Mesophotic coral bleaching associated with changes in thermocline depth

Domain: earth_science
Published: 2023-10-16
Editorial outcome: accept

Abstract
As global temperatures continue to rise, shallow coral reef bleaching has become more intense and widespread. Mesophotic coral ecosystems reside in deeper (30–150 m), cooler water and were thought to offer a refuge to shallow-water reefs. Studies now show that mesophotic coral ecosystems instead have limited connectivity with shallow corals but host diverse endemic communities. Given their extensive distribution and high biodiversity, understanding their susceptibility to warming oceans is imperative. In this multidisciplinary study of an atoll in the Chagos Archipelago in the central Indian Ocean, we show evidence of coral bleaching at 90 m, despite the absence of shallow-water bleaching. We also show that the bleaching was associated with sustained thermocline deepening driven by the Indian Ocean Dipole, which might be further enhanced by internal waves whose influence varied at a sub-atoll scale. Our results demonstrate the potential vulnerability of mesophotic coral ecosystems to thermal stress and highlight the need for oceanographic knowledge to predict bleaching susceptibility and heterogeneity.

Introduction
Coral reefs represent one of the most iconic, diverse and valuable ecosystems on Earth, hosting almost 30% of all marine fish species and possibly more than a million species overall1,2. In spite of their limited spatial coverage (0.5% of the marine world), they support more species per unit area than any other marine environment3. Living close to their thermal limit, however, shallow corals are threatened by the global increase in sea surface temperatures (SSTs) and subsequent coral bleaching; current estimates suggest that 70–90% of the reefs will be lost with a 1.5 °C rise and 99% if the increase in temperatures reaches 2 °C4,5. Bleaching events are increasing in their severity, frequency and duration6,7, yet our knowledge of the impacts of these events is centred around shallow-water coral reefs. Mesophotic coral ecosystems (MCEs) reside between the depths of 30–150 m and have been estimated to occupy two-thirds of the total depth range of zooxanthellate coral environments8,9. It was previously hypothesised that these communities are buffered against anthropogenic changes as they are located in deeper, cooler water, and may therefore offer refuge to shallow-water corals through the dispersal of larvae8,10. However, recent studies have shown that MCEs have limited ecological and genetic connectivity to their shallow-water counterparts and are biologically and ecologically valuable in their own right, hosting diverse communities with high levels of endemism11–14. Given the extensive distribution of MCEs and the high biodiversity they support, understanding the susceptibility of these communities to bleaching in the face of warming oceans is imperative.

Mesophotic corals are thought to be buffered from the thermal stress experienced by shallow-water corals as they live in deeper waters and particularly within the thermocline across which temperature decreases abruptly8,15. Vertical perturbations in the depth of the thermocline expose benthic fauna and flora to rapid, and pronounced, changes in temperature. Recent results demonstrate that internal waves breaking over submarine slopes lift the thermocline, drawing cold water upwards and relieving thermal stress16,17. Rather than the relatively easily monitored SST, however, the dynamical processes responsible for modulating the thermocline depth occur independently of surface warming and are much harder to monitor with in situ sensors. Thus, whilst the threat of shallow coral bleaching can be assessed, and early warning indicators provided through products such as the National Oceanic Atmospheric Administration (NOAA) Coral Reef Watch (CRW), a metric which nonetheless has to be interpreted with caution)18,19, the susceptibility of MCEs to thermal stress requires an understanding of the physical oceanographic drivers of temperature variability beneath the surface, which is a considerably more challenging prospect than predictions of large-scale surface temperatures. The problem is further compounded by the practical and technological challenges of monitoring the coral community at mesophotic depths.

Here, we reveal the susceptibility of MCEs to bleaching events at depths of up to 90 m at two sites within an isolated atoll within the Chagos Archipelago in the central Indian Ocean (Fig. 1). This is the deepest example of coral bleaching on record and occurred in the absence of shallow-water coral bleaching. We demonstrate an association with the prevailing physical oceanographic regime in, firstly, triggering a mesophotic coral bleaching event at the basin scale due to a strong Indian Ocean Dipole (IOD) event and, secondly, in potentially modulating the extent of bleaching at this depth around the atoll due to the internal wave field.

Together, our results confirm that bleaching of scleractinian corals can occur within MCEs at depths of up to 90 m and, in the absence of shallow-water bleaching, we show the limitations of using surface bleaching susceptibility indicators to represent the threat to MCEs. Our observations also highlight the critical role played by the physical oceanographic regime at multiple spatiotemporal scales in setting the subsurface thermal regime.

Results
Coral bleaching at depth
We used a combination of remotely operated vehicle (ROV) surveys to obtain high-resolution digital imagery of the coral colonies and their bleaching state from shallow (15 m) to lower mesophotic depths (90 m), moored in-situ measurements of the physical oceanographic regimes over the slopes surrounding the atoll to resolve the dynamical processes modulating the thermocline depth, and high-resolution numerical modelling to simulate the change in oceanographic conditions between the two sites surveyed. Publicly available numerical model outputs of conditions across the Indian Ocean were also used to understand the regional scale conditions that reflected the influence of the IOD. The IOD is a key interannual cycle operating with a periodicity of 3–7 years that modulates surface wind fields, ocean currents and thermocline depth throughout the tropical Indian Ocean in a similar manner as El Niño Southern Oscillation (ENSO) in the Pacific20.

Video surveys of MCEs were conducted at two contrasting sites within Egmont Atoll, Ile de Rats (IDR) on the North-western flank and Manta Alley (MA), located on the North-eastern side of the atoll (Fig. 1), during November 2019, when the IOD exhibited its strongest positive phase on record, and March 2020 by which time the IOD was weakly negative. Coral bleaching was assessed using two metrics. Firstly, bleaching prevalence was estimated as the percentage of affected individual colonies in the population. Secondly, bleaching severity was estimated as the bleaching extent within a single colony, calculated using a bleaching index (BI).

During November 2019, coral bleaching was virtually absent on shallow-water (15–20 m) and upper-mesophotic reefs (30–40 m), with a BI < 2% and < 10% of all colonies bleached at both sites (Fig. 2a, b; full results can be viewed in Supplementary Tables S6 and S7). In contrast, mid- and lower-mesophotic depths (60–70 and 80–90 m, respectively) experienced significant coral bleaching in both severities (BI > 26; Fig. 2a; November 2019—Kruskal–Wallis chi-squared = 2393.1, df = 6, p-value < 0.001; March 2020—Kruskal–Wallis chi-squared = 804.64, df = 6, p-value < 0.001, see supplementary materials for full details) and prevalence (> 78%; Fig. 2b; November 2019—Kruskal–Wallis chi-squared = 2422.5, df = 6, p-value < 0.001. March 2020—Kruskal–Wallis chi-squared = 883.55, df = 6, p-value < 2.2e−1, see supplementary materials for full details) at both sites. The bleaching prevalence and severity values recorded on MCEs here are comparable to those measured globally on shallow-water reefs during several previous mass bleaching events21–23. During March 2020, five months later, coral bleaching at MA at mid- and lower-mesophotic depths was significantly less severe and widespread compared to November 2019, indicating partial overall coral community recovery (Fig. 2a, b).

The shallow-water reefs in the Chagos Archipelago experienced high mortality following the 2014–2017 global-scale bleaching event, with coral cover decreasing to <10% on many reefs24,25. The highest mortality was recorded on reefs at depths < 15 m (our surveys started at 15 m deep), and coral cover on shallow-water reefs at Egmont Atoll was observed to increase between 2012 and 201624,25. Further recovery of the reefs in the Archipelago has been observed in subsequent years26. Despite the high mortality experienced on reefs following the 2014–2017 bleaching event, over 3000 live colonies from 36 genera and 127 morphospecies of scleractinian corals were surveyed between 15 and 20 m in the current study (Supplementary Table S1). Thus, the low prevalence and severity of bleaching observed on reefs between 15 and 20 m in the current study is unlikely to be due to the low number of colonies present at this depth.

Shallow-water reefs in the Chagos Archipelago may now be composed of a higher proportion of heat-tolerant genera and species of scleractinian corals than before the mass bleaching events of 2014–2017, which is possibly reflected by the low prevalence of bleaching recorded on shallow-water reefs in the current study. However, the thermal stress of surface waters was not detected in the four months preceding and the four months subsequent to our cruise by the modelled local temperature fluctuations in the Archipelago between 2016 and 2021 (supplementary Fig. S3), in addition to NOAA Coral Reef Watch18 (although this metric must be taken with caution19. Previous studies within the Archipelago have shown that temperatures above 29.5 °C can induce bleaching24. During our surveys in 2019, the CTD mounted on the ROV continuously monitored temperature throughout the dives and recorded temperatures above 29.5 °C (in water < 25 m) in only two of the 12 dives conducted during our expedition (supplementary Fig. S2; Dive 14 at IDR and Dive 18 at MA). The water temperature during all other dives remained below 29.5 °C for the duration of the dives. Thus, the lack of bleaching observed on shallow-water reefs (15–20 m) is likely due to an absence of thermal stress rather than a lack of coral colonies on the reef and/or a high proportion of thermally tolerant individuals. As mesophotic corals live in low irradiance zones, and could potentially be affected by a change in water transparency, irradiance data with depth collected in 2020 and 2022 are also provided to the reader for their perusal in Supplementary Table S7, while a difference of > 10% in cloud cover has been observed between the two sampling periods.

On shallow-water reefs, high bleaching variability at local scales has been found to be partly due to differences in species composition in terms of both taxa and abundances22,27–29. In this study, significant differences in coral community composition were observed between depth bands within each site (PERMANOVA test on abundance data, 999 permutations, results in Supplementary Tables S2-1, S2-2). However, less difference in community structure was observed between the two sites at the same depth compared to two different depths within a site (Supplementary Tables S2-1, S2-2), and clear grouping of communities from the two sites at the same depth are shown in Fig. S1. At the same depth, the two survey sites share a high number of coral species (Table S3) and it is likely that the significant difference in coral community structure detected in the PERMANOVA is driven by the presence of a low number of rare coral species. Furthermore, the few coral species that span the depth distribution from upper-mesophotic waters (30–40 m) down to the lower mesophotic zone (60–70, and 80–90 m for Leptoseris spp.) experienced more severe bleaching in terms of prevalence and severity at mesophotic depths, with more coral bleaching observed at MA compared to IDR (Supplementary Table S4), indicating that coral composition is not the only driver of differences in coral bleaching along the depth gradient.

Thermocline deepening
The unprecedented depth to which coral bleaching occurred at Egmont Atoll during 2019 was likely attributable to the deepening of the thermocline that led to the presence of warm surface waters at a depth normally associated with the thermocline. This subsurface internal response is entirely distinct from the usual indicator of coral bleaching threat, which is essentially a function of SST alone. Analysis of the NOAA CRW database18 for the Chagos Archipelago region and wider central Indian Ocean over the four months before and after November 2019 confirmed that no coral bleaching warning was recorded within this period, in addition to the modelled local temperature fluctuations in the Archipelago between 2016 and 2021 (Supplementary Fig. S3). Thus, it would normally be assumed that there was no thermal stress (or associated bleaching) in shallow-waters (< 30 m) around Egmont, demonstrating that SST is likely a poor predictor of coral bleaching at mesophotic depths30.

Instead, the observed bleaching during 2019 coincided with the strongest positive phase of the IOD observed since records began (Fig. 3b), causing an enhancement in easterly winds throughout the eastern and central Indian Ocean and a sustained westward current throughout the surface mixed layer. The central and western Indian Ocean thermocline deepened31 (Fig. 3a), rendering coral communities that usually reside within the thermocline susceptible to bleaching through exposure to warmer surface waters32. Specifically, the 22 °C isotherm deepened from a depth of 60–140 m throughout a period of 3 months centred on November 2019. The depressed thermocline subsequently propagated westwards toward critical coral habitats in the Seychelles and Mauritius, where similar impacts on deep reefs would be expected. Five months later, as the IOD transitioned to a weakly negative phase, the thermocline had recovered to more typical depths of 40–50 m and the coral at depth displayed less evidence of bleaching (Fig. 3c–e).

Local-scale variation in bleaching influenced by internal waves
The differences in bleaching severity and extent between MA and IDR suggest that, whilst the basin-scale impact attributable to the IOD deepened the thermocline throughout the region, a local influence further modulated the thermocline depth and relieved thermal stress at IDR. To investigate the source of this variability, we analysed data from sub-surface moorings equipped with oceanographic sensors to measure current velocity and temperature throughout the entire water column at both sites. The observations were complemented by and contributed to the validation and tuning of, a high-resolution numerical model that further benefitted from a multibeam bathymetry survey of the entire atoll to depths of 400 m that we conducted prior to the ROV surveys in November 2019.

The thermocline in MA shoaled as expected between November 2019 and March 2020 (Fig. 4a) but, when observed over shorter periods, also underwent vertical excursions of > 20 m amplitude at tidal timescales (Fig. 4b). As opposed to the frequently observed generation of internal tides by cross-slope orientated currents over continental slope margins, the internal waves at MA were coincident with signals in along-slope currents; the resulting near-bed temperature fronts varied in their character, resembling at times turbulent bores and, at other times, nonlinear wave trains. Furthermore, increases in near bed temperature (evident as downward deflected isotherms in Fig. 4c, corresponding tidal height in Fig. 4d) are accompanied at shallower depth by decreases in interior temperature, with isotherms deflected upwards. Such behaviour is consistent with Mode 2 internal waves, a less frequent observation throughout the ocean where attention frequently highlights the importance of Mode 1 waves within which the direction of vertical movement of isotherms is consistent throughout the whole water column.

The numerical model output, supported by the moored observations, confirms that the headland at IDR is characterised by a notably different internal wave regime, with waves of larger amplitude which tend to draw cold water up the slope rather than depress warm water downwards (Supplementary Fig. S8). Thus, in a time-averaged sense, the internal waves could enhance warming at the depth of the thermocline in MA where bleaching was observed by preferentially advecting warm surface waters downslope. At IDR, the waves could have an opposite effect by predominantly advecting cold, sub-thermocline water up the slope and relieving thermal stress in the benthic environment.

To understand the discrepancy in internal wave activity and coral bleaching between the two sites, the numerical model was forced with tides at both diurnal and semi-diurnal frequencies following analysis of the long-term current data (see modelling methods). The model was run for a period of 15 days, to include a spring-neap cycle, initialised with a vertical temperature profile obtained in the deep water surrounding Egmont Island that represents oceanographic conditions undisturbed by internal waves over the slopes. The model replicated the observed pattern of temperature variability within the thermocline in terms of the frequency and amplitude of perturbations (Fig. 5c, based on in-situ observations, Fig. 5d). Most significantly, the Mode 2 internal wave activity causes a sustained increase in the time-averaged temperature at the seabed relative to the undisturbed regime within MA at the depths where bleaching was most pronounced, between 60 and 90 m deep (Fig. 5a; Supplementary Fig. S5). The same impact was absent at IDR due to the cooling, rather than warming, influence of internal waves on the northern flank of the atoll, demonstrating the highly localised potential influence of internal waves on coral bleaching within MCEs (Supplementary Figs. S4, S6, S7).

The temperature measured by the ROV during the dives to survey MCEs corroborates this result. In-situ temperatures at the seabed were consistently higher than the background values obtained from a vertical profile obtained nearby but in deeper water away from the influence of the slope (Fig. 5b, supplementary Fig. S5b; not as pronounced for IDR, Fig. S6b). Thus, internal waves could elevate the time-mean temperature at a depth beyond the values that would be experienced by corals without any tidal forcing, exacerbating the impact of basin-scale dynamics and potentially modulating bleaching in MCEs over horizontal distances of O(1 km). Additional impacts may also be generated by remotely forced internal waves that, after generation at other sites, radiate out into the surrounding ocean before, potentially, breaking over the slopes surrounding islands such as Egmont.

In summary, our results demonstrate that scleractinian corals at mesophotic depths from the Chagos Archipelago, in the Indian Ocean, are susceptible to thermal stress and bleaching in the same manner as that experienced by shallow-water reefs. This is in contrast to previous studies on mesophotic corals from different geographic areas27,33–35, highlighting the need to incorporate these unique ecosystems within conservation planning13,36,37. Our study adds further weight to the increasing evidence demonstrating that MCEs are not a universal refugia for shallow-water coral reefs12,37–40. In addition, SST as a measure of thermal stress is a poor indicator of coral bleaching at mesophotic depths in the Indian Ocean, revealing the urgent need to consider the impact of subsurface dynamical processes on thermocline depth41. Here, the IOD was potentially the dominant mechanism responsible for coral bleaching at a regional, monthly, scale and is projected to increase in frequency and severity with global warming42, similarly to ENSO in the Pacific region. At local scales, internal waves, especially Mode 2, were suggested to have an impact on the thermal regime at mesophotic depths and could be responsible for deep bleaching over distances < 1 km, which realistically requires high-resolution numerical modelling to fully understand. As shown in this paper, the internal wave influence on coral bleaching is sensitive to the details of the bathymetry, stratification and forcing, all of which vary over both space and time. At different locations, other modes of variability may play a significant role in modulating the near-bed temperature regime. Currently, remotely sensed products and/or numerical output with typical resolutions of 5 km are used to evaluate the threat to surface corals from bleaching and are considered state-of-the-art, yet are clearly deficient for resolving subsurface dynamical processes at local, atoll-scales. Concernedly, it is likely that many mesophotic bleaching events go unnoticed due to the lack of appropriate monitoring techniques for deeper reefs. As researchers spend increasing amounts of time on MCEs, records of bleaching events at mesophotic depths are likely to increase. However, numerical models that are able to incorporate dynamical processes at local scales will further our understanding of the frequency and severity of bleaching on MCEs. To conclude, additional data on the composition, dynamics and threats to MCEs are required to better understand these critical ecosystems and to develop sound conservation and resource management criteria.

Methods
Study area
This study focuses on Egmont Atoll, within the Chagos Archipelago (Fig. 1), where two research cruises were undertaken in November 2019 and March 2020. Egmont Atoll has a total surface area of 40 km2 and is composed of six islands and several distinct areas43. Mesophotic coral ecosystems were investigated at two sites: Ile Des Rats (IDR) on the North-western coast, and Manta Alley (MA) (also called Egmont Mid) along the North-eastern coast (Fig. 1).

Biological data
Data collection. A Falcon Seaeye Remotely Operated Vehicle (ROV) was used to collect underwater imagery at all sites. The ROV was equipped with four SAAB Seaeye LED daylight white lamps (34 W, 3520 Lumens), with two mounted on a tilt platform with a SAAB Seaeye camera in the centre (recording live video in standard resolution (720p) with wide-angled lens (91o in water), functioning with low light, with an information overlay displaying depth, time, heading, pitch and roll). A second camera (GoPro Hero 4) was positioned directly below the Seaeye camera and recorded footage in High Definition (2.7k, 24 fps, wide field of view). Dive duration was limited by the GoPro battery length, which was ~3 h. In addition, a Valeport Modus conductivity–temperature–depth (CTD; serial number 31027) was mounted on the ROV (calibrated on 23/04/2015 and 10/12/2020 with no modification required between the two dates).

Due to the presence of a strong current at many sites in the Chagos Archipelago, it was difficult to maintain a constant heading at an altitude close to the seabed to undertake linear video transects. Thus, still image samples were collected along transects. To collect image samples, the ROV descended to the appropriate depth and approached the seabed (altitude < 1.5 m) with the cameras positioned at an oblique angle to the seabed. Still, frames were captured in order to collect high-quality images that allow specimen identification and maximise the field of view of the seabed. While digital imagery has its limitations, non-destructive image collection techniques such as those used in this study are regularly employed to quantify benthic habitat composition in shallow and deep-sea ecosystems and contribute significantly to surveying and monitoring vulnerable habitats44–47.

For each image, the time, depth, latitude and longitude of the sampling position were recorded, and 90 images were collected per depth, with a total of 1080 images from the two sites. Along the depth gradient, six depth bands, chosen a priori and based on the literature, were surveyed to cover the shallow and mesophotic zone: 15–20; 30–40; 60–70, to 80–90, 110–120 and 150–160 m. Depth bands were also chosen to facilitate ROV operation and counteract the strong upwelling and downwelling currents occurring in the Archipelago. The two deepest depth bands were not included in the analysis for this study as scleractinian corals were not observed at these depths. Surveys were undertaken along the entire depth gradient at both IDR and MA in November 2019. In March 2020, only surveys at MA were possible due to an extremely dynamic current regime close to the atoll, directed from West to East, preventing safe access to IDR. Scale, enabling the calculation of image area, could not be quantified due to technical issues related to the ROV lasers. However, the collection of benthic imagery was standardised by ensuring that the camera angle was consistent throughout the dives and ensuring the ROV was as close to the seabed as possible when still images were captured. Hence, this study focuses on the proportion of bleached colonies observed from the total number of colonies surveyed at each depth, rather than an area-based survey.

Coral bleaching prevalence (number of individuals in the population affected, %) and severity (bleaching extent within a single colony, bleaching index, BI) were assessed in November 2019 and March 2020, using still images extracted from video transects, from shallow and upper mesophotic (15–20 and 30–40 m) to mid and lower mesophotic depths (60–70 and 80–90 m).

Image analysis. Still images collected along each transect were annotated using the online annotation platform, BIIGLE48. All benthic organisms > 1 cm within each image were identified and quantified (Fig. 6). All organisms identified as distinct morphospecies were assigned an Operational Taxonomic Unit (OTU) and were identified to the highest taxonomic resolution possible. However, morphospecies may correspond to species, genus, family or higher taxonomic levels. Alongside the image analysis, a morphospecies catalogue was created for the region following the global standardised marine taxon reference image database suggested by Howell et al.49. For the purposes of this study, only morphospecies identified as zooxanthellate corals were analysed.

Hard coral bleaching identification
Bleaching extent and severity. Edmunds et al.50 indicated that subjective rankings of bleaching based on coral colour are strongly associated with Symbiodinium density, chlorophyll a concentration, and the intensity of green, blue and red colour spectrums. Subjective ranking may therefore be a good indicator of disruption of the symbiosis for bleaching events23,50. Thus, the bleaching extent within a single colony, also called bleaching severity, can be calculated based on coral colour. In addition, a bleaching index (BI) can be used to assess a species’ overall health. Following previously published methods23,50–52 4 bleaching categories were created in order to classify each scleractinian colony observed in the images to provide a precise measure of coral health: (1) unaffected (normal coloration), (2) light (combining pale, a lighter colour than usual for the time of year, and 0–20% of the coral surface bleached), (3) moderate (20–80% bleached) (4) severe (80–100% bleached and bleached with partial mortality). Total mortality was not taken into account to avoid counting corals that had not bleached during this event. The four categories are identical to those used in a previous mesophotic study51.

As the images did not include a uniform Lambertian reference material, a combination of methods was used to assign colonies to these four categories: the still image itself when fully saturated by light; the video footage from which the images were sampled to verify the bleaching category of a colony when the image itself was not sufficient; different bleaching severities within the same image, thus exposure to the same light conditions; physical samples of hard coral from different species and different depths with the corresponding underwater image; and both images and physical samples of healthy corals collected in a subsequent expedition in 2022, to compare with the samples of the present study.

The bleaching index (BI) was calculated from the percentage of coral colonies observed in each of the above four bleaching categories:
BI = (0 * C1 + 1 * C2 + 2 * C3 + 3 * C4) / 3 (1)
where Ci is the percentage of observations in each of the above four bleaching categories.

These categories were created in BIIGLE software and assigned to every zooxanthellate scleractinian coral identified during the image annotation (Fig. 7).

Bleaching prevalence. Bleaching prevalence has been used by several authors in coral bleaching studies, and is the number of individuals in the population affected (see references in Quimpo et al.28). Here, bleaching prevalence was calculated as a percentage by dividing the number of bleached colonies by the total number of colonies recorded and multiplying by 100, using the same categories in BIIGLE described above.

Statistics
In order to detect differences in terms of coral bleaching between the two sites, the two seasons and the six depth bands, using R software53, a Kruskal–Wallis test was performed with pairwise comparisons using post-hoc Wilcoxon rank sum test with continuity correction and Benjamini–Hochberg (BH) adjusted method for both BI and bleaching prevalence calculations. Differences in hard coral community composition between sites and depths were investigated using a multi-dimensional scaling (MDS) plot and permutational analysis of variance (PERMANOVA) test on abundance data, square-root transformed and Bray–Curtis similarity, with a dummy variable added to account for zero-inflated data54–56 using PRIMER v6. A test was significant when the p-value was < 0.05.

Sea surface temperature via NOAA satellites
Degree heating weeks (DHW) data were extracted from the National Oceanic Atmospheric Administration (NOAA) Coral Reef Watch (CRW) database18 for the Chagos Archipelago region (−8 to −4° S; 70 to 73° E) and wider central Indian Ocean (−30 to 20° S; 40 to 100° E). DHW shows accumulated heat stress (HotSpots) by accumulating the instantaneous bleaching heat stress during the most recent 12-week period, with significant coral bleaching usually occurring when the DHW value reaches 4 °C-weeks18. However, this metric should be taken with caution as research has shown that its ability to predict bleaching varies with geographic location19.

Moored measurements
Data were obtained at two locations within Egmont from three separate moorings, two collocated in MA, and one at IDR. The current meter mooring within MA consisted of a near-bed (z = 2 m above bed) upwards looking Signature 500 kHz ADCP, whilst a secondary mooring located within 100 m horizontally comprised a taut-line mooring on which were mounted two RBR Concerto conductivity–temperature–depth (CTD) sensors at the top and bottom of the mooring and 23 RBR solo-T temperature sensors spaced at 2 m vertical intervals between z = 4–50 m. At IDR a single taut-line mooring contained temperature-depth sensors (top and bottom), and 25 temperature sensors spaced at vertical intervals of 2–4 m, and an inline upwards looking Aquadopp 400 kHz ADCP. All thermistors and temperature–depth sensors were logged at 1 Hz, and CTDs logged at 0.2 Hz. The Nortek Signature ADCP operated on a dual sampling regime, providing 10 min average velocities at 2 m vertical intervals and 23 min of 1 Hz burst velocity data in 1 m vertical bins and 1 Hz echosounder data at 6 min intervals at the start of every hour.

Temperature data were interpolated to regular 2 m vertical intervals and cleaned in both spatial and temporal dimensions with a maximum deviation filter and running mean window. Noise issues in the echosounder data necessitated correcting with a dynamic level adjustment to a common noise floor as well as gain normalisation via a logarithmic fit for acoustic decay with range. In the case of Fig. 4a temperature data have been binned to 1-day samples and further low passed with a 6-day cut-off to better visualise long-term evolution.

Remote sensed data
Indian Ocean dipole (IOD) index data is taken from the Ocean Observations Panel for Climate Dipole Mode Index dataset (https://psl.noaa.gov/gcos_wgsp/Timeseries/DMI/). Remotely sensed temperature is taken from the Copernicus Marine Service Global Ocean Forecast (from 2019) and Reanalysis (before 2019). Time series were extracted from 8.125° S and 73.875° E in deep water to the east of the Archipelago to minimise the effect of perturbations arising from flow–topography interaction in the Chagos Archipelago and highlight the basin-scale evolution of the thermocline due to the IOD.

High-resolution oceanographic numerical model
Modelling the tidal motions in Egmont Atoll was conducted using the nonlinear nonhydrostatic Massachusetts Institute of Technology general circulation model (MITgcm)57. The topography used in the model is presented in Fig. 8A; bathymetric data were collected during a multibeam survey of Egmont to depths of 400 m during 2019 and gridded to 5 m horizontal resolution. Beyond depths of 400 m, data were interpolated to match the GEBCO bathymetry. The vertical model resolution was 5 m and the horizontal resolution in the central part of the model domain was 25 m in both horizontal directions. The model simulation encompassed 16 days to allow for a day of spin-up and 15 days of predicted currents and temperature variability. Reflection of barotropic tidal waves from the domain boundaries was excluded through the application of Orlanski-type boundary conditions.

According to the TPXO inverse tidal model predictions58 and in-situ data from ADCP moorings the tidal currents in the area consist of comparable values of diurnal and semi-diurnal harmonics. Figure 8B and C show depth-integrated zonal (u) and meridional (v) velocities without long-term oscillations at MA. Both currents show a 15-day periodicity that results from a combination of semidiurnal M2 and diurnal K1 tidal harmonics.

The combination of semidiurnal M2 and diurnal K1 tidal harmonics was activated in the model using a methodology described in Vlasenko and Stashchuk59. The temperature/salinity profiles were taken from CTD profiles acquired in deep water, away from the internal wave activity over the slopes, during 2019 and 2020 near Egmont. The observed vertical profiles represent the undisturbed fluid stratification required for the model initialisation. The temperature profile for March 2020 is shown in Fig. 5b by the black solid line. The modelled temperature, salinity, and velocities were compared with the ADCP mooring and thermistor chain data in MA. Figure 8D and E show depth-averaged time series of u and v velocities at the same position as the mooring. The background non-tidal currents were deleted from the original raw ADCP records. D and E Tidal currents reproduced by the model at the position of the mooring.

From the coincidence between Fig. 8C, B and D, E, it is seen that the model correctly reproduces tidal currents in terms of phase and amplitude.

Depending on the combination of buoyancy frequency N(z), bottom topography H(x), Coriolis parameter f = 2Ωsinθ (Ω is the angular velocity of the Earth and θ is the latitude), and the tidal velocity Um, a variety of generation scenarios are possible60. The periodic response in time, t, with frequency, σ, of internal waves propagating horizontally in the ocean along the x-axis with wavenumber k are given as q(z) = sin(kx − σt). In terms of the boundary value problem, the vertical structure q(z) of these waves is defined by the following boundary value problem (BVP):
qzz + k2 * ((N(z)2 − σ2) / (σ2 − f2)) * q = 0 (2)
q = 0; at z = 0; z = −H (3)
Note that the above-mentioned BVP has solutions, q1(z), q2(z), q3(z),… with horizontal wavenumbers k1, k2, k3,…, that define the vertical structure qi(z) and horizontal scale ki (i = 1, 2, 3,…) of generated internal waves. The BVP shown above is applied to a very general case which includes both strong and weak Earth rotation. For the Chagos Archipelago, the Coriolis parameter f at the latitude of Egmont Atoll, 6.5o, is small compared to the tidal frequency σ. If so, the direct theoretical consequence from the BVP for the considered area is that the properties of internal waves are the same for both semidiurnal and diurnal baroclinic tidal constituents.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "Review of Deep Coral Bleaching Driven by Hidden Changes in Thermocline Depth for Nature\nCommunications\nI am now reviewing this revised manuscript for the second time and as previously stated I am impressed\nwith the physical oceanography and its causal role in the observed bleaching of scleractinian corals on\nMCEs in the Indian Ocean. I also appreciate the authors response to the previous reviewer’s comments.\nNonetheless, I still believe there are issues that should be addressed.\nLine 18; Suggest this reads as follows; “Our results demonstrate the potential vulnerability…”\nLine 26; Here, and throughout the manuscript “Scleractinian” is not capitalized. It is not a taxon and\nshould be in lower case.\nLine 27; Suggest this reads as follows; “…sea surface temperatures (SSTs) and subsequent coral\nbleaching; current estimates…”\nLine 32; Suggest this reads as follows; “…depths of 30-150 m and have been estimated to occupy…”\nLine 33-34; Suggest this reads as follows; “It has been hypothesized that these communities are buffered\nagainst anthropogenic changes, and therefore might represent a refuge that replenishes shallow-water\ncoral species with vertically dispersed larvae8,10. Or words to that effect…..\nLine 51; “in-situ” is not hyphenated and should be italicized as it is Latin.\nLine 53; Per my previous review. The fact that a flawed metric (i.e., DHW) is being used by a large\nproportion of the community is not a justification for its continued use. If the authors insist on using this\nmetric, knowing these flaws as I pointed out in my last review, then they must at least tell the\ncommunity that there are known problems, with references, especially as it relates to its predictive\ncapabilities.\nLine 63; Reviewer #2 had some keen insights on this, and I will be interested in seeing how the authors\ndeal with the issue of post-bleaching coral communities being dominated by “winners” as a reason for\nlittle to no bleaching on shallow reefs compared to potentially more thermally sensitive corals at MCE\ndepths. The recovery you discussed in response to the reviewer, in the absence of any seascape genetic\ndata, was likely a result of recruitment from local populations, or the winners so likely more resistant to\nthermal stress. Also, 3000 corals in 2019 and 1000 in 2020 on shallow reefs-what happened here?\nFigure 1. The euphotic zone, classically defined in the oceanographic community is 0-200 m and the\nmesopelagic zone is 200-1000 m. The MCE depth definition is placed, or should be placed, over these\nlong accepted oceanographic depth descriptions as near coastal benthic habitat.\nLine 110; “5” should be “five”\nLine 128-135; There it is-the “winners” argument, but then you try and support your interpretation with\na flawed metric. Again, if you are going to do this you must state clearly for the readers the flawed\naspects of the metric.\nFigure 2; Need a fuller description of statistics. As requested in my previous review what primary\nanalysis, and post hoc analysis, was run? What were the DF, F-value, p value corrections for multiple\ncomparisons, etc. as applicable.\nLines 155 and elsewhere; ANOSIM provides a test to detect differences in two or more groups of\n“sampling units” based on ranked similarities. First, why not present the results as an NMDS or cluster\nplot? Would be much easier for the reader to see the depth comparisons of coral communities between\ndepths and sites. Did the authors ensure that the heterogeneity of dispersion, which ANOSIM is very\nsensitive to, is equivalent or at least similar between depths and sites? Also, why the more permissive p\nvalue of 0.1 to start with? Is it possible that at a minimum p value of 0.05 some of these comparisons\nwould not have been significant?\nLine 165; “spp.” is not italicized.\nLine 250; Is this supposed to say; “(See modelling methods)”?\nLine 283; Suggest this sentence reads as follows; “In summary, our results show that scleractinian corals\nat mesophotic depths from the Chagos Archipelago in the Indian Ocean are susceptible to thermal\nstress, and bleach in a similar manner to that observed for shallow-water corals in contrast to other\nstudies on mesophotic corals from different geographic areas26, 32-34.”\nLine 286; Suggest this reads as follows; “Our study adds more evidence that MCEs are not, a priori, a\nuniversal source of coral recruits for replenishing shallow water coral reefs12, 13, 37-39.”\nLines 334-338; So, transects were employed. How long were they? How many images were taken at\neach depth? Were the same number of images taken at both sites at both times? What was the angle of\nthe oblique imagery?\nLine 339-342; The statement that non-orthogonal, or oblique, imagery is taken by the deep-sea\ncommunities is true. But they usually collect those images, along with scale (!), and analyze them a priori\nknowing that different techniques (i.e., multiple lasers, Canadian grids) will be needed to obtain\northorectified images and accurate community characterizations for multiple ecological metrics such as\nabundance and percent cover. Regardless of whether plot or plotless designs are incorporated the\nimagery must be orthorectified.\nLine 347; Why were the depth bands discontinuous?\nLines 362-372; You only present the “community” analysis on zooxanthellate corals for the\npresence/absence data. The additional information is unnecessary. Amend it for the analysis presented\nin the manuscript.\nLine 386; “coral colour” is actually a function of its reflectance captured by the image under a specific\nlight field. Without a reference, a control, based on a simultaneous image of a Lambertian surface you\ncannot accurately and consistently quantify image to image difference in “coral colour” even with a\nknown light source. More on this later.\nLines 414-418; As stated previously; “Also, there is no indication of how bleaching prevalence was\nactually calculated because to compare between sites one would have to/should know the aerial extent\nof the survey. That is the percentage of bleached coral at site A was 50% and site B was 75% based on a\n100 m2 survey. Or better yet do transects at each depth, even plotless transects would be fine as long as\nthe areas surveyed were the same. Just like Quimpo et al. 2020, the paper the authors reference, did in\ntheir paper.\nResponse to authors comments of prior review\nI appreciate the efforts of the authors to examine both irradiance and cloud cover at their sites as it\nrelates to coral bleaching. I also understand that corals at mesophotic depths are probably naïve to\ntemperature increases of 3-7°C. Figure C1 is helpful although changing the scale to allow a closer\nexamination of the changes in irradiance at mesophotic depths would have been more informative.\nHowever, the authors do provide calculations of optical depths for the irradiance data they do have that\nare based on calculated Kd. The authors state that only 1% of surface PAR reaches 90 m so irradiance is\nnot an issue as it relates to bleaching. But the corals at these depths are acclimatized to these extremely\nlow irradiances. Any change in the optical properties may allow increased water transparency and\nincreased irradiances, albeit small when thinking in terms of shallow coral reefs, but not inconsequential\nfor extreme low-light acclimatized corals. For instance, the Kd for the 1% OD of 63 m is 0.073 while for\n97.8 m the Kd is 0.047 from your table. These are not inconsequential differences and suggest significant\nchanges in water transparency which could have consequences related to the role of light in bleaching\nat mesophotic depths, which on shallow reefs is primarily a light driven phenomenon; temperature sets\nthe table, but light drives the process. The authors should give the reader the data and a chance to\nassess. Provide the OD data, give an example and say it is possible that these oceanographic processes,\nespecially internal waves, could change the transparency of the water column and could have\ncontributed to the bleaching process.\nOn the issue of using coral color as an index of bleaching extent and severity. As suggested above again,\nthe calculation of a bleaching index based on coral color requires that all colonies being assessed in the\nimage be orthoganol, and at the same height above the substratum so that the light source illuminates\nthe coral evenly and at the same intensity. If this does not occur then this index, basically a measure of\ncoral reflectance, requires, for each image, a reference to compare against. The reference material must\nbe Lambertian in nature; a commonly used material is Spectralon, which can provide a diffuse reflection\nthat is equal across all visible wavelengths. This allows the user to compare the reflectance of the\nstandard to the reflectance of the subject under the same light source (and any differences associated\nwith light intensity). For images that are not orthogonal such as used here multiple references would be\nneeded since the distance from the light to the subject varies, and therefore so des light intensity across\nthe image. This can be all entered in the authors BIIGLE program for appropriate annotation and is\nessential to compare coral bleaching between sites, and between years.\nAs far as bleaching prevalence I still believe that to compare between depths or sites one would have\nto/should know the aerial extent of the survey. That is the percentage of bleached coral at site A was\n50% and site B was 75% based on a 100 m2 survey. The authors describe taking images, and the number\nof images, but do not adequately describe the process-see comments above for Lines 334-338.\nThe authors contend that using the number of individuals to assess species diversity is a valid approach\nas described by Gotelli and Cowell 2001. Their techniques utilize rarefication curves and I see no\ndescription of that in the M+M of this manuscript. Also, my reading of Gotelli and Colwell 2002 suggest\nthat using species density, versus species diversity/richness would be a more appropriate metric to\nderive for quantitative studies, and therefore requires a knowledge of area analyzed. This is best\naccomplished using orthogonal images.\nAgain, the physical oceanography is amazing! The authors should couple that data to the bleaching\nprevalence data alone, once the M+M for the bleaching prevalence data is better explained, and omit\neverything else.", "reviewer_3": "Review of NCOMMS-23-12279-T\nI was brought in to review the physical oceanography reported in this manuscript. I have\nexpertise in studying the dynamics of internal waves in the ocean using observations similar\nto those reported here.\nIn general, there is a reasonably detailed set of measurements of the physical state of the\nocean at the two study sites. These observations come from moorings with temperature,\nsalinity, and currents. Based on the description in the methods, the mooring design and the\ndata that the moorings collected seems appropriate to assess the variability of temperature\nover the upper ~100 m with good vertical resolution on frequencies from minutes to weeks.\nHaving this data is very good and an absolute prerequisite here. Unfortunately, however, the\nmooring time series start after (dec 2020) the primary bleaching period (nov 2020), and the\ndata for whatever reason is given second billing to two numerical models.\nMITgcm is used by the authors to model the internal wave variability. It is initialised by a CTD\nprofile the authors collected, and forced by the semidiurnal and diurnal barotropic tides. The\nmodel is (sort of) compared to the data, and then the authors create a number of plots of\nmodel output that they use to argue about differences between the two reef sites. The\nauthors settle on “mode 2” internal waves as differing between the two sites. I am fairly\nsceptical that the analysis of the model in the way presented here supports that conclusion\nto the exclusion of other hypotheses. I would have preferred to see more analysis of the\ndata, and a deeper dive into the model insight about how the internal wave climate is\ndifferent between the two sites.\nIt should be understood that my comments that follow are in an effort to get the best out of\nthese data, and that I don’t believe that the manuscript should be rejected due to the PO\ncomponent of the paper. That said, I have a number of fairly significant concerns with the\npresentation and interpretation.\nFor the record, I actually do not believe that “definitively” identifying the presence of some\ninternal wave pattern or another is a precondition for this being a valuable contribution.\nSimply identifying, in the data first, and the model second, that the different reefs have\ndifferent internal wave climates is probably enough to POSE the hypothesis that this is the\nreason why one bleach and the other did not. More data/modelling would be needed to\ndefinitely show this.\nFinally, there has been some fairly strident back-and-forth between the authors and the first\ntwo reviewers about the value of SST and “coarse” numerical models in predicting bleaching\nrisk in mesophotic corals. My take is the following: of course a mode-derviedl “early warning”\nproduct tuned to the ocean surface mixed layer and shallow (<30 m depth) corals would\nhave questionable application to 40-80 m depths. Is there actually debate about this? As the\nauthors point out, because of the importance of internal wave variability, any global model\ndriven early warning system is likely to be quite challenged. (As an aside, I will note that\nglobal models like mercator do not get the internal waves correct *anywhere* and so by\ndefinition can not at present capture this impact for any depth). Simply pointing out that\ncurrent generation “bleaching warming systems” are not going to be as effective for\nmesophotic corals because of internal wave variability, without getting into the “difficulties” of\nmeasuring the position of the thermocline – which is actually not that hard and is regularly\ndone with moorings all over the world – is plenty of a conclusion enough in that realm for a\npaper like this.\nI hope the authors find these comments useful. I have written many of them in what follows.\nIt is not my position that every suggestion has to be followed up on. But I do worry that at\npresent the PO story is incomplete and in some ways confusing and potentially even wrong.\nWe want to get as much as that out of the paper as possible before it is published.\nMajor comments about the PO:\n1) The presentation in Fig. 3 is confusing. First of all, Fig 3 is from a model reanalysis..\nIt is not data, it is the output of a model. The model does assimilate data, but it needs\nto be clearly understood that these are not actual observations, including within the\nfigure/caption itself.\nI have comments below about each subpanel.\na) There really is no need to show the entire reanalysis period. Why is this\ndone? I much prefer the presentation in Fig. S2. Fig 3 a and b are far too\ncluttered and this story is about 2019-2020, not the decade beforehand. I\nstrongly suggest that this be re thought. It is almost impossible to understand\nanything about the temperature fluctuations in fig 3 a.\nb) Fig 3 b should be zoomed into a much tighter time range. Again, there is little\nvalue in showing a long time series, since the point of the paper seems to be\nthat 1) regional oceanography was anomalous (this has been shown by\nothers and comes with a few references in the text) and 2) local effects\nmatter. Neither fig 3 a or 3 b needs a decadal perspective.\nc) Fig 3 c d and e are unnecessary. While somewhat interesting that the\nthermocline position was anomalous regionally, I don't think this strengthens\nthe paper. For one, again, these are the results of a model with coarse\ngridding in space and time (the authors later point out that such models are to\nbe taken with a grain of salt in areas with complex local bathymetry and local\ndynamics). More generally, this paper should rely mainly on the observations\ncollected and the MITgcm model. I dont think the cluttered presentation in Fig.\n3 really adds anything and it could be simplified with a net positive benefit on\npresentation.\n2) Fig 4.\na) Fig 4 a— I cannot understand why the data is “averaged to daily values and\nthen low passed” with a 6 d cut off. I do not believe this is necessary… plus if\nyou are going to filter a time series, it is not necessary to average it\nbeforehand. I dont think the filtering actually probably adds that much and I\nwould avoid it.\nb) This is nice (real, unfiltered data!!) and should be bigger and the main point of\nthis figure. In fact, I think the authors should be comparing IDR and MA with\nthis figure, showing a zoom in like this for both sites. But either way, these are\nthe observations we need to see!\nc) Ok… I have experience with Nortek instruments in ecosounder mode and I\ncan confidently say that it is not scientifically accepted that the returns in that\ninstrument mode can be simply ascribed to “turbulence” as the authors do\nhere. This is a contentious claim, and the authors have no other turbulence\ndata that I see to justify it. Moreover, why is this even necessary? Why have a\nfigure about turbulence and then never talk about mixing processes in the\ntext? The authors are mainly interested in the actions of the internal waves in\ntransporting cold (or trapping warm) water to the reef. This doesn’t need\nqualitative hand waving about turbulence, even if the internal waves are\nimportant to mixing and mixing is important to bleaching. You just don’t have\nthe necessary data to say anything quantitative, so it would be much better to\nremove this. Finally, I bet you are seeing enhanced scattering from biological\nsources (zooplankton, etc) that are beings advected up and down by the\ninternal waves. Even if it IS turbulence causing this signal, you can’t quantify\nit in these data so you are better off leaving it out.\nd) Why is tidal elevation here? These internal waves are (probably) baroclinic\nresponses to barotropic tidal forcing. The surface tide will not give you much\nor any insight to the subsurface internal tide, especially over a hand picked 18\nh segment… What is this supposed to show?\n3) Lines 242-243: “The influence of internal waves, both at tidal and higher frequencies,\nwas far less pronounced during 2019 when the thermocline was depressed due to\nthe IOD.” Where is the evidence for this statement? Your time series starts in Dec\n2019. Are you saying that there were less internal waves in Dec 2019 than in the rest\nof the time series? Do you mean that the appearance of sub thermocline water on\nthe reef due to internal waves was less common or absent in 2019? Either way, this\nstatement is a very important one that absolutely needs to be justified if it is going to\nbe in here.\n4) Fig. 5\na) Ok… I have spent a few days trying to puzzle out what exactly is being shown\nin Fig 5 a (and again in S3, S4a and S5a). This is my best guess: The model\nis initialised with a density profile taken by the authors on some day in some\noffshore place. This is used as the initial density profile at all locations in the\nmodel. Then the model is run for 15 days. Then (now I am getting into\nspeculation territory) the authors extract the bottom temperature values at all\ntimes over the reefs of interest, form some sort of average in time at each\nnear bottom location, then take the temperature at the corresponding depth\nfrom the initial, offshore profile and subtract that offshore temperature from\nthe model temperature. Therefore, “red” means that at that depth it is warmer\nthan the offshore initial condition. Is this more or less what is being done?\nIf so, this needs to be explained somewhere!! The title of the plots is variously\nreferred to as “model mean temperature” and “bottom mean temperature\nvariations.” Arguably the quantity you are plotting is not accurately described\nby either of these titles. It would be more correct to refer to this as an anomaly\nrelative to the initial state or similar.\nSecond, the CTD cast that you choose to initialise the model is itself simply a\nsnapshot at one time of the evolving vertical position and gradient of the\nthermocline. Did you test other stratifications? To this reviewer, it would have\nbeen a better use of the modelling to compare the internal wave climate\nunder several different stratifications (i.e. at peak positive 2019 IOD vs\n“normal” conditions.. These initializations need not be collected by the\nauthors, but instead could come from ARGO or even the model reanalysis.\nThe MITgcm is best used to test the hypothesis that changing stratification\nimpacts internal wave variability at both locations, in addition to exploring how\nthe internal waves are different at the two locations.\nFinally, and most importantly, this approach to analyzing the model does not\nactually tell you anything about the presence or absence of mode-2\ninternal waves (or any internal waves). These plots need to be re-thought and\npotentially abandoned entirely. They are confusing and do not speak to what\nyou are trying to assess.\nb) In general, it is confusing to me why there would be so much model shown and\nso little data in Fig 5 c and d. You have weeks of data… why not show it?\nI don’t think what is being shown here is very convincing in terms of\ndata/model comparison (see next comment).\n5) The model… I found myself trying to figure out what exactly was done with the\nmodel. While the spatial resolution was mentioned, the size of the domain was not.\nHow far into the open ocean does it extend? I couldn’t figure out the time step either.\nI will note that it is somewhat rare to fire up a model and “run it for 15 days” without a\nspin up period, but perhaps there was one. In general the modelling details were\nsparse and need to be filled in a bit.\nI was likewise a bit confused about the model/data comparison. Yes, this is difficult to\ndo quantitatively, but no attempt has been made here to do so. Instead it is asserted\nthat the model captures the internal wave variability, with a nod to the figures that\nshow wiggly lines from the data and wiggly lines from the model. (I note here that\nthere is –presumably– a typo: these would be depth-AVERAGED velocities, not\ndepth-integrated velocities… or they are plotted in the wrong units). Comparing depth\naveraged velocities between a model and data is a bit of a funny thing to do if you\ncare about the baroclinic internal wave response, which is not a depth-averaged sort\nof quantity. So yeah… I’m not sure outside of qualitatively for the depth averaged\ncurrents that there is any evidence that the model is recreating the internal wave\nfeatures in the data.\nIn S6 both model and a short snapshot of ADCP data in depth and time are shown.\nBut I am confused why the data is only shown for a 2.5 day period, but the full 15 d\nmodel time series is shown (see previous comment about fig 5 c and d in the main\npart of the paper).\n6) Regarding the “mode-2” structure of the tidal variability at MA.\na) First comment is that mode-2 variability is commonly observed and often\nstudied and written about in the literature, so I would remove the statement\n“relatively rare observation throughout the ocean where attention has largely\nfocused on Mode 1 waves within which the direction of vertical movement of\nisotherms is consistent throughout the whole water column.” which while\nperhaps not strictly incorrect, requires a lot of work by the modifiers\n“relatively” and “largely.”\nb) You have the data to show whether or not MA and IDR have a different\nvertical structure of the internal tide. You *do not* need the model for this.\nInstead you would use the model to diagnose WHY the internal wave\nstructure is different in the different locations. I would suggest an EOF or\nother modal decomposition to show this from the data.\nc) For the record… internal waves cannot “warm” the water. The can transport\nheat from one place to another (advective heat flux), and they can give up\nenergy to turbulence, which in turn can lead to mixing, which, then, in the\npresence of a temperature gradient, can lead to a heat flux (mixing-driven\nheat flux). What you are showing in the model is that the (I think time mean)\nvertical temperature profile at MA is different from the initial condition (and\nIDR) particularly in the mid-reef. You do appear to have some data in fig 4\nthat shows one example of isotherms separating. I would suggest you lean\nmore on these observations. I do NOT think this paper needs to “discover”\nthat the internal wave climate is complicated over complicated bathymetry, or\nthat the oceanography can be different on different sides of an atoll, even a\nsmall one, in order to be an impactful contribution.\nMinor comments:\n1) Lines 182-183: The discussion of SST being a “poor predictor” of thermocline depth\nand thus the potential that CRW not being good for mesophotic zone corals needs to\nbe more carefully made… the index the authors show in figure 3 b is, in fact, the\ndifference in SSTs between the western and equatorial Indian Ocean. The authors\nassert that the IOD index captures the anomalous thermocline deepening (which is\ndue most likely to a westward propagating Rossby wave). Nevertheless, after saying\nthat SST as represented in CRW is obscures risk to deep corals, in the very next\nthought they use an SST index as predictive of stress to deep corals. This should be\ncleaned up.\n2) Lines 221-222: “resembling at times turbulent bores and, at other times, nonlinear\nwave trains” Where is the evidence for this? This is speculation and should be\nremoved, it doesn’t add anything.", "reviewer_1_final": "The authors do have a nice piece of work here. It is flawed in some ways as all studies are, and has been discussed in several iterations of the review process. I have had my say in this regard and now leave it in the hands of the editors. One final suggestion;\nLines 429-431; suggest it reads as \"As the images did not include a uniform Lambertian reference material, a combination of methods was used to assign colonies to these 4 categories:\"", "reviewer_3_final": "I have reviewed the response of the authors to my initial comments regarding the physical oceanography in the paper. I have also reviewed the revised manscript and SI. The authors fixed some of the minor things that I pointed out, but largely rebutted the major comments, arguing that their analysis and presentation was sufficiently strong.\nI continue to find the presentation of the PO analysis unnecessarily complicated and in places unclear. This is not (and should not be) a paper about the oceanographic details of the internal wave climate in the vicinity of the study site. The analysis and the modelling effort (and probably the data) are not comprehensive enough to perform a detailed study of the dynamics. Of course, a regional study like that would not likely be broadly interesting enough for Nature Communications even if it was comprehensive.\nSo the authors are in a tough spot. They are trying to make a limited statement about the physical dynamics relative to 1) how out of the ordinary 2019 was and 2) the comparison of the two study sites. The assertion that 2019 was an anomalous year in the central equatorial Indian Ocean oceanography is not novel. Internal waves being important for coral reef thermal stress is not novel. Pointing out internal wave heat flux can differ between adjacent areas in regions of complex bathymetry is also not novel.\nI believe the oceanography here can and should be boiled down to two statements: 1) 2019 was regionally an anomalous year with widespread potential for thermal stress even at mesophotic depths, and that 2) even in the context of regionally high potential for stress, the exposure to internal waves matters on a sub-atoll scale.\nTo me, this simple case can be made in one or at most 2 figures. I do not believe it matters or is even really that well justified that the internal waves have more of a “mode-2” character. For example, I do not find that having detailed plots of velocity from the models with qualitative comparison to the little data they have is necessary to make the case that they need to make, I find the plan view of the time mean model bottom temperature anomaly relative to the initial condition to be a strange metric for internal wave exposure, etc.\nIn short there is too much detail and speculation for a paper that is mainly about something else (coral bleaching), and too little for a scientifically defensible study of the oceanography at the sub-atoll scale (a totally different study). It feels as though the compromise the authors have taken with the level of detail leaves the paper in an awkward position. I wish I could be more positive but I think the following statement from the authors sums up my problem:\n“We agree with the reviewer that these environments are extremely complicated and other factors may play a role; however, given the challenge of obtaining observation data from this environment and the need to explain the observed bleaching characteristics, we have prioritised the most plausible mechanism for which we have observational and modelling evidence.” (emphasis mine)\nIf the aim is to provide “plausible mechanisms” because of a “need to explain” – well I would have thought a much more limited presentation of the oceanography would suffice. I disagree with the author’s language here – “needing” to explain something is not hypothesis driven science – but that alone isn’t a deal killer for me.\nI thought I had provided perhaps a somewhat over-caffeinated but pretty clear pathway forward for the oceanography part of this paper. It bums me out that I can’t really strongly support this aspect of this study at this stage. I think the paper is important and probably the main finding and presentation is worthy of a high impact journal. It isn’t far away… but right now the oceanography is holding the rest of the story back."}, "author_response": "Response to authors comments of prior review\nI appreciate the efforts of the authors to examine both irradiance and cloud cover at their sites as it\nrelates to coral bleaching. I also understand that corals at mesophotic depths are probably naïve to\ntemperature increases of 3-7°C. Figure C1 is helpful although changing the scale to allow a closer\nexamination of the changes in irradiance at mesophotic depths would have been more informative.\nHowever, the authors do provide calculations of optical depths for the irradiance data they do have that\nare based on calculated Kd. The authors state that only 1% of surface PAR reaches 90 m so irradiance is\nnot an issue as it relates to bleaching. But the corals at these depths are acclimatized to these extremely\nlow irradiances. Any change in the optical properties may allow increased water transparency and\nincreased irradiances, albeit small when thinking in terms of shallow coral reefs, but not inconsequential\nfor extreme low-light acclimatized corals. For instance, the Kd for the 1% OD of 63 m is 0.073 while for\n97.8 m the Kd is 0.047 from your table. These are not inconsequential differences and suggest significant\nchanges in water transparency which could have consequences related to the role of light in bleaching\nat mesophotic depths, which on shallow reefs is primarily a light driven phenomenon; temperature sets\nthe table, but light drives the process. The authors should give the reader the data and a chance to\nassess. Provide the OD data, give an example and say it is possible that these oceanographic processes,\nespecially internal waves, could change the transparency of the water column and could have\ncontributed to the bleaching process.\nOn the issue of using coral color as an index of bleaching extent and severity. As suggested above again,\nthe calculation of a bleaching index based on coral color requires that all colonies being assessed in the\nimage be orthoganol, and at the same height above the substratum so that the light source illuminates\nthe coral evenly and at the same intensity. If this does not occur then this index, basically a measure of\ncoral reflectance, requires, for each image, a reference to compare against. The reference material must\nbe Lambertian in nature; a commonly used material is Spectralon, which can provide a diffuse reflection\nthat is equal across all visible wavelengths. This allows the user to compare the reflectance of the\nstandard to the reflectance of the subject under the same light source (and any differences associated\nwith light intensity). For images that are not orthogonal such as used here multiple references would be\nneeded since the distance from the light to the subject varies, and therefore so des light intensity across\nthe image. This can be all entered in the authors BIIGLE program for appropriate annotation and is\nessential to compare coral bleaching between sites, and between years.\nAs far as bleaching prevalence I still believe that to compare between depths or sites one would have\nto/should know the aerial extent of the survey. That is the percentage of bleached coral at site A was\n50% and site B was 75% based on a 100 m2 survey. The authors describe taking images, and the number\nof images, but do not adequately describe the process-see comments above for Lines 334-338.\nThe authors contend that using the number of individuals to assess species diversity is a valid approach\nas described by Gotelli and Cowell 2001. Their techniques utilize rarefication curves and I see no\ndescription of that in the M+M of this manuscript. Also, my reading of Gotelli and Colwell 2002 suggest\nthat using species density, versus species diversity/richness would be a more appropriate metric to\nderive for quantitative studies, and therefore requires a knowledge of area analyzed. This is best\naccomplished using orthogonal images.\nAgain, the physical oceanography is amazing! The authors should couple that data to the bleaching\nprevalence data alone, once the M+M for the bleaching prevalence data is better explained, and omit\neverything else.\nReviewer #3 (Remarks to the Author):\nSee attached document\nReview of NCOMMS-23-12279-T\nI was brought in to review the physical oceanography reported in this manuscript. I have\nexpertise in studying the dynamics of internal waves in the ocean using observations similar\nto those reported here.\nIn general, there is a reasonably detailed set of measurements of the physical state of the\nocean at the two study sites. These observations come from moorings with temperature,\nsalinity, and currents. Based on the description in the methods, the mooring design and the\ndata that the moorings collected seems appropriate to the variability of temperature\nover the upper ~100 m with good vertical resolution on frequencies from minutes to weeks.\nHaving this data is very good and an absolute prerequisite here. Unfortunately, however, the\nmooring time series start after (dec 2020) the primary bleaching period (nov 2020), and the\ndata for whatever reason is given second billing to two numerical models.\nMITgcm is used by the authors to model the internal wave variability. It is initialised by a CTD\nprofile the authors collected, and forced by the semidiurnal and diurnal barotropic tides. The\nmodel is (sort of) compared to the data, and then the authors create a number of plots of\nmodel output that they use to argue about differences between the two reef sites. The\nauthors settle on “mode 2” internal waves as differing between the two sites. I am fairly\nsceptical that the analysis of the model in the way presented here supports that conclusion\nto the exclusion of other hypotheses. I would have preferred to see more analysis of the\ndata, and a deeper dive into the model insight about how the internal wave climate is\ndifferent between the two sites.\nIt should be understood that my comments that follow are in an effort to get the best out of\nthese data, and that I don’t believe that the manuscript should be rejected due to the PO\ncomponent of the paper. That said, I have a number of fairly significant concerns with the\npresentation and interpretation.\nFor the record, I actually do not believe that “definitively” identifying the presence of some\ninternal wave pattern or another is a precondition for this being a valuable contribution.\nSimply identifying, in the data first, and the model second, that the different reefs have\ndifferent internal wave climates is probably enough to POSE the hypothesis that this is the\nreason why one bleach and the other did not. More data/modelling would be needed to\ndefinitely show this.\nFinally, there has been some fairly strident back-and-forth between the authors and the first\ntwo reviewers about the value of SST and “coarse” numerical models in predicting bleaching\nrisk in mesophotic corals. My take is the following: of course a mode-derviedl “early warning”\nproduct tuned to the ocean surface mixed layer and shallow (<30 m depth) corals would\nhave questionable application to 40-80 m depths. Is there actually debate about this? As the\nauthors point out, because of the importance of internal wave variability, any global model\ndriven early warning system is likely to be quite challenged. (As an aside, I will note that\nglobal models like mercator do not get the internal waves correct *anywhere* and so by\ndefinition can not at present capture this impact for any depth). Simply pointing out that\ncurrent generation “bleaching warming systems” are not going to be as effective for\nmesophotic corals because of internal wave variability, without getting into the “difficulties” of\nmeasuring the position of the thermocline – which is actually not that hard and is regularly\ndone with moorings all over the world – is plenty of a conclusion enough in that realm for a\npaper like this.\nI hope the authors find these comments useful. I have written many of them in what follows.\nIt is not my position that every suggestion has to be followed up on. But I do worry that at\npresent the PO story is incomplete and in some ways confusing and potentially even wrong.\nWe want to get as much as that out of the paper as possible before it is published.\nMajor comments about the PO:\n1) The presentation in Fig. 3 is confusing. First of all, Fig 3 is from a model reanalysis..\nIt is not data, it is the output of a model. The model does assimilate data, but it needs\nto be clearly understood that these are not actual observations, including within the\nfigure/caption itself.\nI have comments below about each subpanel.\na) There really is no need to show the entire reanalysis period. Why is this\ndone? I much prefer the presentation in Fig. S2. Fig 3 a and b are far too\ncluttered and this story is about 2019-2020, not the decade beforehand. I\nstrongly suggest that this be re thought. It is almost impossible to understand\nanything about the temperature fluctuations in fig 3 a.\nb) Fig 3 b should be zoomed into a much tighter time range. Again, there is little\nvalue in showing a long time series, since the point of the paper seems to be\nthat 1) regional oceanography was anomalous (this has been shown by\nothers and comes with a few references in the text) and 2) local effects\nmatter. Neither fig 3 a or 3 b needs a decadal perspective.\nc) Fig 3 c d and e are unnecessary. While somewhat interesting that the\nthermocline position was anomalous regionally, I don't think this strengthens\nthe paper. For one, again, these are the results of a model with coarse\ngridding in space and time (the authors later point out that such models are to\nbe taken with a grain of salt in areas with complex local bathymetry and local\ndynamics). More generally, this paper should rely mainly on the observations\ncollected and the MITgcm model. I dont think the cluttered presentation in Fig.\n3 really adds anything and it could be simplified with a net positive benefit on\npresentation.\n2) Fig 4.\na) Fig 4 a— I cannot understand why the data is “averaged to daily values and\nthen low passed” with a 6 d cut off. I do not believe this is necessary… plus if\nyou are going to filter a time series, it is not necessary to average it\nbeforehand. I dont think the filtering actually probably adds that much and I\nwould avoid it.\nb) This is nice (real, unfiltered data!!) and should be bigger and the main point of\nthis figure. In fact, I think the authors should be comparing IDR and MA with\nthis figure, showing a zoom in like this for both sites. But either way, these are\nthe observations we need to see!\nc) Ok… I have experience with Nortek instruments in ecosounder mode and I\ncan confidently say that it is not scientifically accepted that the returns in that\ninstrument mode can be simply ascribed to “turbulence” as the authors do\nhere. This is a contentious claim, and the authors have no other turbulence\ndata that I see to justify it. Moreover, why is this even necessary? Why have a\nfigure about turbulence and then never talk about mixing processes in the\ntext? The authors are mainly interested in the actions of the internal waves in\ntransporting cold (or trapping warm) water to the reef. This doesn’t need\nqualitative hand waving about turbulence, even if the internal waves are\nimportant to mixing and mixing is important to bleaching. You just don’t have\nthe necessary data to say anything quantitative, so it would be much better to\nremove this. Finally, I bet you are seeing enhanced scattering from biological\nsources (zooplankton, etc) that are beings advected up and down by the\ninternal waves. Even if it IS turbulence causing this signal, you can’t quantify\nit in these data so you are better off leaving it out.\nd) Why is tidal elevation here? These internal waves are (probably) baroclinic\nresponses to barotropic tidal forcing. The surface tide will not give you much\nor any insight to the subsurface internal tide, especially over a hand picked 18\nh segment… What is this supposed to show?\n3) Lines 242-243: “The influence of internal waves, both at tidal and higher frequencies,\nwas far less pronounced during 2019 when the thermocline was depressed due to\nthe IOD.” Where is the evidence for this statement? Your time series starts in Dec\n2019. Are you saying that there were less internal waves in Dec 2019 than in the rest\nof the time series? Do you mean that the appearance of sub thermocline water on\nthe reef due to internal waves was less common or absent in 2019? Either way, this\nstatement is a very important one that absolutely needs to be justified if it is going to\nbe in here.\n4) Fig. 5\na) Ok… I have spent a few days trying to puzzle out what exactly is being shown\nin Fig 5 a (and again in S3, S4a and S5a). This is my best guess: The model\nis initialised with a density profile taken by the authors on some day in some\noffshore place. This is used as the initial density profile at all locations in the\nmodel. Then the model is run for 15 days. Then (now I am getting into\nspeculation territory) the authors extract the bottom temperature values at all\ntimes over the reefs of interest, form some sort of average in time at each\nnear bottom location, then take the temperature at the corresponding depth\nfrom the initial, offshore profile and subtract that offshore temperature from\nthe model temperature. Therefore, “red” means that at that depth it is warmer\nthan the offshore initial condition. Is this more or less what is being done?\nIf so, this needs to be explained somewhere!! The title of the plots is variously\nreferred to as “model mean temperature” and “bottom mean temperature\nvariations.” Arguably the quantity you are plotting is not accurately described\nby either of these titles. It would be more correct to refer to this as an anomaly\nrelative to the initial state or similar.\nSecond, the CTD cast that you choose to initialise the model is itself simply a\nsnapshot at one time of the evolving vertical position and gradient of the\nthermocline. Did you test other stratifications? To this reviewer, it would have\nbeen a better use of the modelling to compare the internal wave climate\nunder several different stratifications (i.e. at peak positive 2019 IOD vs\n“normal” conditions.. These initializations need not be collected by the\nauthors, but instead could come from ARGO or even the model reanalysis.\nThe MITgcm is best used to test the hypothesis that changing stratification\nimpacts internal wave variability at both locations, in addition to exploring how\nthe internal waves are different at the two locations.\nFinally, and most importantly, this approach to analyzing the model does not\nactually tell you anything about the presence or absence of mode-2\ninternal waves (or any internal waves). These plots need to be re-thought and\npotentially abandoned entirely. They are confusing and do not speak to what\nyou are trying to assess.\nb) In general, it is confusing to me why there would be so much model shown and\nso little data in Fig 5 c and d. You have weeks of data… why not show it?\nI don’t think what is being shown here is very convincing in terms of\ndata/model comparison (see next comment).\n5) The model… I found myself trying to figure out what exactly was done with the\nmodel. While the spatial resolution was mentioned, the size of the domain was not.\nHow far into the open ocean does it extend? I couldn’t figure out the time step either.\nI will note that it is somewhat rare to fire up a model and “run it for 15 days” without a\nspin up period, but perhaps there was one. In general the modelling details were\nsparse and need to be filled in a bit.\nI was likewise a bit confused about the model/data comparison. Yes, this is difficult to\ndo quantitatively, but no attempt has been made here to do so. Instead it is asserted\nthat the model captures the internal wave variability, with a nod to the figures that\nshow wiggly lines from the data and wiggly lines from the model. (I note here that\nthere is –presumably– a typo: these would be depth-AVERAGED velocities, not\ndepth-integrated velocities… or they are plotted in the wrong units). Comparing depth\naveraged velocities between a model and data is a bit of a funny thing to do if you\ncare about the baroclinic internal wave response, which is not a depth-averaged sort\nof quantity. So yeah… I’m not sure outside of qualitatively for the depth averaged\ncurrents that there is any evidence that the model is recreating the internal wave\nfeatures in the data.\nIn S6 both model and a short snapshot of ADCP data in depth and time are shown.\nBut I am confused why the data is only shown for a 2.5 day period, but the full 15 d\nmodel time series is shown (see previous comment about fig 5 c and d in the main\npart of the paper).\n6) Regarding the “mode-2” structure of the tidal variability at MA.\na) First comment is that mode-2 variability is commonly observed and often\nstudied and written about in the literature, so I would remove the statement\n“relatively rare observation throughout the ocean where attention has largely\nfocused on Mode 1 waves within which the direction of vertical movement of\nisotherms is consistent throughout the whole water column.” which while\nperhaps not strictly incorrect, requires a lot of work by the modifiers\n“relatively” and “largely.”\nb) You have the data to show whether or not MA and IDR have a different\nvertical structure of the internal tide. You *do not* need the model for this.\nInstead you would use the model to diagnose WHY the internal wave\nstructure is different in the different locations. I would suggest an EOF or\nother modal decomposition to show this from the data.\nc) For the record… internal waves cannot “warm” the water. The can transport\nheat from one place to another (advective heat flux), and they can give up\nenergy to turbulence, which in turn can lead to mixing, which, then, in the\npresence of a temperature gradient, can lead to a heat flux (mixing-driven\nheat flux). What you are showing in the model is that the (I think time mean)\nvertical temperature profile at MA is different from the initial condition (and\nIDR) particularly in the mid-reef. You do appear to have some data in fig 4\nthat shows one example of isotherms separating. I would suggest you lean\nmore on these observations. I do NOT think this paper needs to “discover”\nthat the internal wave climate is complicated over complicated bathymetry, or\nthat the oceanography can be different on different sides of an atoll, even a\nsmall one, in order to be an impactful contribution.\nMinor comments:\n1) Lines 182-183: The discussion of SST being a “poor predictor” of thermocline depth\nand thus the potential that CRW not being good for mesophotic zone corals needs to\nbe more carefully made… the index the authors show in figure 3 b is, in fact, the\ndifference in SSTs between the western and equatorial Indian Ocean. The authors\nassert that the IOD index captures the anomalous thermocline deepening (which is\ndue most likely to a westward propagating Rossby wave). Nevertheless, after saying\nthat SST as represented in CRW is obscures risk to deep corals, in the very next\nthought they use an SST index as predictive of stress to deep corals. This should be\ncleaned up.\n2) Lines 221-222: “resembling at times turbulent bores and, at other times, nonlinear\nwave trains” Where is the evidence for this? This is speculation and should be\nremoved, it doesn’t add anything.\n\nWe are grateful to the former reviewer and the new reviewer for taking the time to review our\nmanuscript and provide constructive comments. Please find our detailed responses below.\nReviewers’ comments:\nReviewer #1 (Remarks to the Author):\nReview of Deep Coral Bleaching Driven by Hidden Changes in Thermocline Depth for Nature\nCommunications\nI am now reviewing this revised manuscript for the second time and as previously stated I am\nimpressed with the physical oceanography and its causal role in the observed bleaching of\nscleractinian corals on MCEs in the Indian Ocean. I also appreciate the authors response to the\nprevious reviewer’s comments. Nonetheless, I still believe there are issues that should be addressed.\n• Thank you for accepting to review this manuscript again, we are grateful for the constructive\ncomments.\nLine 18; Suggest this reads as follows; “Our results demonstrate the potential vulnerability…”\n• We have edited the sentence as suggested.\nLine 26; Here, and throughout the manuscript “Scleractinian” is not capitalized. It is not a taxon and\nshould be in lower case.\n• We have edited the words as suggested.\nLine 27; Suggest this reads as follows; “…sea surface temperatures (SSTs) and subsequent coral\nbleaching; current estimates…”\n• We have edited the sentence as suggested.\nLine 32; Suggest this reads as follows; “…depths of 30-150 m and have been estimated to occupy…”\n• We have edited the sentence as suggested.\nLine 33-34; Suggest this reads as follows; “It has been hypothesized that these communities are\nbuffered against anthropogenic changes, and therefore might represent a refuge that replenishes\nshallow-water coral species with vertically dispersed larvae8,10. Or words to that effect…..\n• We have edited the sentence as suggested.\nLine 51; “in-situ” is not hyphenated and should be italicized as it is Latin.\n• We have edited the word.\nLine 53; Per my previous review. The fact that a flawed metric (i.e., DHW) is being used by a large\nproportion of the community is not a justification for its continued use. If the authors insist on using\nthis metric, knowing these flaws as I pointed out in my last review, then they must at least tell the\ncommunity that there are known problems, with references, especially as it relates to its predictive\ncapabilities.\n• More details have been added to the text, including reference to the literature to highlight\npotential flaws with this metric. Furthermore, in our previous revisions to the manuscript we\nadded text and data to demonstrate that the NOAA CRW predictions were supported by the\nmodelled local temperature fluctuations shown in supplementary figure S2, and in situ\ntemperature data recorded by the CTD mounted on the ROV (supplementary figure S1),\nwhich both indicate no thermal stress in shallow waters in November 2019.\nLine 63; Reviewer #2 had some keen insights on this, and I will be interested in seeing how the\nauthors deal with the issue of post-bleaching coral communities being dominated by “winners” as a\nreason for little to no bleaching on shallow reefs compared to potentially more thermally sensitive\ncorals at MCE depths. The recovery you discussed in response to the reviewer, in the absence of any\nseascape genetic data, was likely a result of recruitment from local populations, or the winners so\nlikely more resistant to thermal stress. Also, 3000 corals in 2019 and 1000 in 2020 on shallow reefs-\nwhat happened here?\n• In our last revision of the manuscript, we added some additional information to the\nmanuscript in response to the reviewers’ comments regarding the presence of ‘thermally-\nresistant colonies in shallow water’ to support our conclusions that lack of bleaching in\nshallow waters was more likely a result of no thermal stress rather than a lack of colonies\nobserved.\n• From line 132, we state that “Shallow-water reefs in the Chagos Archipelago may now be\ncomposed of a higher proportion of heat-tolerant genera and species of scleractinian corals\nthan before the mass bleaching events of 2014-2017, which is possibly reflected by the low\nprevalence of bleaching recorded on shallow-water reefs in the current study […]. The water\ntemperature during all other dives remained below 29.5°C for the duration of the dives.\nThus, the lack of bleaching observed on shallow-water reefs (15-20 m) is likely due to an\nabsence of thermal stress rather than a lack of coral colonies on the reef and/or a high\nproportion of thermally tolerant individuals […]. On shallow-water reefs, high bleaching\nvariability at local scales has been found to be partly due to differences in species\ncomposition in terms of both taxa and abundances. In this study, significant differences in\ncoral community composition were observed between depth bands within each site […]. At\nmesophotic depths (from 60 m to 90 m), no significant differences in coral community\ncomposition were detected between the two sites […]. Furthermore, the few coral species\nthat span the depth distribution from shallow to upper-mesophotic waters (30-40 m) down\nto the lower mesophotic zone (60-70 m, and 80-90 m for Leptoseris spp.) experienced more\nsevere bleaching in terms of prevalence and severity at mesophotic depths, with more coral\nbleaching observed at MA compared to IDR (supplementary table S4), indicating that coral\ncomposition is not the only driver of differences in coral bleaching along the depth gradient.”\n• We agree that mesophotic corals may also be more thermally-sensitive, and our data\ndemonstrate a temperature difference of 3-7°C above the normal seasonal range at\nmesophotic depths, unlike in the shallow waters, where no thermal stress was detected at\nthe time of our survey (from in situ measurements and satellite derived predictions).\n• The difference between the number of corals assessed between 2019 and 2020 is because\nwe had differing number of images surveyed between 2019 and 2020. In March 2020, we\nwere unable to survey all locations due to poor weather conditions and the Covid pandemic\ncutting short the second cruise. In total in 2019, we surveyed 150 images in the 15-20m\ndepth zone, while we surveyed only 30 images in March 2020 (see Table S1, supplementary\nmaterial).\nFigure 1. The euphotic zone, classically defined in the oceanographic community is 0-200 m and the\nmesopelagic zone is 200-1000 m. The MCE depth definition is placed, or should be placed, over these\nlong accepted oceanographic depth descriptions as near coastal benthic habitat.\n• Thank you for highlighting the discrepancies here. The categories in Figure 1 should refer\nonly to the benthic zones rather than oceanographic depth descriptions. This has been\nclarified in the figure legend.\nLine 110; “5” should be “five”\n• We have edited the word, thank you.\nLine 128-135; There it is-the “winners” argument, but then you try and support your interpretation\nwith a flawed metric. Again, if you are going to do this you must state clearly for the readers the\nflawed aspects of the metric.\n• Thank you for highlighting this. We have added specifics to the text to highlight that this\nmetric has limitations. In our previous revisions to the manuscript, we added additional text\nand data to support the predictions made by the NOAA CRW that there was no thermal\nstress in shallow water in November 2019 (we support our interpretations with temperature\ndata collected in the field from the ROV in 2019).\nFigure 2; Need a fuller description of statistics. As requested in my previous review what primary\nanalysis, and post hoc analysis, was run? What were the DF, F-value, p value corrections for multiple\ncomparisons, etc. as applicable.\n• A full description of the statistics was provided in the methods section of the manuscript\npreviously submitted. However, detailed results were missing from the main text in the\nresults section and the figure legend. We apologise for this oversight, and we have added\nspecific details to the results text, figure legend and detailed results in supplementary tables\nS5 & S6.\nLines 155 and elsewhere; ANOSIM provides a test to detect differences in two or more groups of\n“sampling units” based on ranked similarities. First, why not present the results as an NMDS or\ncluster plot? Would be much easier for the reader to see the depth comparisons of coral communities\nbetween depths and sites. Did the authors ensure that the heterogeneity of dispersion, which\nANOSIM is very sensitive to, is equivalent or at least similar between depths and sites? Also, why the\nmore permissive p value of 0.1 to start with? Is it possible that at a minimum p value of 0.05 some of\nthese comparisons would not have been significant?\n• We didn’t originally show the MDS plot to save space within the manuscript and we felt it\nwas appropriate just to show the statistical results. However, we have added the MDS plot to\nthe supplementary materials (based on the PERMANOVA analysis described below).\n• We have re-analysed our scleractinian coral community data using PERMANOVA, with a\nbalanced design (please see results in the supplementary materials). There is significant\nheterogeneity of variance among some of the groups of sites/depths, but the largest\ndifferences are between communities at different depths rather than between two sites at\nthe same depth (see boxplot and PERMDISP results in table below). PERMANOVA with a\nbalanced design is robust to the issues of heterogeneity of variances among groups.\nFurthermore, we are mainly interested in the variance in coral community structure between\nthe two sites at the same depth. The PERMDISP results and boxplot below show significant\nhomogeneity of variance for Ile des Rats and Manta Alley at 60m and 80m, with significant\nheterogeneity of variance between the two sites at 15m and 30m (although the t-value is\nfairly low here). Thus, the PERMANOVA results can be considered robust.\nGroups t P(perm)\n(IDR-15,IDR-30) 5.3373 0.0010\n(IDR-15,IDR-60) 5.9659 0.0010\n(IDR-15,IDR-80) 10.789 0.0010\n(IDR-15,MA-15) 4.1261 0.0010\n(IDR-15,MA-30) 3.5192 0.0030\n(IDR-15,MA-60) 4.0816 0.0010\n(IDR-15,MA-80) 12.081 0.0010\n(IDR-30,IDR-60) 10.54 0.0010\n(IDR-30,IDR-80) 15.025 0.0010\n(IDR-30,MA-15) 0.74318 0.4860\n(IDR-30,MA-30) 6.8273 0.0010\n(IDR-30,MA-60) 8.7443 0.0010\n(IDR-30,MA-80) 16.723 0.0010\n(IDR-60,IDR-80) 4.7789 0.0010\n(IDR-60,MA-15) 9.2125 0.0010\n(IDR-60,MA-30) 0.81446 0.4900\n(IDR-60,MA-60) 1.782 0.1330\n(IDR-60,MA-80) 5.4262 0.0010\n(IDR-80,MA-15) 13.599 0.0010\n(IDR-80,MA-30) 4.593 0.0010\n(IDR-80,MA-60) 6.517 0.0010\n(IDR-80,MA-80) 0.3041 0.7740\n(MA-15,MA-30) 6.0994 0.0010\n(MA-15,MA-60) 7.4954 0.0010\n(MA-15,MA-80) 14.999 0.0010\n(MA-30,MA-60) 0.55073 0.6050\n(MA-30,MA-80) 5.0361 0.0010\n(MA-60,MA-80) 7.3036 0.0010\n• The PERMANOVA results indicate significant differences in the coral communities between\nsites and depths. We would expect differences between depths as the environmental\nconditions change over the depth gradient, and thus, so do the benthic communities.\nHowever, the differences between sites at the same depth are minimal (see overlap of data\npoints on the MDS plot above and the low t-values from the PERMANOVA analysis, Table S2-\n1, and the number of shared coral species between sites at the same depth, Table S3). Thus,\nthe significant difference in coral community composition at the two sites at the same\ndepths is likely driven by the presence of a low number of rare coral species. Thus, we can be\nconfident that the difference in bleaching between sites at the same depth is not due to\nlarge differences in the coral species present at the two sites as these are largely the same,\naside from a few rare species.\n• The p-value presented in the previous version of the manuscript for the ANOSIM results is on\nthe contrary less permissive, as 0.1% is equivalent to 0.001. However, this is now irrelevant\nas we are using PERMANOVA instead of ANOSIM and the results text has been updated\naccordingly.\nLine 165; “spp.” is not italicized.\n• It has been edited, thank you.\nLine 250; Is this supposed to say; “(See modelling methods)”?\n• Indeed, it has been edited, thank you.\nLine 283; Suggest this sentence reads as follows; “In summary, our results show that scleractinian\ncorals at mesophotic depths from the Chagos Archipelago in the Indian Ocean are susceptible to\nthermal stress, and bleach in a similar manner to that observed for shallow-water corals in contrast\nto other studies on mesophotic corals from different geographic areas26, 32-34.”\n• We have edited the sentence as suggested.\nLine 286; Suggest this reads as follows; “Our study adds more evidence that MCEs are not, a priori, a\nuniversal source of coral recruits for replenishing shallow water coral reefs12, 13, 37-39.”\n• We have edited the sentence as suggested.\nLines 334-338; So, transects were employed. How long were they? How many images were taken at\neach depth? Were the same number of images taken at both sites at both times? What was the angle\nof the oblique imagery?\n• As described previously, linear transects were not employed due to the nature of the\ncurrents around Egmont Atoll preventing the ROV from operating along a linear line.\nHowever, a set number of still images of the seabed were collected from each depth zone\nspecified (90 images per depth). The number of images taken per site/depth has been added\nto the supplementary table S1, for clarification.\nLines 339-342; The statement that non-orthogonal, or oblique, imagery is taken by the deep-sea\ncommunities is true. But they usually collect those images, along with scale (!), and analyze them a\npriori knowing that different techniques (i.e., multiple lasers, Canadian grids) will be needed to obtain\northorectified images and accurate community characterizations for multiple ecological metrics such\nas abundance and percent cover. Regardless of whether plot or plotless designs are incorporated the\nimagery must be orthorectified.\n• As mentioned previously, we experienced significant issues in piloting the ROV in difficult\ncurrents and uneven topography around Egmont Atoll. In addition, the lasers on the SD\ncamera broke prior to the first surveys being undertaken. We were not able to repair the\nlasers and as we were two days steam from the nearest port, we had to continue with our\ndata collection without them. We fully understand the need to collect images along with a\nmeasure of scale to standardise data collection and subsequent analysis. Given our\npredicament in a remote location, the needs of other researchers on the cruise and the\nfunds already spent on ship time and transporting equipment to the ship, we continued with\nour surveys and standardised image collection from the seabed as much as was possible. As\ndetailed in the manuscript, the angle of the camera was kept in the same position and we\nmaintained a consistent altitude above the seabed when taking the still image. We have\nbeen as transparent as we can about how the data were collected, and we have added an\nadditional information to the manuscript to ensure the reader is fully aware of the\ncircumstances of the data collection. Although we are unable to quantify bleaching over a\ngiven area, we believe our standardised method of image collection enables us to compare\nbleaching prevalence and severity within our study using assessments of individual colonies\n(similar to McClanahan et al., 2001). We believe that the technical elements have no\nmaterial impact on the validity of the findings of the manuscript.\nLine 347; Why were the depth bands discontinuous?\n• The depth bands were discontinuous to align with the specific depths previously surveyed in\nthe literature. Furthermore, we were taking part in a multidisciplinary cruise and time had to\nbe allocated equally amongst researchers. Thus, we had to maximise our time in the water\nand chose to target discrete depth bands rather than undertake continuous surveys across\nthe entire depth gradient.\nLines 362-372; You only present the “community” analysis on zooxanthellate corals for the\npresence/absence data. The additional information is unnecessary. Amend it for the analysis\npresented in the manuscript.\n• We have edited the text as suggested.\nLine 386; “coral colour” is actually a function of its reflectance captured by the image under a specific\nlight field. Without a reference, a control, based on a simultaneous image of a Lambertian surface\nyou cannot accurately and consistently quantify image to image difference in “coral colour” even with\na known light source. More on this later.\n• We appreciate this and do not deny that image analysis of bleached coral should include\nreference to a standard material. However, we are unable to return to the field to\nphotograph a reference material. At the time of the survey, our aim was to collect baseline\ndata on the diversity and distribution of benthic communities from shallow to mesophotic\ndepths. We did not anticipate observing bleaching on the reefs and we did not go prepared\nto survey bleaching. However, the presence of bleaching on the reefs on our arrival offered\nan unprecedented opportunity to document bleaching at mesophotic depths in parallel to\noceanographic data being collected at the same time for the same site. We have a number of\nimages of bleached corals at different depths that were subsequently sampled for genetic\nanalysis and thus, were verified as bleached onboard the ship (images also available). The\npresence of the bleached colonies across the depth zones was striking and the bleached\ncolonies were frequently visible from 15-20 m above the seabed during our decent with the\nROV. We have different bleaching severities within the same image (thus exposed to the\nsame light conditions). Images for analysis were selected only if they had even lighting and\nthe presence of video data meant we could review the colonies from multiple angles using\nthe video footage to further verify the presence of bleaching.\nLines 414-418; As stated previously; “Also, there is no indication of how bleaching prevalence was\nactually calculated because to compare between sites one would have to/should know the aerial\nextent of the survey. That is the percentage of bleached coral at site A was 50% and site B was 75%\nbased on a 100 m2 survey. Or better yet do transects at each depth, even plotless transects would be\nfine as long as the areas surveyed were the same. Just like Quimpo et al. 2020, the paper the authors\nreference, did in their paper.\n• Methodological detail on how images were collected across survey sites was provided in the\nmethodology and the specific number of images per site and depth has been added to the\nsupplementary table S1. While we are unable to quantify the area surveyed, we believe that\nassessing individual colonies for bleaching and determining the proportion of colonies\nbleached is an adequate measure for the study described here. Assessing individual colonies\non a reef rather than surveying a given area of reef has been undertaken previously (e.g\nMcClanahan et al., 2001). While we understand the survey design is not perfect, due to the\nreasons described above, we still believe that the data tell a compelling story and should be\nshared with the research community. We have been transparent in how we collected the\ndata in the manuscript.\nResponse to authors comments of prior review\nI appreciate the efforts of the authors to examine both irradiance and cloud cover at their sites as it\nrelates to coral bleaching. I also understand that corals at mesophotic depths are probably naïve to\ntemperature increases of 3-7°C. Figure C1 is helpful although changing the scale to allow a closer\nexamination of the changes in irradiance at mesophotic depths would have been more informative.\nHowever, the authors do provide calculations of optical depths for the irradiance data they do have\nthat are based on calculated Kd. The authors state that only 1% of surface PAR reaches 90 m so\nirradiance is not an issue as it relates to bleaching. But the corals at these depths are acclimatized to\nthese extremely low irradiances. Any change in the optical properties may allow increased water\ntransparency and increased irradiances, albeit small when thinking in terms of shallow coral reefs,\nbut not inconsequential for extreme low-light acclimatized corals. For instance, the Kd for the 1% OD\nof 63 m is 0.073 while for 97.8 m the Kd is 0.047 from your table. These are not inconsequential\ndifferences and suggest significant changes in water transparency which could have consequences\nrelated to the role of light in bleaching at mesophotic depths, which on shallow reefs is primarily a\nlight driven phenomenon; temperature sets the table, but light drives the process. The authors should\ngive the reader the data and a chance to assess. Provide the OD data, give an example and say it is\npossible that these oceanographic processes, especially internal waves, could change the\ntransparency of the water column and could have contributed to the bleaching process.\n• We have added the table of light optical depth, which we provided in our previous response\nto your comments, to the supplementary materials file (table S7), as well as specific details in\nthe manuscript text.\n• Any comment on the impact of internal waves on water clarity would be entirely speculative\nand also assumes detailed knowledge and understanding of the temporal scales over which\nlight may be attenuated (presumably by elevated resuspension) and the response of the\ncoral to this. We recognise that this may be an interesting consideration within a future study\nbut is beyond the scope of the present paper.\nOn the issue of using coral color as an index of bleaching extent and severity. As suggested above\nagain, the calculation of a bleaching index based on coral color requires that all colonies being\nassessed in the image be orthoganol, and at the same height above the substratum so that the light\nsource illuminates the coral evenly and at the same intensity. If this does not occur then this index,\nbasically a measure of coral reflectance, requires, for each image, a reference to compare against.\nThe reference material must be Lambertian in nature; a commonly used material is Spectralon, which\ncan provide a diffuse reflection that is equal across all visible wavelengths. This allows the user to\ncompare the reflectance of the standard to the reflectance of the subject under the same light source\n(and any differences associated with light intensity). For images that are not orthogonal such as used\nhere multiple references would be needed since the distance from the light to the subject varies, and\ntherefore so des light intensity across the image. This can be all entered in the authors BIIGLE\nprogram for appropriate annotation and is essential to compare coral bleaching between sites, and\nbetween years.\n• We appreciate this and do not deny that image analysis requires reference to a standard\nmaterial. However, we are unable to return to the field to photograph a reference materials\nand add them to Biigle. Biigle only allows adjustment of contrast, brightness, hue and\nsaturation, thus our images in Biigle cannot be corrected for colour. We could apply a colour\ncorrection to all our images outside of Biigle, however, we would need to seek additional\nsupport and advice on how to undertake this. However, we believe that the bleached\ncolonies were very obvious on the reef and have verified bleached colonies viewed at\nmultiple depths on camera with coral fragments brought to the surface.\n• At the time of the survey, our aim was to collect baseline data on the diversity and\ndistribution of benthic communities from shallow to mesophotic depths. We did not\nanticipate observing bleaching on the reefs and we did not go prepared to survey bleaching.\nHowever, the presence of bleaching on the reefs on our arrival offered an unprecedented\nopportunity to document bleaching at mesophotic depths in parallel to oceanographic data\nbeing collected at the same time for the same site. While we are unable to photograph\nreference material, we have a number of images of bleached coral at different depths that\nwere subsequently sampled for genetic analysis and thus, were verified as bleached onboard\nthe ship (images also available). The presence of the bleached colonies across the depth\nzones was striking and the bleached colonies were frequently visible from 15-20 m above the\nseabed during our decent with the ROV. While our data were not collected under a perfect\nexperimental design, we believe the story is extremely valuable and should be shared with\nthe research community.\nAs far as bleaching prevalence I still believe that to compare between depths or sites one would have\nto/should know the aerial extent of the survey. That is the percentage of bleached coral at site A was\n50% and site B was 75% based on a 100 m2 survey. The authors describe taking images, and the\nnumber of images, but do not adequately describe the process-see comments above for Lines 334-\n338.\n• Methodological detail on how images were collected across survey sites was provided in the\nmethodology and the specific number of images per site and depth has been added to\nsupplementary Table S1. While we are unable to quantify the area surveyed, we believe that\nassessing individual colonies for bleaching and determining the proportion of colonies\nbleached is an adequate measure for the study described here. Assessing individual colonies\non a reef rather than surveying a given area of reef has been undertaken previously (e.g\nMcClanahan et al 2001). While we understand the survey design is not perfect, due to the\nreasons described above, we still believe that the data tell a compelling story and should be\nshared with the research community. We have been transparent in how we collected the\ndata in the manuscript.\nThe authors contend that using the number of individuals to assess species diversity is a valid\napproach as described by Gotelli and Cowell 2001. Their techniques utilize rarefication curves and I\nsee no description of that in the M+M of this manuscript. Also, my reading of Gotelli and Colwell 2002\nsuggest that using species density, versus species diversity/richness would be a more appropriate\nmetric to derive for quantitative studies, and therefore requires a knowledge of area analyzed. This is\nbest accomplished using orthogonal images.\n• The reference to Gotelli and Colwell 2001 was made in our previous response to the\nreviewer comments on assessing species diversity from images of the seabed – the reviewer\ncomment was made in reference to our example image from Biigle showing our annotations.\nWe discussed in our previous reply that individual-based rarefaction can be used to enable\ndirect comparison of species diversity among sites/depths based on the number of\nindividuals encountered, thus we do not need to know the area of the image being\nannotated. We have not assessed species diversity using rarefaction curves within this\nmanuscript; thus details are not provided on this in the M&M.\nAgain, the physical oceanography is amazing! The authors should couple that data to the bleaching\nprevalence data alone, once the M+M for the bleaching prevalence data is better explained, and omit\neverything else.\n• Thank you for your comments. We have improved our explanation of the bleaching\nprevalence and severity data and how these were determined, and we have been completely\ntransparent about the limitations of our data.\nReviewer #3\nI was brought in to review the physical oceanography reported in this manuscript. I have expertise in\nstudying the dynamics of internal waves in the ocean using observations similar to those reported\nhere.\n• We appreciate the thorough review from a specialist in the oceanographic element of this\nstudy.\nIn general, there is a reasonably detailed set of measurements of the physical state of the ocean at\nthe two study sites. These observations come from moorings with temperature, salinity, and currents.\nBased on the description in the methods, the mooring design and the data that the moorings\ncollected seems appropriate to assess the variability of temperature over the upper ~100 m with\ngood vertical resolution on frequencies from minutes to weeks. Having this data is very good and an\nabsolute prerequisite here. Unfortunately, however, the mooring time series start after (dec 2020)\nthe primary bleaching period (nov 2020), and the data for whatever reason is given second billing to\ntwo numerical models.\n• We appreciate the reviewer’s comment regarding the start of observations being in\nDecember 2019, after the bleaching was observed during November of the same year.\nHowever, we did in fact deploy moorings for 2-3 weeks during the November cruise but did\nnot include them in this paper because the data were almost entirely from within the SML\ndue to the extremely deep thermocline at the time. The temperature data from November\nthus demonstrate a vertically homogenous surface layer to a depth of 60 m, which is the\nlimit of the moorings at this site due to the steep slopes below this depth that prohibit the\ndeployment of moorings other than at a couple of sites that we identified from the\nmultibeam survey. It is for this reason that the MITgcm simulations referred to below were\nso important, in filling in the unavoidable gaps in the observations and providing an\nassessment of how the internal waves potentially impact the thermal regime at depth,\nbelow the depths for which we have observational evidence.\nMITgcm is used by the authors to model the internal wave variability. It is initialised by a CTD profile\nthe authors collected and forced by the semidiurnal and diurnal barotropic tides. The model is (sort\nof) compared to the data, and then the authors create a number of plots of model output that they\nuse to argue about differences between the two reef sites. The authors settle on “mode 2” internal\nwaves as differing between the two sites. I am fairly sceptical that the analysis of the model in the\nway presented here supports that conclusion to the exclusion of other hypotheses. I would have\npreferred to see more analysis of the data, and a deeper dive into the model insight about how the\ninternal wave climate is different between the two sites.\n• We agree with the reviewer that these environments are extremely complicated and other\nfactors may play a role; however, given the challenge of obtaining observation data from\nthis environment and the need to explain the observed bleaching characteristics, we have\nprioritised the most plausible mechanism for which we have observational and modelling\nevidence. This is not meant to exclude other mechanisms that would require (prohibitively\ncomplex) additional observations and we trust we have not been too bold in our language in\nsuggesting that other mechanisms are not to be excluded. We have checked our language to\nthis effect but we also believe we have been thorough in our assessment of the role played\nby the mode 2 waves through the modal decomposition that the reviewer may have missed\nas it’s at the end of the Supplementary Material (as we felt it would be too technical and\nwould distract from the main story for the wider audience that is likely to be more\nbiologically-orientated).\nIt should be understood that my comments that follow are in an effort to get the best out of\nthese data, and that I don’t believe that the manuscript should be rejected due to the PO\ncomponent of the paper. That said, I have a number of fairly significant concerns with the\npresentation and interpretation.\nFor the record, I actually do not believe that “definitively” identifying the presence of some\ninternal wave pattern or another is a precondition for this being a valuable contribution.\nSimply identifying, in the data first, and the model second, that the different reefs have\ndifferent internal wave climates is probably enough to POSE the hypothesis that this is the\nreason why one bleach and the other did not. More data/modelling would be needed to\ndefinitely show this.\n• We understand the reviewer’s concerns and attempted to write the paper without being too\nbullish about the certainty of our results. As referred to above, we have tried to be\ntransparent regarding the uncertainties but we also consider that the observations, obtained\nfrom an enormously challenging location due to bottom slope steepness, and numerical\nmodelling represents compelling evidence for our interpretation.\nFinally, there has been some fairly strident back-and-forth between the authors and the first\ntwo reviewers about the value of SST and “coarse” numerical models in predicting bleaching\nrisk in mesophotic corals. My take is the following: of course a mode-derviedl “early warning”\nproduct tuned to the ocean surface mixed layer and shallow (<30 m depth) corals would\nhave questionable application to 40-80 m depths. Is there actually debate about this?\n• Our key contribution to this aspect of the study is that there is very little argument to this\n(i.e. mesophotic reefs) because it’s simply not yet received the same level attention of\nshallow reefs whilst, also, the dynamics responsible for controlling the thermal environment\nare completely different.\nAs the authors point out, because of the importance of internal wave variability, any global model\ndriven early warning system is likely to be quite challenged. (As an aside, I will note that\nglobal models like mercator do not get the internal waves correct *anywhere* and so by\ndefinition can not at present capture this impact for any depth). Simply pointing out that\ncurrent generation “bleaching warming systems” are not going to be as effective for\nmesophotic corals because of internal wave variability, without getting into the “difficulties” of\nmeasuring the position of the thermocline – which is actually not that hard and is regularly\ndone with moorings all over the world – is plenty of a conclusion enough in that realm for a\npaper like this.\n• Yes, we agree that we could limit our findings to this but we would then be missing the point\nthat those interested in bleaching of mesophotic coral reefs need to consider using higher\nresolution, internal wave-resolving models than currently offered by the global models.\nI hope the authors find these comments useful.\n• We are very grateful to have the perspective of an oceanographer in reviewing this paper\nand we trust that the reviewer appreciates the time we have put into our response to their\nreview that we are grateful to have received as we look to continually improve the paper.\nI have written many of them in what follows.\nIt is not my position that every suggestion has to be followed up on. But I do worry that at\npresent the PO story is incomplete and in some ways confusing and potentially even wrong.\nWe want to get as much as that out of the paper as possible before it is published.\nMajor comments about the PO:\n1) The presentation in Fig. 3 is confusing. First of all, Fig 3 is from a model reanalysis… It is not data, it\nis the output of a model. The model does assimilate data, but it needs to be clearly understood that\nthese are not actual observations, including within the figure/caption itself.\n• We were not under the impression that we suggested the figure was developed from data\nrather than model output but have checked to ensure that this is the case. We have\nhowever included explicit reference to the use of the CMEMS model output in generating\nthe figure to avoid any misunderstanding.\nI have comments below about each subpanel.\na) There really is no need to show the entire reanalysis period. Why is this done? I much prefer the\npresentation in Fig. S2. Fig 3 a and b are far too cluttered and this story is about 2019-2020, not the\ndecade beforehand. I strongly suggest that this be re thought. It is almost impossible to\nunderstand anything about the temperature fluctuations in fig 3 a.\n• We can certainly understand the reviewer’s perspective on this but we wished to use the\nopportunity to demonstrate how anomalous 2019 was within the context of recent history,\nfor which preseenting the thermocline depth as far back as 1994 is helpful because one can\nsee the deep thermocline in 1998 and again 2006. We agree that this makes the detail more\ndifficult to discern but that is not the purpose of this panel.\nb) Fig 3 b should be zoomed into a much tighter time range. Again, there is little value in showing a\nlong time series, since the point of the paper seems to be that 1) regional oceanography was\nanomalous (this has been shown by others and comes with a few references in the text) and 2) local\neffects matter. Neither fig 3 a or 3 b needs a decadal perspective.\n• We appreciate the reviewer’s concerns but, as with the point above, these two panels\nprovide the temporal context to how anomalous 2019 was; whilst others have shown that\nthe regional oceanography was anomalous, none have (as far as we are aware) done so\nwithin the context of thermocline depth. Given the critical role played by the thermocline in\nsetting the depth range over which internal waves may exert an influence, it is important to\ndemonstrate the time evolution of thermocline depth over a long period to highlight where\n2019 sits within the context of the ocean state over the past 2 -3 decades.\nc) Fig 3 c d and e are unnecessary. While somewhat interesting that the thermocline position was\nanomalous regionally, I don't think this strengthens the paper. For one, again, these are the results of\na model with coarse gridding in space and time (the authors later point out that such models are to\nbe taken with a grain of salt in areas with complex local bathymetry and local dynamics).\n• These panels demonstrate the thermocline depth over the Indian Ocean, for which the\nglobal model output is much more robust than around the regions of complex bathymetry.\nThe importance of these panels lies in demonstrating the spatial extent of this thermocline\nevolution over the Indian Ocean. We were acutely aware of the importance of\ndemonstrating that our results weren’t a special case that had limited applicability\nelsewhere. These panels demonstrate that the thermocline deepening due to the IOD\nextended throughout the central, equatorial and western Indian Ocean, thereby influencing\nthe MCE in locations such as La Reunion, Mauritius, Seychelles and the Maldives. We trust\nthat the reviewer agrees that making it clear how this basin-scale evolution of the\nthermocline impacts multiple locations is important to bring to the reader’s attention.\nMore generally, this paper should rely mainly on the observations collected and the MITgcm model. I\ndon’t think the cluttered presentation in Fig. 3 really adds anything and it could be simplified with a\nnet positive benefit on presentation.\n• We appreciate the reviewer’s perspective but hope that our explanation above is accepted.\n2) Fig 4.\na) Fig 4 a— I cannot understand why the data is “averaged to daily values and then low passed” with\na 6 d cut off. I do not believe this is necessary… plus if you are going to filter a time series, it is not\nnecessary to average it beforehand. I dont think the filtering actually probably adds that much and I\nwould avoid it.\n• The daily averaging was an initial step taken to enable an assessment of the data before the\nfiltering was decided up on for the purpose of the presentation in Figure 4a. We agree that\nthe explanation is perhaps confusing but would stress that the 6 day filtering is necessary for\nthe purpose of presentation; without it, the tidal influence renders the long-term evolution\nmuch more difficult to discern because of the higher frequency variability present in the\ndata. Please note that the key finding from this panel is that, in support of the indications\noffered by the global model output, the thermocline was below the depth of observations\nduring November 2019 (this why we don’t include moored observations from that cruise)\nand then shoaled to more typical depths up the second cruise in March 2020 when the coral\ndemonstrated good recovery.\nb) This is nice (real, unfiltered data!!) and should be bigger and the main point of this figure. In fact, I\nthink the authors should be comparing IDR and MA with this figure, showing a zoom in like this for\nboth sites. But either way, these are the observations we need to see!\n• We agree that a direct comparison could be useful but also recognise the limitations on\nspace and the rather subtle differences in the equivalent data from IDR and MA. For this\nreason the figure requested by the reviewer is in fact already in the paper but within the\nSupplementary material in Figure S7 (where we trust the reviewer agrees, the differences\nare subtle and more likely distracting to include the main text). We would thus prefer to\nretain the presentation of Figure 4 as it currently is because the panels demonstrate a) the\nlocal evolution (shoaling) of the thermocline suggested by the basin-scale model analysis\npresented in Figure 3, b) the tidal periodicity in thermocline behaviour over the slope at MA\nand c) the detailed structure of individual tidal excursions at that location.\nc) Ok… I have experience with Nortek instruments in ecosounder mode and I\ncan confidently say that it is not scientifically accepted that the returns in that\ninstrument mode can be simply ascribed to “turbulence” as the authors do\nhere. This is a contentious claim, and the authors have no other turbulence\ndata that I see to justify it. Moreover, why is this even necessary? Why have a\nfigure about turbulence and then never talk about mixing processes in the\ntext? The authors are mainly interested in the actions of the internal waves in\ntransporting cold (or trapping warm) water to the reef. This doesn’t need\nqualitative hand waving about turbulence, even if the internal waves are\nimportant to mixing and mixing is important to bleaching. You just don’t have\nthe necessary data to say anything quantitative, so it would be much better to\nremove this. Finally, I bet you are seeing enhanced scattering from biological\nsources (zooplankton, etc) that are beings advected up and down by the\ninternal waves. Even if it IS turbulence causing this signal, you can’t quantify\nit in these data so you are better off leaving it out.\n• We agree that the echosounder certainly doesn’t represent turbulence and have revised the\ntext to moderate our reference to turbulence. We did actually measure turbulence directly\nwith our MSS profiler during our last cruise in March 2022 and the high scattering layers in\nthe echosounder are turbulent (but could also include biological scatterers) but we\nappreciate that this analysis isn’t (and won’t be because it’s beyond the scope as the\nreviewer correctly points out) included in the current paper.\nd) Why is tidal elevation here? These internal waves are (probably) baroclinic responses to barotropic\ntidal forcing. The surface tide will not give you much or any insight to the subsurface internal tide,\nespecially over a hand picked 18 h segment… What is this supposed to show?\n• The elevation was included at a late stage in the manuscript preparation to provide a\nreference for the interpretation of currents depicted in Figure 4c. The instantaneous\ncurrents are phase-locked to the barotropic tide because the baroclinic response is local\nrather than associated with remotely-generated internal waves that then break upon the\nslopes surrounding Egmont. This a good point of the reviewer because we are acutely aware\nthat the archipelago as a whole is inevitably going to be an effective generator of internal\nwaves that radiate away into the surrounding ocean; we obviously cannot robustly include\nthese effects (because the GEBCO bathymetry we’d to use completely misrepresents the\nslope angles) in the modelling despite their potential role which is why we explain this\npossible role towards the end of the paper.\n3) Lines 242-243: “The influence of internal waves, both at tidal and higher frequencies,\nwas far less pronounced during 2019 when the thermocline was depressed due to\nthe IOD.” Where is the evidence for this statement?\n• Apologies that this isn’t clear in the text and we have modified the MS accordingly. We were\nreferring to the impact of internal waves in MA (so at a depth of 60-70 m) during November\n2019 when the thermocline was at 100 m. As a result, MA was inundated with warm surface\nwaters and was vertically homogenous, so internal waves were unable to exist at those\ndepths until the thermocline recovered to more typically depths during early 2020.\nYour time series starts in Dec2019. Are you saying that there were less internal waves in Dec 2019 than in the rest\nof the time series? Do you mean that the appearance of sub thermocline water on the reef due to internal waves was less common or absent in 2019? Either way, this statement is a very important one that absolutely needs to be justified if it is going to be in here.\n• As stated above, our observations started in November 2019 but almost all of the moored\nmeasurements were within the upper 100 m and thus failed to capture the deeper internal\nwaves. The only exception was a mooring that (fortuitously!) sank after sliding down the\nvery steep slope at IDR during November 2019. This is used to compare with the numerical\nmodelling output in Figure S6. We have revised the text to clarify that the November\nconditions meant cold water didn’t reach the shallow reefs although we trust the reviewer\nappreciates that this paper is specifically concerned with the mesophotic reef rather than\nthe shallow reefs.\n4) Fig. 5\na) Ok… I have spent a few days trying to puzzle out what exactly is being shown in Fig 5 a (and again\nin S3, S4a and S5a). This is my best guess: The model is initialised with a density profile taken by the\nauthors on some day in some offshore place.\n• Correct; the model is initialised with a deep CTD profile taken from the channel to the north\nof Egmont and where, we assume, the local influence of internal waves is minimised such\nthat the CTD profile is representative of unperturbed conditions.\nThis is used as the initial density profile at all locations in the model.\n• Correct\nThen the model is run for 15 days.\n• Correct\nThen (now I am getting into speculation territory) the authors extract the bottom temperature values\nat all times over the reefs of interest, form some sort of average in time at each near bottom location, then take the temperature at the corresponding depth from the initial, offshore profile and subtract that offshore temperature from the model temperature.\n• Correct, although we would suggest referring to the offshore profile as an ‘unperturbed’\nprofile\nTherefore, “red” means that at that depth it is warmer than the offshore initial condition.\n• Correct – red means that the seabed is experiencing, in a time-averaged sense, warmer\nconditions than would be found in the absence of the internal waves.\nIs this more or less what is being done?\n• Yes – perfect!\nIf so, this needs to be explained somewhere!! The title of the plots is variously referred to as “model mean temperature” and “bottom mean temperature variations.” Arguably the quantity you are plotting is not accurately described by either of these titles. It would be more correct to refer to this as an anomaly relative to the initial state or similar.\n• We agree that this needs to be clarified and we have carefully examined the text to ensure\nthat our approach is understandable.\nSecond, the CTD cast that you choose to initialise the model is itself simply a snapshot at one time of\nthe evolving vertical position and gradient of the thermocline.\n• To an extent; it was indicative of the unperturbed (in the sense of internal evolution over the\nslopes) environment during November 2019 when the bleaching occurred. So, yes it was a\nsnapshot but it was a snapshot at the time of interest when the bleaching needed to be\nexplained.\nDid you test other stratifications?\n• Yes, we ran the model with the stratification for both November 2019 and March 2020. The\ntwo scenarios are presented in Figure 5 (MA, March 2020) and S3 (IDR, March 2020) and for\nNovember 2019, S4 (MA) and S5 (IDR)\nTo this reviewer, it would have been a better use of the modelling to compare the internal wave\nclimate under several different stratifications (i.e. at peak positive 2019 IOD vs “normal” conditions..\n• As stated above, this is precisely what we did and trust that the reviewer agrees our\napproach was therefore correct.\nThese initializations need not be collected by the authors, but instead could come from ARGO or even\nthe model reanalysis.The MITgcm is best used to test the hypothesis that changing stratification\nimpacts internal wave variability at both locations, in addition to exploring how the internal waves are\ndifferent at the two locations. Finally, and most importantly, this approach to analyzing the model does\nnot actually tell you anything about the presence or absence of mode-2 internal waves (or any internal\nwaves). These plots need to be re-thought and potentially abandoned entirely. They are confusing and\ndo not speak to what you are trying to assess.\n• As stated towards the end of the Methods (lines 503-521), the modal decomposition was\nperformed to identify the role of Mode 2 waves. The point of this analysis and the\npresentation of Figure 5 is to demonstrate that the internal wave exacerbates the heating\nexperienced at depths where the bleaching was observed, i.e, the red shading in Figure 5a.\nComparing the panel with Figure S3 which shows the equivalent impact at IDR where no\nbleaching was observed, we can see an absence of red shading because the internal waves\nhave a minimal impact on the near-bed thermal regime. So the point of Figure 5 is to show\nthe reader that internal waves further enhance warming and, most importantly, the absence\nof an equivalent effect at a nearby location at the same island highlights the fine-scale\napproach one must take in understanding bleaching throughout the MCE.\nb) In general, it is confusing to me why there would be so much model shown and so little data in Fig\n5 c and d. You have weeks of data… why not show it? I don’t think what is being shown here is very\nconvincing in terms of data/model comparison (see next comment).\n• There are gaps in what the observations show, i.e. the deep thermocline in November 2019\nmeant all moorings, that couldn’t be deployed any deeper because the slopes were too\nsteep (as experienced on the Nov. 2019 cruise when we tried and the mooring slipped 100 m\ndown-slope) were within the SML. Furthermore, the moorings provide high temporal and\nvertical resolution at a couple of fixed locations, limiting the evaluation of how the internal\nwaves influence the wider slope region. This is why the model output is so important and we\ntrust we have struck a good balance.\n5) The model… I found myself trying to figure out what exactly was done with the model. While the\nspatial resolution was mentioned, the size of the domain was not. How far into the open ocean does\nit extend? I couldn’t figure out the time step either. I will note that it is somewhat rare to fire up a\nmodel and “run it for 15 days” without a spin up period, but perhaps there was one. In general the\nmodelling details were sparse and need to be filled in a bit.\n• Agreed – we felt it appropriate to limit the detail in this paper that is motivated by the coral\nbleaching and likely to be of most interest to biologists. Further papers have been submitted\nthat consider, in isolation, the modelling and we wished to avoid confusing readers with\nmore detail than useful. We have nonetheless added some more fundamental details as\nrequested to the text.\nI was likewise a bit confused about the model/data comparison. Yes, this is difficult to do\nquantitatively, but no attempt has been made here to do so. Instead it is asserted that the model\ncaptures the internal wave variability, with a nod to the figures that show wiggly lines from the data\nand wiggly lines from the model. (I note here that there is –presumably– a typo: these would be\ndepth-AVERAGED velocities, not depth-integrated velocities…\n• Thank you – yes they are depth averaged.\nor they are plotted in the wrong units). Comparing depth averaged velocities between a model and\ndata is a bit of a funny thing to do if you care about the baroclinic internal wave response, which is\nnot a depth-averaged sort of quantity. So yeah… I’m not sure outside of qualitatively for the depth\naveraged currents that there is any evidence that the model is recreating the internal wave features\nin the data.\n• The depth averaged, i.e. barotropic, currents are those used to force the model and this is\nwhat is being verified in Figure 8 rather than the baroclinic response; as TPXO7 predictions\nare subject to uncertainty in regions of such bathymetric complexity, we need to be careful\nin determining whether the model forcing is accurate, thus the value of comparing the\namplitudes of predicted and observed tidal velocities.\nIn S6 both model and a short snapshot of ADCP data in depth and time are shown. But I am confused\nwhy the data is only shown for a 2.5 day period, but the full 15 d model time series is shown (see\nprevious comment about fig 5 c and d in the main part of the paper).\n• As stated above, we were lucky enough that a mooring was deployed over a slope in\nNovember 2019 that was steeper than expected (it was before the multibeam survey!) and\nas a result slipped down the slope to ~130 m. The benefit for us was that we obtained 2.5\ndays of data from below the thermocline before the emergency recovery; these are the data\nused to compare with the model output for November 2019 and are the only observations\navailable from those depths where the bleaching was observed and which we can compare\nwith the model for those depths.\n6) Regarding the “mode-2” structure of the tidal variability at MA.\na) First comment is that mode-2 variability is commonly observed and often studied and written\nabout in the literature, so I would remove the statement “relatively rare observation throughout the\nocean where attention has largely focused on Mode 1 waves within which the direction of vertical\nmovement of isotherms is consistent throughout the whole water column.” which while\nperhaps not strictly incorrect, requires a lot of work by the modifiers “relatively” and “largely.”\n• OK, although we retain words to the effect that Mode 1 receives more attention which we\ntrust the reviewer accepts.\nb) You have the data to show whether or not MA and IDR have a different vertical structure of the\ninternal tide. You *do not* need the model for this. Instead you would use the model to diagnose\nWHY the internal wave structure is different in the different locations. I would suggest an EOF\nor other modal decomposition to show this from the data.\n• The modal decomposition was performed for the model rather than data because of the lack\nof useful data during November 2019 at depths where the bleaching was observed. We\nagree that such an approach tp the data analysis would be preferred but given the lack of\ndata at 100 m in MA during November 2019 when the bleaching occurred, we would prefer\nto avoid further complicating the technical aspects of the oceanography in this biologically-\nmotivated paper.\nc) For the record… internal waves cannot “warm” the water. The can transport heat from one place\nto another (advective heat flux), and they can give up energy to turbulence, which in turn can lead to\nmixing, which, then, in the presence of a temperature gradient, can lead to a heat flux (mixing-driven\nheat flux). What you are showing in the model is that the (I think time mean) vertical temperature\nprofile at MA is different from the initial condition (and IDR) particularly in the mid-reef. You do\nappear to have some data in fig 4 that shows one example of isotherms separating. I would\nsuggest you lean more on these observations. I do NOT think this paper needs to “discover”\nthat the internal wave climate is complicated over complicated bathymetry, or\nthat the oceanography can be different on different sides of an atoll, even a small one, in order to be an impactful contribution.\n• We completely agree and thank the reviewer for pointing out that our language may not\nhave been as accurate as it should have been – we have addressed this in the text.\n• We hope that the reviewer recognises that we are not stressing our discovery of the\ncomplexity of internal waves in such environments but rather demonstrating their potential\n(or likely) role in driving a response in the mesophotic coral ecosystem.\nMinor comments:\n1) Lines 182-183: The discussion of SST being a “poor predictor” of thermocline depth\nand thus the potential that CRW not being good for mesophotic zone corals needs to\nbe more carefully made… the index the authors show in figure 3 b is, in fact, the\ndifference in SSTs between the western and equatorial Indian Ocean. The authors\nassert that the IOD index captures the anomalous thermocline deepening (which is\ndue most likely to a westward propagating Rossby wave). Nevertheless, after saying\nthat SST as represented in CRW is obscures risk to deep corals, in the very next\nthought they use an SST index as predictive of stress to deep corals. This should be\ncleaned up.\n• This is perhaps a detail that could be debated but ultimately becomes rather technical, and\nthus distracting given the intended audience, insofar as yes, the IOD index is based on SST\nvalues but is quite different to the application of those SST values to a determination of\nlikelihood of shallow coral bleaching. The IOD index simply serves as a metric of how large\nthe IOD influence may be; the subsequent response is subsurface and not in itself related to\nthe SST that serves of an indicator of the basin-scale state.\n2) Lines 221-222: “resembling at times turbulent bores and, at other times, nonlinear\nwave trains” Where is the evidence for this? This is speculation and should be\nremoved, it doesn’t add anything.\n• This is one the challenges we experienced when writing this paper – how many examples to\nuse and for what purpose? We have multiple examples of the form taken by the waves\n(more or less every tidal cycle during 2020 for a start) but can’t present them all, despite\ntheir interest to physical oceanographers. So, whilst we agree that we’d like to include\nevidence for this statement in the form of figures, we cannot for practical purposes in this\npaper.\n\nREVIEWERS' COMMENTS\nReviewer #1 (Remarks to the Author):\nThe authors do have a nice piece of work here. It is flawed in some ways as all studies are, and has been\ndiscussed in several iterations of the review process. I have had my say in this regard and now leave it in\nthe hands of the editors. One final suggestion;\nLines 429-431; suggest it reads as \"As the images did not include a uniform Lambertian reference\nmaterial, a combination of methods was used to assign colonies to these 4 categories:\"\nReviewer #3 (Remarks to the Author):\nI have reviewed the response of the authors to my initial comments regarding the physical\noceanography in the paper. I have also reviewed the revised manscript and SI. The authors fixed some of\nthe minor things that I pointed out, but largely rebutted the major comments, arguing that their analysis\nand presentation was sufficiently strong.\nI continue to find the presentation of the PO analysis unnecessarily complicated and in places unclear.\nThis is not (and should not be) a paper about the oceanographic details of the internal wave climate in\nthe vicinity of the study site. The analysis and the modelling effort (and probably the data) are not\n are not\ncomprehensive enough to perform a detailed study of the dynamics. Of course, a regional study like that\nwould not likely be broadly interesting enough for Nature Communications even if it was\ncomprehensive.\nSo the authors are in a tough spot. They are trying to make a limited statement about the physical\ndynamics relative to 1) how out of the ordinary 2019 was and 2) the comparison of the two study sites.\nThe assertion that 2019 was an anomalous year in the central equatorial Indian Ocean oceanography is\nnot novel. Internal waves being important for coral reef thermal stress is not novel. Pointing out internal\nwave heat flux can differ between adjacent areas in regions of complex bathymetry is also not novel.\nI believe the oceanography here can and should be boiled down to two statements: 1) 2019 was\nregionally an anomalous year with widespread potential for thermal stress even at mesophotic depths,\nand that 2) even in the context of regionally high potential for stress, the exposure to internal waves\nmatters on a sub-atoll scale.\nTo me, this simple case can be made in one or at most 2 figures. I do not believe it matters or is even\nreally that well justified that the internal waves have more of a “mode-2” character. For example, I do\nnot find that having detailed plots of velocity from the models with qualitative comparison to the little\ndata they have is necessary to make the case that they need to make, I find the plan view of the time\nmean model bottom temperature anomaly relative to the initial condition to be a strange metric for\ninternal wave exposure, etc.\nIn short there is too much detail and speculation for a paper that is mainly about something else (coral\nbleaching), and too little for a scientifically defensible study of the oceanography at the sub-atoll scale (a\ntotally different study). It feels as though the compromise the authors have taken with the level of detail\nleaves the paper in an awkward position. I wish I could be more positive but I think the following\nstatement from the authors sums up my problem:\n“We agree with the reviewer that these environments are extremely complicated and other factors may\nplay a role; however, given the challenge of obtaining observation data from this environment and the\nneed to explain the observed bleaching characteristics, we have prioritised the most plausible\nmechanism for which we have observational and modelling evidence.” (emphasis mine)\nIf the aim is to provide “plausible mechanisms” because of a “need to explain” – well I would have\nthought a much more limited presentation of the oceanography would suffice. I disagree with the\nauthor’s language here – “needing” to explain something is not hypothesis driven science – but that\nalone isn’t a deal killer for me.\nI thought I had provided perhaps a somewhat over-caffeinated but pretty clear pathway forward for the\noceanography part of this paper. It bums me out that I can’t really strongly support this aspect of this\nstudy at this stage. I think the paper is important and probably the main finding and presentation is\nworthy of a high impact journal. It isn’t far away… but right now the oceanography is holding the rest of\nthe story back.\n\nREVIEWERS' COMMENTS\nReviewer #1 (Remarks to the Author):\nThe authors do have a nice piece of work here. It is flawed in some ways as all studies are,\nand has been discussed in several itera(cid:415)ons of the review process. I have had my say in this\nregard and now leave it in the hands of the editors. One final sugges(cid:415)on;\nLines 429-431; suggest it reads as \"As the images did not include a uniform Lamber(cid:415)an\nreference material, a combina(cid:415)on of methods was used to assign colonies to these 4\ncategories:\"\nThe lines have been changed accordingly.\nReviewer #3 (Remarks to the Author):\nI have reviewed the response of the authors to my initial comments regarding the physical\noceanography in the paper. I have also reviewed the revised manscript and SI. The authors\nfixed some of the minor things that I pointed out, but largely rebutted the major comments,\narguing that their analysis and presentation was sufficiently strong.\nWe sincerely appreciate the time taken to review the paper again and recognise that the\nreviewer is frustrated that we largely chose to retain our version of the manuscript. We\ngenuinely endeavoured to address the scientific flaws raised by the reviewer whilst\nretaining our right as the authors to present the story in the manner that we think\nappropriate. We appreciate that the reviewer would prefer certain elements to be removed\nbut we consider that those elements are a critical component of the message and removing\nthem would be to the significant detriment of the paper. To be completely clear, we firmly\nbelieve that it is precisely because of the detailed insight into the oceanography as a means\nof explaining why the coral bleached, and why it didn’t elsewhere, that makes this paper so\nimportant.\nI continue to find the presentation of the PO analysis unnecessarily complicated and in places\nunclear. This is not (and should not be) a paper about the oceanographic details of the\ninternal wave climate in the vicinity of the study site. The analysis and the modelling effort\n(and probably the data) are not comprehensive enough to perform a detailed study of the\ndynamics. Of course, a regional study like that would not likely be broadly interesting\nenough for Nature Communications even if it was comprehensive.\nThroughout the presentations at conferences over the past 2 years, and based on the other\ntwo reviewers who were not oceanography specialists, we are unable to agree that the PO\nis complicated at all; indeed we have been very careful to present the complex aspects in a\nmanner that will be accessible to non-specialists and have been repeatedly commended for\nintegrating the PO in a way that is comprehensible to a wider audience.\nSo the authors are in a tough spot. They are trying to make a limited statement about the\nphysical dynamics relative to 1) how out of the ordinary 2019 was and 2) the comparison of\nthe two study sites. The assertion that 2019 was an anomalous year in the central equatorial\nIndian Ocean oceanography is not novel. Internal waves being important for coral reef\nthermal stress is not novel. Pointing out internal wave heat flux can differ between adjacent\nareas in regions of complex bathymetry is also not novel.\nWe strongly disagree with this statement and are frustrated by the absence of evidence (in\nthe form of references) provided by the reviewer to demonstrate how the elements of our\nstudy are not novel. Internal waves have been invoked as a mechanism responsible for\nrelieving thermal stress in shallow corals (for which warming surface temperatures are\ncritical) but we would welcome the provision of references identifying the role of internal\nwaves in modulating the mesophotic reef, which is a completely different environment.\nSecondly, the anomalous conditions of 2019 have been identified in a few papers that we\nourselves referenced (as it is only 2023 we would be surprised if there was already a\nsubstantial body of work on this event already) but to suggest that identifying the\nthermocline deepening resulting from the IOD event as the principal driver of coral\nbleaching in the mesophotic reef is nothing new seems very disingenuous.\nI believe the oceanography here can and should be boiled down to two statements: 1) 2019\nwas regionally an anomalous year with widespread potential for thermal stress even at\nmesophotic depths, and that 2) even in the context of regionally high potential for stress, the\nexposure to internal waves matters on a sub-atoll scale.\nThis is the reviewer’s view on how the paper could be written and they are entitled to their\nopinion but it is equally our right as the authors to retain our version. We stress that the\nreviewer is not suggesting that the science is flawed but is instead making editorial\nsuggestions that have not been suggested by anyone else during the presentation of this\nwork.\nTo me, this simple case can be made in one or at most 2 figures. I do not believe it matters or\nis even really that well justified that the internal waves have more of a “mode-2” character.\nFor example, I do not find that having detailed plots of velocity from the models with\nqualitative comparison to the little data they have is necessary to make the case that they\nneed to make, I find the plan view of the time mean model bottom temperature anomaly\nrelative to the initial condition to be a strange metric for internal wave exposure, etc.\nAgain, this is the reviewer’s opinion and we disagree. Specifically, we consider that it does\nmatter that we are able to identify the role of Mode 2 waves are being important because\nthis will be applicable across tropical regions with comparable stratification. In future\nstudies during which biologists may work with oceanographers to evaluate how internal\nwaves may alleviate thermal stress, it is obviously enormously helpful for this specific\ndynamic process to be targeted from the outset as will hopefully be achieved through the\nreading of this paper. If we withheld this information, for no scientific reason, we would be\nholding back precisely the kind of helpful information that scientific papers are published to\npromote throughout the community. Regarding the plan view, we struggle to understand\nhow this is strange; it demonstrates how the depth bands within which coral bleaching was\nobserved correspond to those depths subjected to elevated temperatures due to the\ninternal waves. We have not heard of any difficulty in understanding this figure and result\nfrom any other member of an audience and genuinely consider that the figure is quite easy\nto understand.\nIn short there is too much detail and speculation for a paper that is mainly about something\nelse (coral bleaching), and too little for a scientifically defensible study of the oceanography\nat the sub-atoll scale (a totally different study).\nThe entire reason this paper is submitted to Nature/Nature Communications is because of\nthe insight into why the coral bleached as a response to the oceanographic conditions. We\nconsider, as do everyone else to who the results have been presented, that the\ninterpretation is robust so we would appreciate what aspect of the study then reviewer\nconsiders to be flawed. Similarly, we consider that the level of detail is appropriate and\nwould consider that the support from the first two reviewers (who were specialists oin the\ncoral) for the oceanography attests to this.\nIt feels as though the compromise the authors have taken with the level of detail leaves the\npaper in an awkward position. I wish I could be more positive but I think the following\nstatement from the authors sums up my problem:\n“We agree with the reviewer that these environments are extremely complicated and other\nfactors may play a role; however, given the challenge of obtaining observation data from\nthis environment and the need to explain the observed bleaching characteristics, we have\nprioritised the most plausible mechanism for which we have observational and modelling\nevidence.” (emphasis mine)\nThis is becoming a philosophical debate that we are unable to respond to in a critical,\nobjective manner without the clear identification of what aspects the reviewer would\nsuggest be removed and why.\nI thought I had provided perhaps a somewhat over-caffeinated but pretty clear pathway\nforward for the oceanography part of this paper.\nWe genuinely appreciate the time taken to provide the review but the recommendations\nwere based on the reviewers vision for what the paper may look like, and they appear to be\nannoyed that we didn’t make major revisions based on their editorial opinion rather than\naddressing any scientific flaws. Again, we appreciate the reviewers suggestions but in the\nabsence of specific points that relate to scientific weakness and/or flaws, we have found it\nchallenging to identify elements that could be changed to strengthen, rather than weaken,\nthe paper.\nIt bums me out that I can’t really strongly support this aspect of this study at this stage. I\nthink the paper is important and probably the main finding and presentation is worthy of a\nhigh impact journal. It isn’t far away… but right now the oceanography is holding the rest of\nthe story back.\nThis is an opinion that hasn’t been expressed by any other individuals yet and we simply\ndisagree that the PO is anything other than ‘excellent’ as indicated by the initial reviewers."}]

Decision letter