*Review* **A Review of Current and New Optical Techniques for Coral Monitoring**

**Jonathan Teague 1,\*, David A. Megson-Smith 1, Michael J. Allen 2,3, John C.C. Day <sup>1</sup> and Thomas B. Scott <sup>1</sup>**


**Abstract:** Monitoring the health of coral reefs is essential to understanding the damaging impacts of anthropogenic climate change as such non-invasive methods to survey coral reefs are the most desirable. Optics-based surveys, ranging from simple photography to multispectral satellite imaging are well established. Herein, we review these techniques, focusing on their value for coral monitoring and health diagnosis. The techniques are broadly separated by the primary method in which data are collected: by divers and/or robots directly within the environment or by remote sensing where data are captured above the water's surface by planes, drones, or satellites. The review outlines a new emerging technology, low-cost hyperspectral imagery, which is capable of simultaneously producing hyperspectral and photogrammetric outputs, thereby providing integrated information of the reef structure and physiology in a single data capture.

**Keywords:** coral reef monitoring; reef health; review; hyperspectral imaging; marine optics

**1. Introduction**

Coral reefs are strategically important for coastal nations in tropical and subtropical regions due to the valuable ecosystem goods and services they provide [1]. However, reef systems are now being impacted on a global scale by a variety of conditions, namely, "coral bleaching" [2,3], diseases [4,5], nutrient pollution [6] and algal overgrowth [7], coastal engineering [8] and sedimentation [9], crown-of-thorns [10] and sea-urchin predation [11]. Corals are particularly susceptible to environmental changes as they have low tolerance to variations in temperature, salinity, and solar radiation [12]. Sustained periods of stress can lead to coral colony death, and, in some instances, to whole reef collapse [13]. This represents a significant concern for the 275 million people who live within 30 km of these ecosystems, and who rely on these reefs for their livelihoods and food security [14].

While coral bleaching is most commonly associated with changes in sea surface temperature (SST) [3,15], it can also be a response to other external factors or triggers such as ocean acidification [16], bacterial infection [17] or shading caused by extreme turbidity [18]. The term 'bleaching' refers to the loss of the symbiont algal cells of the family Symbiodiniaceae, which are normally the main provider of coral colour [19,20]. The white or bleached appearance of the coral results from the calcium carbonate exoskeleton becoming visible, since the coral tissue itself is translucent [19], or as a result of polyp death.

Coral disease is another of the main causes of reef degradation and has been increasing worldwide since first studied in the 1970s in the Red Sea [21]. It has become particularly prevalent in the Caribbean [22,23], but has also been increasingly recorded in other reef systems such as the Great Barrier Reef [4,22,24,25]. Coral can become more susceptible to disease due to factors such as a decline in water quality and fish stocks, heat stress and,

**Citation:** Teague, J.; Megson-Smith, D.A.; Allen, M.J.; Day, J.C.; Scott, T.B. A Review of Current and New Optical Techniques for Coral Monitoring. *Oceans* **2022**, *3*, 30–45. https://doi.org/10.3390/ oceans3010003

Academic Editor: Michael W. Lomas

Received: 1 May 2021 Accepted: 13 January 2022 Published: 20 January 2022

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more recently identified, to ocean acidification driven by anthropogenic activity [26–28]. In some cases, specific pathogens have been identified as a primary contributor [22,29]. A diverse array of diseases have now been observed, with approximately 30 diseases and syndromes affecting the health of 150 different species worldwide [5,30]. The term 'disease' is used to describe symptoms arising from a known pathogen, while 'syndrome' refers to effects arising from an unknown causative agent, whether it be a pathogen, pollutant, or climate condition such as ocean warming [19].

Visible changes associated with coral ill-health can provide a valuable metric for the monitoring of colonies. Affected corals are frequently characterised (and named accordingly) by abnormal or decreased pigmentation in compromised tissue [31]. To date, white, brown, pink, yellow, and black line diseases have all been described [26–28,32].

Bleaching or disease is often identifiable by the absence of specific pigments in individual corals [33–36]. These pigments have specific wavelength peaks characteristic of their optical reflectance or fluorescence spectra. These pigments include chlorophyll-a absorption (676 nm) [37], chlorophyll-a fluorescence (685 nm), peridinin (574 nm) [38], diatoxanthin (607 nm) [38], and green fluorescent protein (GFP) (511 nm) [39].

The photosynthetic pigment chlorophyll-a and accessory pigments peridinin and diatoxanthin provide a direct insight into the symbiont density [40,41]. As these pigments are only found within the corals' symbiotic partner Symbiodiniaceae, they provide a direct bleaching indicator. GFP fluorescence provides different insights as it is highly responsive to thermal fluctuations [15,42,43] and is often spectrally more distinctive, namely in its intensity when compared to chlorophyll fluorescence [33].

This observed specificity lends itself to utilising automated image-based techniques that can objectively quantify and monitor compromised colonies based on spectroscopic optical measurements. Current observations by human divers are unavoidably subjective and provide less robust and detailed data.
