The ISME Journal (2020) 14:325–334 https://doi.org/10.1038/s41396-019-0548-z REVIEW ARTICLE Down to the bone: the role of overlooked endolithic microbiomes in reef coral health 1 1 2,3 2,3 2,3 Mathieu Pernice ● Jean-Baptiste Raina ● Nils Rädecker ● Anny Cárdenas ● Claudia Pogoreutz ● Christian R. Voolstra2,3 Received: 2 April 2019 / Revised: 17 October 2019 / Accepted: 28 October 2019 / Published online: 5 November 2019 © The Author(s) 2019. This article is published with open access Abstract Reef-building corals harbour an astonishing diversity of microorganisms, including endosymbiotic microalgae, bacteria, archaea, and fungi. The metabolic interactions within this symbiotic consortium are fundamental to the ecological success of corals and the unique productivity of coral reef ecosystems. Over the last two decades, scientific efforts have been primarily channelled into dissecting the symbioses occurring in coral tissues. Although easily accessible, this compartment is only 2–3 mm thick, whereas the underlying calcium carbonate skeleton occupies the vast internal volume of corals. Far from being devoid of life, the skeleton harbours a wide array of algae, endolithic fungi, heterotrophic bacteria, and other boring eukaryotes, 1234567890();,: 1234567890();,: often forming distinct bands visible to the bare eye. Some of the critical functions of these endolithic microorganisms in coral health, such as nutrient cycling and metabolite transfer, which could enable the survival of corals during thermal stress, have long been demonstrated. In addition, some of these microorganisms can dissolve calcium carbonate, weakening the coral skeleton and therefore may play a major role in reef erosion. Yet, experimental data are wanting due to methodological limitations. Recent technological and conceptual advances now allow us to tease apart the complex physical, ecological, and chemical interactions at the heart of coral endolithic microbial communities. These new capabilities have resulted in an excellent body of research and provide an exciting outlook to further address the functional microbial ecology of the “overlooked” coral skeleton. Looking below the surface: abundance and Earth [1]. In terrestrial systems, these microenvironments diversity of endolithic communities typically provide protection from intense solar radiation and desiccation, as well as sources of nutrients, moisture, Endolithic environments—the pore spaces within solid and substrates derived from minerals [2, 3]. In marine substrates—are ubiquitous habitats for microbial life on systems, endolithic communities similarly exploit the rocky seafloors, but also dwell into limestone and miner- alised skeleton of a broad range of marine animals [4, 5]. A These authors contributed equally: Mathieu Pernice and Jean- wide spectrum of boring microorganisms was already Baptiste Raina described in the late 1880s, with several species of cyano- bacteria, fungi, and eukaryotic green algae known to * Jean-Baptiste Raina penetrate coastal carbonate rocks and the shells of molluscs [email protected] [6]. Coral endolithic microorganisms forming distinct and * Christian R. Voolstra fi [email protected] visible bands in the skeleton were rst characterized not long after, in 1902 [7], a mere 19 years after the description of the unicellular symbiotic algae in coral tissues [8]. While 1 Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia the past 120 years have seen a vast improvement in our understanding of the ecology, physiology, metabolism, 2 Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of diversity, and genetics of Symbiodiniaceae [9], the photo- Science and Technology (KAUST), Thuwal, Saudi Arabia synthetic microalgal symbionts inhabiting the tissue of 3 Department of Biology, University of Konstanz, 78457 corals, less effort was channelled into the characterization of Konstanz, Germany endolithic microorganisms. Their ecological significance 326 M. Pernice et al. remains underexplored and detailed descriptions of their of corals [11, 26–28]. High abundance of cyanobacteria and in situ microenvironment and activity are still scarce. anoxygenic phototrophic bacteria was suggested by spectral signatures of bacteriochlorophylls in the green and deeper Endolithic microalgae bands of coral skeletons [18, 29]. Diversity surveys based on 16S rRNA gene amplicon sequencing have revealed The dense green band in the skeleton that can be observed more than 90 unclassified cyanobacterial OTUs (>97% underneath the tissue of many coral species is often domi- similarity cut off) across the skeleton of 132 coral fragments nated by the filamentous green algae Ostreobium spp. [19]. In addition, anaerobic green sulphur bacteria from the (Siphonales, Chlorophyta) [10]. This diverse genus can genus Prosthecochloris were found prevalent in the skele- penetrate both dead carbonate substrates as well as live ton of Isopora palifera [30]. corals [11], and has been recorded in the aragonite skeletons of Atlantic, south Pacific, and Caribbean reef corals including Pocillopora spp., Stylophora spp., Acropora spp., Physicochemical characteristics of the coral Favia spp., Montastrea spp., Porites spp., and Goniastrea skeleton spp. [11–18]. Recent molecular studies have revealed the astonishing genetic diversity of this group, with up to 80 The coral skeleton is a porous substrate with unique phy- taxonomic units at the near-species level [19–22]. High- sicochemical characteristics [29, 31–33], which are derived throughput amplicon sequencing has also revealed the from the influence of the overlying coral tissue and the presence of other, less abundant, boring green microalgae internal structure of the skeleton itself. These specific closely related to Phaeophila, Bryopsis, Chlorodesmis, physicochemical characteristics likely drive the spatial Cladophora, Pseudulvella, and red algae from the Ban- structure, interspecies interactions, ecophysiology, and giales order in coral skeletons [19]. functions of coral endolithic communities. Endolithic fungi Light Endolithic fungi are as prevalent as microalgae in coral Photosynthetically active radiation (PAR)—the waveband skeletons. They penetrate the calcium carbonate micro- of solar radiation ranging from 400 to 700 nm used by most structures and ultimately interact with Ostreobium cells algae for photosynthesis—are strongly attenuated by [23]. The first endolithic fungi isolated from coral skeletons absorption from the Symbiodiniaceae cells within the coral in the Caribbean and the South Pacific belonged to the tissue and intense scattering from the skeleton [34]. Earlier divisions Ascomycota and Basidiomycota [24]. The intru- estimates suggested that up to 99% of the incident PAR sion of fungal filaments into the polyp zone of the herma- were absorbed or scattered before reaching the endoliths typic coral Porites lobata is known to prompt a defence [14, 35, 36]; similar values were derived from more recent mechanism involving a dense deposition of skeleton, in situ measurements, with 0.1–10% of incident PAR resulting in pearl-like structures [23]. These observations reaching the endolithic communities [29]. Besides water were extended to acroporid and pocilloporid corals, sug- depth, internal irradiance is also strongly influenced by gesting that endolithic fungi are geographically and tax- coral species through variation in tissue thickness and onomically widespread [25]. Along with endolithic skeletal morphology [29]. algae, fungi are present in the newly deposited coral ske- Although endolithic oxygenic phototrophs subsist in leton [5, 25], and exhibit rapid growth to match skeletal extremely low levels of PAR, their light environment in accretion [23]. shallow waters is not as depleted in near-infrared radiation (NIR) (wavelengths from >700 to 1000 nm) [29], as NIR is Endolithic prokaryotes not absorbed by the coral tissue and penetrates much deeper into the skeleton [18]. These wavelengths can be exploited Only a few studies have characterized the diversity of coral by bacteria harbouring bacteriochlorophyll which sustains endolithic bacteria, but often ignored the potential spatial anoxygenic photosynthesis [37], and by other long heterogeneity within this coral compartment. Species of wavelength-absorbing pigments (e.g., chlorophyll d and f) filamentous marine cyanobacteria, such as Plectonema ter- in oxygenic phototrophs [38, 39]. However, since irradiance ebrans, Mastigocoleus testarum, and Halomicronema attenuation increases for higher wavelengths, the amount excentricum, were some of the first described prokaryotes of NIR available for the endolithic communities is from green bands of coral skeletons. These cyanobacteria strongly constrained by water depth. Therefore, NIR can were initially observed in shells of mussels and barnacles only sustain photosynthetic activity in reefs shallower than and subsequently found in association with a great diversity 15 metres [29]. Down to the bone: the role of overlooked endolithic microbiomes in reef coral health 327 Oxygen and pH For example, dense skeletons cause higher light attenuation compared to skeletons that are less dense. Consequently, Photosynthesis and respiration from endolithic communities denser skeletons more strongly promote the development of generate diurnal fluctuations in the pH and oxygen con- anoxic microenvironments, favouring anaerobic micro- centrations within the skeleton