2006, the Upper and Lower Keys show the greatest loss in mean percent stony coral cover (Fig. 3.6, NOAA 2006). Figure 3.6. Mean percent stony coral cover in the Florida Keys by region, Up per, Middle and Lower Keys. The Upper and Lower Keys stations continue to show the greatest loss in mean percent stony coral cover since the beginning of the project. Mean percent coral cover in the Middle Keys has not changed significantly since 1999. Be tween 2005 and 2006, a notable decline in mean percent stony coral cover at CREMP stations Sanctuary

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51 wide occurs in all three regions (from Callahan et al. 2006). Because CDOM is carried reefward from terrestrial sources during low tide, and is diluted by ocean water during high tide, the timing of sampling with respect to the tidal cycle was recorded (Tables 3.3a,b). Tidal tables were obtained from the websites: http://www.ndbc.noaa.go v/station_page.php?station=mlrf1 for Molasses Reef and http://co ops.nos.noaa.gov/tides04/tab2ec3d.html for Carysfort Reef and Largo Sound, Key Largo. Table 3.3a. Tidal information for s ampling sites (Key Largo 6m (KL6m) Reef, Algae Reef) on dates sampled in 2004. Molasses Reef high low Largo Sound 25 o 08.4'N 80 o 23.7W high low Carysfort Reef 25 o 13.3' N 80 o 12.7' W high low Ma y 25, 2004 1:14 am 7:24 am 1:22 pm 7:34 pm 3:36 am 10:19 am 3:44pm 10:29 pm July 6, 2004 12:09 am 6:21 am 12:30 pm 6:33 pm 2:31 am 9:16 am 2:52 pm 9:36 pm 00:37 am 6:51 am 12:58 pm 7:11 pm July 7, 2 004 10:02 am 17:34 pm Sept. 28, 2004 2:46 am 9:02 am 3:10 pm 9:18 pm 9:30 am 3:41 pm 9:46 pm 3:58 pm Sept. 30, 2004 4:38 am 10:55 am 5:03 pm Table 3.3b. Sampling (water collection) ti mes for Carysfort, Algae and Key Largo 6m (KL6m) Reefs, May, July, and September 2004. sampling times May July September Key Largo 6m (KL6m) 25 o 01.0 92'N 80 o 23.844' W 13:05 May 25 high tide 10:35 July 7 high tide 17:20 September 28 close to high tide A lgae 25 o 08.799'N 80 o 17.579' W 10:35 May 25 between tides 12:04 July 6 high tide 11:03 September 28 between tides Carysfort 10m 25 o 13.160'N 80 o 12.428' W 13:45 September 30 between tides (low)

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52 3.3.2. In situ and incident irradiance measurements On most sampling dates in 2004 and before July 2005, the underwater light field was quantified using hand lowered in situ instruments, including a Licor 192SA underwater quantum sensor for measuring PAR (400 700 nm). Above water incident spectral irradiance, E d0+ ( $ ) was measured using a LICOR 1800 Spectroradiometer from 8:30 am to 6:30 pm on most days of sampling in 2004 (280 850 nm, 1.5 nm intervals, sampling frequency 10 20 minutes). Beginning in July 2005, a Biospherical Instruments BIC submersible radiom eter was used to measure in situ irradiance, E dz ( $ ) The BIC was equipped to measure 10 nm wavebands of downwelling cosine irradiance centered at 305, 330, 380 nm ("W/cm<=/nm), recording the center wavelength, and integrated PAR (400 700nm) ("Einsteins/m< =/s). A "dark reading", which measured the signal at each wavelength with the BIC on deck and the black cap covering the sensor, was made each day of sampling. The dark reading is subtracted from each light measurement at all wavelengths, to correct for the background (voltage) measurement by the BIC The dark reading is especially important for the UV measurements at 305 and 330 nm, because this correction could make a substantial difference in irradiance when correcting low signals at these wavelengths These in situ irradiance data were used to calculate the attenuation coefficient K d and to calibrate my model for calculating UV irradiance from absorption measurements (see section 3.3.3 ).

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53 3.3.3. Water samples: collection and in lab optical measureme nts During all cruises, water samples were collected from the surface and bottom by SCUBA divers or use of Niskin bottles; additional water samples were collected if stratification was observed. Simultaneous measurements of conductivity and temperature wer e made on some dates (see Tables 3.2a,b, and c). Sampling typically occurred sometime intermediate between high and low tide, for example in September 2004, sampling occurred between high and low tide, therefore during falling tide (Tables 3.3a,b). For abs orption measurements, discrete water samples (2 3 l) collected just below the surface and at depth of coral growth were filtered through glass fiber/fine (GFF) and 0.2 m filters to determine the separate contributions of absorption due to dissolved and particulate material. The 0.2 m filtrate and the GFF filters were analyzed on a UV Visible spectrophotometer (Perkin Elmer Lambda 18, Hitachi U 3300) respectively for sp ectral a g ( $ ) and spectral absorption due to particles ( a p ( $ ) ), from 300 800 nm. The quantitative filter pad method was used to determine a p ( $ ) (Mitchell 1990, Mitchell et al. 2000). Spectral absorption due to phytoplankton, a phi ( $ ) was determined by met hanol extraction of the filter pads, and spectral absorption due to detritus, a d ( $ ) was determined as the difference between the whole minus methanol extracted filter pad absorption: a d ( $ )= a p ( $ ) a phi ( $ ) (3.1) To estimate the between site compositional differences in a g I compared the slope of a g ( $ ) in the UV region (Del Vecchio and Blough 2002) for inshore reefs to offshore, clear water reefs. Spectral slope of a g( $ ) for the the UVB region (280 312 nm)

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54 was calculated using least squar es linear regression of natural logarithm converted a g( $ ) (Carder et al 1989): S (280 312) = ln( ag ( 312 )/ ag ( 280 )) ( 312 280 ) (3.2) Differences in spectral slope may indicate different composition and source of CDOM as well as differences in the degree of CDOM photobleachi ng (Zanardi Lamardo et al. 2004). The spectral range 280 312 nm was used to represent UVB radiation as well as to avoid the error due to inflections in spectral CDOM absorption that occur at wavelengths higher than 312 nm. Chlorophyll concentrations ( [c hl] ) were measured on solutions of hot methanol extracted pigments from the GFF filters used for absorption measurements using a Turner Fluorometer and methods described by Holm Hansen and Riemann (1978). 3.3.4. Calculating underwater irradiance from in lab absorption measurements In the water column, total diffuse attenuation of downwelling irradiance, K d is due to absorption ( a ) and scattering ( b ) by water molecules, dissolved material, and particulate material, and the angular distribution of ligh t, expressed as : Kd= ( a + b)w p g/ (3.3) where = cos # and # is the zenith angle (angle between the sun and plane perpendicular to the surface. Because coral reef waters are typically characteri zed by low mineral/particle concentrations in the absence of in situ scattering measurements, the diffuse attenuation coefficient for downwelling irradiance, K d can be estimated as the sum of a g a p (absorption due to particulate material), and a w (abso rption due to pure water, Morel et al.

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55 2007, Fry 2008). When scattering is constant and light measurements are made within two hours of solar noon, the effect of is negligible and the total diffuse attenuation of downwelling irradia nce can be estimated solely from absorption: K d = a g + a p + a w (3.4) Irradiance reaching the sea floor ( E dz ) can then be estimated as: E dz ( $ )= E d0+ ( $ )e K_d*z where z = depth (3.5) (Kirk 199 4 ). The intensity of irradiance reaching th e benthos, E dz decreases exponentially as a function of depth ( z ) and K d where E d0+ is the irradiance intensity above the water surface. The relationship in equation (11) can be used to evaluate the discrepancy between measured K d and calculated total absorption, a t (where a t = a g + a p + a w ) see Table 3.4, Fig. 3.9) and to compare between sites (see Chapter 6): Kd= ( a )w p g/ => Kd= at/ or = at/ Kd (3.6) For collimated light, equals one and thus K d = a t (Kirk 199 4 ). As light becomes more diffuse (or scattered), decreases. The relationship between absorption, a t scattering, b, and the average cosine, and its im portance to UV exposure on coral reefs, is discussed in Chapter 6. 3.3.5. Sources of Error 3.3.5.1. Irradiance and absorption due to particles In 2004 and 2005, E d0+ measured using a Li COR 1800 spectroradiometer, combined with in lab absorption measurem ents, a t were used to estimate K dz according to Equations (3.4) and (3.6) On all subsequent sampling dates, in situ i rradiance (UVR and

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56 PAR), measured using a BIC radiometer (Biospherical Instruments, San Diego, CA) were used to calculate K dz as well as to test the model for calculating K d from a t and E d0+ Variations of in lab a t from in situ K d may be due to the angular structure of the light field ( ) or errors in measuring a t (see below). Overestimation of a t would result in ove restimation of K d Considering inshore and offshore sites together, the median ratio a t : K d ranged from 0.866 to 0.959 for the UV wavelengths (305, 330 and 380 nm) but was markedly lower, namely 0.274, for PAR (Table 3.4, Fig. 3.7). Thus, because the mean a t : K d is close to unity for the UV dataset but not for PAR, a t is a good estimate of K d for the UV but not for the PAR dataset. Table 3.4. Median a t /K d and 25 th 75 th percentile ranges for inshore and offshore reefs. a t /K d 305 nm 330 nm 380 nm PAR Medi an a t /K d inshore 0.909 0.890 0.842 0.270 25th percentile 0.784 0.749 0.714 0.208 75 th percentile 0.990 0.975 0.924 0.324 Median a t /K d offshore 1.019 1.038 0.981 0.274 25th percentile 0.246 0.475 0.586 0.229 75 th percentile 1.147 1.234 1.203 0.382 Med ian a t /K d inshore and offshore 0.959 0.911 0.886 0.274 25th percentile 0.832 0.804 0.737 0.191 75 th percentile 1.098 1.130 1.100 0.355

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57 Figure 3.7. Ratio of in lab a t to in situ K d ( a t /K d ) for inshore (x) and offshore (o) reef sites, 2005 2008. Da shes represent medians. Highest outliers occurred at offshore sites Considering inshore and offshore reef sites separately, a t : K d was higher for offshore reefs than for inshore reefs (see Table 3.4) This could be because particles play a slightly greater role in total absorption at offshore sites (see Table 3.5) and thus cause more scatter in measuring absorption on the filter pad, and consequently, higher a t In addition, the pathlength corrections using the QFT for a p may cause the overestimate of a p an d thus proportionately overestimate a t (Finkel & Irwin 2001). Although the quantitative filter technique is the accepted and widely used method for measuring absorption due to particles ( a p ), the coefficients used for correcting for the pathlength may vary based on the size and type of particles as well as type of measurement

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58 equipment (spectrophotometer) and sample preparation techniques (Finkel & Irwin 2001) Table 3.5. Median a g /a t and a p /a t and 25 th 75 th percentile ranges for inshore and offshore r eefs. 305 nm 330 nm 380 nm PAR Median a g /a t inshore 0.892 0. 852 0. 753 0.509 25 th percentile 0.867 0.799 0.684 0.346 75 th percentile 0.928 0.899 0.841 0.638 Median a g /a t offshore 0.871 0.7 809 0.678 0.347 25 th percentile 0.825 0.758 0.605 0.212 75 th percentile 0.903 0.851 0.764 0.465 Median a p /a t inshore 0.090 0.104 0.116 0.192 25 th percentile 0.0583 0.0741 0.0787 0.126 75 th percentile 0.109 0.141 0.158 0.263 Median a p /a t offshore 0.106 0.135 0.155 0.268 25 th percentile 0.082 0.107 0.126 0.216 75 th percentile 0.134 0.174 0.195 0.339 Recent studies have shown that freezing the filter pads may result in exaggeration of the MAA peak due to extracellular release of MAAs, compared to lower absorption in their normal, intact shape (Laurion et al. 2 003). Using a ratio such as relative MAA expression (see Chapter V) can cancel out this exaggeration, but large MAA peaks may affect a p especially a p330 Also, the MAA absorption observed using the frozen filter QFT method may not represent in vivo abso rption by MAAs, where the pigments would be intact in the cells (Laurion et al. 2003). Large colloids (diameter ~ 0.4 1 m) can be captured on the GFF filters (nominal pore size 0.7 m) and thus can also be a source of measurement error, because they pla y a significant role in particulate scattering: in the water column, scattering by large colloids can exceed that of pure water by an order of magnitude.

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59 3.3.5.2. Absorption due to colloids Small colloids range from 0.01 0.02 m, and thus can be present in the 0.2 m filtrate used to determine absorption due to CDOM ( a g ). Small colloids can play an important role in the overall colloidal backscattering in the ocean. The combined backscattering of small and large colloids is typically higher than that of pure seawater over most of the visible spectrum: the scattering coefficient of large colloids from 350 700 nm can be up to two orders of magnitude higher than that due to pure water (Stramski and Wozniak 2005). Small colloids can contribute 44% to total backscattering at 350 nm (Stramski and Wozniak 2005) and thus can be a significant cause of pathlength amplification (error in a g ) in the UVR. Thus, the contribution of colloids to particulate backscattering may result in overestimation of a g Optimally, t o account for all size components in the water column, the 0.2 m filtrate used in this study to measure a g should be subtracted from the 0.7 m filtrate (from a p preparation) to determine absorption due to particulate material and colloids ( a p ) between 0. 2 and 0.7 m. This size fraction has not been accounted for in my dataset. Typical organisms in the 0.2 to 0.7 m size fraction include prochlorophytes, very small green phytoplankton, as well as some small cyanobacteria (blue green algae) (Carder et al. 1986), thus their exclusion could also result in underestimates of [ chl ] The warm, oligotrophic water loving cyanobacteria Trichodesmium sp. was visually observed in the water column at many sampling sites, and was also often observed as "puffs" and "tufts", referring to their shape, on the GFF filter upon measuring a p in turn resulting in higher a p as well as [ chl ] (see section 3.3.3.).

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60 4. Colored dissolved organic material p rotects c oral reefs by controlling exposure to UVR 1 4.1. Introduction Corals worldwide have been declining since the 1970's and the prognosis for the future is not improving ( Birkeland 2004, Hoegh Guldberg et al. 20 07). Coral bleaching has become a worldwide phenomenon, and the frequency and intensity of bleaching is increasing ( Hoegh Guldberg 1999, Wilkinson 2002 ). While the relationship between coral mass bleaching events and elevated sea surface temperature (SST) is well established (Hoegh Guldberg 1999), increasing numbers of studies are revealing that light plays a vital role in coral bleaching. For example, Lesser and Farrell (2004) found that corals do not bleach in the absence of light. Low wavelength ultravi olet radiation (UVR) and blue light can stimulate production of reactive oxygen species causing gene mutation and other damaging consequences to marine invertebrates (Lesser 2006, Levy et al. 2006). Mass bleaching events typically occur when sea condition s are unusually calm ( e.g. Fabricius et al. 2004) and thermal bleaching appears to be caused by photoinhibition and photodamage to photosystem II of the zooxanthellae (e.g., Lesser and Farrell 2004, Smith Much of this chapter will be published by Ayo ub L, Hallock P, Coble P as Colored Dissolved Organic Material Increases Resiliency of C oral Reefs by Controlling Exposure to UVR" in the Proceedings of the 11th International Coral Reef Symposium, Ft. Lauderdale, Florida, 7 11 July 2008.

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et al. 2005). The fact that clouds or direct shading can reduce bleaching in corals provides more evidence for the necessary role of light ( e.g. Mumby et al. 2001; Fabricius et al. 2004). More recent studies are linking coral disease and photooxidative stress (Lesser 2006). UVR specifically has been shown to cause DNA damage, DNA mutations or cell death in marine organisms such as corals (Shick et al. 1996). Although it is generall y thought that UVR attenuates quickly, some natural water bodies are characterized by high transparency to UVR (Gleason and Wellington 1993). Pure water absorbs minimally at wavelengths below 490 nm, thus attenuation of the shorter wavelengths of light is primarily due to dissolved and particulate matter (Kirk 1996). Light absorption by colored dissolved organic matter (CDOM) is highest at the shortest wavelengths and exponentially decreases with increasing wavelength. Moreover, the absorption of high ene rgy radiation causes bleaching and degradation of CDOM (Zepp et al. 2008). Spectrally, photobleaching of CDOM increases with decreasing wavelength from 500 to 280 nm, with the most effective photobleaching occurring in the UV A region (320 400 nm) (Osbur n et al. 2001). While an increase in rates of CDOM breakdown may not be biologically significant in turbid, CDOM rich waters, it may be a major reason why corals in clear waters are reportedly more susceptible to bleaching ( e.g. West and Salm 2003) and po ssibly also to diseases that are not directly related to pollution. For example, as a consequence of the 4% global reduction in stratospheric ozone following the Mt. Pinatubo eruption (Randel et al. 1995), the resultant approximately 8% increase in UV B r eaching the sea surface (Schick et al. 1996) could have increased the rate of CDOM degradation by as much as 24% (Zepp

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62 2003). Other studies estimate a lower percentage change, for example, a 25% increase in UV B results in a 10% increase in photobleaching according to studies on temperate lakes (Osburn et al. 2001). As a defense against UVR, corals and other aquatic organisms produce UV absorbing pigments called mycosporine like amino acids (MAAs) (Shick et al. 1996). Maximum absorption for MAAs occurs be tween 305 and 360 nm. Thus, the presence of MAAs can indicate photic stress (Morrison and Nelson 2004). Exposure to UVR has been increasing in recent decades due to stratospheric ozone depletion, resulting in increased photobleaching of CDOM and, in turn, deleterious effects on marine biota (Fig. 4.1). We propose that CDOM is protecting inshore patch reefs from exposure to the most extreme solar radiation and damaging effects of photooxidative stress.

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63 Figure 4.1. Atmospheric, optical, and biological fact ors affecting CDOM absorptivity and related biological effects (after Morris and Hargreaves 1997; Zepp et al. 2008). 4.2. Material and Methods In late May, early July and late September 2004, and early May and mid July 2005, water samples and in situ opti cal data were collected at several reefs in the upper and middle Florida Keys. In addition, in September 2004, absorption due to CDOM ( a g ) was measured along a transect (red arrow in Fig. 4.2) from offshore at 75 m depth, shoreward to 50 m and 25 m depths, inshore to Carysfort and Algae Reefs, and finally within a mangrove lined canal in John Pennekamp State Park. In summer 2006 and 2007, sampling sites included inshore and offshore coral reefs in the Upper, Middle and Lower

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64 Keys that lie within the Florida Keys National Marine Sanctuary (FKNMS) and are part of the Coral Reef Evaluation and Monitoring Program (CREMP) (Fig. 4.2). Figure 4.2. Study sites in the Lower, Middle and Upper Florida Keys included offshore reefs and inshore (patch) reefs that diffe r in degree of development of associated shoreline. In 2006 and 2007, study sites also included inshore and offshore CREMP study sites in the Lower, Middle and Upper Florida Keys ( image adapted from A. Ramirez). Total absorption can be partitioned into ab sorption due to dissolved material, a g particulate material, a PM and pure water, a w (Kirk 1994). Using measured a g and a p and published values of a w (Morel et al. 2007): a t ( $ ) = a g + a p + a w (4.1)

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65 In natural systems, light is not collimated bu t diffuse. Measuring irradiance consistently within 2 hours of solar noon minimizes the effect of sun angle and thus pathlength on light attenuation. Total attenuation is due to scattering as well as absorption. Scattering is small compared to absorption f or this study (Ivey, unpubl. data). Thus, the diffuse attenuation coefficient of downwelling irradiance ( K d ) can be estimated from total absorption (Kirk 1994): K d = a g + a PM + a w (4.2) Water samples were collected from the subsurface (~ 0.5 m) and a t the depth of coral growth by SCUBA divers or using Niskin bottles. After filtration, water samples were frozen and transported back to the lab, where spectral absorption (300 800 nm) for CDOM ( a g ( $ ) ) was measured according to the method described in Mitchell et al. (200 0 ) and a PM ( $ ) was measured according to Mitchell (1990) using a UV Visible spectrophotometer (Perkin Elmer Lambda 18 or Hitachi U 3300). Spectral absorption due to detritus, a d ( $ ) was determined by methanol extraction of pigments and subtracted from a PM ( $ ) to determine spectral absorption due to phytoplankton, a phi ( $ ) : a d ( $ ) = a p ( $ ) a phi ( $ ) (4.3) (Kirk 1994). Relative MAA expression was determined using the method of Morrison and Nelson (2004). In July 2004 incident solar irradiance reaching the sea surface was measured using a LiCor 1800 Spectroradiometer (280 850 nm) at a nearby land site at 10 20 minute intervals from 8:30 am 6:30 pm daily. Intensity of irradiance reaching the benthos was calculated from measurements of in lab absorption a t ( $ ) and the in situ incident downwelling irradiance E d0 ( $ ) according to eqn. (4.3) and:

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66 E dz ( $ )= E d0 ( $ ) e Kd( $ )* z (4.4) where z represents depth in meters (Kirk 1994). After July 2005, K d was calculated from in situ underwater downwelling cosin e irradiance ( E d ( )) measured at 305, 330, 380 nm (10 nm wavebands, recorded at maximum wavelength minus 5 nm) and the visible wavelengths (integrated from 400 700 nm) using a BIC (Biospherical Instruments, Inc.) radiometer. 4.3. Results and Discussion Absorption due to CDOM decreased going offshore from mangroves to inshore reefs, offshore reefs and finally blue water (Fig. 4.3), exhibiting the progressive dilution of land sourced CDOM. Figure 4.3. Transect of absorption due to CDOM at 320 an ( a g 320 ). a g 320 decreased going from mangrove canals in John Pennekamp Park to inshore and offshore reefs to offshore blue water. Downwelling UV irradiance at 320 nm at depth = 6m ( E d6m 320nm ), modeled from a t320 and incident irradiance ( E d0 ), was higher at ree fs associated with developed shoreline,

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67 such as KL6m ( E d6m 320nm = 0.01 0.084 W/m 2 ) than at reefs offshore from extensive mangrove shoreline, such as Algae Reef ( E d 320nm = 0.008 0.057 W/m 2 ) (Fig. 4.4). Figure 4.4. E d6m 320 at intact shoreline asso ciated reefs compared to developed shoreline associated reefs as computed from a t 320 and E d0 320 E d6m 320 was consistently lower at intact shoreline associated reefs. Over the period of sampling, 2004 2007, the contribution of absorption due to CDOM, a g to total absorption, a t increased with decreasing wavelength, ranging from 60% at 380 nm to over 90% at 305 nm. Thus, CDOM is the major attenuator of UVR. Over the course of each summer a g / a t typically decreased, likely due to photobleaching of CDOM (Fig. 4.5). The observed increase in a g / a t from May to July 2005 may be due to the higher rainfall which occurred in June and July, causing greater runoff and thus

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68 increased CDOM over the reef ( http://www.ncdc.noaa.gov/oa/climate/research /monitoring.html#ustempprcp). Figure 4.5. R elative contribution of a g to a t in the UV at 305, 320, 330, 380 nm. R elative contribution of a g to a t in the UV at 305, 320, 330, 380 nm ranged from 62% at 380 nm to 91% at 305 nm and from 18 62 % for visible light; mean a g / a t typically declined at all wavelengths as the summer progressed. The difference in E d6m (ex: E d6m 320 ) between intact and developed reefs may be due to a g (ex: a g 320 ), which was higher at intact shoreline associated reefs compared to developed shoreline associated reefs considering all dates sampled in 2004 2007 (Fig. 4.6, Table 4.1).

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69 Figure 4.6. a g 320 at intact shoreline associated reefs ( n = 10) compared to developed shoreline associated reefs ( n = 10). Comparing medians, a g 320 was higher at intact shoreline associated reefs. Table 4.1. Medians and 25 th 75 th percentile ranges for a g 320 at intact shoreline associated reefs compared to developed shoreline associated re efs. median 25 th 75 th percentile intact developed intact developed a g 320 0.357 0.232 0.311 0.443 0.210 0.286 Comparing a g between inshore and offshore reefs, a g was higher at inshore reefs at all wavelengths (e.g., a g330 Fig. 4.7). a g 330 wa s higher at inshore reefs ( n = 26, median = 0.665, 25 th percentile = 0.362, 75 th percentile = 1.516) than offshore reefs ( n = 22, median = 0.361, 25 th percentile = 0.240, 75 th percentile = 0.488). K d 330 was also higher at inshore reefs ( n = 26, median = 0 .670, 25 th percentile = 0.458, 75 th percentile = 0.878) than

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70 offshore reefs ( n = 22, median = 0.419, 25 th percentile = 0.254, 75 th percentile = 0.548). Concurrently, K d calculated from in situ measurements using a BIC radiometer was higher at inshore reefs (ex: K d 330 Fig. 4.7; Table 4.2). The difference in K d between inshore and offshore reefs decreased with increasing wavelength, excepting discrepancy from this trend at 305 nm due to immeasurably low irradiance intensities (Table 4.2). Thus, difference in water transparency between inshore and offshore reefs was greater for UVR than for PAR. Results for both a g and K d two independent measures of UV transparency, illustrate that coral reef biota are exposed to lower intensities of UV irradiance at inshor e reefs compared to offshore reefs in the Florida Keys. Figure 4.7. Absorption due to CDOM at 330 nm ( a g 330 ) and the attenuation coefficient of downwelling irradiance at 330 nm, K d 330 a g 330 was higher at inshore reefs ( n = 26, median = 0.665, 25 th p ercentile = 0.362, 75 th percentile = 1.516) than offshore reefs ( n = 22, median = 0.361, 25 th percentile = 0.240, 75 th percentile = 0.488). K d 330 was higher at inshore reefs ( n = 26, median = 0.670, 25 th percentile = 0.458, 75 th percentile = 0.878)

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71 than o ffshore reefs ( n = 22, median = 0.419, 25 th percentile = 0.254, 75 th percentile = 0.548). Dashes represent median s. Table 4.2. Comparison of K d between inshore and offshore reefs. median 25 th 75 th percentile K d( $ ) inshore offshore inshore offshore K d 305 1.14 0.77 0.78 1.74 0.57 1.06 K d 330 0.76 0.50 0.53 1.25 0.38 0.65 K d 380 0.35 0.23 0.22 0.58 0.21 0. 30 K dPAR 0.22 0.17 0.20 0.29 0.13 0.22 The ratio of downwelling irradiance at 6m ( E d6m ) to incident irradiance above the water surface ( E d0 ), E d6m / E d0 for 305, 330, 380 nm and PAR for inshore versus offshore reefs was calculated from in situ measurements of K d according to equation (4.4) (Figs. 4.8a,b). Median E d6m / E d0 at each wavelength was consistently lower at inshore reefs compared to offshore reefs, although the 25 th to 75 th percentile ranges consistently overlap (Table 4.3). Thus, likely as a result of higher a g and thus higher K d inshore reefs were exposed to higher UVR and visible light than offshore reefs. Outliers occurred at 380 nm (2.42) and PAR (6.64) but are not included in this data analysis. The euphotic zone depth, E d6m / E d0 of 1% for PAR reflects the depth where PAR is 1% of its surface value ( Lee et al 2007 ) Significant ly, E d6m / E d0 for all UV wavelengths exceeded 1%.

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72 Figure 4.8a. E d6m /E d0 for 305, 330, and 380 nm for inshore versus offshore reefs sampled 2004 2007 (in = inshore, off = offshore). Dashes represent medians. Figure 4.8b. E d6m /E d0 for PAR for inshor e versus offshore reefs sampled in 2004 2007 (in = inshore, off = offshore). Dashes represent medians.

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73 Table 4.3. Medians and 25 th to 75 th percentile ranges for E d6m /E d0 at 305, 330, 380 nm and PAR. median 25 th 75 th percentile E d6m /E d0 ( $ ) inshore offshore inshore Offshore E d6m /E d0 305 0.00105 0.0192 n 26 32 8.31E 06 0.0102 0.00457 0.0580 E d6m /E d0 330 0.0104 0.0678 n 27 32 2.09E 04 0.0463 0.0337 0.215 E d6m /E d0 380 0.123 0.245 n 27 31 0.0243 0.272 0.188 0.460 E d6m /E d0 PAR 0.267 0.390 n 27 31 0.169 0.287 0.272 0.474 Spectral slope of a g in the UV, S (280 312 nm) was higher at offshore sites compared to inshore sites (Fig. 4.9, Table 4.4). Comparing inshore reefs by region, median S was the same in the Lower an d Middle Keys, and higher in the Upper Keys. Comparing offshore reefs by region, median S for was lowest in the Lower Keys and increased going from the Middle to Upper Keys. Thus, in addition to higher exposure to UVR (Fig. 4.8, Table 4.3), because S incre ases with increasing photobleaching of CDOM (Del Vecchio and Blough 2002), CDOM at offshore reefs was more highly photobleached.

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74 Figure 4.9. Spectral slope, S, (280 312 nm) for the Upper, Middle, and Lower Keys, inshore versus offshore sites. Dashes r epresent medians. Medians for inshore reefs in the Lower and Middle Keys were equal, and lower than that for the Upper Keys. Median for offshore reefs was lowest in the Lower Keys and increased going from the Middle to Upper Keys. Table 4.4. Medians and 2 5 th to 75 th percentile ranges for S (280 312 nm) for inshore versus offshore reefs by region (Lower, Middle, and Upper Keys). median 25 th 75 th percentile S inshore offshore inshore offshore Lower Keys 0.0253 0.0282 n 10 10 0.0240 0.0270 0.0262 0.0292 Middle Keys 0.0253 0.0294 n 3 6 0.0251 0.0256 0.0272 0.0317 Upper Keys 0.0271 0.0314 n 34 10 0.0249 0.0293 0.0306 0.0333

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75 As presented in section 4.1, we propose that declining percent stony coral cover in the Florida Keys ma y be exacerbated by increased exposure to UVR. Comparing percent stony coral cover and a g 320 low percent stony coral cover co occurs most frequently with low a g 320 (Fig. 4.10) and the sites where this occurs are mostly offshore sites where a g is low (Fi g. 4.11). Co occurrence of low percent stony coral cover with low a g 320 was high (17 (1 1) and 15 (1 2)), while co occurrence of higher scaled combinations were relatively low (between 0 and 5). In all but two cases (combination 1 3), low % coral cov er was consistently accompanied by low a g 320 (Table 4.5). Percent stony coral cover was consistently higher at inshore reef sites compared to offshore reefs, and did not always co occur with high a g 320 (Fig. 4.9). An explanation of the negative relations hip between a g 320 and percent stony coral cover may be that corals need light for photosynthesis, so the inshore reefs may be light limited at high a g Inshore reefs are more often exposed to high a g than low a g suggesting that longer term light history ha s greater influence o n percent coral cover than instantaneous a g measurements.

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76 Figure 4.10. The number of occurrences of different combinations of scaled % stony coral cover and a g 320 There were large numbers of low % stony coral cover low a g 320 (17 (1 1) and 15 (1 2), while occurrences of higher scaled combinations were relatively low (between 0 and 5). In all but 2 cases (combination 1 3), low % coral cover was consistently accompanied by low a g 320

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77 Figure 4.11. Percent stony coral cov er versus a g 320 for the CREMP sites sampled in 2006 and 2007. Low percent stony coral cover (% coral cover) co occurs most frequently with low a g 320 High percent coral cover occurs only at inshore reefs. Percent coral cover data courtesy of M. Callahan, CREMP, FWRI, St. Petersburg, FL. Table 4.5. Scaling gradients for % stony coral cover (%cc) and a g 320 1 2 3 %CC < 0.1 0.1 < %CC < 0.2 %CC > 0.2 a g 320 < 0.4 0.4 < a g 320 <0.8 a g 320 > 0.8 Relative expression of MAAs declined with increasing a g 320 (Fig. 4.12). Throughout the sampling period 2004 2007, r elative MAA expression was significantly higher at reefs associated with developed than at reefs associated with intact shoreline (see Chapter 5, Fig. 5.7).

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78 Figure 4.12. Relative expression o f MAAs declined with increasing a g 320 for intact and developed reefs in 2004 2005. 4.4. Conclusions Though traditionally it has been thought that corals require clear water for photosynthesis, recent trends show that the clearer water reefs are experie ncing higher rates of coral decline. In the Florida Keys, distance from shoreline as well as shoreline quality may influence reef health as recent declines in percent coral cover and coral biodiversity have been greater at offshore reefs than inshore reefs (Somerfield et al. 2008) and coral lesion recovery rates are higher at inshore (patch) reefs near intact shoreline than developed shoreline (Fisher et al. 2007). Inshore reefs may be closer to seagrass beds, mangroves, wetlands, and other terrestrial sour ces of CDOM. Our work shows that differences in water transparency, and the resulting spectral differences in

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79 solar radiation reaching the benthos, may contribute to different rates of decline in coral cover between inshore patch reefs and offshore shallow reefs. This study helps to support/explain previous observations in the Florida Keys: 1) lower rates of decline at inshore reefs than offshore reefs ( e.g. Somerfield et al. 2008); 2) consistently higher bleaching in larger foraminifers at a reef associ ated with clearer water (Conch Reef) than at a reef influenced by Florida Bay water (Tennessee Reef) (Williams 2002); 3) occurrence of bleaching in benthic foraminifers ( Amphistegina gibbosa ) in the Florida Keys follows solar cycle, not SST cycle, and incr eases with increasing UV:PAR (Williams 2002); and 4) higher coral cover, coral lesion recovery rates and abundances of larger foraminifers at a reef associated with intact shoreline (Algae Reef) compared to a reef associated with developed shoreline (KL6m Reef) (Fisher 2007). Prior studies also show deleterious effects of UVR on reef organisms Lab experiments have shown that bleaching in A. gibbosa is exacerbated by exposure to blue or UV wavelengths (Williams and Hallock 2004). Studies of bleaching in corals indicate that decline in zooxanthellate photosynthetic capacity follows increase in daylight and precedes temperature peak (Warner et al. 2002 ) and that UVR and PAR exacerbate supraoptimal temperature effects (Lesser and Farrell 2004). Although MAA s are photoprotective, the energetic cost of MAA production may inhibit growth and recovery from stress (Hoogenboom et al. 2006 ) and high solar radiation may depress MAA production (Lesser and Farrell 2004 ). Based on modeled entire water column photoblea ching in lakes photobleaching can cause 0.6 to 1.4% decrease in CDOM light absorption over the timescale of tidal flushing (12 hours) (Reche et al. 2000). O ffshor e reefs and developed shoreline associated reefs

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80 that do not receive consistent, tidally flus hed pulses of CDOM are particularly susceptible to increased UV transparency due to photobleaching of CDOM. In conclusion, UV irradiance may contribute to photooxidative stress and reef decline in the Florida Keys. Management of shorelines to protect sour ces of photo protective CDOM such as mangroves, seagrasses, and wetlands may reduce susceptibility to bleaching in corals.

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81 5. Mycosporine like Amino Acids as indicators of photo oxidative stress 5.1 Introduction Mycosporine like amino acids (MAAs) are UV absorbing compounds with maximal absorbance at 310 360 nm (Shick et al. 1999). MAAs also may have an antioxidant activity (Dunlap and Yamamoto 1995, Kim et al. 2001, Suh et al. 2003). Because MAAs are induced by exposure to UVR (Dunl ap et al. 1986, Banaszak et al. 1998, Lesser 2000), theories on MAA induction are relevant to my study of photobiology and photochemistry of CDOM and coral reefs. MAAs can be produced by symbiotic zooxanthellae (Shick et al. 1999) as well as by phytoplank ton (Morrison and Nelson 2004). While exposing corals to UVR can induce UV protective mechanisms such as production of MAAs (Shick et al. 1996, Dunlap and Shick 1998, Morrison and Nelson 2004, Shick 2004) and DNA repair enzymes (Banaszak and Lesser 1995, K uffner et al. 1995, Anderson et al. 2001), prolonged overexposure to UVR can also reduce photosynthetic rates and simultaneously reduce MAA production (Lesser and Farrell 2004). In addition, production of MAAs may decrease with increasing temperature, leav ing zooxanthellae more susceptible to damage caused by exposure to UVR (Lesser et al. 1990). Results from studies monitoring visible light (400 700 nm) and MAA production have been ambiguous (Jokiel et al. 1997, Moisan and Mitchell 2001). Increases in bl ue wavelengths of light can induce production of UV absorbing MAAs, however, visible

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82 and UVR co vary, thus as blue wavelengths of light increase, the concurrent increase in UVR may actually be responsible for MAA induction. Another hypothesis proposes that photosynthetically usable energy (PUR) absorbed in excess of the processing capacity of cellular biochemistry may be passed on to a genetic pathway to induce MAAs (Moisan and Mitchell 2001). Goes et al. (1995) suggest that disruption of a metabolic pathwa y may cause MAA accumulation. According to Hader, MAAs, which are located in the outer cytoplasmic layers of the algal cell, prevent up to 7 out of 10 UV photons from reaching the central targets (e.g., the DNA in the nucleus) (http://www.photobiology.inf o/Hader.html). MAAs are a diverse group of compounds and as such display a range of absorption maxima ( http://www.photobiology.info/Hader.html ). The MAAs can be extracted from the cells and separated by HPLC. The absorption spectra of the separated MAAs show different absorption maxima spread out over the UV A region (http://www.photobiology.info/Hader.html; Figure 5.1). Light absorption by MAAs occurs between 310 to 360 nm and depends on the organism s sampled (Dunlap and Shick 1998). Other compounds, such as DNA and amino acids, absorb at lower UV wavelengths (Fig. 5.2).

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83 Figure 5.1. Absorption spectra for several different MAAs. The absorption spectra of the separated MAAs show different absorptio n maxima spread out over the UV A region ( http://www.photobiology.info/Hader.html ) Figure 5.2. Relative MAA expression is calculated from the spectral absorption due to phytoplankton, a phi or It is the ratio of the peak to the trough in the UV range

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84 Phytoplankton rely on negative and positive phototaxis to optimize their exposure to light. Over the course of the morning, phytoplankton can move from the surface to deeper depths (http://www.photobiology.info/Hader.html). Nevertheless, phytoplankton ma y utilize MAAs as a means of adapting to high light environments (Klisch and Haeder 2000). For example, Morrison and Nelson (2004) found that in clear ocean waters, absorption in the UV region by surface dwelling phytoplankton is typically associated wit h MAAs and is higher in the summer than winter, indicating that MAAs are produced in response to higher exposure to solar radiation. Although many studies have investigated MAA production (see Dunlap and Shick 1998), few studies have compared seasonal and geographical differences in MAA production in reefal waters. My study provides the first analysis of water column MAA production on reefs in the Florida Keys. Not only do MAAs protect organisms from UV damage, but, because MAA production is induced by UVR as well as visible light, their presence in the water column may reflect UV exposure and thus photic stress. This project tests the following hypotheses: 1) within sites, MAA production does not depend on depth, and 2) between sites, MAA production does n ot differ comparing offshore reefs and inshore reefs and comparing intact and developed reefs. The expected results are that, due to higher exposure of solar irradiance at the surface and offshore, respectively, relative MAA expression will be higher at th e surface compared to the bottom, offshore compared to inshore, and at developed compared to intact shoreline associated reefs.

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85 5.2. Methods Spectral absorption due to phytoplankton ( a phi ) (see Chapter 3) for intact and developed shoreline associ ated reefs was examined for MAA peaks in the UV range. I used relative MAA expression (relative UV pigment peak height, Morrison and Nelson 2004; see Figure 5.2) as an expression of organismal stress due to exposure to solar radiation, especially UVR. Usin g chlorophyll as an indicator of phytoplankton biomass, I compared the absorption peak at 320 nm to chlorophyll concentration ([ chl ], g/l) (see Chapter 3), to determine whether MAA production is proportional to phytoplankton biomass. I also examined the r atio maximum MAA absorption: maximum absorption by chlorophyll ( a phi 683 ) to determine the amount of MAA produced relative to absorption due to chlorophyll. 5.3 Results and Discussion Chlorophyll concentration [ chl ], an indicator of phytoplankton biomas s, did not correlate with relative MAA expression (Fig. 5.3). Relative MAA expression tended to range from 1 2 regardless of [ chl ]. Relative MAA expression values above 2 were due to surface samples (blue box in Fig. 5.3) and in one case, the lowest valu e above 2, due to a bottom sample at a developed shoreline associated reef (KL6m). Thus, MAA production does not increase with increasing [ chl ]. Because [ chl ] is an index of phytoplankton biomass (Huot et al. 2007), it can be deduced that relative MAA pr oduction is not solely dependent on phytoplankton biomass, and low relative MAA production is not indicative of low phytoplankton biomass.

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86 Figure 5.3. Relative MAA expression versus [ chl ] for all dates sampled from 2004 2007 where data for both relativ e MAA expression and [ chl ] were available. Figure 5.4 illustrates relative MAA expression versus a g 320 for all sites sampled in 2004 through 2007. The highest values for relative MAA expression occurred at low (< 0.5 m 1 ) a g 320 I determined from the n umber of observations of relative MAA expression greater than 2 ( n = 8) and the number of observations of a g 320 less than 0.5 ( n = 34) compared to the total number of observations ( n = 63), that the probability of all eight relative MAA values greater tha n 2 occurring by chance is (34/63) 8 = 0.007 or 0.7%. Therefore, there is high probability that high relative MAA production is associated with low a g 320 In addition, while many samples, surface and bottom, had lower values of relative MAA production co o ccurring with a g 320 less than 0.5 m 1 all relative MAA

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87 expression values greater than 2 were surface samples with a g 320 less than 0.5 m 1 Thus depth, i.e. exposure to light, as well as a g plays an important role in MAA production. Figure 5.4. Rela tive MAA expression versus a g 320 for all sites sampled in 2004 through 2007 where data for both a g 320 and relative MAA expression were available. The chance of all eight relative MAA values greater than 2 occurring by chance is 0.007 (0.7%). Because the surface is exposed to higher intensities of solar irradiance compared to the bottom (see Chapter 2), it would be expected that, within sites, relative MAA expression would be higher for surface samples compared to bottom samples. Relative MAA expression t ended to be higher and more variable for surface samples (median = 1.346, 25 th to 75 th percentile range = 1.195 to 1.615) than for bottom samples (median = 1.208, 25 th to 75 th percentile range =1.125 to 1.356, Figure 5. 5 ).

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88 Figure 5.5. Relative MAA expres sion for surface samples compared to bottom samples. Dashes represent medians. Relative MAA expression tended to be higher and more variable for surface samples (median = 1.346, 25 th to 75 th percentile range = 1.195 to 1.615) than for bottom samples (media n = 1.208, 25 th to 75 th percentile range =1.125 to 1.356). Because of the discrepancy between surface and bottom samples, I compared surface and bottom samples separately for relative MAA expression at inshore versus offshore reefs (Fig. 5.6, Table 5.1). Comparing surface and bottom samples, relative MAA expression was significantly higher at the surface at offshore reefs. For inshore reefs, though the median was higher at the surface than the bottom, the 25 th 75 th percentile ranges overlapped, thus I c an only conclude that the inshore surface samples tended to be higher but the difference may not be signif i cant. Comparing medians for surface and bottom samples at inshore versus offshore reefs, relative MAA expression

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89 tended to be higher at offshore surf ace compared to inshore surface and at offshore bottom compared to inshore bottom. Figure 5.6. Relative MAA expression comparing surface and bottom samples at inshore versus offshore reefs. Dashes represent medians Table 5.1. Medians, 25 th 75 th perce ntile ranges, and number of samples ( n ) for relative MAA expression at inshore versus offshore reefs, surface versus bottom. Relative MAA expression inshore surface inshore bottom offshore surface offshore bottom median 1.290 1.000 1.506 1.115 25 th perc entile 1.082 1.050 1.354 1.001 75 th percentile 1.371 1.322 1.922 1.233 N 30 14 21 10 R elative expression of MAAs decreased with increasing a g 320 for intact and developed shoreline associated reefs in 2004 2005 (Figure 4.7). Throughout the sampling p eriod 2004 2007, r elative MAA expression was significantly higher at reefs

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90 associated with developed shoreline (median = 1.190 25 th to 75 th percentile range = 1.109 to 1.220, than at reefs associated with intact shoreline (median = 1.353, 25 th to 75tth percentile range = 1.337 1.650, Fig. 5.7). Values of relative MAA expression above 2 were for surface samples, and were higher for developed shoreline associated reefs. At the same time, a g 320 was significantly higher and had a lower range at intact s horeline associated reefs (see Fig. 4.6, Table 4.1) where relative MAA expression was lower. Thus a g 320 may be playing a photo protective role against UVR. Figure 5.7. Relative MAA expression of intact shoreline associated reefs compared to develope d shoreline associated reefs. Dashes represent medians. Comparing medians for relative MAA expression for surface samples only by region Upper, Middle and Lower Keys, relative MAA expression tended to be highest in the Middle Keys and the 25 th 75 th percentile ranges all overlap (Fig. 5.8, Table 5.2). The Lower Keys has the lowest 25 th to 75 th percentile range. The outliers for the Upper

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91 Keys are as follows: the highest outlier is an offshore reef near developed shoreline (Molasses), the second highes t outlier is an inshore reef near developed shoreline (KL6m Reef); and the third highest outlier is an inshore reef near intact shoreline (Algae Reef). The two outliers in the Middle Keys occurred at an offshore site, Tennessee Reef (deep and shallow site, sampled on the same date). Figure 5.8. Relative MAA expression by region, Lower, Middle, and Upper Keys. Dashes represent median s. Table 5.2. Medians, 25 th 75 th percentile ranges, and number of samples ( n ) for relative MAA expression comparing regio ns, Lower, Middle and Upper Keys. Relative MAA expression Lower Keys Middle Keys Upper Keys median 1.325 1.625 1.315 25 th percentile 1.220 1.294 1.178 75 th percentile 1.466 1.751 2.487 n 13 3 11

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92 At the same time, mean a g 3 3 0 at the surface was sig nificantly lower and had a lower range in the Upper Keys compared to the Lower Keys (Fi g 5.9, Table 5.3) a g 3 3 0 for the Middle Keys tended to be lower than the Lower Keys and higher than the Upper Keys. Thus, in the Lower Keys, low relative MAA expressi on co occurred with high a g 3 3 0 Th e Lower Keys have more extensive of mangroves compared to the Upper Keys (Lidz et al. 2003), and while the Middle Keys receive CDOM rich waters from Florida Bay, the constancy and proximity of terrest r ial sourced, loca lly produced CDOM with each tidal cycle might play a bigger role in UV photo protection in the Lower Keys than the pulses of CDOM rich water from Florida Bay in the Middle Keys. Although median relative MAA expression as well as a g 3 3 0 were low in the Upp er Keys, the Upper Keys had more and higher outliers compared to the Lower Keys.

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93 Figure 5.9. a g 330 at only the surface for the Florida Keys by region, Lower, Middle and Upper Keys. Table 5.3. a g 330 at the surface only for the Florida Keys by region Lower, Middle and Upper Keys. a g 330 surface only Lower Keys Middle Keys Upper Keys a g 330 median (m 1 ) 0.539 0.352 0.272 25 th percentile 0.364 0.272 0.214 75 th percentile 0.614 0.593 0.311 n 19 12 29 Considering surface and bottom samples togeth er, the trends in a g 330 between Upper, Middle and Lower Keys are the same as for surface samples only (Fig. 5.10, Table 5.4), while the median a g 330 considering surface and bottom samples together were slighting higher. Thus, a g 330 for surface samples a re generally lower than bottom samples.

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94 Figure 5.10. a g 330 at the bottom and surface for the Florida Keys by region, Lower, Middle and Upper Keys. Table 5.4. a g 330 at the surface and bottom for the Florida Keys by region, Lower, Middle and Upper Keys. a g 330 surface & bottom Lower Keys Middle Keys Upper Keys a g 330 median (m 1 ) 0.543 0.419 0.281 25 th percentile 0.421 0.427 0.270 75 th percentile 0.635 0.870 0.386 n 52 23 28 In conclusion, relative MAA expression was higher at the surface than at the bottom, at offshore reefs compared to inshore reefs, and at developed shoreline associated reefs compared to intact shoreline associated reefs. In general, high relative MAA expression co occurred with lower a g 320 or 330

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95 The species composition at the surface may produce higher amounts of MAAs as a means of adapting to the high intensities and durations of low wavelength radiation at the surface Surface dwelling phytoplankton may accumulate higher amounts of MAAs compared to bottom dwelling phytoplankton, in response to high irradiance, allowing them to adapt to conditions of high irradiance at the surface (Klisch and Haeder 2000). MAA production may also decrease in nitrogen deficient waters, making organisms in N poor waters more susceptibl e to UV damage (Klisch and Haeder 2008). Variability in relative MAA expression increased going from the Lower to Upper Keys. Given the degree of shoreline development in the Key Largo area of the Upper Keys, in contrast with the significant amount of man grove shoreline at John Pennekamp Park, the high variance in the Upper Keys may be due to greater variability in the degree of shoreline development in this region (Appendix A). While the Middle Keys receive substantial input from CDOM and particle rich F lorida Bay (Lidz et al 2006, Porter 2002), the lowest relative MAA expression was seen in the Lower Keys, w h ich has the highest amount of intact shoreline. Because surface samples, offshore sites, and sites near developed shoreline have higher amounts of MAAs compared to bottom samples, inshore sites, and sites near intact shoreline, where a g UV is higher, I deduced that offshore sites and sites near developed shoreline sites are exposed to higher levels of photic stress. The phytoplankton apparently have a cclimated to high light by producing more MAAs. Photic stress compromises resistance to other biotic and abiotic stressors on reefs, and can contribute to the relative decline in offshore, clearer water reefs, relative to inshore, less transparent reefs (see Chapter 4). Combined with CREMP's observations of higher rates of decline at offshore

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96 reefs, these results on MAA production allow me to reject the hypothesis that UVR does not play an important role in coral reef decline. CDOM, as a photoprotective b arrier to UVR, may protect coral reefs from photooxidative stress. Chlorophyll concentration ([ chl ], g/l) was significantly lower in the Upper Keys (mean=0.252, SD=0.111) compared to the Middle (mean=0.326, SD=0.109) and Lower Keys (mean=0.342, SD=0.079) ( p = 0.0313 and 0.00168, respectively). Comparing the Middle and Lower Keys, [chl] was not significa ntly different ( p = 0.597) ( Figure 5.11, Table 5.5). At the same time, a g 320 was lowest and relative MAA expression was relatively high in the Upper Keys, especially compared to the Lower Keys. Thus, high CDOM co occurs with lower production of UV protect ing compounds (MAAs) and higher production of chlorophyll, an indicator of phytoplankton biomass. These results support the hypothesis that CDOM may be protecting organisms, as exhibited here by phytoplankton, from photo oxidative stress.

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97 Figure 5.11 [ chl ] by region in the Lower, Middle, and Upper Keys. Dashes represent medians. Table 5.5. Median s, 25 th and 75 th percentiles, and number of samples ( n) for [ chl ] for the Lower, Middle, and Upper Keys. [ chl ] g/l lower middle upper median 0.345 0.33 4 0.239 25 th percentile 0.286 0.263 0.177 75 th percentile 0.398 0.403 0.323 n 22 16 35 5.4 Future Work The dynamic nature of exposure to solar radiation, behavioral and physiological species acclimations to solar radiation, and the time scales of th ese processes are an exciting aspect that this project did not address. While some studies have

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98 investigated the time scales of MAA production at one depth in culture, other studies have investigated MAA production over seasonal time scales, in situ analys is of phytoplankton number and species, together with time scales of phototaxis and MAA production, should be explored further.

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99 Chapter 6. Spatial Variability of Inherent and Apparent Optical Properties on Coral Reefs 6.1. Background Coral reefs in the Florida Keys, as well as worldwide, are experiencing decline in coral cover, increase in disease and bleaching, and associated stresses that result in overall decline in coral health (see Chapter 3). Among fact ors that have been implicated in the cause of coral reef decline are temperature and solar radiation (Lesser and Farrell 2004). The underwater light field is a result of incident irradiance interacting with the absorption and scattering processes that occ ur in the water column, as well as the pathlength (depth). Gregg (2002) describes the angular structure of the underwater light field: The direct downwelling stream contains the irradiance directly transmitted by the sun, traversing the air sea interface and proceeding forward at an angle described by the solar zenith angle modified by the refractive index of seawater. Each scattering and absorbing event in the water column removes irradiance from the direct downwelling stream. Whereas the downwelling direct irradiance receives no contributions in the water column and steadily decreases as the result of absorption and scattering processes, the downwelling diffuse irradiance gains forward scattered downwelling direct irradiance and backscattered upwellin g diffuse irradiance in the water column. This irradiance stream

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100 travels along a path defined as the average cosine for downwelling diffuse irradiance" ( Gregg 2002, p. 6) Thus, diffuse irradiance is amplified by scattering and the downwelling light stream is enhanced by forward scattering. A coral reef where overlying water is characterized by relatively lower absorption may incur higher irradiances due to the angular distribution of light through the water column until it ultimately reaches the bottom. T he reflective properties of the bottom may also increase the amount of upward scattering of light, and thus light, reaching the benthos (Lee et al. 1998, 1999; Boss and Zanefeld 2003). 6.2. Objectives The goal of this chapter is to use field data from two Upper Keys patch (inshore) reefs to compare differences in the amount of light reaching the benthos based on modeled radiance distribution determined using Hydrolight 6.3. Methods See Chapter 3 for sample collection and field measurements. Scattering, b was measured using an ac 9 (WET labs ) according to Voss et al (2003). Methods for in lab measurements of absorption ( a g a p ) and chlorophyll concentration [chl] are also detailed in Chapter 3, as are field site locations and characteristics. KL6m is located near developed shoreline, while Algae Reef is located near intact mangrove shoreline (Fig 3.1). Hydrolight ( Sequoia Scientific), a radiance distribution modeling program, was used to derive radiance distribution parameters K d and d from in lab measurements of

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101 total absorption, a t and in situ measurements of scattering, b for two inshore reefs KL6m Reef and Algae Reef differing in UV transparency as a result of differences in a g Because in situ scattering, b was measure d only on September 28, 2004, this analysis is limited to one dataset collected at each site on this date. Hydrolight derived (modeled) attenuation coefficients for downwelling irradiance, K d and the average cosine of downwelling irradiance, $ d at fo ur different UV wavelengths, 305, 320, 330 and 380 nm, were compared between sites. Also, modeled K d was compared to estimates of K d based on in lab measurements of a t 6.3.1. Calculating underwater irradiance The natural light field is not collimated but diffuse. In the water column, total diffuse attenuation of downwelling irradiance, K d is due to absorption ( a ) and scattering ( b ) by water molecules, dissolved material, and particulate material, and the angular distribution of light, the average cosine of downwelling irradiance, d : Kd= ( a + b)w p g/ d (6.1) where d = (E d E u )/E d0 = cos & and & is the zenith angle (angle between the sun and plane perpendicular to the surface; see following section for derivation). When scattering is constant and light measurements are made within two hours of solar noon, the effect of d is negligible and the total diffuse attenuation of downwelling irradiance can be estimated solely from abso rption. K d = a g + a p + a w (6.2) where a p is absorption due to particulate material and a w is absorption due to pure water. Irradiance reaching the sea floor ( E dz ) can then be estimated as:

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102 E dz ( $ )= E d0 ( $ )e K_d*z where z = depth (6.3) (Kirk 1994). When is not constant and b << a the following is true: Kd= ( a )w p g/ or Kd= at/ (6.4) where a t is total absorption due to water molecules, particulate material and gelbstoff. 6.3.2. Th e a ngular distribution of light According to Kirk ( 1994 p. 9 10 ) Irradiance (at a point of a surface), E is the radiant flux incident on an infinitesimal element of a surface, containing the point under consideration, divided by the area of that el ement; it is the radiant flux per unit area of a surface: E = d /d S (6.5) Irradiance has the units W m 2 or quanta (or photons) s 1 m 2 where one mol photons is 6.02 x 10 23 (Avogadros number) photons. One mole of photons is frequently referred to as an einstein The relationship between E, radiant flux per unit surf ace area, and radiance, L, is shown in my Figure 6.1. T he projected area of the element of surface is d S cos & and the corresponding element of solid angle is d % Thus, the radiant flux on the element of surface within the solid angle d % is: d = L( &,") d S cos & d % (6.6)

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103 Figure 6.1. Radiance ( L ) on a point in a surface, from a given direction, is the radiant flux in the specified direction per unit solid angle per unit projected area of the surface ( after Kirk 1994). Then, Irradiance, E, can be exp ressed as: E = d /d S = L( &,") d S cos & d %/ d S = = L( &,") cos & d % The total downward irradiance at that point in the surface is obtained by integrating with respect to solid angle over the whole upper hemisphere: Ed= L (",#) cos"d2$%& (6.7) The scalar i rradiance, E 0 is the integral of the radiance distribution at a point over all

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104 directions about that point: E0= L (",#) d4$%& (6.8) Scalar irradiance is thus a measure of the radiant intensity at a point, which treats radiation from all directions e qually. In the case of irradiance, on the other hand, the contribution of the radiation flux at different angles varies in proportion to the cosine of the zenith angle of incidence of the radiation: a phenomenon based on purely geometrical relations (Figur e 6.1, eqn. 6.9) and sometimes referred to as the Cosine Law. The downward scalar irradiance, E 0d is the integral of the radiance distribution over the upper hemisphere (Kirk 1994, pp. 9 10): E0 d= L (",#) d2$%& (6.9) Because the object of my stud y is to estimate the amount of light reaching the bottom, or benthos, the parameter of concern is the average cosine, in the downward direction, d Again, quoting Kirk (1994, p. 10), The average cosine for downwelling light, d at a particular poi nt in the radiation field, may be regarded as the mean value, in an infinitesimally small volume element at that point in the field, of the cosine of the zenith angle of all the downwelling photons in the volume element. It can be calculated by summing (i. e., integrating) for all elements of solid angle (d % ) comprising the upper hemisphere, the product of the radiance in that element of solid angle and the value of cos & (i.e. L( &," ) cos & ), and then dividing by the total radiance originating in that hemisphere: d = EdE0 d = L (",#) cos"d$2%&L (",#) d$2%& (6.10)

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105 Thus, d is related to the cosine of the zenith angle as the downward irradiance at a point compared to the radiance distribution over the upper hemisphere. Consequently, d is also called the average cosine for downwelling light and is unitless. The a verage cosine of light describes the angular structure of the light field ranging from collimated light plane perpendicular to the surface, where the zenith angle ( & ) is 0 (cos 0 = 1 and thus ! d = 1) to maximally diffuse light, where & = 90 ¡ (cos 90 = 0 and thus ! d = 0). Multispectral K d and ! d can be estimated or modeled from single wavelength estimates of a g and b using Hydrolight (version 5). The ratio of in lab measurements of total absorption, a t to independently measured, in situ K d is an estimate of the average cosine of light, = a t /K d (6.11) (Kirk 1994). Except when the single scattering albedo is very low (less than 0.1), which onl y occurs in very clear oceanic water at long wavelengths (greater than 650nm), scattering dominates ! d Otherwise the effect of absorption dominates ! d : light that does not have the shortest pathlength is more rapidly removed (absorbed), so that the li ght that is traveling vertical to the surface of the water penetrates most deeply; secondarily scattered light results in increase of light in the forward direction, leaving the underwater light field more vertical and making ! d closer to 1 (Berwald et a l. 1995; Kirk 1994). For optically clear waters, where absorption dominates light attenuation, d will be close to one for the entire depth profile and at infinite depths ! d would be close to one as well, consistent with the absorption effect. Thus, l ight becomes more vertical or collimated at deeper depths, and ! d increases (becomes closer to unity). In more highly

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106 scattering, low absorbing waters, scattering plays a greater role, light becomes more diffuse and d decreases (deviates from unity). 6.4. Results and Discussion Table 6.1 compares calculated estimates of K d and d at 330 nm ( K d330nm ) using Hydrolight (version 5), laboratory measurements of absorption, in situ measurements of scattering ( b ), as well as other meteorological and optic al parameters for KL6m and Algae Reefs. d can also be estimated as the ratio of measured total absorption coefficient ( a t ) to modeled K d (see Eqn. 6.5). Comparing modeled ( Hydrolight derived) d between sites, modeled d was lower at the reef site wi th the lower a g developed shoreline associated KL6m Reef (Table 6.1, Table 6.2, Figure 6.2), showing that the light field is more diffuse at KL6m Reef compared to intact shoreline associated Algae Reef. In addition, modeled reflectance, R was also co nsistently higher at KL6m (Table 6.3).

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107 Table 6.1. Meteorological data, salinity and bottom type, as well as optical parameters used as input, model bottom type, and output ("modeled") for Hydrolight version 5.0 for for Algae Reef and KL6 m Reef on September 28, 2004 Algae Reef September 28, 2004 25.1467 o N, 80.2931 o W KL6m September 28, 2004 25.0184 o N, 80.3972 o W surface (0.5 m) bottom (6m) Surface (0.5 m) Bottom (6m) Julian Day 272 272 272 273 Time (GMT) 16.25 16.25 21.50 17.75 temperature ( o C) 28.0 28.0 28.8 28.8 Salinity (PSU) 36.0 36.0 36.0 36.0 Hydrolight solar zenith angle ( o ) 30.47 30.5 30.5 28.7 Hydrolight total ozone (DU) 278 278 278 265 actual bottom type 50% to mostly sand, coral 50% to mostly sand, coral san d, seagrass, coral sand, seagrass, coral Winds (m/s) 6.7 6.7 2.5 1.5 [chl] ( g/l) 0.324 No data No data 0.321 a t330nm in lab (m 1 ) 0.576 0.532 0.323 0.300 a g330nm (m 1 ) 0.505 0.446 0.257 0.236 b 330 (m 1 ) 0.801 1.987 1.374 1.462 computed b b330nm (m 1 ) 0.0219 0.0433 0.0142 0.0447 Hydrolight K d330nm (m 1 ) 0.718 0.809 0.461 0.5 25 a t330nm / K d330nm 0.802 0.657 0.700 0.571 Hydrolight d ([mineral] = 0) 0.838 0.733 0.745 0.699 Hydrolight model bottom type avg coral avg coral avg coral avg coral

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108 Figure 6.2. Comparison of d for Algae and KL6m Reef surface and bottom at 305, 320, 330 and 380 nm. d at Algae Reef is higher at all wavelengths than at KL6m, at the surface as well as bottom. See Table 6.3 for values and 25th 75 th percentile ranges Table 6.2. Comparison of d for Algae and KL6m Reef surface and bottom at 305, 320, 330 and 380 nm. Medians and 25th 75 th percentile ranges. d Algae surface KL6m surface Algae bottom KL6m bottom 305 nm 0.84650 0.72930 0.73580 0.69470 320 nm 0.83970 0.72480 0.72930 0.69360 330 nm 0.83830 0.76625 0.73370 0.69840 380 nm 0.83020 0.77305 0.73720 0.72640 median 0.83900 0.74778 0.73475 0.69655 25th percentile 0.836275 0.728175 0.7326 0.694425 75th percentile 0.8414 0.76795 0.73615 0.7054 Table 6.3. Inherent and Apparent Optical Properties (IOPs and AOPs) computed by Hy drolight (version 5) for Algae and KL6m Reef, surface and bottom, at 305, 320, 330

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109 and 380 nm, based upon in situ absorption, a and scattering, b. m_bar_d = d . E d for Algae and KL6m Reef, surface and bottom, as computed by Hydrolight (version 5), w as higher at the surface but lower at the bottom at Algae Reef. Although E d was not appreciably different at the surface comparing KL6m Reef and Algae Reef, downwelling irradiance reaching the bottom, E d6m was consistently one order of magnitude hig her at KL6m Reef than at Algae Reef, and this effect increased with decreasing wavelength, due to the combined effect of lower a g and lower d at KL6m Reef relative to Algae Reef (Figs. 6.3, 6.4, Table 6.4).

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110 Figure 6.3. Although modeled E d at the sur face was not very different at Algae Reef compared to KL6m, due to lower a g and lower d at the bottom, E d at the bottom was approximately an order of magnitude higher at KL6m compared to Algae Reef (see Table 6.2). Because a g was lower at KL6m Reef t han Algae Reef for all sampling dates (2004 2007) (for example, a g 330 Figure 6.4, Table 6.3), these results for d for one day in September 2004, where a g was lower at KL6m Reef, can be considered generally representative for these sites. Sources of e rror include measurement of a p and a g (see Chapter 3), sky conditions, and in situ scattering ( b ).

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111 Figure 6.4. a g 330 at Algae and KL6m Reefs, surface and bottom, for all sampling dates from 2004 2007. a g 330 was lower at KL6m than Algae Reef, consid ering surface and bottom samples separately. Dashes represent medians. Table 6.4. Medians and 25 th 75 th percentile ranges for a g 330 at Algae and KL6m reefs, surface and bottom, for all sampling dates from 2004 2007. a g 330 median 25 th 75 th percen tile range Algae surface 0.313 0.291 0.374 KL6m surface 0.211 0.184 0.272 Algae bottom 0.296 0.266 0.364 KL6m bottom 0.203 0.177 0.232 6.5. Conclusions Higher diffuseness of the light field (lower d ) increases the amount of UV irradiance re aching the corals, beyond the increase in scattering with decreasing wavelength according to 4.32 (Kirk 1994). Particle scattering by phytoplankton, detritus or minerals also increases with decreasing wavelength (Gregg 2002). This study shows

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112 that UVR re aching the benthos can be higher at reefs with lower a g due to both the lower absorptivity and higher diffuseness of light and these effects increase with decreasing wavelength. Fisher et al. (2007) reported that lesion recovery in corals, which is a bio indicator of coral condition, was significantly faster at Algae Reef, where a g as well as a p (absorption due to particulate material, a p = a t a g ) (Table 6.1), are greater than at KL6m reef. Thus, the recovery of corals from physical damage may be enhanc ed under lower UV conditions. A typical value for d at 400 nm for natural waters illuminated by sun and sky is 0.71 (Mobley 1994, p. 551). At lower wavelengths d would be lower. Thus, to check the accuracy of a t330nm / K d330nm in estimating d at 33 0 nm, one can multiply by approximately a value lower than 0.71, because d decreases as wavlength decreases. However, because a t330nm / K d330nm is already lower than modeled d there is either an error (underestimation) in measuring a t330nm an error ( overestimation) in modeled K d330nm or an error (overestimation) in modeling d It is not likely that a p has been underestimated, because typically, it is overestimated due to scattering in the cuvette or in the filter pad (see Chapter 3). The error in m odeling the apparent optical properties K d330nm and d which are dependent upon the angular structure of the light field as well as the components of the water column, therefore may be due to sky conditions. Thus, differences in actual versus modeled cl oud cover could also account for some of the difference between modeled and measured d (see Table 6.1, a t330nm / K d330nm compared to d ). Modeled d is consistently higher than measured d Modeled d accounts for sky conditions, while measured d d oes not. In the case of increased cloud cover, light is scattered through the atmosphere and the incident light on the ocean

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113 surface is more diffuse under cloudy sky conditions than under clear sky conditions (Gregg 2002, see Fig. 6.5). Cloud cover also a lters the spectral distribution of light: cloudy, diffuse sky UV spectra (350 400 nm) represent a greater proportion than clear, diffuse sky UV spectra (20.5%), while cloudy sky red spectra (650 700 nm) represent a smaller proportion than clear sky red spe ctra ( 9.4%) (Fig. 6.6). Frederick et al (2000) found that monthly integrated broadband UV irradiance usually has peaks in June to July and that the large variability in UV irradiance reaching the earth's surface is consistent with changing cloudiness. Figure 6.5. Depiction of the pathways of irradiance under clear and cloudy skies, and in the oceans. The sizes of the arrows indicate the relative proportions of direct (E d ) and diffuse (E s ) irradiance for clear skies and cloudy skies. Some of the surfa ce irradiance is reflected off the sea surface (1 #). These pathways continue into the ocean where an additional diffuse upwelling (E u ) path exists (from Gregg, 2002).

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114 Figure 6.6. Spectral surface irradiance just below the sea surface (after spectral s urface reflectance) for clear skies and cloudy skies. The cloudy sky simulation represents the effects of 80 g m 2 liquid water path, which produces about half the total surface solar irradiance as the clear sky model for the same solar zenith angle and at mospheric optical properties (from Gregg 2002). Because cloudy, diffuse sky conditions present a greater amount of irradiance to the surface than clear, diffuse sky conditions (Gregg 2002), corals at the benthos "see" relatively higher intensity low wav elength, more damaging UVR. Thus, the danger of photo oxidative stress is potentially greater (Lesser and Farrell 2004) under cloudy, diffuse sky conditions compared to clear, diffuse sky conditions (Fig. 6.6). In conclusion, the spectral quality of li ght reaching the benthos on coral reefs is affected by atmospheric variables (clouds, aerosols) as well as by water column properties (pathlength, absorption and scattering by minerals, phytoplankton, and CDOM). Understanding the variables affecting the di ffuse nature of light is important in

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115 studying the effects of solar radiation on coral reef biota. Observations of the coincidence of maximum bleaching with maximum solar radiation in the Keys, especially UV radiation, found in my study (Chapters 3, 4, and 5) indicate the necessity of understanding radiative transfer processes, including apparent optical properties such as d The cumulative effects of high irradiance over the course of the summer increase coral reef susceptibility to photo oxidative str ess when later summer temperatures peak. Atmospheric and water column effects on the diffuseness of the underwater light field may exacerbate incident solar and temperature stress. Algae Reef, the intact shoreline, higher a g associated reef, was characteri zed by higher a g and d and lower E d bottom Thus, these results agree those presented previously (see Chapters 3, 4 and 5). Diffuseness increases with decreasing wavelength (Kirk 1994). The results in this chapter show that increased diffuseness may caus e increase in short wavelength solar radiation reaching the benthos. In conclusion intact shoreline can be an important source of CDOM protecting coral reefs from photooxidative stress.

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116 Chapter 7. Conclusions and Future Research 7.1. Conclusions C oral reefs have long been characterized by their remarkable productivity and diversity while thriving in the clearest, most nutrient poor oceanic regions (e.g., Odum and Odum 1955; Wells 1957). Thus, a major paradox of the response of Florida's coral reef s to ongoing environmental change is that offshore reefs have declined much faster than inshore reefs (Somerfield et al 2008). Coral disease and bleaching are considered among the most important causes of decline in coral populations and percent coral co ver on reefs. Mass coral bleaching is so strongly correlated with elevated temperature that NOAA has developed a hotspot bleaching warning system ( http://coralreefwatch. noaa.gov/satellite/methodology/ methodology.html ). Yet the physiological mechanism of bleaching is actually photo oxidative stress (Lesser 2006). This means that sunlight is required for bleaching to occur. Fitt and Warner (1995) and others have shown th at shorter wavelengths of light, either visible or UV, trigger bleaching at lower temperatures than does higher wavelength visible light. Thus, the underlying goal that prompted my study is to provide evidence that can help to resolve the paradox of why coral populations, in what historically were the best environments, have declined the fastest over the past several decades. My working hypothesis is that CDOM in reef waters can protect corals from the photic component of

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117 photo oxidative stress that caus es mass bleaching, and that human activities have resulted in reduced CDOM concentrations in reef tract waters. Major ways that human activities have influenced CDOM distributions in coastal waters is by widespread alteration of watersheds and coastlines including removal of coastal vegetation and changes in coastal hydrology (e.g., construction of causeways between islands in south Florida). An undeveloped watershed slowly releases its colored (i.e., higher CDOM) freshwater; a developed watershed sheds more and muddier runoff during the rainy season, and minimal runoff during the dry season. This is in contrast with undeveloped shorelines with coastal hammocks and mangroves, which trap sediments coming from both land and offshore, while releasing CDOM with every tidal cycle. While increased CDOM can be photoprotective, sediments, which can smother and block visible light needed for photosynthesis from corals, are not beneficial to coral reefs. Therefore when coastal vegetation is replaced by seawalls an d urban or agricultural development, depending upon local weather, coastal waters are alternatively more turbid and more transparent, properties that are stressful for corals and other benthic organisms. Thus, undeveloped and intact shorelines with mangrov e and coastal hammocks can support coral reefs by supplying photoprotection via CDOM and reducing smothering and blocking of visible light by sediments. My study investigated distribution of CDOM in waters of the Florida reef tract. In general, UV absorbin g CDOM was more prevalent on inshore reefs and reefs near intact shorelines, compared to offshore reefs and reefs with developed shorelines. Intact shoreline associated reefs and inshore reefs were characterized by lower photic stress as illustrated by l ower production of UV absorbing substances in the water column, lower

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118 UVR reaching the benthos, lower rates of CDOM photobleaching and higher percent coral cover compared to developed shoreline associated reefs and offshore reefs. Individual findings can be summarized as follows: 1. In reef areas near intact shoreline, where mangroves are a major source of CDOM, absorption due to CDOM ( a g ) decreases going offshore from mangrove coastline to ocean waters beyond the reef. Absorption due to CDOM in the UV ( a g UV ) is higher at inshore reefs compared to offshore reefs, for example, absorption due to CDOM at 320 nm ( a g 320 ) at offshore reefs is only 64% of that at inshore reefs. 2. CDOM is the major attenuator of UVR: for all reefs sampled, a g UV / a t UV range d from 62% at 380 nm to 91% at 305 nm ; over the course of each summer a g UV / a t UV decreased, likely due to photobleaching of CDOM. 3. In very shallow waters, less UVR is reaching the bottom at intact shoreline associated reefs compared to developed shoreline assoc iated reefs. 4. Considering inshore and offshore reefs together, a g UV is higher in the Lower Keys, which are characterized by larger amounts of mangrove coastline and Middle Keys, which receive CDOM rich water inputs from Florida Bay, compared to the Uppe r Keys. 5. The attenuation coefficient for downwelling irradiance in the UV ( K d UV ) is higher at inshore reefs compared to offshore reefs, while the difference in K d PAR between inshore and offshore reefs is not as great.

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119 6. Considering each site individually, f or the CREMP sites sampled in 2006 and 2007, o n a 3 tiered scale of low to high coral cover and low to high a g 320 the predominant combination is low % stony coral cover accompanied by low a g 320 Percent stony coral cover as well as a g 320 were general ly higher at inshore reefs compared to offshore reefs 7. Relative expression of the UV absorbing MAAs was lower at intact shoreline associated reefs compared to developed shoreline associated reefs and tended to be lower at inshore reefs compared to offshor e reefs. 8. Considering the Florida Keys by region, relative MAA expression was higher in the Upper Keys compared to the Lower Keys at the same time a g 320 was lower in the Upper Keys compared to the Lower Keys and Middle Keys. 9. Spectral slope, S was higher in offshore reef waters, indicating extensive photobleaching of CDOM, compared to inshore reefs. 10. Diffuseness of the underwater light field increases the probability of light exposure for benthic organisms. Diffuseness was lower at the higher CDOM, intact shoreline associate reef compared to the developed shoreline associated reef Thus, all of the measured parameters indicate that the inshore reefs, especially those near undeveloped shoreline, are more photo protected by CDOM than are more developed sh oreline and offshore reefs, consistent with my working hypothesis.

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120 The results of this study show that intact shoreline such as mangroves, and other terrestrial sources of CDOM, such as wetlands influencing Florida Bay, play an important role in limiting p hoto oxidative stress on Florida Keys reefs. Increasing restrictions on shoreline development to preserve mangrove sources of CDOM to reef tract waters, and protecting wetlands that through estuaries, bays, and rivers may provide CDOM rich waters to the re ef tract, are an important strategy for reducing photo oxidative stress and thus increasing resiliency of coral reefs. The Florida reef tract is well monitored, but monitoring in itself has not slowed the decline of coral populations. Increased focus on p rotection of CDOM sources will enhance efforts to protect Florida's coral reefs, and coral reefs worldwide, from degrading in the face of ocean warming and acidification projected for the future ( Hoegh Guldberg et al. 2007, Baker et al. 2008) 7.2 Future research To further quantify the role of mangroves and other terrestrial sources of CDOM in protecting coral reefs, controlled lab experiments should continue to study CDOM breakdown rates and processes in response to increasing temperature and acidificati on. Moreover, ecosystem based studies should more closely examine the role of CDOM ( a g ) in coral reef health as expressed by indicators of coral health, such as coral cover, disease and bleaching Sources of CDOM can be quant ified using fluorescence spectroscopy and fluorescence Excitation Emission Matrices (EEMS) (Moran et al. 1991, Coble 2007).

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121 In addition to local management and monitoring, global networking and monitoring is essential to protecting reefs for the future. Satellite sensors that can measure UVR and CDOM for large spatial areas are planned for future deployment, and algorithms for shallow, reflective coastal waters are continually being improved. The spectral slopes found in this study can be used with existi ng satellite measurements of PAR irradiance to estimate UVR in these coastal regions, where satellite images are difficult to correct due to bottom reflectance (Lee et al. 1998). With cooperation between optical, physical, and biological oceanographers, cu rrent products can be improved and expanded upon, so that, hopefully, the delicate balance of coral reefs and other ocean ecosystems can be maintained.

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130 Banks. Coral Reefs 23: 152 160 Pait AS, DeSouza AE, Farrow DRG (1992) Agricultural pesticide use in coastal areas: a national summary. Strate gic Environmental Assessments Division, NOAA, Maryland Peters M, Palandro D Hallock P, Shinn E (in press) Assessing patterns of patch reef distribution in the Lower Florida Keys, USA, using IKONOS satellite imagery. Proc 11 th Int Coral Reef Symp Pomeroy LR, Wiebe JJ (1988) Energetics of microbial food webs. Hydrobiologia 159:7 18 Pope RM, F ry ES (1997) Absorption spectrum (380 700 nm) of pure water. II. Integrating cavity measurements. Appl Opt 36: 8710 8723 Porter JW, Lewis SK, Porter KG (1999) The effect of multiple stressors on the Florida Keys coral reef ecosystem: a landscape hy pothesis and a physiological test. Limnol Oceanogr 44: 941 949 Porter KG (2002) Water Quality in the FKNMS I n : Porter JW, Porter KG (eds) The Everglades, Florida Bay, and Coral Reefs of the Florida Keys: An Ecosystem Sourcebook. p 625 Ramirez A, Ayoub LM, Duncan Baker R, Hallock P (2007) Foraminifers as indicators of photo oxidative stress: comparing bleaching prevalence in foraminifers with rate s of decline in coral cover in the Florida Keys, USA. GSA Denver Annual Meeting (28 31 October 2007), paper no 154 1 Randazzo AF, Halley RB (1997) The Geology of the Florida Keys. In : Randazzo AF, Jones DS ( ed s) The g eology of Florida. Universi ty Press of Florida Gainesville Randel WJ, Wu F, Russell JM III, Waters JW, Froidevaux L (1995) Ozone and temperature changes following the eruption of Mt. Pinatubo. J Geophys Res 100:16753 16764 Reche I, Pace ML, Cole JJ (2000) Modeled effects of disso lved organic carbon and solar spectra on photobleaching in lake ecosystems. Ecosystems 3:419 432 Risk MJ (1999) Paradise lost: how marine science failed the world's coral reefs. Mar Fresh w Res 50: 831 837 Roscoe HK (2001) The risk of lar ge volcanic eruptions and the impact of this risk on future ozone depletion. Natural Hazards 23: 231 246 Roth AA, Clausen CD, Yahiku PY, Clausen VE, Cox WW (1982) Some effects of light on coral growth. Pac Sci 36 (1): 65 82 Rundel R (1983) Acti on spectra and estimation of biologically effective UV radiation. Physiologia Plantarum 58 : 360 366 Rundel RD, Nachtwey DS (1978) Skin cancer and ultraviolet radiation. Photochem Photobiol 28 (3): 345 356 Schlichter D, Fricke HW, Weber W (1986) Light harvesting by wavelength transformation in a symbiotic coral of the Red Sea twilight zone. Mar Biol 91, 403 407 Shick JM (2004) The continuity and intensity of ultraviolet irradation affect the kinetics of biosynthesis, accumulation, and conversion of my cosporine like amino acids (MAAs) in the coral Stylophora pistillata Limnol Oceanogr 49(2): 442 4458 Shick JM, Lesser MP, Dunlap WC, Stochaj WR, Chalker BE, Wu Won J (1995) Depth dependent responses to solar ultraviolet radiation and oxidative stress in the zooxanthellate coral Acropora microphthalma Mar Biol 122: 41 51 Shick JM Lesser MP Jokiel PL ( 1996) Effe cts of ultraviolet radiation on corals and other coral reef organisms. Global Change Biol 2(6): 527 545

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131 Shick JM, Romaine Lioud S, Ferrier Page % s C, Gattuso J P (1999) Ultraviolet b radiation stimulates shikimate pathway dependent accumulation of mycosporine like amino acids in the coral Stylophora pistillata despite decreases in its population of symbiotic dinoflagel lates. Limnol Oceanogr 44: 1667 1682 Siegel DA, Maritorena S, Nelson NB, Hansell DA, Lorenzi Kayser M (2002) Global distribution and dynamics of colored dissolved and detrital organic materials. J Geophys Res 107(12) : 3228 Smith RC, Cullen JJ (1995) E ffects of UV radiation on phytoplankton. Rev Geophys 33 : 121 1 1 223 Smith NP, Lee TN (2003) Volume transport through tidal channels in the Middle Florida Keys. J Coastal Res 10(2): 254 260 Smith DJ, Suggett DJ, Baker NR (2005) Is photoinhi bition of zooxanthellae photosynthesis the primary cause of thermal bleaching in corals? Global Change Biol 11:1 11 Somerfield PJ, Jaap WC, Clarke KR, Callahan M, Hackett K, Porter J, Lybolt M, Tsoko C, Yanev G (2008) Changes in coral reef comm unities among the Florida Keys, 1996 2003. Coral Reefs [doi 10.1007/s00338 008 0390 7] Stabenau ER, Zepp RG, Bartels E, Zika RG (2004) Role of the seagrass Thalassia testudinum as a source of chromophoric dissolved organic matter in coastal south Flori da. Mar Ecol Prog Ser 282: 59 72 Stabenau ER, Hendee JC, Floritt L (2006) Investigating the Interactive Effects of Light and Temperature on Coral Photosynthetic Health. Ocean Sciences Meeting 2006. Abstract OS46L 09. http://www.agu.org/meetings/os06/os06sessions/os06_OS46L.html Stedmon C, Marager S (2001) The optics of chromophoric dissolved organic matter (CDOM) in the Greenland Sea: an algorithm for differentiat ion between marine and terrestrially derived organic matter. Limnol Oceanogr 46(8): 2087 2093 Steinberg DK, Nelson NB, Carlson CA, Prusak AC (2004) Production of chromophoric dissolved organic matter (CDOM) in the open ocean by zooplankton and the co lonial cyanobacterium Trichodesmium spp. Mar Ecol Prog Ser 267: 45 56 Stevenson FJ (1982) Humus chemistry: genesis, composition, reactions. Wiley, New York Stramski, D., and S. B. Wozniak. 2005. Light scattering by marine colloids ASLO 2005 Aquatic Sciences Meeting, Salt Lake City, Utah, USA. Abstract Book, p. 107. Suh H, Lee H, Jung J (2003) Mycosporine glycine protects biological systems against photodynamic damage by quenching singlet oxygen with a high efficiency. Photochem P hotobiol 78: 109 113 Swart PK, Healy G Greer L Lutz M Saied A Anderegg D Dodge RE Rudnick D (1999) The use of proxy chemical records in coral skeletons to ascertain past environmental conditions in Florida Bay. Estuaries 22(B)384 397 Twardowski M S, Boss E, Sullivan JM, Donaghay, PL (2004) Modeling the spectral shape of absorption by chromophoric dissolved organic matter. Mar Chem 89: 69 88 United Nations Environment Programme (UNEP) (2003) Environmental Effects of Ozone Depletion: 2002 Ass essment. The Secretariat for The Vienna Convention for the Protection of the Ozone Layer and The Montreal Protocol on Substances that Deplete the Ozone Layer, ISBN 92 807 2312 X

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132 Vincent WF, Kumagai M, Belzile C, Ishikawa K, Hayakawa K (2001) Effects of seston on ultraviolet attenuation in Lake Biwa, Limnology 2(3):179 184 Vincent WF, Neale PJ (2004) Mechanisms of UV damage to aquatic organisms. In : d e Mora S, Demers S, Vernet M ( eds) The effects of UV radiation in the marine environment. Cambridge Univ ersity Press, Cambridge, pp 149 176 Vodacek A, Blough NV, DeGrandpre MD, Peltzer, ET, Nelson RK (1997) Seasonal variation of CDOM and DOC in the Middle Atlantic Bight: terrestrial inputs and photooxidation. Limnol Oceanogr 42:674 686 Voss KJ, Mobley CD, Sundman LK, Ivey JE, Mazel CH ( 2003 ) The spectral upwelling radiance distribution in optically shallow waters Limnol Oceanogr 48 ( 2):364 373 Walker ND, Rouse Jr LJ, Fargion GS (1994) T he Great Flood of Summer 1993: Mississippi River Discharge Studied. Earth in Space 7(3): 11 14 Waksman SA (1932) Humus. Williams and Wilkins, Baltimore Warner ME, Chilcoat GC, McFarland FK, Fitt WK (2002) Seasonal fluctuations in the photosynthetic capacity of photosystem II in symbiotic dinoflagellates in the Caribbean reef building coral Montastrea Mar Biol 141:31 38 Wells JW (1957) Coral Reefs. Geological Society of America, Memoir 67(1):609 631 West JM, Salm RV ( 2003 ) Resistance and resilience to coral bleaching: implications for coral reef conservation and management Conserv Biol 17:956 967 Wilkinson C (2002) Status of coral reefs of the world: 2002. Global Coral Reef Monitoring Network, Aust ralian Institute of Marine Science, Townsville http://www.aims.gov.au/ pages/research/coralbleaching/s2/ scr 00.html Williams DE (2002) Population ecology of bleaching stressed Amphistegina gibbosa in the Florida Keys (1991 1999): i nfluence of solar radiation on reef dwelling foraminifera. Ph.D. thesis, University of South Florida Williams DE, Hallock P (2004) Light requirements and bleaching in Amphistegina gibbosa : observations from laboratory experiments. M ar Biol 145:641 649 Wotton RS, Wotton WS (1994) The Biology of Particles in Aquatic Systems. CRC Press Yentsch CS, Yentsch CM, Cullen JJ, Lapointe B, Phinney DA, Yentsch SW (2002) Sunlight and water transparency: cornerstones in coral researc h. J Exp Mar Biol Ecol 268(2): 171 183 Zanardi Lamardo E, Moore CA Zika RG (2004) Seasonal variation in molecular mass and optical properties of chrom ophoric dissolved organic material in coastal waters of southwest Florida. Mar Chem 89(1): 37 54 Zepp RG (2003) UV exposure of coral assemblages in the Florida Keys. EPA Report: EPA/600/R 03/095 September 2003. http://www.epa.gov/athens/publications/ Zepp RG, Callaghan TV, Erickson III DJ (2002) Interactive effects of ozone depletion and climate change on biogeochemical cycles. Photochem Photobiol Sci 2: 51 61 Zepp RG, Moran MA, Stabenau E, White EM (2002) Photochemical and biological degradation of CDOM in waters from selected coastal regions of the southeastern United States. EOS Trans AGU 83: OS278. American Geophysical Union, Washington, D.C. Zepp RG, Shank GC, Stabenau E, Patterson KW, Cyterski M, Fisher W, Bartels E, Anderson, SL (2008) Spatial and temporal variability of solar ultraviolet exposure of coral assemblages in the Florida Keys: importance of colored dissolved organic matter. Limnol Oceanogr 53:109 1922

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133 Appendices

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134 Appendix A: Map of Florida Keys with waterways, cities, management areas and reefs

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135 Appendix B: Appendix of Important Terms and Abbreviations (source: http://www.epa.gov/uvnet/glo ssary.html#totalcolumn) I. Irradiance related terms: Irradiance The power transferred to a unit area of a surface by radiation from all directions within a hemisphere, measured in watts per square meter (W/m& ). Ultraviolet (UV) / Ultraviolet Radiation (UVR) A portion of the electromagnetic spectrum with wavelengths shorter than visible light. The sun produces UV, commonly split into three bands: UV A, UV B, and UV C. Solar UV Index The solar UV index (UVI) describes the level of solar UV radiation at the Earth's surface. The values of the index range from zero upward the higher the index value, the greater the potential for damage to the skin and eye, and the less time it takes for ha rm to occur. The UV index is computed using forecasted ozone levels, a computer model that relates ozone levels to UV incidence on the ground, forecasted cloud amounts, and the elevation of the forecast cities. Some countries also use ground observations ( UNEP 2002). Spatial and Temporal Variation in UV Exposure The combination of total ozone and solar zenith angle, which is determined by the geographical position, season and time of the day, can lead to a variety of UV exposure situations (UNEP 2002). D iffey Weighting A weighting function that indicates which UV wavelengths are most efficient at burning human skin. When the weighting is multiplied by spectral irradiance and the product is integrated over all wavelengths, the result is diffey weighted ir radiance, a single number indicating the rate at which fair skin will redden. DUV Diffey weighted UV irradiance (watts/m& ) Direct Sun Refers to a measurement based only on direct radiation from the sun's disk and excluding indirect radiation from the remainder of the sky.

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136 II. Ozone related terms: O 3 (Ozone) A molecule consisting of three oxygen atoms. Ozone strongly absorbs short wavelength ultraviolet light and consequently protects life on earth from the damaging effects of this radiation. It is also a very reactive compound, which makes it a harmful air pollutant at the surface. Repeated exposure to ozone can make people more susceptible to respiratory infection and lung inflammation, and can aggravate preexisting respiratory diseases, such as asthma. Sometimes people refer to "good" (stratospheric) ozone and "bad" (surface) ozone. Ozone layer That level of the atmosphere which encompasses a peak in ozone concentrations, roughly 12 to 30 km above the surface. Total Column Ozone The total amount of ozone in a column of air stretching from the eart h's surface to space. More than 90% of the ozone is in the ozone layer at high altitude. Dobson Unit (DU) The unit of measure for total ozone or other gases. If you were to take all the o zone in a column of air stretching from the surface of the earth to space, and bring all that ozone to standard temperature (0 Celsius) and pressure (1013.25 millibars, or one atmosphere (atm)), the column would be about 0.3 centimeters thick. Thus, the to tal ozone would be 0.3 atm cm, or 300 Dobson Units (DU). III. Photospectroscopic and optical terms and abbreviations: a g absorption due to CDOM (gelbstoff) a p absorption due to particulate material a phi absorption due to pigmented material or phytopla nkton a w absorption due to pure water d average cosine of downwelling irradiance E irradiance I radiance b scattering K d attenuation coefficient for downwelling irradiance azimuth angle radiant flux % solid angle & zenith angle [chl ] chlorophyll concentration CDOM colored dissolved organic matter gelbstoff or gilvin yellow substance, also referred to as CDOM

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137 IV. Biological Response Terms MAAs Mycosporine like Amino Acids UVR absorbing compounds with broadband absor ption from 310 360 nm (Lesser 2006) HSP Heat Shock Proteins generalized stress response that is evolutionarily conserved; under stressful conditions, HSPs interact with proteins to maintain their conformation and function or in targeting damaged proteins for degradation (Lesser 2004)

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About the Author Lore M. Ayoub received her Bachelors degree in Biology from Bloomsburg University in 1982. She attended Lehigh University where she completed a M.S. Degree in Aquatic Ecosystems/Environmental Science, st udying the relative contributions of dissolved and particulate material to UV attenuation in temperate lakes. Thereafter she was employed in Bermuda as a scientist and educator Her graduate work at the University of South Florida with Dr. Pamela Hallock Muller and Dr. Paula Coble in the College of Marine Science has focused on factors controlling UV attenuation in the Florida Keys, and its influence on coral reef health. Her other projects at USF included population assemblages of fossil foraminifera literature research on storm water runoff in South Florida teaching assistant ship in Population Ecology and public outreach She led one scientific field mission using SCUBA for her doctoral research, and received advanced SCUBA certifications including AAUS Scientific Diver and NAUI Nitrox.


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Can colored dissolved organic material protect coral reefs by reducing exposure to ultraviolet radiation?
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ABSTRACT: Although mass coral bleaching events are generally triggered by high seawater temperatures, experiments have demonstrated that corals and reef-dwelling foraminifers bleach more readily when exposed to high energy, short wavelength solar radiation (blue, violet and ultraviolet [UVR]: Lambda ~ 280 490 nm). In seawater, colored dissolved organic matter (CDOM), also called gelbstoff, preferentially absorbs these shorter wavelengths, which consequently bleach and degrade the CDOM. Alteration of watersheds and destruction of coastal wetlands have reduced natural sources of CDOM to reefal waters. I tested the null hypothesis that CDOM does not differ between reefs that differ in coral health, and that water transparency to UVR is not a factor in reef health. I measured absorption of UVR and UV irradiance at various reefs in the Florida Keys that differ in distance from shore and degree of anthropogenic development of the adjacent shoreline.My results show that intact shoreline associated reefs and inshore reefs tend to be exposed to lower intensities of UVR, and lower degrees of photic stress, than developed shoreline associated reefs and offshore reefs. Absorption due to CDOM (ag320) was higher, and photic stress, as revealed by increased production of UV-absorbing compounds, Mycosporine like Amino Acids (MAAs), was lower at the surface compared to the bottom. The following results support my conclusion: ag320 and UV attenuation coefficients (Kd 's) were higher at intact compared to developed shoreline associated reefs, and at inshore compared to offshore reefs. Spectral slope, S, was higher at offshore compared to inshore reefs, indicating a higher degree of photobleaching of CDOM. Relative expression of MAAs was higher at developed compared to intact shoreline associated reefs, at offshore reefs compared to inshore reefs, and at the surface compared to the bottom.Solar energy reaching the benthos at two inshore reefs of the same depth (6m) was approximately an order of magnitude higher at the reef near developed shoreline compared to the reef near intact shoreline, and may be due to greater degree of diffuseness of the underwater light field combined with lower ag at the developed shoreline-associated reef.
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