Teague, J. , Willans, J., Allen, M., Scott, T., & Day, J. (2019). Hyperspectral imaging as a tool for assessing coral health utilising natural fluorescence. Journal of Spectral Imaging, 8, [a7]. https://doi.org/10.1255/jsi.2019.a7 Publisher's PDF, also known as Version of record License (if available): CC BY Link to published version (if available): 10.1255/jsi.2019.a7 Link to publication record in Explore Bristol Research PDF-document This is the final published version of the article (version of record). It first appeared online via IMPublications at https://www.impopen.com/jsi-abstract/I08_a7 . Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ J. Teague et al., J. Spectral Imaging 8, a7 (2019) 1 volume 1 / 2010 JsI ISSN 2040-4565 JOURNAL OF SPECTRALPeer Reviewed Paper Paper Presented at HSI 2018, October 2018, Coventry, UK IMAGING openaccess In thIs Issue: spectral preprocessing to compensate for packaging film / using neural nets to invert Hyperspectralthe PROSAIL canopy model imaging as a tool for assessing coral health utilising natural fluorescence Jonathan Teague,a,* Jack Willans,b Michael J. Allen,c Thomas B. Scottd and John C.C. Daye aInterface Analysis Centre (IAC), HH Wills Physics Laboratory, Tyndall Ave, Bristol BS8 1TL, UK. E-mail: [email protected], https://orcid.org/0000-0001-7817-6434 bSealife London Aquarium, County Hall, Westminster Bridge Rd, Lambeth, London SE1 7PB, UK. cPlymouth Marine Laboratory (PML), Prospect Place, The Hoe, Plymouth PL1 3DH, UK and University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK. https://orcid.org/0000-0001-8504-7171 dInterface Analysis Centre (IAC), HH Wills Physics Laboratory, Tyndall Ave, Bristol BS8 1TL, UK. https://orcid.org/0000-0003-2263-6088 eInterface Analysis Centre (IAC), HH Wills Physics Laboratory, Tyndall Ave, Bristol BS8 1TL, UK. https://orcid.org/0000-0002-1719-5065 Fluorescent proteins are a crucial visualisation tool in a myriad of research fields including cell biology, microbiology and medicine. Fluorescence is a result of the absorption of electromagnetic radiation at one wavelength and its reemission at a longer wavelength. Coral communities exhibit a natural fluorescence which can be used to distinguish between diseased and healthy specimens, however, current methods, such as the underwater visual census, are expensive and time-consuming constituting many manned dive hours. We propose the use of a remotely operated vehicle mounted with a novel hyperspectral fluorescence imaging (HyFI) “payload” for more rapid surveying and data collection. We have tested our system in a laboratory environment on common coral species including Seriatopora spp., Montipora verrucosa, Montipora spp., Montipora capri- cornis, Echinopora lamellose, Euphyllia ancora, Pocillopora damicornis and Montipora confusa. With the aid of hyperspectral imaging, the coral speci- mens’ emission wavelengths can be accurately assessed by capturing the emission spectra of the corals when excited with light emitting diodes (395–405 and 440 nm). Fluorescence can also provide an indicator of coral bleaching as shown in our bleaching experiment where we observe fluorescence reduction alongside coral bleaching. Keywords: coral, fluorescence, fluorescent proteins (FPs), chlorophyll, hyperspectral imaging Introduction Corals are marine invertebrates in the class Anthozoa to the “Stoney corals” group or Scleractinia. Hermatypic of the phylum Cnidaria, they often live in sessile colo- corals contain photosynthetic algae, specifically dino- nies of many individual polyps. Reef-building corals are flagellates belonging to the genus Symbiodinium often geographically distributed in tropical and subtropical referred to as Zooxanthellae, that live symbiotically waters, typically occurring between the 300° north and within its cells. The algae provide the coral with energy 300° south latitudes.1 Corals primarily responsible for synthesised through photosynthesis and in exchange building modern reefs are Hermatypic corals, belonging receive protection and nutrients required to conduct Correspondence Citation Jonathan Teague ([email protected]) J. Teague, J. Willans, M.J. Allen, T.B. Scott and J.C.C. Day, “Hyperspectral imaging as a tool for assessing coral health utilising natural Received: 15 October 2018 fluorescence”, J. Spectral Imaging 8, a7 (2019). https://doi.org/10.1255/ Revised: 21 February 2019 jsi.2019.a7 Accepted: 1 March 2019 © 2019 The Authors Publication: 5 March 2019 This licence permits you to use, share, copy and redistribute the paper in doi: 10.1255/jsi.2019.a7 any medium or any format provided that a full citation to the original ISSN: 2040-4565 paper in this journal is given. 2 Hyperspectral Imaging as a Tool for Assessing Coral Health Utilising Natural Fluorescence Figure 1. The symbiotic relationship between Hermatypic corals and Symbiodinium. photosynthesis (Figure 1). Ahermatypic corals do not For example, if an object’s emission wavelength is possess this symbiosis.2 around 420–460 nm (blue) it can be excited with ultra- Hermatypic coral communities exhibit a natural fluo- violet (UV). This means for an excitation light source we rescence, both from the coral host and the Symbiodinium, can use LEDs that emit in UV or blue which will excite the significance of which is yet to be determined. across a wide range of the spectrum. This will allow us Previous studies have suggested many possibilities for to see the whole spectrum of coral fluorescence proteins the role that fluorescent proteins (FPs) play in corals: described by Alieva et al.,8 as corals mainly fluoresce in acting as a sunscreen by providing a photobiological the green 478–512 nm and cyan 485–495 nm. system for regulating the light environment;3 or as a host Green FP (GFP) are key colour determinants in reef- stress response, through their action as antioxidants; building corals (class Anthozoa, order Scleractinia).9 downregulation of FPs frequently occurs in injured or Reef-building corals have symbiotic relationships with compromised coral tissue;4 and even to attract prey.5 dinoflagellates (Zooxanthellae) that contain chlorophyll With such broad functional activity, the presence of and associated photosynthetic pigments adding further FPs can potentially be exploited as a proxy for meas- splendour to an already impressive spectral palette. uring coral health. Analysis of the natural variability in Coral FPs are major determinants of the colour diversity, fluorescence intensity for a given species, as well as the accounting for practically every visible coral colour other differences between diseased and healthy specimens, than the brown of the photosynthetic pigments of algal enables the development of an index relating fluores- symbionts.10 Known coral GFP-like proteins11,12 can be cence to disease.6 arbitrarily subdivided into several “colour types”: cyan, Fluorescence is the processes in which molecules emit shortwave green, longwave green, yellow, red and a non- light from electronically excited states created by either fluorescent purple-blue.8,10 a physical (absorption of light), mechanical (friction) or Cyan proteins typically have an emission peak between chemical mechanism. Fluorescence is observed when 485 nm and 495 nm, although more blue-shifted vari- light is absorbed by fluorochromes, a fluorescent chem- ants can occasionally be found, down to 477 nm.8 Green ical compound that can emit light upon light excitation. fluorescent colour is the most common in corals and Electrons are promoted from a ground state to an excited is the most conspicuous of all the fluorescent colours state and, as the excited molecule returns to its ground in situ.10 The position of the peak excitation wave- state, the relaxation process involves the emission of a length in the green proteins is around 478–512 nm.8 photon of lower energy and hence longer wavelength There are two known wild-type yellow FP with emis- than the absorbed photon.7 sion maxima between 525 nm and 570 nm: zoanYFP J. Teague et al., J. Spectral Imaging 8, a6 (2019) 3 from a Zoanthidea representative (emission maximum specialised equipment or post-survey data processing, 538 nm) and a hydromedusan protein phiYFP (emission but it does require the observer to have a high level of maximum 535 nm).8 Corals that excite in red can contain diagnostic expertise in coral taxonomy and disease iden- either the DsRed-type or Kaede-type red FP. Kaede-type tification.15 proteins are mostly associated with Scleractinian corals of suborder Faviina. Red FP from all other organisms studied Bleaching thus far, including other suborders of reef-building corals Bleaching refers to the loss of colour in symbioses (Scleractinia), all sea anemones (Actiniaria) and two more between Zooxanthellae and marine benthic animals, Corallimorpharia representatives, possess the DsRed-like this is not restricted to corals but is displayed by all chromophore. DsRed proteins typically have an emission animals in symbiosis with Zooxanthellae. Bleaching often peak between 560 nm and 589 nm and Kaede around displays with depressed growth and increased coral 574 nm.8 mortality; always considered as a detrimental physi- ological response.19 The causes