Optical properties of corals distort variable chlorophyll ... · 5 96 actinic irradiance levels, rETR versus irradiance curves (i.e. light curves) can be determined, 97 which enables

1

Short title: Coral optics and variable chlorophyll fluorescence 1

Corresponding authors: [email protected], [email protected] 2

3

Optical properties of corals distort variable chlorophyll fluorescence 4

measurements 5

6

Daniel Wangpraseurt1,2,3a

, Mads Lichtenberg1, Steven L Jacques

4, Anthony WD Larkum

5, 7

Michael Kühl1,5a

8

9

1Marine Biological Section, Department of Biology, University of Copenhagen, 10

Strandpromenaden 5, DK-3000 Helsingør, Denmark 11

2Department of Chemistry, University of Cambridge, Lensfield Road, UK 12

3Scripps Institution of Oceanography, University of California, San Diego, USA 13

4Tufts University, USA 14

5Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, 15

Australia. 16

aCorresponding authors 17

18

Author contributions: D.W., M.L., A.W.D.L., M.K. conceived and designed the experiments; 19

D.W., M.L. and A.W.D.L. performed experiments, D.W., S.L.J. and M.K. analysed and 20

interpreted data; D.W. and S.L.J. developed optical models. D.W. wrote the article with 21

contributions from all authors. 22

23

Funding: This study was supported by a Carlsberg Foundation distinguished postdoctoral 24

fellowship (D.W.), a Carlsberg Foundation instrument grant (M.K.), and a Sapere-Aude 25

Advanced grant from the Independent Research Fund Denmark ǀ Natural Sciences (M.K.). 26

27

One-sentence summary: Variable chlorophyll fluorescence is distorted by the optical properties 28

of corals as demonstrated by experimental studies on hydrogel slabs and optical simulations. 29

30

Plant Physiology Preview. Published on January 28, 2019, as DOI:10.1104/pp.18.01275

Copyright 2019 by the American Society of Plant Biologists

www.plantphysiol.orgon June 2, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

mailto:[email protected]

mailto:[email protected]

http://www.plantphysiol.org

2

31

ABSTRACT 32

Pulse amplitude modulated (PAM) fluorimetry is widely used in photobiological studies of 33

corals, as it rapidly provides numerous photosynthetic parameters to assess coral ecophysiology. 34

Coral optics studies have revealed the presence of light gradients in corals, which are strongly 35

affected by light scattering in coral tissue and skeleton. We investigated whether coral optics 36

affects variable chlorophyll fluorescence measurements and derived photosynthetic parameters 37

by developing planar hydrogel slabs with immobilized microalgae and with bulk optical 38

properties similar to those of different types of corals. Our results show that PAM-based 39

measurements of photosynthetic parameters differed substantially between hydrogels with 40

different degrees of light scattering but identical microalgal density, yielding deviations in 41

apparent maximal electron transport rates by a factor of 2. Furthermore, system settings such as 42

the measuring light intensity affected F0, Fm and Fv/Fm in hydrogels with identical light 43

absorption but different degrees of light scattering. Likewise, differences in microalgal density 44

affected variable chlorophyll fluorescence parameters, where higher algal densities led to greater 45

Fv/Fm values and relative electron transport rates. These results have important implications for 46

the use of variable chlorophyll fluorimetry in ecophysiological studies of coral stress and 47

photosynthesis, as well as other optically dense systems such as plant tissue and biofilms. 48

49



3

INTRODUCTION 50

The ecological success of coral reefs is largely due to the successful symbiotic relationship 51

between the coral animal host and its photosymbiotic microalgae belonging to the genus 52

Symbiodinium. This highly efficient symbiotic interaction is susceptible to changes in 53

environmental conditions, such as excess solar radiation and above-average seawater 54

temperatures, which can lead to the breakdown of the coral-algal symbiosis and the visible 55

paling of the coral colony known as coral bleaching (Weis, 2008). Given the importance of 56

Symbiodinium photosynthesis for coral health, coral photosynthesis has been studied intensively 57

from molecular to environmental scales (Dubinsky and Falkowski, 2011; Falkowski et al., 1990). 58

Coral photosynthesis can be studied with techniques quantifying photosynthetic O2 production or 59

carbon fixation (Hoogenboom et al., 2012; Kühl et al., 1995; Osinga et al., 2012), but 60

photophysiological measurements based on variable chlorophyll (Chl) a fluorescence are now 61

widely used in coral research and many other areas of terrestrial and aquatic photosynthesis 62

research (Ralph and Gademann, 2005; Szabó et al., 2014; Warner et al., 1996; Warner et al., 63

2010). In contrast to gas exchange or C-fixation measurements that require significant sample 64

handling, variable chlorophyll fluorescence relies on optical light pulsing schemes that are 65

applied externally with minimal sample manipulation or directly in the natural habitat, and a 66

variety of commercial instruments for cuvette-based, fiber-optic or imaging measurements are 67

available (e.g. Schreiber, 2004). In coral reef science, pulse amplitude modulated (PAM) 68

chlorophyll a fluorimeters are by far the most commonly used instrument to probe 69

photosynthesis (Warner et al., 2010). 70

Variable chlorophyll fluorimetry quantifies the fate of absorbed light energy trapped by 71

the photosynthetic apparatus via changes in Chl a fluorescence, which tracks the redox status of 72



4

photosystem (PS) II and the balance between photochemical and non-photochemical quenching 73

processes. PAM-based measurements employ the so-called saturation pulse method (Schreiber, 74

2004). The PAM technique generates multiple photochemical charge separations (multiple 75

turnover) and fully reduces QA via the application of 50–1000-ms multiple turnover flashlets 76

(‘fat flashes’) (see Kromkamp and Forster, 2003). The fluorescence yield prior to the saturation 77

pulse indicates the level of fluorescence when QA is maximally oxidized and PSII reaction 78

centres are fully open. Such minimum fluorescence yield is denoted as F0 and F, referring to 79

dark- and light-acclimated samples, respectively. The saturation pulse is assumed to lead to the 80

complete closure of PSII reaction centers, such that photochemical quenching is fully inhibited 81

(Schreiber et al., 1993). Consequently, fluorescence emission is maximal and this parameter is 82

known as the maximal fluorescence yield, where Fm and Fm’ refer to dark- and light-acclimated 83

samples, respectively (Schreiber, 2004). From these measurements, many derived parameters 84

describe the photophysiology of the investigated sample. 85

In coral reef science, the most frequently used fluorescence parameter is the maximum 86

PSII quantum yield, which is calculated from saturation pulse measurements on dark-acclimated 87

samples as follows: Fv/Fm = (Fm-F0)/Fm. The Fv/Fm parameter is considered a key proxy for coral 88

health, and differences in Fv/Fm between coral measurements are interpreted as a change in coral 89

fitness (Jones et al., 2000; Wiedenmann et al., 2013). The effective quantum yield of PSII, 90

ФPSII= (Fm’-F)/Fm’, is determined via a saturation pulse measurement under a known actinic 91

irradiance of photosynthetic active radiation (PAR) (Genty et al., 1989). An estimate of the 92

relative PSII-derived photosynthetic electron transport rate is calculated as rETR = ФPSII x PAR 93

(Ralph and Gademann, 2005), whereas determination of the absolute ETR requires information 94

about the PSII absorption cross section (Szabó et al., 2014). When calculated over a range of 95



5

actinic irradiance levels, rETR versus irradiance curves (i.e. light curves) can be determined, 96

which enables the calculation of the maximum electron transport rate (ETRmax) and the light-use 97

efficiency factor (α), i.e., the initial slope of the rETR vs irradiance curve. Measurement 98

protocols for the application of PAM on corals are well-described (e.g. Warner et al. 2010), and 99

the maximum PSII quantum yield and rETR vs irradiance curve parameters are frequently used 100

to interpret the health and photo-physiological acclimation state of Symbiodinium within the 101

coral host (Ralph et al., 2005). 102

However, the application of variable chlorophyll fluorescence is based on the 103

assumptions that all photosynthetic entities (cells/chloroplasts) are (i) equally exposed to the 104

incident actinic light levels, (ii) equally exposed to the measuring light and emitting fluorescence 105

equally, and (iii) effectively saturated by the saturation pulse (Schreiber et al., 1996; Serôdio, 106

2004). In other words, it is assumed that (1) each photosynthetic cell has identical fluorescence 107

excitation/emission, and (2) the generated fluorescence from each cell has equal probability to be 108

detected by the fluorimeter. These assumptions are only met, if the light distribution within the 109

sample is homogenous, such as in optically dilute algal cultures (see e.g. Ting and Owens, 1992). 110

In contrast, most photosynthetic tissues exhibit strong scattering and absorption, leading to a 111

heterogenous distribution of irradiance within the sample (e.g., Evans, 2009; Evans et al., 2017; 112

Oguchi et al., 2011, Lichtenberg et al., 2017; Serôdio, 2004; Szabó et al., 2014). For instance, 113

steep light gradients exist in biofilms (Kuhl et al. 1994) which can lead to an effective 114

overestimation of ФPSII and ETR (Serôdio, 2004). Such gradients can also affect measurements 115

of the Chl a fluorescence kinetics (Susila et al., 2004). Re-absorption of fluorescence emission 116

can pose a challenge for Chl a fluorimetry in optically dense tissues (Naus et al., 1994; 117

Bartošková et al., 1999). A method for correcting variable fluorescence measurements in 118



6

optically dense algal media under constant optical geometries (e.g. cuvettes) has been proposed 119

(Klughammer and Schreiber, 2015), but this approach assumes a simple exponential light 120

attenuation (Lambert-Beer’s law), which is too simplistic for light-scattering photosynthetic 121

tissues (Kuhl et al. 1994, Wangpraseurt et al. 2016). 122

Knowledge of the tissue inherent optical properties (IOPs) allows us to predict light 123

propagation by solving the radiative transfer equation. The IOPs are defined as the probability of 124

light absorption per infinitesimal path length (µa, [mm-1

]), the probability of light scattering per 125

infinitesimal path length (µs, [mm-1

]), the anisotropy of scattering (g) (i.e. the average cosine 126

⟨cos θ⟩ of the scattering angle θ), and the refractive index (n). In strongly light-scattering 127

samples, µs is combined with g to define the reduced scattering coefficient µs’ = µs · (1-g) 128

(Jacques et al. 2013). The reduced scattering coefficient describes photon diffusion in a random 129

walk of step sizes of 1/ µs’, where each step involves isotropic scattering. Recent progress in 130

coral optics (Swain et al., 2016; Wangpraseurt et al., 2016a; Wangpraseurt et al., 2014b) revealed 131

that coral tissues and skeletons can be strongly light-scattering and that µs’ is variable between 132

coral species. For instance, µs’ of coral skeletons can vary by one order of magnitude (Marcelino 133

et al., 2013), thus substantially affecting the amount of light that is backscattered into the 134

overlying algal layer (Marcelino et al., 2013; Wangpraseurt et al., 2016a). Thick-tissued corals 135

can have light-scattering host pigments (e.g. green fluorescent protein, GFP) situated on top of 136

the algal layer (Lyndby et al., 2016; Wangpraseurt et al., 2017b). In such a scenario, light is 137

effectively scattered before it reaches Symbiodinium cells, leading to a strong surface 138

enhancement of scalar irradiance, E0 (=fluence rate) (Lyndby et al., 2016). 139

The absorption coefficient (µa) of corals is largely dependent on Symbiodinium cell 140

density and Chl a content per cell (Wangpraseurt et al. 2016). Algal densities in corals vary 141



7

seasonally (Chen et al., 2005) and in response to environmental stress (Glynn, 1996). 142

Symbiodinium density affects vertical light attenuation, where densely pigmented corals are 143

characterised by steep light gradients, while less-pigmented corals have a diffusely enhanced 144

tissue light environment (Wangpraseurt et al. 2017). The photosynthetic yield of Symbiodinium 145

can be vertically stratified within the coral tissue (Lichtenberg et al., 2016; Wangpraseurt et al., 146

2016b). During coral bleaching, microalgal symbionts experience photoinhibition (Warner et al., 147

1999) and such damage is likely more prominent in the light-exposed top layers of coral tissue 148

(Lichtenberg et al., 2016; Wangpraseurt et al., 2016b). Corals thus represent a challenging study 149

organism for variable Chl fluorimetry; yet, to our knowledge, no studies have aimed at ground 150

truthing the central assumptions of PAM measurements on corals. 151

The use of natural coral samples for such study would be easily contrived by variability 152

of the inherent optical properties of individual samples (e.g. changes in µa, µs’). To avoid this 153

variability, we developed optical analogues to corals using a biomedical tissue optics approach. 154

Optical phantoms are often created to solve problems related to the propagation of light in 155

scattering tissues, e. g., for calculating the light dose in photodynamic therapy and cancer 156

treatment (Pogue and Patterson, 2006). The optical response of human tissue is mimicked by 157

optical phantoms consisting of (1) a gel-like planar matrix (e.g. gelatin, agar or agarose), (2) 158

light-scattering particles (e.g. SiO2, TiO2, polystyrene microspheres) and (3) light absorbers (e.g. 159

intralipid, india ink) (Tuchin, 2007). 160

In this study, we created multiple planar hydrogel slabs to replicate the bulk optical 161

properties of corals and characterised their variable Chl fluorescence-derived parameters, 162

including Fv/Fm, Y(II) and rETR (Supplemental Table S1). Specifically, we examined the role of 163

light scattering by replicating three major coral categories: (1) corals with strongly 164



8

backscattering skeletons (‘skeleton’ hydrogel), (2) corals with low-scattering skeletons 165

(‘transparent’ hydrogel) and (3) corals with light scattering in skeleton and tissue (e.g. due to 166

GFP host pigments) (‘GFP’ hydrogel). We also assessed the role of light absorption for Chl a 167

fluorimetry by creating hydrogels with different microalgal densities and PS II efficiencies. 168

Furthermore, we developed a light-propagation model (chlorophyll fluorescence Monte Carlo 169

simulation, Chf-MC) that allows for prediction of the generated fluorescence and detected 170

fluorescence as a function of tissue optical properties. Although we focused on the widely 171

applied PAM method, it is also relevant for other variable Chl fluorescence methods such as fast 172

repetition rate fluorimetry (Gorbunov et al., 2001). The optical phantom approach (Fig. 1) and 173

numerical models can easily be altered to address identical questions in other light-scattering 174

samples such as leaves and biofilms. 175

RESULTS 176

Effects of measuring light settings and light scattering on variable chlorophyll fluorescence 177

Hydrogels with identical absorber density but different light-scattering properties showed up to 178

5-fold differences in F0 for the same measuring light (ML) intensity (Fig. 2 a-d). Highest F0 179

values were achieved for the skeleton hydrogel (F0=0.162, Fig. 2 b,d). ML intensity also affected 180

measurements of the maximal fluorescence yield (Fm) and the calculation of Fv/Fm (Fig. 2 e-f). 181

For ML=3-4, Fv/Fm values were about 0.74 for all three coral-mimicking hydrogels, while for 182

ML=<3 and >5, Fv/Fm values differed by up to 0.1 (Fig. 2f). 183

The in vivo light microenvironment measured with fibre optic microsensors differed for 184

the three coral-mimicking hydrogels, and photon scalar irradiance (400–700 nm) at the hydrogel 185

surface reached 109% (±0.85 SE; n=8) of the downwelling photon irradiance, Ed (Supplemental 186



9

Table S1) for the transparent hydrogel, 142% Ed (±9 SE; n=8) for the skeleton hydrogel, and 187

244% Ed (± 12.3 SE; n=8) for the GFP hydrogel (Fig. 3). The steepest light attenuation was 188

measured in the GFP hydrogel, and the lowest, in the transparent hydrogel (Fig. 3). The top layer 189

(0 µm to 750 µm) of the light-scattering GFP hydrogel (Fig. 1d) created a subsurface maximum 190

in scalar irradiance (at about 250 µm below the hydrogel surface); this was followed by rapid 191

light attenuation within the light-absorbing algal layer (750 µm to 1500 µm). For the skeleton 192

hydrogel, light attenuated to 125% Ed within the first 300 µm, after which light scattering by the 193

underlying layer caused a subsurface maximum around 700 µm from the hydrogel surface that 194

reached 170% Ed (Fig. 3). 195

Steady-state light curves revealed that the effective quantum yield of PSII (ФPSII) and the 196

derived relative electron transport rates (rETR) differed between the three coral-mimicking 197

hydrogels (Fig. 4a-d), where the shape of the curves depended on the light field parameter used 198

to quantify the actinic light level. When plotted as a function of downwelling photon irradiance 199

(Ed), the ФPSII was higher for the GFP hydrogel than for the skeleton and transparent hydrogel, 200

and this difference was larger for rETR calculations. For instance, at Ed =1000 µmol photons m-2

201

s-1

, rETR was about 1.5 times higher for the GFP vs the other two hydrogels (Fig. 4c). Correction 202

of ETR for in vivo scalar irradiance (E0) led to similar patterns between the GFP and skeleton 203

hydrogel, which now both showed higher rETRs than the transparent hydrogel (Fig. 4d). 204

Effects of light absorption on variable chlorophyll fluorescence 205

We constructed hydrogels with identical scattering properties but different light absorption 206

properties (Fig. 1j-m). Surface photon scalar irradiance (400–700 nm) in the hydrogel with 207

medium algal density (1.0 x 106 cells cm

-2) was about 1.4-fold higher than that in the hydrogel 208



10

with high algal density (3.5 x 106 cells cm

-2) (205% Ed ±. 0.27 SE vs 146% Ed ±. 0.51 SE; n=4). 209

This difference increased as a function of vertical depth, and measurements at depths of >2000 210

µm showed up to 3-fold enhanced scalar irradiance values in the medium- vs high–algal-density 211

hydrogel (Fig. 5a). 212

Microalgal density had a significant effect on estimates of the maximum quantum yield, where 213

hydrogels with 3.5 x 106 cells cm

-2 showed about 0.04 units higher Fv/Fm values than hydrogels 214

with 1.0 x 106 cells cm

-2 (student’s t-test: t(6)=11.25, p<0.01, Fig. 5b). Likewise, microalgal 215

density affected rETR, and at Ed=500 µmol photons m-2

s-1

, rETR was about 2.7-fold higher for 216

the high vs medium algal density hydrogel (rETR= 41.1 ± 0.1 vs 14.7 ± 0.8; n=4) (Fig. 5c). 217

Additionally, rETR values were corrected for the in vivo scalar irradiance, as determined with 218

scalar irradiance microsensors for each respective photic zone (i.e. the hydrogel layer that 219

contained microalgal cells). Correction for in vivo scalar irradiance slightly improved this 220

discrepancy, but calculations of rETRmax and the light-use efficiency factor (α) were still about 221

1.35 (rETRmax=80 vs 59) and 2-fold higher (α=0.22 and 0.11) for high- vs medium–algal-density 222

hydrogels. 223

Effects of bio-optical properties and simulated coral bleaching on variable chlorophyll 224

fluorescence 225

Hydrogels mimicking a stressed but not bleached coral, i.e., harbouring a top layer with high 226

algal density but low photosynthetic potential, showed low rETR and onset of photoinhibition 227

(Fig. 6). However, hydrogels mimicking a partially bleached and stressed tissue, i.e., harbouring 228

a top layer with reduced microalgal density and photosynthetic potential, showed moderate rETR 229

with rETRmax = 38 (at Ed> 500 µmol photons m-2

s-1

) and no signs of photoinhibition (Fig. 6). 230



11

DISCUSSION 231

Variable chlorophyll fluorimetry is a key tool for probing photosynthesis in vivo (Baker, 2008). 232

However, the assumptions underlying the calculation of variable chlorophyll fluorescence 233

parameters might not be fulfilled when measuring externally on highly stratified and dense 234

photosynthetic tissues, such as corals, biofilms and plant tissues (Evans, 2009; Serôdio, 2004; 235

Szabó et al., 2014). Our results showed that F0, Fm and Fv/Fm were affected by the scattering 236

properties of coral-mimicking hydrogels (Fig. 2). In a first approximation, we can describe the 237

detected F0 signal by using three simple terms: (1) the measuring light intensity incident on an 238

algal cell, i.e., fluorescence excitation, (2) the fluorescence emission per cell, which is governed 239

by the bio-physical properties of the cell, such as Chl a content and dark acclimation (Warner et 240

al., 2010), and (3) the probability that such emitted fluorescence is detected by the imaging 241

instrument (fluorescence escape) (see supplementary information). Because algal cells can 242

collect light from all directions, the excitation term is not described by the downwelling 243

irradiance of the measuring light, but by the scalar irradiance (=fluence rate) of measuring light 244

(Kühl et al., 1995), which in turn is affected by the tissue optical properties (Jacques, 2013) (see 245

optical simulations in supplementary information). In the first experiment (Fig. 1), we kept µa 246

constant while modulating µs’, which created characteristic differences in the light 247

microenvironment between three different coral tissue mimics (Fig. 3). The enhancement of 248

photon irradiance at the tissue surface of the skeleton hydrogel was due to the strong 249

backscattering (Fig. 3). In contrast, light attenuation was described by a simple exponential 250

attenuation for the transparent hydrogel (Fig. 3). 251

The observed differences in the F0 signal between the skeleton and transparent hydrogels 252

for a given measuring light intensity were due to two mechanisms (Fig. 7). Firstly, the fluence 253



12

rate of the measuring light was enhanced in the absorbing layer (0–750 µm depth) for the 254

skeleton vs. the transparent hydrogel (Fig. 3). The higher fluence rate led to an increased chance 255

of photon absorption and thus higher levels of fluorescence generation (see optical simulations in 256

Supplemental Figure S2). Secondly, although an individual algal cell acts as an isotropic point 257

source (i.e. emitting fluorescence equally well in all directions) (Schreiber, 2004), the detected 258

fluorescence signal depends on the propagation of fluorescent light from this point source, 259

through the tissue towards the fluorimeter (Welch et al., 1997). Because intact corals are 260

typically monitored externally using a fiber or camera in backscattering configuration, the 261

reflectivity of the skeleton controls the upwelling fluorescence towards the detector. For the 262

transparent hydrogel, the downwelling fluorescence was essentially lost, while backscattering by 263

the skeleton hydrogel led to an effective redirection of the otherwise-lost downwelling 264

fluorescence (Fig. 7). 265

For the GFP hydrogel, the light-scattering elements were placed on top of the light-266

absorbing algal layer (Fig. 1). Scattering diffuses the incident light, and diffuse light penetrates 267

less into biological tissue than collimated light (Tuchin, 2007; Wangpraseurt and Kühl, 2014) 268

(Supplemental Figure S2). Thus, although intense scattering in the top tissue layer would 269

enhance the chance of fluorescence emission and subsequent upwelling of generated 270

fluorescence, it also leads to a steep attenuation of the measuring light within the algal layer 271

(Lyndby et al., 2016; Fig. 3, Supplemental Figure S2). The vertical attenuation of photon scalar 272

irradiance (400–700 nm) within the light-absorbing layer was described according to Lambert–273

Beer’s law for the transparent and GFP hydrogels, yielding an attenuation coefficient that was 274

1.4-fold higher for the GFP vs. transparent hydrogel (1.7 mm-1

and 1.2 mm-1

, respectively; data 275

not shown). Together, these results exemplify that the F0 signal can be strongly affected by the 276



13

scattering properties of the photosynthetic tissue and the spatial arrangement of light-scattering 277

vs light-absorbing elements in the tissue. 278

Our results suggest that coral light-scattering modulated (i) the ability of the saturation 279

pulse to fully saturate PSII, (ii) the likelihood for actinic effects during ML probing, and (iii) the 280

operational volume that is probed during Fv/Fm measurements (Fig. 7). Fv/Fm values for the 281

skeleton hydrogel were more than 0.1 units (dimensionless) higher than for the transparent and 282

GFP hydrogels when probed with low ML intensities (Fig. 2). This likely indicates that skeleton 283

backscattering facilitated the full saturation of all photosynthetic cells within the tissue volume, 284

creating a homogenous light environment (Fig. 3) (Enriquez et al., 2005). In contrast, the steep 285

light gradient in the GFP hydrogels led to rapid attenuation of the saturation pulse light (Fig. 3), 286

leaving only about 50% of Ed in the lowest layers of the photic zone. In such a scenario, the 287

likelihood of incomplete PSII saturation increases with vertical tissue depth (Serôdio, 2004), thus 288

inducing lower Fm values for deeper tissue layers. Optical simulations using Chf-MC showed that 289

increased tissue scattering (from µs’=1 mm-1

to 10 mm-1

) reduced the tissue depth for which PSII 290

was fully saturated by >50% (for µa=0.1–1 mm-1

) (see supplementary information and 291

Supplemental Figure S4b). Chf-MC can serve as an initial point of reference for assessing the 292

likelihood of incomplete PSII saturation in the sample (Supplemental Figure S4b). Other 293

approaches, including the multiphase flash method, which uses ~1-s–long multiphase flashes to 294

saturate PSII, could provide additional instrument improvements that reduce the likelihood of 295

incorrect Fm’ estimates (Loriaux et al., 2013). 296

Optical scattering affected the ML intensity within the photosynthetic tissue and thus the 297

likelihood of ML inducing actinic effects (Supplemental Figure S5). The relationship between 298

measuring light used to probe for F and Fm can be nonlinear at higher light intensity settings, 299



14

leading to a decrease in the Fm to F ratio and thus a reduction in Fv/Fm values (Ting and Owens, 300

1992). Such non-linearity is caused by instrument optics, and although this has been tested only 301

for the PAM 101 (Ting and Owens, 1992), it is likely that the same artefacts contributed to the 302

observed decrease in Fv/Fm for higher ML settings when using the I-PAM system (Fig. 2f). 303

Light scattering affected the operational volume of the PAM instrument, i.e. the 304

contribution of fluorescence from different vertical tissue depths to observed fluorescence from 305

the sample (Supplemental Figures S2, S4a). For samples containing photosynthetic cells with 306

variable intrinsic PS II efficiency, differences in the operational volume could lead to a complex 307

mixture of fluorescence signals from different tissue depths (Fig. 6). Such mixed fluorescence 308

signals could theoretically be decomposed by calculating the depth-specific contribution to 309

observed fluorescence using Chf-MC (supplementary information). However, it is a pre-requisite 310

that the intrinsic properties of PS II efficiency are known (Klughammer and Schreiber, 2015). 311

The effective quantum yield of PSII (ФPSII) and rETR differed between the three light-312

scattering coral mimics (Fig. 4), and the rETR of the GFP hydrogel was greater than that of the 313

skeleton and transparent hydrogels when calculated with Ed as a measure of actinic light (Fig. 314

4c). Using the average E0 within the photic zone as a measure of actinic light reduced the 315

difference in rETR between the GFP and skeleton hydrogels, and the two light curves were 316

identical for E0 <400 µmol photons m-2

s-1

. This suggests that for low actinic light levels, 317

measurements of the average in vivo scalar irradiance within the entire photic zone can, to some 318

extent, correct for rETR estimates from corals with different degrees of light scattering 319

(Marcelino et al., 2013). For higher actinic irradiance, such correction was not successful, and 320

rETR was greater for the GFP hydrogel than for the skeleton hydrogel (Fig. 4d). The 321

enhancement of rETR in the GFP scenario was likely due to the presence of the steep light 322



15

gradient (Fig. 3), ensuring that the irradiance incident on lower cell layers enabled optimal 323

conditions for photosynthesis. 324

We found that both Fv/Fm and rETR were reduced for hydrogels with lower microalgal 325

cell density (Fig. 5b-d). Lower microalgal cell density decreased light absorption, which 326

enhanced the internal light microenvironment (Fig. 5a) and consequently lowered ФPSII. Given 327

that rETR is calculated by multiplying ФPSII with PAR, differences in the internal light 328

microenvironment can lead to substantial artefacts in the calculation of rETR (Fig. 4c). 329

Additionally, correct calculations of absolute ETR require knowledge of the absorption factor 330

(AF), which in itself is affected by optical scattering (Supplemental Figure S6; Szabo et al. 331

2014). 332

The Fv/Fm measurements were performed for hydrogels with different absorber densities 333

(at ML=2), which yielded the same F0 but higher Fm values for the hydrogel with enhanced 334

microalgal cell densities. Although the exact mechanisms underlying these differences are 335

unclear, these first measurements have important implications for coral science, given that 336

microalgal cell density is highly variable between coral species (Drew, 1972) and within a 337

species due to factors such as differences in light acclimation (Falkowski and Dubinsky, 1981), 338

seasonal fluctuations (Chen et al., 2005), and environmental stress (e.g. coral bleaching) (Weis, 339

2008). Bleached corals can exhibit an approximate doubling of the fluence rate within coral 340

tissues compared to healthy corals (Swain et al., 2016; Wangpraseurt et al., 2017a), and such 341

change in the internal light microenvironment was successfully mimicked with our hydrogels 342

with different absorber densities (Fig. 5a). Thus, differences in Fv/Fm and rETR between coral 343

individuals with different algal cell densities should be interpreted with caution and might, to 344



16

some extent, reflect different optical properties as well as differences in photophysiological 345

status. 346

PAM-based measurements are often used to assess changes in photochemical efficiency 347

during coral bleaching (Jones et al., 2000; Rodriguez-Roman et al., 2006). During such 348

environmental stress, both the optical properties of the coral and ФPSII of the algal symbiont 349

undergo changes over time (Iglesias-Prieto et al., 1992; Wangpraseurt et al., 2017a). Cells from 350

top layers exposed to supra-optimal irradiance are likely to be stressed to a greater extent than 351

cells from deeper layers (Lichtenberg et al., 2016; Wangpraseurt et al., 2016b). We found that 352

changes in cell density and spatial differences in ФPSII lead to a misinterpretation of variable 353

fluorescence signals. For instance, hydrogels mimicking stressed corals by containing a top layer 354

with normal algal cell density but with reduced photochemical efficiency, showed much lower 355

rETR than hydrogels mimicking bleached corals (see Fig. 1 and Table 1 for hydrogel 356

configurations). The high density of the low-performing cells in the top hydrogel layer, limited 357

the operational volume in the stressed-coral scenario. In contrast, a reduction in the cell density 358

of top layers, enhanced the operational volume to measurements of well-performing lower cell 359

layers, effectively enhancing rETR (Fig. 6). 360

The present experimental study has shown that coral optical properties can contrive the 361

interpretation of PAM-based fluorescence measurements. The next step is to develop theoretical 362

models that predict the likelihood of optical artefacts in a sample and ideally correct for such 363

artefacts. We have taken first steps by developing a Chl a fluorescence Monte Carlo model (Chf-364

MC) for photosynthetic tissues that allows for predicting the likelihood of PSII saturation, the 365

actinic effects of ML, the operational volume and depth distribution of the collected fluorescence 366

(see supplementary information). The simulations can be adjusted to account for absorption of 367



17

emitted fluorescence. The optical model is limited to a 1-layer system, which is best applicable 368

to structurally simple photosynthetic tissues. Future efforts should include the modelling of 369

chlorophyll a fluorescence in multiple tissue layers and in a 3D architecture (Fang, 2010). The 370

use of tissue phantoms with defined optical properties is a promising approach to examine and 371

qualify the precision of variable chlorophyll fluorimetry in plant tissues and biofilms. 372

Quantification of inherent optical parameters in photosynthetic tissues might furthermore lay the 373

experimental basis for better light-propagation models (Jacques, 1998; Mycek and Pogue, 2003; 374

Swartling et al., 2003), which will enable optimal measurement protocols and instrument 375

configurations. 376

METHODS 377

Experimental approach 378

Experiment 1 was aimed at understanding how differences in coral light scattering affect variable 379

chlorophyll fluorescence measurements in identical algal populations, i.e., same algal culture at 380

identical cell densities. Thick-tissued faviid corals often have light-scattering GFP granules on 381

top of the light-absorbing algal layer, which is also subject to light scattering from the coral 382

skeleton (Lyndby et al., 2016; Wangpraseurt et al., 2017b). The ‘GFP’ hydrogel consisted of a 3-383

layer system with a thin (750 µm) light-scattering upper layer (mimicking GFP scattering), a 384

light-absorbing layer (algae), and a thick light-scattering base layer (skeleton) (Fig. 1, Table 1). 385

However, not all corals follow this tissue arrangement, and other corals do not have light-386

scattering GFP granules. In thin-tissued corals, light scattering can be dominated by the 387

backscattering properties of the skeleton (Enriquez et al., 2005). To mimic this optical 388

configuration, the ‘skeleton hydrogel’ was prepared to be identical to the GFP hydrogel but 389



18

without the top GFP layer. In the ‘transparent’ hydrogel, the light-scattering skeleton layer was 390

replaced with a 1% agarose gel layer (see schematics in Fig. 1). 391

In Experiment 2, we examined how changes in coral light absorption might affect 392

variable chlorophyll fluorescence measurements. In healthy corals, algal densities can vary 393

seasonally from approximately 1.5 to 6 x 106 cells cm

-2 (Chen et al., 2005). We therefore created 394

hydrogels with microalgal densities of 3.5 x 106 cells cm

-2 (‘high density’) and 10

6 cells cm

-2 395

(‘medium density’) (Fig. 1, Table 1). 396

Experiment 3 mimicked a coral stress scenario in order to explore systematically, how 397

combined changes in microalgal density and photophysiology affect variable chlorophyll 398

fluorescence measurements in corals. We mimicked a ‘stressed coral’, where top algal layers 399

have reduced photosynthetic quantum yields, while lower layers are operating with high yields. 400

For this, we created a light-absorbing algal layer with Nanochloropsis sp. (thickness = 750 µm, 401

algal density = 2 x 106 cells cm

-2) on top of a Rhodomonas salina layer (thickness = 750 µm, 402

algal density = 2 x 106 cells cm

-2), exhibiting a Fv/Fm = 0.7. The double layer was placed on top 403

of the light-scattering skeleton hydrogel. We also created a hydrogel mimicking a ‘stressed and 404

bleached coral’ by using a reduced density of Nanochloropsis (3 x 105 cells cm

-2) in the top layer 405

(Table 1). The ‘healthy coral’ consisted of two layers of Rhodomonas salina (each 750 µm thick 406

and with an algal density of 2 x 106 cells cm

-2) on top of the high-backscatter hydrogel. 407

Hydrogel fabrication 408

To develop a hydrogel with light-scattering properties similar to those of corals, we used a 409

protocol developed for human tissues (Wagnières et al., 1997), where hydrogels with tissue-like 410

properties for visible light were constructed with a reduced scattering coefficient of µs’= 1.5 – 411



19

3.4 cm-1

between 400 to 450 nm (Wagnières et al., 1997). The reduced scattering coefficient of 412

coral skeletons is highly variable, with µs’ ranging between 3 and 140 cm-1

(Marcelino et al., 413

2013; Swain et al., 2016), and the optical properties of living coral tissue apparently exhibit a 414

similar variability (Wangpraseurt et al., 2016a). Given the variability in coral scattering, we did 415

not aim to quantify in detail the reduced scattering coefficient of our hydrogel, but rather to 416

develop a hydrogel that falls within the bulk part of light scattering observed in corals. 417

The developed hydrogels were composed of (1) a gel-like matrix, (2) light-scattering 418

particles, and (3) light-absorbing algae. We used a 1% agarose (Ultrapure low-melting-point 419

agarose; Thermo Scientific, Rochford, USA) solution in filtered (0.2 µm) seawater, which is 420

rather optically clear in the visible part (Wagnières et al., 1997). The agarose was prepared by 421

heating the agarose-seawater mixture in a microwave, ensuring that the solution was clear and 422

free of gas bubbles. The low agarose concentration ensured that the hydrogel was mechanically 423

similar to soft tissues such as coral tissue and exhibited gas diffusion properties similar to 424

seawater. Light scattering was achieved by mixing the hydrogel with defined concentrations of 425

silicon dioxide particles (size fraction: 99% between 0.5 – 10 µm and 80% between 1-5 µm, 426

Sigma Aldrich, USA) to achieve the desired scattering (see Table 1) (Wagnières et al., 1997). 427

Such silicon dioxide particles are non-toxic to microalgae and cyanobacteria (Dickson and Ely, 428

2013) and exhibit a good broadband scattering of white light at the chosen particle size 429

distribution (Wagnières et al., 1997). 430

After adding the silicon dioxide particles, the agarose solution was vortexed for about 30 431

seconds, ensuring a homogenous distribution of the light-scattering particles. The solution was 432

cooled down to about 30ºC, after which the microalgae were added at defined concentrations 433

(see Fig. 1). We selected two types of light-absorbing microalgae, Symbiodinium sp. and 434



20

Rhodomonas salina. Preliminary experiments were performed with Symbiodinium sp., while the 435

main experiments were performed with Rhodomonas salina, which was similar in cell size (8–10 436

µm) and was easier to grow and maintain in a healthy state. For both algal species, PAM-437

relevant blue light absorption is dominated by Chl a along with additional contributions by Chl c 438

(Kaňa et al., 2013; Wangpraseurt et al., 2014). However, for the purpose of this study, the type of 439

algal strain is largely irrelevant, as we investigated the effect of basic light-scattering 440

mechanisms on variable Chl a fluorescence measurements. The solution of agarose, SiO2 and 441

microalgae was transferred rapidly into petri dishes (diam. 35 mm, height 10 mm), where they 442

were left to cure for at least 30 min. 443

Apparent optical properties of tissue hydrogels 444

The light microenvironment of coral mimics was measured in vivo using scalar irradiance 445

microsensors (Rickelt et al., 2016) as described in detail elsewhere (Kühl, 2005; Wangpraseurt et 446

al., 2012). Briefly, scalar irradiance probes were constructed with a spherical isotropic light-447

collecting tip of ~80 µm (Rickelt et al. 2016). The probe was mounted on a motorised 448

micromanipulator (PyroScience GmbH, Germany) controlled by a PC running dedicated 449

software (Profix; PyroScience GmbH, Germany) and oriented at an angle of ~45º relative to the 450

vertically incident light. Measurements of spectral scalar irradiance were performed from the 451

surface of the hydrogel in vertical step sizes of 80 µm. The spectral scalar irradiance was then 452

integrated over the spectral range of photosynthetically active radiation (PAR, 400–700 nm) and 453

expressed in percentage of the incident downwelling irradiance (Ed) (Kühl 2005). 454

Variable chlorophyll fluorescence imaging 455



21

We used a variable chlorophyll fluorescence imaging system (Mini I-PAM, Walz, Effeltrich, 456

Germany) (Ralph et al., 2005; Kühl and Polerecky, 2008). The I-PAM was equipped with blue 457

LEDs (460 nm) and delivered a maximum saturation pulse intensity (SP =10) of >2700 µmol 458

photons m-2

s-1

. The ML intensity was calibrated for ML1-12 at frequency 1 using a fast data 459

logger (ULM 500, Walz GmbH, Germany) connected to cosine-corrected PAR sensor, yielding 460

an average photon irradiance output of 0.3, 0.4, 0.6, 0.8, 1, 1.2, 1.4, 1.6, 1.8, 2.1, 2.3, 2.6 µmol 461

photons m-2

s-1

. The I-PAM system was mounted on a heavy stand and the hydrogels 462

illuminated vertically from above. Initial measurements were performed to calibrate the focal 463

distance and aperture settings between the camera head and hydrogel samples, after which, focus 464

and aperture were fixed. All measurements were performed with the hydrogels within petri 465

dishes that were placed on top of a black light-absorbing surface. Measurements were performed 466

in a darkened room. 467

Measurements were performed with dark-acclimated samples (after about 30 min in 468

darkness) to examine differences in the background fluorescence between the ‘transparent, 469

‘skeleton’ and ‘GFP’ hydrogels. For each measurement, the PAM settings were fixed (measuring 470

light intensity, ML= 4, gain=1, damping=2, frequency=1). Measurements were also performed to 471

examine the effects of changes in measuring light intensity on F0, Fm and the calculated Fv/Fm. 472

Each sample was measured at a range of measuring light intensities (ML settings ranging 473

between 1 and 12), beginning with the lowest measuring light intensity setting. For each 474

measuring light intensity, a saturation pulse was applied for 720 ms (intensity setting =10, 475

yielding 2700 µmol photons m-2

s-1

), and a resting period of 1 min was used between saturation 476

pulses. 477



22

We also examined the effects of light scattering on samples illuminated with defined 478

actinic irradiance levels, i.e., light-acclimated samples. Steady-state light curves of rETR versus 479

photon irradiance were measured over a range of actinic incident photon irradiances of PAR 480

(400–700 nm) ranging from 0 to about 1600 µmol photons m-2

s-1

. For each light curve, the 481

sample was dark-acclimated for about 15 min before a light curve was measured using an 482

exposure time of 5 min at each irradiance level. Prior to starting the steady-state light curves, the 483

measuring light intensity was adjusted such that F0 for the different coral mimics yielded 484

comparable values (i.e. F0=0.08). Likewise, measuring light intensity was adjusted such that 485

F0=0.08 for experiments 2 and 3 (Fig. 1). 486

Data analysis 487

The effective photosynthetic quantum yield of PSII was calculated as ФPSII= (Fm’-F)/Fm’ and 488

relative photosynthetic PSII electron transport rates were calculated as rETR = PAR x ФPSII 489

(Baker, 2008). Calculated rETR versus photon irradiance curves were fitted with an exponential 490

function (Webb et al., 1974) to estimate the maximal relative PSII electron transport rates 491

(rETRmax) and the light-use efficiency factor, α. Non-linear curve fitting was performed in Origin 492

(Origin Pro 9.3, USA) using a Levenberg-Marquart least squares fitting algorithm. 493

Optical simulations 494

A probability light distribution model was developed to calculate the depth-dependent generation 495

and escape of Chl fluorescence (Chf-MC). Details of the model and optical simulations can be 496

found in the supplementary information (Supplemental Text S1). 497

498



23

Supplemental Data 499

500

Supplemental Text S1. Fluorescent Monte Carlo model to simulate the effect of changes in light 501

scattering and pigment density on calculations of the PSII maximum quantum yield. 502

Supplemental Figure S1. Schematic of photon energy flow in PAM-based variable chlorophyll 503

fluorescence measurements. 504

Supplemental Figure S2. Chlorophyll fluorescence Monte Carlo model simulating the 505

penetration of measuring light. 506

Supplemental Figure S3. Chlorophyll fluorescence Monte Carlo model investigating the effect 507

of re-absorption on observed fluorescence. 508

Supplemental Figure S4. Chlorophyll fluorescence Monte Carlo model calculating the 509

penetration depth of the generated fluorescence. 510

Supplemental Figure S5. Chlorophyll fluorescence Monte Carlo model calculating the % of 511

photosynthetic tissue overexposed by ML. 512

Supplemental Figure S6. 2-Layer Monte Carlo Simulation of light absorption by microalgal 513

cells for the skeleton hydrogel showing the effect skeletal backscattering on the tissue absorption 514

factor. 515

Supplemental Table S1. Abbreviations 516

517



24

Supplemental Text S1. Fluorescent Monte Carlo model to simulate the effect of changes in light 518

scattering and pigment density on calculations of the PSII maximum quantum yield (Fv/Fm). 519

Supplemental Figure S1. Schematic of photon energy flow in PAM-based variable chlorophyll 520

fluorescence measurements. 521

Supplemental Figure S2. Chlorophyll fluorescence Monte Carlo model (chf-MC) simulating the 522

penetration of measuring light MLd (675 nm) in J mm-2

(A), the depth-dependent F0 generation [J 523

mm-2

](B), the depth-dependent escape of generated fluorescence Fesc(700 nm) [dimensionless] 524

(C), and the observed fluorescence Fobs [J mm-2

](D). 525

Supplemental Figure S3. Chlorophyll fluorescence Monte Carlo model (chf-MC) investigating 526

the effect of re-absorption on observed fluorescence. The penetration of measuring light MLd 527

(675 nm) in J mm-2

(A), the depth-dependent F0 generation [J mm-2

] (B), the depth-dependent 528

escape of generated fluorescence (700nm) [dimensionless] (C) and the observed fluorescence 529

(D). The absorption coefficient at 675 nm was µa=0.15 mm-1

and the reduced scattering 530

coefficient was µs’= 1 mm-1

. The absorption coefficient of the re-emitted fluorescence was varied 531

between µa=0.05 mm-1

(red), 0.03 mm-1

(black), 0.01 mm-1

(green) and 0 mm-1

(blue). 532

Supplemental Figure S4. Chlorophyll fluorescence Monte Carlo model (chf-MC) calculating 533

the penetration depth, i.e., the depth over which at least 90% of the generated fluorescence 534

originates from (a), and the saturation depth, i.e., the depth for which all photosynthetic cells are 535

saturated by a saturation pulse of 2800 µmol photons m-2

s-1

, assuming a saturation threshold of 536

1500 µmol photons m-2

s-1

(b). The dependency on the reduced scattering coefficient µs’ and µa is 537

modeled using chf-MC. 538



25

Supplemental Figure S5. Chlorophyll fluorescence Monte Carlo model (chf-MC) calculating 539

the % of photosynthetic tissue overexposed by ML, for standard setting of the measuring light of 540

ML=3 (A), ML=4 (B) and ML=5 (C). A threshold for overexposure is assumed (0.5 µmol 541

photons m-2

s-1

). 542

Supplemental Figure S6. 2-Layer Monte Carlo Simulation of light absorption by microalgal 543

cells for the skeleton hydrogel showing the effect skeletal backscattering on the tissue absorption 544

factor. 545

Supplemental Table S1. Abbreviations 546

547

548

Acknowledgements 549

This study was supported by a Sapere-Aude Advanced grant from the Independent Research 550

Fund Denmark ǀ Natural Sciences (MK), and by the Carlsberg Foundation via a distinguished 551

postdoctoral scholarship grant (DW), and an instrument grant (MK). We thank Sofie Jakobsen 552

for excellent technical assistance, and Lars Rickelt for manufacturing scalar irradiance 553

microprobes. 554

555



26

Table 1. Material properties of coral tissue–mimicking hydrogels. The algal species was 556

Rhodomonas salina unless indicated otherwise. 557

Experiment Hydrogel Top layer Mid layer Base layer

Coral

scattering

GFP matrix ASW+ 1% agarose ASW+ 1% agarose ASW+ 1% agarose

SiO2 4% / 5%

algae / 2.5 x 106 cells cm-2 /

thickness 0.75 mm 0.75 mm 2.5 mm

Skeleton matrix / ASW+ 1% agarose ASW+ 1% agarose

SiO2 / / 15%


thickness / 0.75 mm 2.5 mm

Transparent matrix ASW+ 1% agarose ASW+ 1% agarose

SiO2 / / /



Coral absorption High matrix / ASW+ 1% agarose ASW+ 1% agarose

SiO2 / 1% 5%



Medium matrix / ASW+ 1% agarose ASW+ 1% agarose

SiO2 / 1% 5%

algae / 1 x 106 cells cm-2 /


Coral stress Stressed matrix ASW+ 1% agarose ASW+ 1% agarose ASW+ 1% agarose

SiO2 / / 5%

algae 2 x 106 cells cm-2

(N. oculata)

2 x 106 cells cm-2

/


Stressed and

bleached

matrix ASW+ 1% agarose ASW+ 1% agarose ASW+ 1% agarose

SiO2 / / 5%

algae 0.3 x 106 cells cm-2

(N. oculata)

2 x 106 cells cm-2

/


Healthy matrix ASW+ 1% agarose ASW+ 1% agarose ASW+ 1% agarose

SiO2 / / 5%

algae 2 x 106 cells cm-2

2 x 106 cells cm-2

/


558



27

Figure Legends 559

Figure 1: Coral tissue organisation and artificial tissue design. a-c) Basic organisation of 560

scleractinic corals. a) Small fragment of a faviid coral (scale bar = 1 mm). b) close-up of the 561

cross-section, revealing the white coral skeleton, the brown algal layer on top of the skeleton, 562

and the green fluorescent protein like-pigment granules (GFP) on the coral tissue surface (scale 563 bar = 1mm). c) close-up of GFP granules (scale bar = 200 µm). d-i) Coral tissue mimicking 564

hydrogels. Schematics of 3-layer ‘GFP’ (d), 2-layer ‘skeleton’ (e), and 2-layer ‘transparent’(f) 565

designs. g-i) Respective photographs of thin cross sections of hydrogels. j-m) Hydrogels for 566

investigating the effect of changes in coral absorption. j-k) High microalgal density tissue design 567

(j) and top view photograph (k). l-m) Medium microalgal density hydrogel (l) and top view 568

photograph (m). n-p) Hydrogels for investigating the effect of coral stress. n) ‘Healthy’ coral 569

design with 2 layers of Rhodomonas sp., o) ‘Stressed’ coral design with 1 layer of 570

Nanochloropsis sp. on top of 1 layer of Rhodomonas sp., p) ‘Bleaching’ design with 1 layer of 571

Nanochloropsis sp. of a reduced cell density on top of Rhodomonas salina. 572

Figure 2. Effect of light scattering on variable chlorophyll fluorescence parameters of dark 573 acclimated coral tissue mimicking hydrogels. (a-c) Example images of minimal fluorescence 574

yields (F0) for measuring light intensity = 4, showing GFP (a), skeleton (b) and transparent (c) 575

hydrogels. The white circle shows the area over which F0 was integrated. Effect of measuring 576

light intensity on F0, (d), Fm, maximal fluorescence yield (e), and the maximum PSII quantum 577 yield, Fv/Fm (f). Note that no measurements are shown at ML>4 (=0.8 µmol photons m

-2 s

-1) and 578

ML>8 (= 1.6 µmol photons m-2

s-1

) for skeleton and transparent hydrogels, respectively due to 579

indications of actinic effects in these hydrogels at higher measuring light levels. 580

Figure 3. In vivo light microenvironment in coral tissue mimicking hydrogels with different 581 scattering properties. Photon scalar irradiance of PAR (400-700 nm) was normalised to the 582 incident downwelling irradiance of PAR and plotted against the vertical depth (µm) of the coral 583

mimics. The algal layer is distributed between depth = 0 µm to 750 µm for the transparent (red) 584

and skeleton (blue) mimic, while the algal layer is between 750-1500 µm in the GFP (green) 585

mimic. Four replicate gels were measured at 2 random spots (total n=8 ± SE). 586

Figure 4. Effect of light scattering on the effective quantum yield ФPSII (a-b) and relative 587

electron transport rates (rETR) (c-d) of coral tissue mimicking hydrogels. Measured ФPSII 588

and calculated rETR were plotted as a function of the incident downwelling irradiance (Ed) (a,c) 589

and with the corrected in vivo scalar irradiance (E0) (b,d). Symbols with error bars represent 590

means ± SE (n=5 biological replicates). 591

Figure 5. Effect of coral light absorption on the light microenvironment and variable 592

chlorophyll fluorescence measurements. Photon scalar irradiance (400-700 nm) was 593

normalised to the incident downwelling irradiance (Ed) and plotted against the vertical depth 594

(µm) in the coral mimics. The algal layer is distributed between 0-750 µm depth (a). The 595

maximum quantum yield of PSII, Fv/Fm (b). Relative electron transport rates (rETR) calculated 596

as a function of the incident downwelling irradiance (Ed) (c) and corrected for in vivo scalar 597

irradiance (E0) (d). All measurements were performed in coral hydrogels mimicking high algal 598



28

density (3.5 x 106 cells cm

-2) and medium algal density (1.0 x 10

6 cells cm

-2). Symbols represent 599

means ± SE (n=4 biological replicates) in panel a-c. The curve fit shown in panel d was the best 600

fit to the experimental data (R2= 0.98 and 0.80) yielding values of ETRmax= 80 and 59, and 601

α=0.22 and 0.11 for the high and medium algal density coral hydrogels, respectively. 602

Figure 6. Combined effects of bio-optical properties and simulated coral bleaching on 603

measured relative electron transport rates (rETR). Hydrogels mimicking healthy tissue 604

contained two dense layers of R. salina (4 x 106 cells cm

-2), hydrogels mimicking stressed tissue 605

contained one dense layer of N. oculata (2 x 106 cells cm

-2) and one dense layer of R. salina (2 x 606

106 cells cm

-2), and hydrogels mimicking bleached tissue contained one layer of N. oculuata at 607

low density (0.3 x 106 cells cm

-2) and one dense layer of R. salina. Data are means ± SE (n=2-3 608

hydrogel replicates). 609

Figure 7. Propagation of PAM-based measuring light in biological tissues with different 610

scattering coefficients. a-b) Excitation (blue) and chlorophyll fluorescence (red) for transparent 611

hydrogel (a) and skeleton hydrogel (b). The optical properties of the light absorbing top layer 612

(layer 1) are constant (i.e. identical algal density and bio physical properties of an algal cell) for 613

both gels, but layer 2 is either transparent or light scattering. For the transparent hydrogel, 614

measuring light absorption by an algal cell (s) is a function of the primary incident beam (solid 615

blue line), while indirect light (dotted blue lines) is lost through the transparent layer. For the 616

skeleton hydrogel, indirect light is redirected via backscattering by layer 2. Such scattering 617

enhances the chance of measuring light absorption and thus leads to greater fluorescence 618

emission (bold red arrows). Fluorescence emission is an isotropic process but the propagation of 619

fluorescent light is affected by tissue optical properties. For the transparent hydrogel, only 620

primary upwelling fluorescence (Fu1) contributes to the detected fluorescence signal, while for 621

the skeleton hydrogel the downwelling fluorescence (Fd) is redirected and adds to the upwelling 622

fluorescence (Fu2). c) A steep light gradient (green line) leads to an underrepresentation of 623

fluorescence detection from lower cell layers compared to a homogenous light environment 624

(black line), given that the operational volume (dotted lines) from which fluorescence is 625

collected is a function of the theoretical instrument detection limit (Elimit) which is modulated by 626

the in vivo photon scalar irradiance. 627

628

References 629

Baker NR (2008) Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annual Review in 630

Plant Biology 59: 89-113 631

Bartošková H, Nauš J, Výkruta M (1999) The arrangement of chloroplasts in cells influences the 632

reabsorption of chlorophyll fluorescence emission. The effect of desiccation on the 633



29

chlorophyll fluorescence spectra of Rhizomnium punctatum leaves. Photosynthesis 634

Research 62: 251-260 635

Chen, Wang AT, Fang LS, Yang YW (2005) Fluctuating algal symbiont communities in 636

Acropora palifera (Scleractinia : Acroporidae) from Taiwan. Marine Ecology Progress 637

Series 295: 113-121 638

Dickson DJ, Ely RL (2013) Silica sol-gel encapsulation of cyanobacteria: lessons for academic 639

and applied research. Applied Microbiology and Biotechnology 97: 1809-1819 640

Drew EA (1972) The biology and physiology of alga-invertebrates symbioses. II. The density of 641

symbiotic algal cells in a number of hermatypic hard corals and alcyonarians from 642

various depths. Journal of Experimental Marine Biology and Ecology 9: 71-75 643

Dubinsky Z, Falkowski P (2011) Light as a source of information and energy in zooxanthellate 644

corals. Coral Reefs: An Ecosystem in Transition: 107-118 645

Enriquez S, Mendez ER, Iglesias-Prieto R (2005) Multiple scattering on coral skeletons enhances 646

light absorption by symbiotic algae. Limnology and Oceanography 50: 1025-1032 647

Evans JR (2009) Potential errors in electron transport rates calculated from chlorophyll 648

fluorescence as revealed by a multilayer leaf model. Plant and Cell Physiology 50: 698-649

706 650

Evans JR, Morgan PB, von Caemmerer S (2017) Light quality affects chloroplast electron 651

transport rates estimated from Chl fluorescence measurements. Plant and Cell Physiology 652

58: 1652-1660 653

Falkowski PG, Dubinsky Z (1981) Light-shade adaptation of Stylophora pistillata, a hermatypic 654

coral from the Gulf of Eilat. Nature 289: 172-174 655

Falkowski PG, Jokiel PL, Kinzie R (1990) Irradiance and corals. Ecosystems of the World 25: 656

89-107 657

Fang Q (2010) Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates. 658

Biomedical optics express 1: 165-175 659

Genty B, Briantais J-M, Baker NR (1989) The relationship between the quantum yield of 660

photosynthetic electron transport and quenching of chlorophyll fluorescence. Biochimica 661

et Biophysica Acta (BBA) 990: 87-92 662

Glynn PW (1996) Coral reef bleaching: Facts, hypotheses and implications. Global Change 663

Biology 2: 495-509 664

Gorbunov MY, Kolber ZS, Lesser MP, Falkowski PG (2001) Photosynthesis and 665

photoprotection in symbiotic corals. Limnology and Oceanography 46: 75-85 666

Hoogenboom MO, Campbell DA, Beraud E, DeZeeuw K, Ferrier-Pagès C (2012) Effects of 667

light, food availability and temperature stress on the function of photosystem II and 668

photosystem I of coral symbionts. PLoS ONE 7: e30167 669

Iglesias-Prieto R, Matta JL, Robins WA, Trench RK (1992) Photosynthetic response to elevated 670

temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture. 671

Proceedings of the National Academy of Sciences USA 89: 10302-10305 672

Jacques SL (1998) Light distributions from point, line and plane sources for photochemical 673

reactions and fluorescence in turbid biological tissues. Photochemistry and Photobiology 674

67: 23-32 675

Jacques SL (2013) Optical properties of biological tissues: a review. Physics in Medicine and 676

Biology 58: R37 677



30

Jones RJ, Ward S, Amri AY, Hoegh-Guldberg O (2000) Changes in quantum efficiency of 678

photosystem II of symbiotic dinoflagellates of corals after heat stress, and of bleached 679

corals sampled after the 1998 Great Barrier Reef mass bleaching event. Marine and 680

Freshwater Research 51: 63-71 681

Kaňa R, Kotabová E, Prášil O (2013) Presence of flexible non-photochemical quenching in 682

cryptophytes (Rhodomonas salina), Photosynthesis Research for Food, Fuel and the 683

Future. Springer, pp. 489-492 684

Klughammer C, Schreiber U (2015) Apparent PS II absorption cross-section and estimation of 685

mean PAR in optically thin and dense suspensions of Chlorella. Photosynthesis Research 686

123: 77-92 687

Kühl M (2005) Optical microsensors for analysis of microbial communities. Methods in 688

Enzymology 397: 166-199 689

Kühl M, Jørgensen BB (1994) The light-field of microbenthic communities – radiance 690

distribution and microscale optics of sandy coastal sediments. Limnology and 691

Oceanography 39: 1368-1398 692

Kühl M, Cohen Y, Dalsgaard T, Jørgensen BB, Revsbech NP (1995) Microenvironment and 693

photosynthesis of zooxanthellae in scleractinian corals studied with microsensors for O2, 694

pH and Light. Marine Ecology Progress Series 117: 159-172 695

Kühl M, Glud RN, Borum J, Roberts R, Rysgaard S (2001) Photosynthetic performance of 696

surface-associated algae below sea ice as measured with a pulse-amplitude-modulated 697

(PAM) fluorometer and O₂ microsensors. Marine Ecology Progress Series 223: 1-14 698

Lichtenberg M, Kühl M (2015) Pronounced gradients of light, photosynthesis and O2 699

consumption in the tissue of the brown alga Fucus serratus. New Phytologist 207: 559-700

569 701

Lichtenberg M, Larkum AW, Kühl M (2016) Photosynthetic acclimation of Symbiodinium in 702

hospite depends on vertical position in the tissue of the scleractinian coral Montastrea 703

curta. Frontiers in microbiology 7:230 704

Lichtenberg M, Trampe ECL, Vogelmann TC, Kühl M (2017) Light sheet microscopy imaging 705

of light absorption and photosynthesis distribution in plant tissue. Plant Physiology 175: 706

721-733 707

Loriaux SD, Avenson TJ, Welles JM, Mc Dermirr DK, Eckles RD, Riensche B, and Genty B 708

(2013) Closing in on maximum yield of chlorophyll fluorescence using a single 709

multiphase flash of sub-saturating intensity. Plant Cell & Environment 36: 1755-1770 710

Lyndby NH, Kühl M, Wangpraseurt D (2016) Heat generation and light scattering of green 711

fluorescent protein-like pigments in coral tissue. Scientific Reports 6: 26599 712

Marcelino LA, Westneat MW, Stoyneva V, Henss J, Rogers JD, Radosevich A, Turzhitsky V, 713

Siple M, Fang A, Swain TD (2013) Modulation of light-enhancement to symbiotic algae 714

by light scattering in corals and evolutionary trends in nleaching. PLoS ONE 8: e61492 715

Mourant JR, Fuselier T, Boyer J, Johnson TM, Bigio IJ (1997) Predictions and measurements of 716

scattering and absorption over broad wavelength ranges in tissue phantoms. Applied 717

optics 36: 949-957 718

Mycek M-A, Pogue BW (2003) Handbook of biomedical fluorescence. CRC Press 719

Naus J, Klinkovsky T, Ilik P, Cikanek D (1994) Model studies of chlorophyll fluorescence 720

reabsorption at chloroplast level under different exciting conditions. Photosynthesis 721

Research 40: 67-74 722



31

Oguchi R, Douwstra P, Fujita T, Chow WS, Terashima I (2011) Intra‐leaf gradients of 723

photoinhibition induced by different color lights: implications for the dual mechanisms of 724

photoinhibition and for the application of conventional chlorophyll fluorometers. New 725

Phytologist 191: 146-159 726

Osinga R, Iglesias-Prieto R, and Enriquez S (2012) Measuring photosynthesis in symbiotic 727

invertebrates: a review of methodologies, rates and processes, in Applied Photosynthesis, 728

ed. M. Najafpour (Rijeka: InTech), 229–256 729

Pogue BW, Patterson MS (2006) Review of tissue simulating phantoms for optical spectroscopy, 730

imaging and dosimetry. Journal of Biomedical Optics 11: 041102-041102-041116 731

Ralph P, Gademann R, Larkum A, Schreiber U (1999) In situ underwater measurements of 732

photosynthetic activity of coral zooxanthellae and other reef-dwelling dinoflagellate 733

endosymbionts. Marine Ecology Progress Series: 139-147 734

Ralph PJ, Gademann R (2005) Rapid light curves: a powerful tool to assess photosynthetic 735

activity. Aquatic Botany 82: 222-237 736

Ralph PJ, Schreiber U, Gademann R, Kühl M, Larkum AW (2005) Coral photobiology studied 737

with a new imaging pulse amplitude modulated fluorometer. Journal of Phycology 41: 738

335-342 739

Rickelt LF, Lichtenberg M, Trampe ECL, Kühl M (2016) Fiber‐optic probes for small‐scale 740

measurements of scalar irradiance. Photochemistry and Photobiology 92: 331-342 741

Rodriguez-Roman A, Hernandez-Pech X, Thome PE, Enriquez S, Iglesias-Prieto R (2006) 742

Photosynthesis and light utilization in the Caribbean coral Montastraea faveolata 743

recovering from a bleaching event. Limnology and Oceanography 51: 2702-2710 744

Schreiber U (2004) Pulse-amplitude-modulation (PAM) fluorometry and saturation pulse 745

method: an overview. Chlorophyll a Fluorescence: A Signature of photosynthesis. 746

Springer. pp 279-319 747

Schreiber U, Kühl M, Klimant I, Reising H (1996) Measurement of chlorophyll fluorescence 748

within leaves using a modified PAM Fluorometer with a fiber-optic microprobe. 749

Photosynthesis Research 47: 103-109 750

Schreiber U, Neubauer C, Schliwa U (1993) PAM fluorometer based on medium-frequency 751

pulsed Xe-flash measuring light: a highly sensitive new tool in basic and applied 752

photosynthesis research. Photosynthesis Research 36: 65-72 753

Serôdio J (2004) Analysis of variable chlorophyll fluorescence in microphytobenthos 754

assemblages: implications of the use of depth-integrated measurements. Aquatic 755

Microbial Ecology 36: 137-152 756

Sušila P, Lazár D, Ilík P, Tomek P, Nauš J (2004) The gradient of exciting radiation within a 757

sample affects the relative height of steps in the fast chlorophyll a fluorescence rise. 758

Photosynthetica 42: 161-172 759

Swain TD, DuBois E, Gomes A, Stoyneva VP, Radosevich AJ, Henss J, Wagner ME, Derbas J, 760

Grooms HW, Velazquez EM (2016) Skeletal light-scattering accelerates bleaching 761

response in reef-building corals. BMC Ecology 16: 1 762

Swartling J, Pifferi A, Enejder AM, Andersson-Engels S (2003) Accelerated Monte Carlo 763

models to simulate fluorescence spectra from layered tissues. Journal of the Optical 764

Society of America A 20: 714-727 765

Szabó M, Wangpraseurt D, Tamburic B, Larkum AW, Schreiber U, Suggett DJ, Kühl M, Ralph 766

PJ (2014) Effective light absorption and absolute electron transport rates in the coral 767

Pocillopora damicornis. Plant Physiology and Biochemistry 83: 159-167 768



32

Ting CS, Owens TG (1992) Limitations of the pulse-modulated technique for measuring the 769

fluorescence characteristics of algae. Plant Physiology 100: 367-373 770

Tuchin VV (2007) Tissue optics: light scattering methods and instruments for medical diagnosis. 771

Bellingham, WA, USA’ The International Society for Optical Engineering. 772

van der Kooi CJ, Elzenga JTM, Dijksterhuis J, Stavenga DG (2017) Functional optics of glossy 773

buttercup flowers. Journal of the Royal Society Interface 14: 20160933 774

Vogelmann TC, Evans J (2002) Profiles of light absorption and chlorophyll within spinach 775

leaves from chlorophyll fluorescence. Plant, Cell & Environment 25: 1313-1323 776

Wagnières G, Cheng S, Zellweger M, Utke N, Braichotte D, Ballini J-P, van den Bergh H (1997) 777

An optical phantom with tissue-like properties in the visible for use in PDT and 778

fluorescence spectroscopy. Physics in Medicine and Biology 42: 1415 779

Wangpraseurt D, Larkum AWD, Ralph PJ, Kühl M (2012) Light gradients and optical 780

microniches in coral tissues. Frontiers in Microbiology 3:316 781

Wangpraseurt D, Holm JB, Larkum AWD, Pernice M, Ralph PJ, Suggett DJ, Kühl M (2017a) In 782

vivo microscale measurements of light and photosynthesis during coral bleaching: 783

evidence for the optical feedback loop? Frontiers in Microbiology 8:59 784

Wangpraseurt D, Jacques SL, Petrie T, Kühl M (2016a) Monte Carlo modeling of photon 785

propagation reveals highly scattering coral tissue. Frontiers in Plant Science 7:1404 786

Wangpraseurt D, Kühl M (2014) Direct and diffuse light propagation through coral tissue, SPIE 787

BiOS. International Society for Optics and Photonics, 894117-894117-894116 788

Wangpraseurt D, Larkum AWD, Franklin J, Szabo M, Ralph PJ, Kühl M (2014a) Lateral light 789

transfer ensures efficient resource distribution in symbiont-bearing corals. Journal of 790

Experimental Biology 217: 489-498 791

Wangpraseurt D, Pernice M, Guagliardo P, Kilburn MR, Clode PL, Polerecky L, Kühl M 792

(2016b) Light microenvironment and single-cell gradients of carbon fixation in tissues of 793

symbiont-bearing corals. The ISME Journal 10: 788-792 794

Wangpraseurt D, Polerecky L, Larkum AWD, Ralph PJ, Nielsen DA, Pernice M, Kühl M 795

(2014b) The in situ light microenvironment of corals. Limnology and Oceanography 796

59:917-926 797

Wangpraseurt D, Tamburic B, Szabó M, Suggett D, Ralph PJ, Kühl M (2014) Spectral effects on 798

Symbiodinium photobiology studied with a programmable light engine. PLoS ONE 9: 799

e112809 800

Wangpraseurt D, Wentzel C, Jacques SL, Wagner M, Kühl M (2017b) In vivo imaging of coral 801

tissue and skeleton with optical coherence tomography. Journal of the Royal Society 802

Interface 14: 20161003 803

Warner ME, Fitt WK, Schmidt GW (1996) The effects of elevated temperature on the 804

photosynthetic efficiency of zooxanthellae in hospite from four different species of reef 805

coral: A novel approach. Plant Cell and Environment 19: 291-299 806

Warner ME, Fitt WK, Schmidt GW (1999) Damage to photosystem II in symbiotic 807

dinoflagellates: A determinant of coral bleaching. Proceedings of the National Academy 808

of Sciences USA 96: 8007-8012 809

Warner ME, Lesser MP, Ralph PJ (2010) Chlorophyll fluorescence in reef building corals, 810

Chlorophyll a Fluorescence in Aquatic Sciences: Methods and Applications. Springer, 811

pp. 209-222 812

Webb WL, Newton M, Starr D (1974) Carbon dioxise exchange of Alnus Rubra - A 813

mathematical model. Oecologia 17: 281-291 814



33

Weis VM (2008) Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of 815

symbiosis. Journal of Experimental Biology 211: 3059-3066 816

Welch A, Gardner C, Richards‐Kortum R, Chan E, Criswell G, Pfefer J, Warren S (1997) 817

Propagation of fluorescent light. Lasers in Surgery and Medicine 21: 166-178 818

Wiedenmann J, D’Angelo C, Smith EG, Hunt AN, Legiret F-E, Postle AD, Achterberg EP 819

(2013) Nutrient enrichment can increase the susceptibility of reef corals to bleaching. 820

Nature Climate Change 3: 160-164 821



1

Figure 1: Coral tissue organisation and artificial tissue design. a-c) Basic organisation of

scleractinic corals. a) Small fragment of a faviid coral (scale bar = 1 mm). b) close-up of the

cross-section, revealing the white coral skeleton, the brown algal layer on top of the skeleton,

and the green fluorescent protein like-pigment granules (GFP) on the coral tissue surface (scale bar = 1mm). c) close-up of GFP granules (scale bar = 200 µm). d-i) Coral tissue mimicking

hydrogels. Schematics of 3-layer ‘GFP’ (d), 2-layer ‘skeleton’ (e), and 2-layer ‘transparent’(f)

designs. g-i) Respective photographs of thin cross sections of hydrogels. j-m) Hydrogels for

investigating the effect of changes in coral absorption. j-k) High microalgal density tissue design

(j) and top view photograph (k). l-m) Medium microalgal density hydrogel (l) and top view

photograph (m). n-p) Hydrogels for investigating the effect of coral stress. n) ‘Healthy’ coral

design with 2 layers of Rhodomonas sp., o) ‘Stressed’ coral design with 1 layer of

Nanochloropsis sp. on top of 1 layer of Rhodomonas sp., p) ‘Bleaching’ design with 1 layer of

Nanochloropsis sp. of a reduced cell density on top of Rhodomonas salina.



1

Figure 2. Effect of light scattering on variable chlorophyll fluorescence parameters of dark

acclimated coral tissue mimicking hydrogels. (a-c) Example images of minimal fluorescence

yields (F0) for measuring light intensity = 4, showing GFP (a), skeleton (b) and transparent (c)

hydrogels. The white circle shows the area over which F0 was integrated. Effect of measuring

light intensity on F0, (d), Fm, maximal fluorescence yield (e), and the maximum PSII quantum yield, Fv/Fm (f). Note that no measurements are shown at ML>4 (=0.8 µmol photons m

-2 s

-1) and

ML>8 (= 1.6 µmol photons m-2

s-1

) for skeleton and transparent hydrogels, respectively due to

indications of actinic effects in these hydrogels at higher measuring light levels.



1

Figure 3. In vivo light microenvironment in coral tissue mimicking hydrogels with different

scattering properties. Photon scalar irradiance of PAR (400-700 nm) was normalised to the incident downwelling irradiance of PAR and plotted against the vertical depth (µm) of the coral

mimics. The algal layer is distributed between depth = 0 µm to 750 µm for the transparent (red)

and skeleton (blue) mimic, while the algal layer is between 750-1500 µm in the GFP (green)

mimic. Four replicate gels were measured at 2 random spots (total n=8 ± SE).



1

Figure 4. Effect of light scattering on the effective quantum yield ФPSII (a-b) and relative electron transport rates (rETR) (c-d) of coral tissue mimicking hydrogels. Measured ФPSII and calculated rETR were plotted as a function of the incident downwelling irradiance (Ed) (a,c) and with the corrected in vivo scalar irradiance (E0) (b,d). Symbols with error bars represent means ± SE (n=5 biological replicates).



1

Figure 5. Effect of coral light absorption on the light microenvironment and variable

chlorophyll fluorescence measurements. Photon scalar irradiance (400-700 nm) was

normalised to the incident downwelling irradiance (Ed) and plotted against the vertical depth

(µm) in the coral mimics. The algal layer is distributed between 0-750 µm depth (a). The

maximum quantum yield of PSII, Fv/Fm (b). Relative electron transport rates (rETR) calculated

as a function of the incident downwelling irradiance (Ed) (c) and corrected for in vivo scalar

irradiance (E0) (d). All measurements were performed in coral hydrogels mimicking high algal

density (3.5 x 106 cells cm

-2) and medium algal density (1.0 x 10

6 cells cm

-2). Symbols represent

means ± SE (n=4 biological replicates) in panel a-c. The curve fit shown in panel d was the best

fit to the experimental data (R2= 0.98 and 0.80) yielding values of ETRmax= 80 and 59, and

α=0.22 and 0.11 for the high and medium algal density coral hydrogels, respectively.



1

Figure 6. Combined effects of bio-optical properties and simulated coral bleaching on

measured relative electron transport rates (rETR). Hydrogels mimicking healthy tissue

contained two dense layers of R. salina (4 x 106 cells cm

-2), hydrogels mimicking stressed tissue

contained one dense layer of N. oculata (2 x 106 cells cm

-2) and one dense layer of R. salina (2 x

106 cells cm

-2), and hydrogels mimicking bleached tissue contained one layer of N. oculuata at

low density (0.3 x 106 cells cm

-2) and one dense layer of R. salina. Data are means ± SE (n=2-3

hydrogel replicates).



2



1

Figure 7. Propagation of PAM-based measuring light in biological tissues with different

scattering coefficients. a-b) Excitation (blue) and chlorophyll fluorescence (red) for transparent

hydrogel (a) and skeleton hydrogel (b). The optical properties of the light absorbing top layer

(layer 1) are constant (i.e. identical algal density and bio physical properties of an algal cell) for

both gels, but layer 2 is either transparent or light scattering. For the transparent hydrogel,

measuring light absorption by an algal cell (s) is a function of the primary incident beam (solid

blue line), while indirect light (dotted blue lines) is lost through the transparent layer. For the

skeleton hydrogel, indirect light is redirected via backscattering by layer 2. Such scattering

enhances the chance of measuring light absorption and thus leads to greater fluorescence

emission (bold red arrows). Fluorescence emission is an isotropic process but the propagation of

fluorescent light is affected by tissue optical properties. For the transparent hydrogel, only

primary upwelling fluorescence (Fu1) contributes to the detected fluorescence signal, while for

the skeleton hydrogel the downwelling fluorescence (Fd) is redirected and adds to the upwelling

fluorescence (Fu2). c) A steep light gradient (green line) leads to an underrepresentation of

fluorescence detection from lower cell layers compared to a homogenous light environment

(black line), given that the operational volume (dotted lines) from which fluorescence is

collected is a function of the theoretical instrument detection limit (Elimit) which is modulated by

the in vivo photon scalar irradiance.



Parsed CitationsBaker NR (2008) Chlorophyll fluorescence: a probe of photosynthesis in vivo. Annual Review in Plant Biology 59: 89-113

Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Bartošková H, Nauš J, Výkruta M (1999) The arrangement of chloroplasts in cells influences the reabsorption of chlorophyllfluorescence emission. The effect of desiccation on the chlorophyll fluorescence spectra of Rhizomnium punctatum leaves.Photosynthesis Research 62: 251-260


Chen, Wang AT, Fang LS, Yang YW (2005) Fluctuating algal symbiont communities in Acropora palifera (Scleractinia : Acroporidae) fromTaiwan. Marine Ecology Progress Series 295: 113-121


Dickson DJ, Ely RL (2013) Silica sol-gel encapsulation of cyanobacteria: lessons for academic and applied research. AppliedMicrobiology and Biotechnology 97: 1809-1819


Drew EA (1972) The biology and physiology of alga-invertebrates symbioses. II. The density of symbiotic algal cells in a number ofhermatypic hard corals and alcyonarians from various depths. Journal of Experimental Marine Biology and Ecology 9: 71-75


Dubinsky Z, Falkowski P (2011) Light as a source of information and energy in zooxanthellate corals. Coral Reefs: An Ecosystem inTransition: 107-118


Enriquez S, Mendez ER, Iglesias-Prieto R (2005) Multiple scattering on coral skeletons enhances light absorption by symbiotic algae.Limnology and Oceanography 50: 1025-1032


Evans JR (2009) Potential errors in electron transport rates calculated from chlorophyll fluorescence as revealed by a multilayer leafmodel. Plant and Cell Physiology 50: 698-706


Evans JR, Morgan PB, von Caemmerer S (2017) Light quality affects chloroplast electron transport rates estimated from Chlfluorescence measurements. Plant and Cell Physiology 58: 1652-1660


Falkowski PG, Dubinsky Z (1981) Light-shade adaptation of Stylophora pistillata, a hermatypic coral from the Gulf of Eilat. Nature 289:172-174


Falkowski PG, Jokiel PL, Kinzie R (1990) Irradiance and corals. Ecosystems of the World 25: 89-107Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Fang Q (2010) Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates. Biomedical optics express 1: 165-175Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Genty B, Briantais J-M, Baker NR (1989) The relationship between the quantum yield of photosynthetic electron transport andquenching of chlorophyll fluorescence. Biochimica et Biophysica Acta (BBA) 990: 87-92


Glynn PW (1996) Coral reef bleaching: Facts, hypotheses and implications. Global Change Biology 2: 495-509Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Gorbunov MY, Kolber ZS, Lesser MP, Falkowski PG (2001) Photosynthesis and photoprotection in symbiotic corals. Limnology andOceanography 46: 75-85



https://www.ncbi.nlm.nih.gov/pubmed?term=Baker NR %282008%29 Chlorophyll fluorescence%3A a probe of photosynthesis in vivo%2E Annual Review in Plant Biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Baker&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Chlorophyll fluorescence: a probe of photosynthesis in vivo&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Chlorophyll fluorescence: a probe of photosynthesis in vivo&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Baker&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Bartošková H%2C Nauš J%2C Výkruta M %281999%29 The arrangement of chloroplasts in cells influences the reabsorption of chlorophyll fluorescence emission%2E The effect of desiccation on the chlorophyll fluorescence spectra of Rhizomnium punctatum leaves%2E Photosynthesis Research&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Barto�?¡kov�?¡&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The arrangement of chloroplasts in cells influences the reabsorption of chlorophyll fluorescence emission&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The arrangement of chloroplasts in cells influences the reabsorption of chlorophyll fluorescence emission&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Barto�?¡kov�?¡&as_ylo=1999&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Chen%2C Wang AT%2C Fang LS%2C Yang YW %282005%29 Fluctuating algal symbiont communities in Acropora palifera %28Scleractinia %3A Acroporidae%29 from Taiwan%2E Marine Ecology Progress Series&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Chen,&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Fluctuating algal symbiont communities in Acropora palifera (Scleractinia : Acroporidae) from Taiwan&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Fluctuating algal symbiont communities in Acropora palifera (Scleractinia : Acroporidae) from Taiwan&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Chen,&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Dickson DJ%2C Ely RL %282013%29 Silica sol%2Dgel encapsulation of cyanobacteria%3A lessons for academic and applied research%2E Applied Microbiology and Biotechnology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Dickson&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Silica sol-gel encapsulation of cyanobacteria: lessons for academic and applied research&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Silica sol-gel encapsulation of cyanobacteria: lessons for academic and applied research&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Dickson&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Drew EA %281972%29 The biology and physiology of alga%2Dinvertebrates symbioses%2E II%2E The density of symbiotic algal cells in a number of hermatypic hard corals and alcyonarians from various depths%2E Journal of Experimental Marine Biology and Ecology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Drew&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The biology and physiology of alga-invertebrates symbioses&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The biology and physiology of alga-invertebrates symbioses&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Drew&as_ylo=1972&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Dubinsky Z%2C Falkowski P %282011%29 Light as a source of information and energy in zooxanthellate corals%2E Coral Reefs%3A An Ecosystem in Transition&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Dubinsky&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light as a source of information and energy in zooxanthellate corals.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light as a source of information and energy in zooxanthellate corals.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Dubinsky&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Enriquez S%2C Mendez ER%2C Iglesias%2DPrieto R %282005%29 Multiple scattering on coral skeletons enhances light absorption by symbiotic algae%2E Limnology and Oceanography&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Enriquez&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Multiple scattering on coral skeletons enhances light absorption by symbiotic algae&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Multiple scattering on coral skeletons enhances light absorption by symbiotic algae&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Enriquez&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Evans JR %282009%29 Potential errors in electron transport rates calculated from chlorophyll fluorescence as revealed by a multilayer leaf model%2E Plant and Cell Physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Evans&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Potential errors in electron transport rates calculated from chlorophyll fluorescence as revealed by a multilayer leaf model&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Potential errors in electron transport rates calculated from chlorophyll fluorescence as revealed by a multilayer leaf model&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Evans&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Evans JR%2C Morgan PB%2C von Caemmerer S %282017%29 Light quality affects chloroplast electron transport rates estimated from Chl fluorescence measurements%2E Plant and Cell Physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Evans&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light quality affects chloroplast electron transport rates estimated from Chl fluorescence measurements&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light quality affects chloroplast electron transport rates estimated from Chl fluorescence measurements&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Evans&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Falkowski PG%2C Dubinsky Z %281981%29 Light%2Dshade adaptation of Stylophora pistillata%2C a hermatypic coral from the Gulf of Eilat%2E Nature&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Falkowski&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light-shade adaptation of Stylophora pistillata, a hermatypic coral from the Gulf of Eilat&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light-shade adaptation of Stylophora pistillata, a hermatypic coral from the Gulf of Eilat&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Falkowski&as_ylo=1981&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Falkowski PG%2C Jokiel PL%2C Kinzie R %281990%29 Irradiance and corals%2E Ecosystems of the World&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Falkowski&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Irradiance and corals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Irradiance and corals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Falkowski&as_ylo=1990&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Fang Q %282010%29 Mesh%2Dbased Monte Carlo method using fast ray%2Dtracing in Pl�cker coordinates%2E Biomedical optics express&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fang&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fang&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Genty B%2C Briantais J%2DM%2C Baker NR %281989%29 The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence%2E Biochimica et Biophysica Acta %28BBA&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Genty&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The relationship between the quantum yield of photosynthetic electron transport and quenching of chlorophyll fluorescence&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Genty&as_ylo=1989&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Glynn PW %281996%29 Coral reef bleaching%3A Facts%2C hypotheses and implications%2E Global Change Biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Glynn&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Coral reef bleaching: Facts, hypotheses and implications&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Coral reef bleaching: Facts, hypotheses and implications&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Glynn&as_ylo=1996&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Gorbunov MY%2C Kolber ZS%2C Lesser MP%2C Falkowski PG %282001%29 Photosynthesis and photoprotection in symbiotic corals%2E Limnology and Oceanography&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Gorbunov&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthesis and photoprotection in symbiotic corals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthesis and photoprotection in symbiotic corals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Gorbunov&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1


Hoogenboom MO, Campbell DA, Beraud E, DeZeeuw K, Ferrier-Pagès C (2012) Effects of light, food availability and temperature stresson the function of photosystem II and photosystem I of coral symbionts. PLoS ONE 7: e30167


Iglesias-Prieto R, Matta JL, Robins WA, Trench RK (1992) Photosynthetic response to elevated temperature in the symbioticdinoflagellate Symbiodinium microadriaticum in culture. Proceedings of the National Academy of Sciences USA 89: 10302-10305


Jacques SL (1998) Light distributions from point, line and plane sources for photochemical reactions and fluorescence in turbidbiological tissues. Photochemistry and Photobiology 67: 23-32


Jacques SL (2013) Optical properties of biological tissues: a review. Physics in Medicine and Biology 58: R37Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Jones RJ, Ward S, Amri AY, Hoegh-Guldberg O (2000) Changes in quantum efficiency of photosystem II of symbiotic dinoflagellates ofcorals after heat stress, and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event. Marine andFreshwater Research 51: 63-71


Kaňa R, Kotabová E, Prášil O (2013) Presence of flexible non-photochemical quenching in cryptophytes (Rhodomonas salina),Photosynthesis Research for Food, Fuel and the Future. Springer, pp. 489-492


Klughammer C, Schreiber U (2015) Apparent PS II absorption cross-section and estimation of mean PAR in optically thin and densesuspensions of Chlorella. Photosynthesis Research 123: 77-92


Kühl M (2005) Optical microsensors for analysis of microbial communities. Methods in Enzymology 397: 166-199Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Kühl M, Jørgensen BB (1994) The light-field of microbenthic communities – radiance distribution and microscale optics of sandycoastal sediments. Limnology and Oceanography 39: 1368-1398


Kühl M, Cohen Y, Dalsgaard T, Jørgensen BB, Revsbech NP (1995) Microenvironment and photosynthesis of zooxanthellae inscleractinian corals studied with microsensors for O2, pH and Light. Marine Ecology Progress Series 117: 159-172


Kühl M, Glud RN, Borum J, Roberts R, Rysgaard S (2001) Photosynthetic performance of surface-associated algae below sea ice asmeasured with a pulse-amplitude-modulated (PAM) fluorometer and O₂ microsensors. Marine Ecology Progress Series 223: 1-14


Lichtenberg M, Kühl M (2015) Pronounced gradients of light, photosynthesis and O2 consumption in the tissue of the brown algaFucus serratus. New Phytologist 207: 559-569


Lichtenberg M, Larkum AW, Kühl M (2016) Photosynthetic acclimation of Symbiodinium in hospite depends on vertical position in thetissue of the scleractinian coral Montastrea curta. Frontiers in microbiology 7:230


Lichtenberg M, Trampe ECL, Vogelmann TC, Kühl M (2017) Light sheet microscopy imaging of light absorption and photosynthesisdistribution in plant tissue. Plant Physiology 175: 721-733


Loriaux SD, Avenson TJ, Welles JM, Mc Dermirr DK, Eckles RD, Riensche B, and Genty B (2013) Closing in on maximum yield ofchlorophyll fluorescence using a single multiphase flash of sub-saturating intensity. Plant Cell & Environment 36: 1755-1770


Lyndby NH, Kühl M, Wangpraseurt D (2016) Heat generation and light scattering of green fluorescent protein-like pigments in coral www.plantphysiol.orgon June 2, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

https://www.ncbi.nlm.nih.gov/pubmed?term=Hoogenboom MO%2C Campbell DA%2C Beraud E%2C DeZeeuw K%2C Ferrier%2DPag�s C %282012%29 Effects of light%2C food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts%2E PLoS ONE 7%3A e&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hoogenboom&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Effects of light, food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Effects of light, food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hoogenboom&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Iglesias%2DPrieto R%2C Matta JL%2C Robins WA%2C Trench RK %281992%29 Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture%2E Proceedings of the National Academy of Sciences USA&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Iglesias-Prieto&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthetic response to elevated temperature in the symbiotic dinoflagellate Symbiodinium microadriaticum in culture&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Iglesias-Prieto&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Jacques SL %281998%29 Light distributions from point%2C line and plane sources for photochemical reactions and fluorescence in turbid biological tissues%2E Photochemistry and Photobiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jacques&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light distributions from point, line and plane sources for photochemical reactions and fluorescence in turbid biological tissues&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light distributions from point, line and plane sources for photochemical reactions and fluorescence in turbid biological tissues&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jacques&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Jacques SL %282013%29 Optical properties of biological tissues%3A a review%2E Physics in Medicine and Biology 58%3A R&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jacques&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Optical properties of biological tissues: a review.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Optical properties of biological tissues: a review.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jacques&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Jones RJ%2C Ward S%2C Amri AY%2C Hoegh%2DGuldberg O %282000%29 Changes in quantum efficiency of photosystem II of symbiotic dinoflagellates of corals after heat stress%2C and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event%2E Marine and Freshwater Research&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jones&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Changes in quantum efficiency of photosystem II of symbiotic dinoflagellates of corals after heat stress, and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Changes in quantum efficiency of photosystem II of symbiotic dinoflagellates of corals after heat stress, and of bleached corals sampled after the 1998 Great Barrier Reef mass bleaching event&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jones&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ka�?a R%2C Kotabová E%2C Prášil O %282013%29 Presence of flexible non%2Dphotochemical quenching in cryptophytes %28Rhodomonas salina%29%2C Photosynthesis Research for Food%2C Fuel and the Future%2E Springer%2C pp&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ka�?�?a&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Presence of flexible non-photochemical quenching in cryptophytes (Rhodomonas salina), Photosynthesis Research for Food, Fuel and the Future.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Presence of flexible non-photochemical quenching in cryptophytes (Rhodomonas salina), Photosynthesis Research for Food, Fuel and the Future.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ka�?�?a&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Klughammer C%2C Schreiber U %282015%29 Apparent PS II absorption cross%2Dsection and estimation of mean PAR in optically thin and dense suspensions of Chlorella%2E Photosynthesis Research&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Klughammer&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Apparent PS II absorption cross-section and estimation of mean PAR in optically thin and dense suspensions of Chlorella&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Apparent PS II absorption cross-section and estimation of mean PAR in optically thin and dense suspensions of Chlorella&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Klughammer&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=K�hl M %282005%29 Optical microsensors for analysis of microbial communities%2E Methods in Enzymology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kühl&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Optical microsensors for analysis of microbial communities&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Optical microsensors for analysis of microbial communities&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kühl&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=K�hl M%2C J�rgensen BB %281994%29 The light%2Dfield of microbenthic communities %26%23x2013%3B radiance distribution and microscale optics of sandy coastal sediments%2E Limnology and Oceanography&dopt=abstract


https://scholar.google.com/scholar?as_q=The light-field of microbenthic communities ? radiance distribution and microscale optics of sandy coastal sediments&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The light-field of microbenthic communities ? radiance distribution and microscale optics of sandy coastal sediments&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kühl&as_ylo=1994&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=K�hl M%2C Cohen Y%2C Dalsgaard T%2C J�rgensen BB%2C Revsbech NP %281995%29 Microenvironment and photosynthesis of zooxanthellae in scleractinian corals studied with microsensors for O2%2C pH and Light%2E Marine Ecology Progress Series&dopt=abstract


https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kühl&as_ylo=1995&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Kühl M%2C Glud RN%2C Borum J%2C Roberts R%2C Rysgaard S %282001%29 Photosynthetic performance of surface%2Dassociated algae below sea ice as measured with a pulse%2Damplitude%2Dmodulated %28PAM%29 fluorometer and O�?? microsensors%2E Marine Ecology Progress Series&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=K�?¼hl&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthetic performance of surface-associated algae below sea ice as measured with a pulse-amplitude-modulated (PAM) fluorometer and Oâ�?�? microsensors&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthetic performance of surface-associated algae below sea ice as measured with a pulse-amplitude-modulated (PAM) fluorometer and Oâ�?�? microsensors&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=K�?¼hl&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Lichtenberg M%2C K�hl M %282015%29 Pronounced gradients of light%2C photosynthesis and O2 consumption in the tissue of the brown alga Fucus serratus%2E New Phytologist&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lichtenberg&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Pronounced gradients of light, photosynthesis and O2 consumption in the tissue of the brown alga Fucus serratus&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Pronounced gradients of light, photosynthesis and O2 consumption in the tissue of the brown alga Fucus serratus&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lichtenberg&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Lichtenberg M%2C Larkum AW%2C K�hl M %282016%29 Photosynthetic acclimation of Symbiodinium in hospite depends on vertical position in the tissue of the scleractinian coral Montastrea curta%2E Frontiers in microbiology&dopt=abstract


https://scholar.google.com/scholar?as_q=Photosynthetic acclimation of Symbiodinium in hospite depends on vertical position in the tissue of the scleractinian coral Montastrea curta.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthetic acclimation of Symbiodinium in hospite depends on vertical position in the tissue of the scleractinian coral Montastrea curta.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lichtenberg&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Lichtenberg M%2C Trampe ECL%2C Vogelmann TC%2C K�hl M %282017%29 Light sheet microscopy imaging of light absorption and photosynthesis distribution in plant tissue%2E Plant Physiology&dopt=abstract


https://scholar.google.com/scholar?as_q=Light sheet microscopy imaging of light absorption and photosynthesis distribution in plant tissue&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light sheet microscopy imaging of light absorption and photosynthesis distribution in plant tissue&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lichtenberg&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Loriaux SD%2C Avenson TJ%2C Welles JM%2C Mc Dermirr DK%2C Eckles RD%2C Riensche B%2C and Genty B %282013%29 Closing in on maximum yield of chlorophyll fluorescence using a single multiphase flash of sub%2Dsaturating intensity%2E Plant Cell %26 Environment&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Loriaux&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Closing in on maximum yield of chlorophyll fluorescence using a single multiphase flash of sub-saturating intensity&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Closing in on maximum yield of chlorophyll fluorescence using a single multiphase flash of sub-saturating intensity&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Loriaux&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


tissue. Scientific Reports 6: 26599Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Marcelino LA, Westneat MW, Stoyneva V, Henss J, Rogers JD, Radosevich A, Turzhitsky V, Siple M, Fang A, Swain TD (2013)Modulation of light-enhancement to symbiotic algae by light scattering in corals and evolutionary trends in nleaching. PLoS ONE 8:e61492


Mourant JR, Fuselier T, Boyer J, Johnson TM, Bigio IJ (1997) Predictions and measurements of scattering and absorption over broadwavelength ranges in tissue phantoms. Applied optics 36: 949-957


Mycek M-A, Pogue BW (2003) Handbook of biomedical fluorescence. CRC PressPubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Naus J, Klinkovsky T, Ilik P, Cikanek D (1994) Model studies of chlorophyll fluorescence reabsorption at chloroplast level underdifferent exciting conditions. Photosynthesis Research 40: 67-74


Oguchi R, Douwstra P, Fujita T, Chow WS, Terashima I (2011) Intra‐leaf gradients of photoinhibition induced by different color lights:implications for the dual mechanisms of photoinhibition and for the application of conventional chlorophyll fluorometers. NewPhytologist 191: 146-159


Osinga R, Iglesias-Prieto R, and Enriquez S (2012) Measuring photosynthesis in symbiotic invertebrates: a review of methodologies,rates and processes, in Applied Photosynthesis, ed. M. Najafpour (Rijeka: InTech), 229–256


Pogue BW, Patterson MS (2006) Review of tissue simulating phantoms for optical spectroscopy, imaging and dosimetry. Journal ofBiomedical Optics 11: 041102-041102-041116


Ralph P, Gademann R, Larkum A, Schreiber U (1999) In situ underwater measurements of photosynthetic activity of coral zooxanthellaeand other reef-dwelling dinoflagellate endosymbionts. Marine Ecology Progress Series: 139-147


Ralph PJ, Gademann R (2005) Rapid light curves: a powerful tool to assess photosynthetic activity. Aquatic Botany 82: 222-237Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Ralph PJ, Schreiber U, Gademann R, Kühl M, Larkum AW (2005) Coral photobiology studied with a new imaging pulse amplitudemodulated fluorometer. Journal of Phycology 41: 335-342


Rickelt LF, Lichtenberg M, Trampe ECL, Kühl M (2016) Fiber‐optic probes for small‐scale measurements of scalar irradiance.Photochemistry and Photobiology 92: 331-342


Rodriguez-Roman A, Hernandez-Pech X, Thome PE, Enriquez S, Iglesias-Prieto R (2006) Photosynthesis and light utilization in theCaribbean coral Montastraea faveolata recovering from a bleaching event. Limnology and Oceanography 51: 2702-2710


Schreiber U (2004) Pulse-amplitude-modulation (PAM) fluorometry and saturation pulse method: an overview. Chlorophyll aFluorescence: A Signature of photosynthesis. Springer. pp 279-319


Schreiber U, Kühl M, Klimant I, Reising H (1996) Measurement of chlorophyll fluorescence within leaves using a modified PAMFluorometer with a fiber-optic microprobe. Photosynthesis Research 47: 103-109


Schreiber U, Neubauer C, Schliwa U (1993) PAM fluorometer based on medium-frequency pulsed Xe-flash measuring light: a highly www.plantphysiol.orgon June 2, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

https://www.ncbi.nlm.nih.gov/pubmed?term=Lyndby NH%2C K�hl M%2C Wangpraseurt D %282016%29 Heat generation and light scattering of green fluorescent protein%2Dlike pigments in coral tissue%2E Scientific Reports&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lyndby&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Heat generation and light scattering of green fluorescent protein-like pigments in coral tissue.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Heat generation and light scattering of green fluorescent protein-like pigments in coral tissue.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lyndby&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Marcelino LA%2C Westneat MW%2C Stoyneva V%2C Henss J%2C Rogers JD%2C Radosevich A%2C Turzhitsky V%2C Siple M%2C Fang A%2C Swain TD %282013%29 Modulation of light%2Denhancement to symbiotic algae by light scattering in corals and evolutionary trends in nleaching%2E PLoS ONE 8%3A e&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Marcelino&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Modulation of light-enhancement to symbiotic algae by light scattering in corals and evolutionary trends in nleaching.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Modulation of light-enhancement to symbiotic algae by light scattering in corals and evolutionary trends in nleaching.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Marcelino&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mourant JR%2C Fuselier T%2C Boyer J%2C Johnson TM%2C Bigio IJ %281997%29 Predictions and measurements of scattering and absorption over broad wavelength ranges in tissue phantoms%2E Applied optics&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mourant&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Predictions and measurements of scattering and absorption over broad wavelength ranges in tissue phantoms&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Predictions and measurements of scattering and absorption over broad wavelength ranges in tissue phantoms&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mourant&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Mycek M%2DA%2C Pogue BW %282003%29 Handbook of biomedical fluorescence%2E CRC Press&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mycek&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Handbook of biomedical fluorescence.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Handbook of biomedical fluorescence.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mycek&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Naus J%2C Klinkovsky T%2C Ilik P%2C Cikanek D %281994%29 Model studies of chlorophyll fluorescence reabsorption at chloroplast level under different exciting conditions%2E Photosynthesis Research&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Naus&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Model studies of chlorophyll fluorescence reabsorption at chloroplast level under different exciting conditions&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Model studies of chlorophyll fluorescence reabsorption at chloroplast level under different exciting conditions&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Naus&as_ylo=1994&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Oguchi R%2C Douwstra P%2C Fujita T%2C Chow WS%2C Terashima I %282011%29 Intra�?�leaf gradients of photoinhibition induced by different color lights%3A implications for the dual mechanisms of photoinhibition and for the application of conventional chlorophyll fluorometers%2E New Phytologist&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Oguchi&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Intraâ�?�leaf gradients of photoinhibition induced by different color lights: implications for the dual mechanisms of photoinhibition and for the application of conventional chlorophyll fluorometers&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Intraâ�?�leaf gradients of photoinhibition induced by different color lights: implications for the dual mechanisms of photoinhibition and for the application of conventional chlorophyll fluorometers&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Oguchi&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Osinga R%2C Iglesias%2DPrieto R%2C and Enriquez S %282012%29 Measuring photosynthesis in symbiotic invertebrates%3A a review of methodologies%2C rates and processes%2C in Applied Photosynthesis%2C ed%2E M%2E Najafpour %28Rijeka%3A InTech%29%2C 229%26%23x&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Osinga&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Measuring photosynthesis in symbiotic invertebrates: a review of methodologies, rates and processes, in Applied Photosynthesis, ed.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Measuring photosynthesis in symbiotic invertebrates: a review of methodologies, rates and processes, in Applied Photosynthesis, ed.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Osinga&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Pogue BW%2C Patterson MS %282006%29 Review of tissue simulating phantoms for optical spectroscopy%2C imaging and dosimetry%2E Journal of Biomedical Optics&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pogue&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Review of tissue simulating phantoms for optical spectroscopy, imaging and dosimetry&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Review of tissue simulating phantoms for optical spectroscopy, imaging and dosimetry&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pogue&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ralph P%2C Gademann R%2C Larkum A%2C Schreiber U %281999%29 In situ underwater measurements of photosynthetic activity of coral zooxanthellae and other reef%2Ddwelling dinoflagellate endosymbionts%2E Marine Ecology Progress Series&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ralph&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=In situ underwater measurements of photosynthetic activity of coral zooxanthellae and other reef-dwelling dinoflagellate endosymbionts.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=In situ underwater measurements of photosynthetic activity of coral zooxanthellae and other reef-dwelling dinoflagellate endosymbionts.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ralph&as_ylo=1999&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ralph PJ%2C Gademann R %282005%29 Rapid light curves%3A a powerful tool to assess photosynthetic activity%2E Aquatic Botany&dopt=abstract


https://scholar.google.com/scholar?as_q=Rapid light curves: a powerful tool to assess photosynthetic activity&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Rapid light curves: a powerful tool to assess photosynthetic activity&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ralph&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ralph PJ%2C Schreiber U%2C Gademann R%2C K�hl M%2C Larkum AW %282005%29 Coral photobiology studied with a new imaging pulse amplitude modulated fluorometer%2E Journal of Phycology&dopt=abstract


https://scholar.google.com/scholar?as_q=Coral photobiology studied with a new imaging pulse amplitude modulated fluorometer&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Coral photobiology studied with a new imaging pulse amplitude modulated fluorometer&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ralph&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Rickelt LF%2C Lichtenberg M%2C Trampe ECL%2C Kühl M %282016%29 Fiber�?�optic probes for small�?�scale measurements of scalar irradiance%2E Photochemistry and Photobiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rickelt&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Fiberâ�?�optic probes for smallâ�?�scale measurements of scalar irradiance&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Fiberâ�?�optic probes for smallâ�?�scale measurements of scalar irradiance&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rickelt&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Rodriguez%2DRoman A%2C Hernandez%2DPech X%2C Thome PE%2C Enriquez S%2C Iglesias%2DPrieto R %282006%29 Photosynthesis and light utilization in the Caribbean coral Montastraea faveolata recovering from a bleaching event%2E Limnology and Oceanography&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rodriguez-Roman&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthesis and light utilization in the Caribbean coral Montastraea faveolata recovering from a bleaching event&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Photosynthesis and light utilization in the Caribbean coral Montastraea faveolata recovering from a bleaching event&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rodriguez-Roman&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Schreiber U %282004%29 Pulse%2Damplitude%2Dmodulation %28PAM%29 fluorometry and saturation pulse method%3A an overview%2E Chlorophyll a Fluorescence%3A A Signature of photosynthesis%2E Springer%2E pp&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Schreiber&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Pulse-amplitude-modulation (PAM) fluorometry and saturation pulse method: an overview.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Pulse-amplitude-modulation (PAM) fluorometry and saturation pulse method: an overview.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schreiber&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Schreiber U%2C K�hl M%2C Klimant I%2C Reising H %281996%29 Measurement of chlorophyll fluorescence within leaves using a modified PAM Fluorometer with a fiber%2Doptic microprobe%2E Photosynthesis Research&dopt=abstract


https://scholar.google.com/scholar?as_q=Measurement of chlorophyll fluorescence within leaves using a modified PAM Fluorometer with a fiber-optic microprobe&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Measurement of chlorophyll fluorescence within leaves using a modified PAM Fluorometer with a fiber-optic microprobe&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schreiber&as_ylo=1996&as_allsubj=all&hl=en&c2coff=1


sensitive new tool in basic and applied photosynthesis research. Photosynthesis Research 36: 65-72Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Serôdio J (2004) Analysis of variable chlorophyll fluorescence in microphytobenthos assemblages: implications of the use of depth-integrated measurements. Aquatic Microbial Ecology 36: 137-152


Sušila P, Lazár D, Ilík P, Tomek P, Nauš J (2004) The gradient of exciting radiation within a sample affects the relative height of steps inthe fast chlorophyll a fluorescence rise. Photosynthetica 42: 161-172


Swain TD, DuBois E, Gomes A, Stoyneva VP, Radosevich AJ, Henss J, Wagner ME, Derbas J, Grooms HW, Velazquez EM (2016)Skeletal light-scattering accelerates bleaching response in reef-building corals. BMC Ecology 16: 1


Swartling J, Pifferi A, Enejder AM, Andersson-Engels S (2003) Accelerated Monte Carlo models to simulate fluorescence spectra fromlayered tissues. Journal of the Optical Society of America A 20: 714-727


Szabó M, Wangpraseurt D, Tamburic B, Larkum AW, Schreiber U, Suggett DJ, Kühl M, Ralph PJ (2014) Effective light absorption andabsolute electron transport rates in the coral Pocillopora damicornis. Plant Physiology and Biochemistry 83: 159-167


Ting CS, Owens TG (1992) Limitations of the pulse-modulated technique for measuring the fluorescence characteristics of algae. PlantPhysiology 100: 367-373


Tuchin VV (2007) Tissue optics: light scattering methods and instruments for medical diagnosis. Bellingham, WA, USA' TheInternational Society for Optical Engineering.


van der Kooi CJ, Elzenga JTM, Dijksterhuis J, Stavenga DG (2017) Functional optics of glossy buttercup flowers. Journal of the RoyalSociety Interface 14: 20160933


Vogelmann TC, Evans J (2002) Profiles of light absorption and chlorophyll within spinach leaves from chlorophyll fluorescence. Plant,Cell & Environment 25: 1313-1323


Wagnières G, Cheng S, Zellweger M, Utke N, Braichotte D, Ballini J-P, van den Bergh H (1997) An optical phantom with tissue-likeproperties in the visible for use in PDT and fluorescence spectroscopy. Physics in Medicine and Biology 42: 1415


Wangpraseurt D, Larkum AWD, Ralph PJ, Kühl M (2012) Light gradients and optical microniches in coral tissues. Frontiers inMicrobiology 3:316


Wangpraseurt D, Holm JB, Larkum AWD, Pernice M, Ralph PJ, Suggett DJ, Kühl M (2017a) In vivo microscale measurements of lightand photosynthesis during coral bleaching: evidence for the optical feedback loop? Frontiers in Microbiology 8:59

Wangpraseurt D, Jacques SL, Petrie T, Kühl M (2016a) Monte Carlo modeling of photon propagation reveals highly scattering coraltissue. Frontiers in Plant Science 7:1404


Wangpraseurt D, Kühl M (2014) Direct and diffuse light propagation through coral tissue, SPIE BiOS. International Society for Opticsand Photonics, 894117-894117-894116


Wangpraseurt D, Larkum AWD, Franklin J, Szabo M, Ralph PJ, Kühl M (2014a) Lateral light transfer ensures efficient resourcedistribution in symbiont-bearing corals. Journal of Experimental Biology 217: 489-498

Pubmed: Author and Title www.plantphysiol.orgon June 2, 2020 - Published by Downloaded from Copyright © 2019 American Society of Plant Biologists. All rights reserved.

https://www.ncbi.nlm.nih.gov/pubmed?term=Schreiber U%2C Neubauer C%2C Schliwa U %281993%29 PAM fluorometer based on medium%2Dfrequency pulsed Xe%2Dflash measuring light%3A a highly sensitive new tool in basic and applied photosynthesis research%2E Photosynthesis Research&dopt=abstract


https://scholar.google.com/scholar?as_q=PAM fluorometer based on medium-frequency pulsed Xe-flash measuring light: a highly sensitive new tool in basic and applied photosynthesis research&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=PAM fluorometer based on medium-frequency pulsed Xe-flash measuring light: a highly sensitive new tool in basic and applied photosynthesis research&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schreiber&as_ylo=1993&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ser�dio J %282004%29 Analysis of variable chlorophyll fluorescence in microphytobenthos assemblages%3A implications of the use of depth%2Dintegrated measurements%2E Aquatic Microbial Ecology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Serôdio&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Analysis of variable chlorophyll fluorescence in microphytobenthos assemblages: implications of the use of depth-integrated measurements&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Analysis of variable chlorophyll fluorescence in microphytobenthos assemblages: implications of the use of depth-integrated measurements&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Serôdio&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Sušila P%2C Lazár D%2C Ilík P%2C Tomek P%2C Nauš J %282004%29 The gradient of exciting radiation within a sample affects the relative height of steps in the fast chlorophyll a fluorescence rise%2E Photosynthetica&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Su�?¡ila&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The gradient of exciting radiation within a sample affects the relative height of steps in the fast chlorophyll a fluorescence rise&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The gradient of exciting radiation within a sample affects the relative height of steps in the fast chlorophyll a fluorescence rise&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Su�?¡ila&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Swain TD%2C DuBois E%2C Gomes A%2C Stoyneva VP%2C Radosevich AJ%2C Henss J%2C Wagner ME%2C Derbas J%2C Grooms HW%2C Velazquez EM %282016%29 Skeletal light%2Dscattering accelerates bleaching response in reef%2Dbuilding corals%2E BMC Ecology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Swain&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Skeletal light-scattering accelerates bleaching response in reef-building corals.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Skeletal light-scattering accelerates bleaching response in reef-building corals.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Swain&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Swartling J%2C Pifferi A%2C Enejder AM%2C Andersson%2DEngels S %282003%29 Accelerated Monte Carlo models to simulate fluorescence spectra from layered tissues%2E Journal of the Optical Society of America A&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Swartling&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Accelerated Monte Carlo models to simulate fluorescence spectra from layered tissues&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Accelerated Monte Carlo models to simulate fluorescence spectra from layered tissues&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Swartling&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Szab� M%2C Wangpraseurt D%2C Tamburic B%2C Larkum AW%2C Schreiber U%2C Suggett DJ%2C K�hl M%2C Ralph PJ %282014%29 Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis%2E Plant Physiology and Biochemistry&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Szabó&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Szabó&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Ting CS%2C Owens TG %281992%29 Limitations of the pulse%2Dmodulated technique for measuring the fluorescence characteristics of algae%2E Plant Physiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ting&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Limitations of the pulse-modulated technique for measuring the fluorescence characteristics of algae&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Limitations of the pulse-modulated technique for measuring the fluorescence characteristics of algae&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ting&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Tuchin VV %282007%29 Tissue optics%3A light scattering methods and instruments for medical diagnosis%2E Bellingham%2C WA%2C USA%27 The International Society for Optical Engineering&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tuchin&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Tissue optics: light scattering methods and instruments for medical diagnosis.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Tissue optics: light scattering methods and instruments for medical diagnosis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tuchin&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=van der Kooi CJ%2C Elzenga JTM%2C Dijksterhuis J%2C Stavenga DG %282017%29 Functional optics of glossy buttercup flowers%2E Journal of the Royal Society Interface&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=van&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Functional optics of glossy buttercup flowers.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Functional optics of glossy buttercup flowers.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=van&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Vogelmann TC%2C Evans J %282002%29 Profiles of light absorption and chlorophyll within spinach leaves from chlorophyll fluorescence%2E Plant%2C Cell %26 Environment&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vogelmann&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Profiles of light absorption and chlorophyll within spinach leaves from chlorophyll fluorescence&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Profiles of light absorption and chlorophyll within spinach leaves from chlorophyll fluorescence&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vogelmann&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wagni�res G%2C Cheng S%2C Zellweger M%2C Utke N%2C Braichotte D%2C Ballini J%2DP%2C van den Bergh H %281997%29 An optical phantom with tissue%2Dlike properties in the visible for use in PDT and fluorescence spectroscopy%2E Physics in Medicine and Biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wagnières&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=An optical phantom with tissue-like properties in the visible for use in PDT and fluorescence spectroscopy.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=An optical phantom with tissue-like properties in the visible for use in PDT and fluorescence spectroscopy.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wagnières&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Larkum AWD%2C Ralph PJ%2C K�hl M %282012%29 Light gradients and optical microniches in coral tissues%2E Frontiers in Microbiology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wangpraseurt&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Light gradients and optical microniches in coral tissues.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light gradients and optical microniches in coral tissues.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Jacques SL%2C Petrie T%2C K�hl M %282016a%29 Monte Carlo modeling of photon propagation reveals highly scattering coral tissue%2E Frontiers in Plant Science&dopt=abstract


https://scholar.google.com/scholar?as_q=Monte Carlo modeling of photon propagation reveals highly scattering coral tissue.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Monte Carlo modeling of photon propagation reveals highly scattering coral tissue.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C K�hl M %282014%29 Direct and diffuse light propagation through coral tissue%2C SPIE BiOS%2E International Society for Optics and Photonics&dopt=abstract


https://scholar.google.com/scholar?as_q=Direct and diffuse light propagation through coral tissue, SPIE BiOS.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Direct and diffuse light propagation through coral tissue, SPIE BiOS.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Larkum AWD%2C Franklin J%2C Szabo M%2C Ralph PJ%2C K�hl M %282014a%29 Lateral light transfer ensures efficient resource distribution in symbiont%2Dbearing corals%2E Journal of Experimental Biology&dopt=abstract


Google Scholar: Author Only Title Only Author and Title

Wangpraseurt D, Pernice M, Guagliardo P, Kilburn MR, Clode PL, Polerecky L, Kühl M (2016b) Light microenvironment and single-cellgradients of carbon fixation in tissues of symbiont-bearing corals. The ISME Journal 10: 788-792


Wangpraseurt D, Polerecky L, Larkum AWD, Ralph PJ, Nielsen DA, Pernice M, Kühl M (2014b) The in situ light microenvironment ofcorals. Limnology and Oceanography 59:917-926


Wangpraseurt D, Tamburic B, Szabó M, Suggett D, Ralph PJ, Kühl M (2014) Spectral effects on Symbiodinium photobiology studiedwith a programmable light engine. PLoS ONE 9: e112809


Wangpraseurt D, Wentzel C, Jacques SL, Wagner M, Kühl M (2017b) In vivo imaging of coral tissue and skeleton with opticalcoherence tomography. Journal of the Royal Society Interface 14: 20161003


Warner ME, Fitt WK, Schmidt GW (1996) The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae inhospite from four different species of reef coral: A novel approach. Plant Cell and Environment 19: 291-299


Warner ME, Fitt WK, Schmidt GW (1999) Damage to photosystem II in symbiotic dinoflagellates: A determinant of coral bleaching.Proceedings of the National Academy of Sciences USA 96: 8007-8012


Warner ME, Lesser MP, Ralph PJ (2010) Chlorophyll fluorescence in reef building corals, Chlorophyll a Fluorescence in AquaticSciences: Methods and Applications. Springer, pp. 209-222


Webb WL, Newton M, Starr D (1974) Carbon dioxise exchange of Alnus Rubra - A mathematical model. Oecologia 17: 281-291Pubmed: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Weis VM (2008) Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis. Journal of Experimental Biology211: 3059-3066


Welch A, Gardner C, Richards‐Kortum R, Chan E, Criswell G, Pfefer J, Warren S (1997) Propagation of fluorescent light. Lasers inSurgery and Medicine 21: 166-178


Wiedenmann J, D'Angelo C, Smith EG, Hunt AN, Legiret F-E, Postle AD, Achterberg EP (2013) Nutrient enrichment can increase thesusceptibility of reef corals to bleaching. Nature Climate Change 3: 160-164




https://scholar.google.com/scholar?as_q=Lateral light transfer ensures efficient resource distribution in symbiont-bearing corals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Lateral light transfer ensures efficient resource distribution in symbiont-bearing corals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Pernice M%2C Guagliardo P%2C Kilburn MR%2C Clode PL%2C Polerecky L%2C K�hl M %282016b%29 Light microenvironment and single%2Dcell gradients of carbon fixation in tissues of symbiont%2Dbearing corals%2E The ISME Journal&dopt=abstract


https://scholar.google.com/scholar?as_q=Light microenvironment and single-cell gradients of carbon fixation in tissues of symbiont-bearing corals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Light microenvironment and single-cell gradients of carbon fixation in tissues of symbiont-bearing corals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Polerecky L%2C Larkum AWD%2C Ralph PJ%2C Nielsen DA%2C Pernice M%2C K�hl M %282014b%29 The in situ light microenvironment of corals%2E Limnology and Oceanography&dopt=abstract


https://scholar.google.com/scholar?as_q=The in situ light microenvironment of corals&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The in situ light microenvironment of corals&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Tamburic B%2C Szab� M%2C Suggett D%2C Ralph PJ%2C K�hl M %282014%29 Spectral effects on Symbiodinium photobiology studied with a programmable light engine%2E PLoS ONE 9%3A e&dopt=abstract


https://scholar.google.com/scholar?as_q=Spectral effects on Symbiodinium photobiology studied with a programmable light engine.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Spectral effects on Symbiodinium photobiology studied with a programmable light engine.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wangpraseurt D%2C Wentzel C%2C Jacques SL%2C Wagner M%2C K�hl M %282017b%29 In vivo imaging of coral tissue and skeleton with optical coherence tomography%2E Journal of the Royal Society Interface&dopt=abstract


https://scholar.google.com/scholar?as_q=In vivo imaging of coral tissue and skeleton with optical coherence tomography.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=In vivo imaging of coral tissue and skeleton with optical coherence tomography.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wangpraseurt&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Warner ME%2C Fitt WK%2C Schmidt GW %281996%29 The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral%3A A novel approach%2E Plant Cell and Environment&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Warner&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral: A novel approach&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=The effects of elevated temperature on the photosynthetic efficiency of zooxanthellae in hospite from four different species of reef coral: A novel approach&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Warner&as_ylo=1996&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Warner ME%2C Fitt WK%2C Schmidt GW %281999%29 Damage to photosystem II in symbiotic dinoflagellates%3A A determinant of coral bleaching%2E Proceedings of the National Academy of Sciences USA&dopt=abstract


https://scholar.google.com/scholar?as_q=Damage to photosystem II in symbiotic dinoflagellates: A determinant of coral bleaching&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Damage to photosystem II in symbiotic dinoflagellates: A determinant of coral bleaching&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Warner&as_ylo=1999&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Warner ME%2C Lesser MP%2C Ralph PJ %282010%29 Chlorophyll fluorescence in reef building corals%2C Chlorophyll a Fluorescence in Aquatic Sciences%3A Methods and Applications%2E Springer%2C pp&dopt=abstract


https://scholar.google.com/scholar?as_q=Chlorophyll fluorescence in reef building corals, Chlorophyll a Fluorescence in Aquatic Sciences: Methods and Applications.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Chlorophyll fluorescence in reef building corals, Chlorophyll a Fluorescence in Aquatic Sciences: Methods and Applications.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Warner&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Webb WL%2C Newton M%2C Starr D %281974%29 Carbon dioxise exchange of Alnus Rubra %2D A mathematical model%2E Oecologia&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Webb&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Carbon dioxise exchange of Alnus Rubra - A mathematical model&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Carbon dioxise exchange of Alnus Rubra - A mathematical model&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Webb&as_ylo=1974&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Weis VM %282008%29 Cellular mechanisms of Cnidarian bleaching%3A stress causes the collapse of symbiosis%2E Journal of Experimental Biology&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Weis&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Weis&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Welch A%2C Gardner C%2C Richards�?�Kortum R%2C Chan E%2C Criswell G%2C Pfefer J%2C Warren S %281997%29 Propagation of fluorescent light%2E Lasers in Surgery and Medicine&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Welch&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Propagation of fluorescent light&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Propagation of fluorescent light&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Welch&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

https://www.ncbi.nlm.nih.gov/pubmed?term=Wiedenmann J%2C D%27Angelo C%2C Smith EG%2C Hunt AN%2C Legiret F%2DE%2C Postle AD%2C Achterberg EP %282013%29 Nutrient enrichment can increase the susceptibility of reef corals to bleaching%2E Nature Climate Change&dopt=abstract

https://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wiedenmann&hl=en&c2coff=1

https://scholar.google.com/scholar?as_q=Nutrient enrichment can increase the susceptibility of reef corals to bleaching&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

https://scholar.google.com/scholar?as_q=Nutrient enrichment can increase the susceptibility of reef corals to bleaching&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wiedenmann&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


Documents

Optical properties of corals distort variable chlorophyll ... · 5 96 actinic irradiance levels, rETR versus irradiance curves (i.e. light curves) can be determined, 97 which enables