**5. Reef-building corals**

#### **5.1 Scleractinian corals as reef architects**

Scleractinian corals present a rich fossil record dating back approximately 240 million years, i.e. they appeared much more recently than macroalgal lineages (1 billion years) and also than sponges (600 million years).

iv. methane oxidation (Vacelet et al., 1996) and sulfate reduction (Hoffmann et al., 2005).

So-called secondary metabolites may be produced and released according to age and reproductive status, but also as a response to abiotic and biotic stresses, against predation and microbial infection, for resource defense against competitors, etc. The communication chemistry of soft-bodied sessile invertebrates can indeed be regarded as a vocabulary of molecular words, and its transcriptomics can be equated to proper syntax, in order to respond as exactly and as economically as possible to an identifiable conflict. According to their mode of action, these molecules can be volatile (short MW halocarbons), surface or tissue bound, or mucus-borne. The participation of the microbiome to the biosynthesis of sponge metabolites has been established in a number of cases in natural conditions, but cultivated individual strains or functional consortia of interest may not express the desired phenotype (production of a specific molecule), or may not be cultivatable outside their host. Aside from possible applications in human welfare, bacteria provide prime examples of prokaryote-metazoan coevolution which have endured an estimated 600 million years of

The sponge mesohyl provides a broad variety of ecological microniches that host bacterial consortia (Thiel et al., 2007), with varying degrees of dependence to the host, while cortical regions tend to be dominated by cyanobacteria (Li, 2009). Both components are known to be involved in the synthesis of bioactive secondary metabolites which are naturally produced (or prompted) in response to microbial pathogens (antibiotics), space competitors (allelopathic substances), epibionts (antifouling molecules), and predators (antifeedants, intoxicants, serine protease inhibitors). This chemical arsenal, together with the presence of structural (sharp mineral sclerites, or tough spongy texture) and visual (warning or cryptic colors and patterns) defenses, are necessary to the survival of these non-motile and often exposed invertebrates. Most classes of so-called secondary metabolites are represented, making sponges a treasure trove for the discovery of new drugs. Here we are concerned with the global chemodiversity aspect and the reader is prompted to consult updated reviews (for example in the dedicated issues of *Natural Products Reports* since 1977), or texts such as Kornprobst (2010b) that provide a user-friendly review of sponge-derived metabolites, addressing their possible biosynthetic origins and their potential applications. Metagenomic screening to identify key polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, and new cloning and biosynthetic expression strategies may provide a sustainable method to obtain new pharmaceuticals derived from the uncultured bacterial symbionts, e.g. with cyanobacteria (Li, 2009). Novel culturing techniques (e.g. Selvin et al., 2009), including co-culturing of microorganisms modulating the proliferation (through quorum sensing) and the expression of

Scleractinian corals present a rich fossil record dating back approximately 240 million years, i.e. they appeared much more recently than macroalgal lineages (1 billion years) and also

supply to the host (Weisz et al., 2010),

**4.4.2 Communication "secondary" aspects of symbiosis** 

existence and survived major biogeoclimatic changes.

strains of interest are now actively investigated (Dusane et al., 2011).

**5. Reef-building corals** 

than sponges (600 million years).

**5.1 Scleractinian corals as reef architects** 

zooxanthellae (Schönberg et al., 2008) and when present actively contribute to carbon

About half of the 1,300 scleractinian coral species are reef-building, largely colonial, zooxanthellate (hermatypic) and occurring in the clear, shallow and oligotrophic waters of the tropics. The other half of the order is largely solitary and azooxanthellate, occurring in all regions of the oceans, including the greatest depths (Budd et al., 2010). The reef-building corals function as primary ecosystem engineers, constructing the framework that serves as a habitat for all other coral reef-associated organisms (Wild et al., 2011). Scleractinians are actively engaged in the production and transformation of mineral and organic materials. Coral limestone structures are broken down by bioeroding organisms and abiotic processes into sand, itself acting as a natural biocatalytic filter for the cycling of organic matter by resident heterotrophic microorganisms (Wild et al., 2005).

#### **5.2 The coral holobiont: An example of 3-way functional integration**

The term holobiont, sometimes collectively defined as biota engaged in a host-symbiont partnership (Santiago-Vázquez et al., 2006), has been borrowed by coral researchers to conveniently include the coral host and all of its associated interactive life forms (reviewed in Rohwer, 2010). This includes tissue-associated symbiotic photosynthetic microalgae, surface and mucus-dwelling bacteria and archaea (Siboni et al., 2008) and recently investigated viruses (Vega Thurber, 2008). Endolithic algae and fungi that bore into the mineral skeleton (Wegley et al., 2004) may be included in this definition as permanent associates (as in Bourne et al., 2009). Very recently a true symbiotic relationship has been described between the acroporid *Acropora muricata* and the hydrozoan *Zanclea margaritae* (Pantos & Bythell, 2010). "Mobile" associates (crustaceans, mollusks, polychaetes etc.) provided they have developed a specific niche or trophic preference with the host and developed a cryptic or aposematic appearance as a result, should logically be included in this definition in that the host's disappearance would probably signify a loss of this additional biodiversity.

The coral holobiont is now regarded as a functional unit by scientists who are interested in physiology, pathology, biochemistry and environmental issues of reef-buiding anthozoans. A review of the functional microbiota associated with corals is provided by Laming (2010). Fig. 1 illustrates the typical coral holobiont with its associated macro- and micro-organisms.

#### **5.3 The coral holobiont on autotrophic, heterotrophic and mixotrophic feeding modes**

Mixotrophic organisms can functionally combine different modes of nutrition: (i) by using photosynthesis for inorganic carbon fixation; and (ii) by taking up organic sources. Coral polyps are diploblastic and hence have no mesoderm-derived digestive tract or specialized respiratory organ. Nutrient and energy requirements of the whole colony must depend (i) on direct diffusion of dissolved gases and simple organic molecules across the polyp body wall, (ii) on "assisted metabolism" with pseudo-respiratory and pseudo-digestive functions in association, respectively, with symbiotic macroalgae sequestered in the endoderm, and mucus-bound bacterial consortia, (iii) during the night, on heterotrophy, i.e. ingestion of bacteria and planktonic particles that are digested in the coelomic cavity, the organic products being further broken down by other bacteria. During the day, polyps function in autotrophic mode, i.e. relying on oxygen production and carbon photosynthates provided by the symbiotic zooxanthellae. Other commensal members of the "extended" holobiont, i.e. crustaceans, echinoderms, polychaete worms, mollusks, etc., live mostly off the food particles trapped in the coral mucus, or as parasites.

Coral Reef Biodiversity in the Face of Climatic Changes 93

through a photosynthesis-enhanced (i.e. daylight) mechanism, thus providing about one quarter of the polyp's nitrogen requirements (Grover et al., 2008), while dissolved ammonia, nitrate and urea make up for nearly all of the remaining needs. In another study (Fitzgerald & Szmant., 1997) consider that corals can "synthesize" 16 of the 20 amino acids (including the eight regarded as essential), meaning that bacteria metabolize them from degrading mucus and that the coral readily absorbs the amino acids. Agostini et al. (2009) have shown that a resident bacteria produce B12 vitamin that is taken up by the coral in the coelenteron. The zooxanthellae are fertilized with the inorganic nitrogenous and phosphate excreta of the polyp as well as obtaining a sheltered niche in exchange for their essential role in functional maintenance of the holobiont. This feature of acclimatization (nitrogen capture) is considered important in a fluctuating environment (Gates & Edmunds, 1999). Finally, scleractinians are potentially capable of modulating their epibiotic bacterial community by producing antibacterial compounds as part of a constitutive defense mechanism, as demonstrated in alcyonarians by Harder et al., (2003), and a feature shared by other marine diploblastic invertebrates investigated for their pharmacological potential. The detection of QS signals in coral-associated microbiota (Goldberg et al., 2011) might explain the role of the bacterial component in the holobiont dynamics. Bacterial colonization may indeed be modulated at strain-level by molecules produced by the coral host and interfering with

intraspecific (Gram - AHL and Gram + AIP) or interspecific (AI-2) QS inducers.

The carbon requirements for respiration in branching and foliose corals are essentially provided by carbon dioxide fixation by the algal symbiont (Muscatine & Cernichiari, 1969) during daytime photosynthesis. Under normal conditions subsurface branched corals acquire up to 95% of their energy requirements by coupling their primary metabolism with that of their symbiotic zooxanthellae, which perform carbon fixation and provide other

Food capture of nano- and macro-plankton, especially bacteria and zooplankton, affords the heterotrophic alternative to most corals, i.e. it helps with acquisition of other elements that are essential to the functioning of the holobiont, including that of the bacterial compartment. In addition, heterotrophy enables calcification by providing the elements of the organic matrix upon which carbonate biomineralization is initiated. Furthermore, feeding rate is enhanced in bleached corals. Switching between autotrophic and heterotrophic modes of

Evidence of coelenteric digestion in hermatypic corals has been long been documented (Boschma, 1925) and extracoelenteric digestion has been suggested in some corals to be a

Coral mucus represents a major metabolic investment on behalf of the coral (up to half of its carbon budget), and it actively contributes to the carbon budget of coral reef systems by bringing photosynthates and trapped organic matter to lagoon sediment where heterotrophic nutrient recycling operates efficiently (Wild et al., 2004). To the colony, mucus is used primarily for protection against silting (layers are sloughed off regularly) and against

**5.3.2 Respiration and translocation of photosynthates** 

**5.3.3 Food capture and extracoelenteric digestion** 

feeding has been investigated by Houlbrèque & Ferrier-Pagès (2009).

strategy to defend space from competing neighbours (Lang, 1990).

shared benefits, e.g. mucus production.

**5.3.4 Mucus and mixotrophic metabolism** 

Fig. 1. Schematic representation of a typical coral holobiont.

1- The polyp endoderm harbors symbiotic dinoflagellates (various clades of the genus *Symbiodinium*), i.e. the zooxanthellae; 2- polyps produce copious amounts of mucus, a multifunctional interface with the outside world, in which bacteria and viruses are trapped together with food particles; 3- associated organisms that have a permanent (non-mobile forms) or an obligate (mobile forms) relationship with the host.

#### **5.3.1 Direct assimilation of DOM (dissolved organic matter)**

This mode of nutrient acquisition is commonplace in benthic diploblastic organisms. It has also been experimentally demonstrated in sponges (de Goeij et al., 2008), while plankton capture is the most commonly described method for filter feeders in open waters, while POM (particulate organic matter) feeding is generally regarded as assimilation of POM bacterial degradation products. To the holobiont, bacteria are as important in nitrogen fixation as zooxanthellae are in carbon fixation. Corals are opportunists in their nitrogen acquisition modes, as its sources are capable of fluctuating rapidly in an oligotrophic environment. Polyps are capable of absorbing dissolved amino acids non-discriminately

Fig. 1. Schematic representation of a typical coral holobiont.

forms) or an obligate (mobile forms) relationship with the host.

**5.3.1 Direct assimilation of DOM (dissolved organic matter)** 

1- The polyp endoderm harbors symbiotic dinoflagellates (various clades of the genus *Symbiodinium*), i.e. the zooxanthellae; 2- polyps produce copious amounts of mucus, a multifunctional interface with the outside world, in which bacteria and viruses are trapped together with food particles; 3- associated organisms that have a permanent (non-mobile

This mode of nutrient acquisition is commonplace in benthic diploblastic organisms. It has also been experimentally demonstrated in sponges (de Goeij et al., 2008), while plankton capture is the most commonly described method for filter feeders in open waters, while POM (particulate organic matter) feeding is generally regarded as assimilation of POM bacterial degradation products. To the holobiont, bacteria are as important in nitrogen fixation as zooxanthellae are in carbon fixation. Corals are opportunists in their nitrogen acquisition modes, as its sources are capable of fluctuating rapidly in an oligotrophic environment. Polyps are capable of absorbing dissolved amino acids non-discriminately through a photosynthesis-enhanced (i.e. daylight) mechanism, thus providing about one quarter of the polyp's nitrogen requirements (Grover et al., 2008), while dissolved ammonia, nitrate and urea make up for nearly all of the remaining needs. In another study (Fitzgerald & Szmant., 1997) consider that corals can "synthesize" 16 of the 20 amino acids (including the eight regarded as essential), meaning that bacteria metabolize them from degrading mucus and that the coral readily absorbs the amino acids. Agostini et al. (2009) have shown that a resident bacteria produce B12 vitamin that is taken up by the coral in the coelenteron. The zooxanthellae are fertilized with the inorganic nitrogenous and phosphate excreta of the polyp as well as obtaining a sheltered niche in exchange for their essential role in functional maintenance of the holobiont. This feature of acclimatization (nitrogen capture) is considered important in a fluctuating environment (Gates & Edmunds, 1999). Finally, scleractinians are potentially capable of modulating their epibiotic bacterial community by producing antibacterial compounds as part of a constitutive defense mechanism, as demonstrated in alcyonarians by Harder et al., (2003), and a feature shared by other marine diploblastic invertebrates investigated for their pharmacological potential. The detection of

QS signals in coral-associated microbiota (Goldberg et al., 2011) might explain the role of the bacterial component in the holobiont dynamics. Bacterial colonization may indeed be modulated at strain-level by molecules produced by the coral host and interfering with intraspecific (Gram - AHL and Gram + AIP) or interspecific (AI-2) QS inducers.

#### **5.3.2 Respiration and translocation of photosynthates**

The carbon requirements for respiration in branching and foliose corals are essentially provided by carbon dioxide fixation by the algal symbiont (Muscatine & Cernichiari, 1969) during daytime photosynthesis. Under normal conditions subsurface branched corals acquire up to 95% of their energy requirements by coupling their primary metabolism with that of their symbiotic zooxanthellae, which perform carbon fixation and provide other shared benefits, e.g. mucus production.

#### **5.3.3 Food capture and extracoelenteric digestion**

Food capture of nano- and macro-plankton, especially bacteria and zooplankton, affords the heterotrophic alternative to most corals, i.e. it helps with acquisition of other elements that are essential to the functioning of the holobiont, including that of the bacterial compartment. In addition, heterotrophy enables calcification by providing the elements of the organic matrix upon which carbonate biomineralization is initiated. Furthermore, feeding rate is enhanced in bleached corals. Switching between autotrophic and heterotrophic modes of feeding has been investigated by Houlbrèque & Ferrier-Pagès (2009).

Evidence of coelenteric digestion in hermatypic corals has been long been documented (Boschma, 1925) and extracoelenteric digestion has been suggested in some corals to be a strategy to defend space from competing neighbours (Lang, 1990).

#### **5.3.4 Mucus and mixotrophic metabolism**

Coral mucus represents a major metabolic investment on behalf of the coral (up to half of its carbon budget), and it actively contributes to the carbon budget of coral reef systems by bringing photosynthates and trapped organic matter to lagoon sediment where heterotrophic nutrient recycling operates efficiently (Wild et al., 2004). To the colony, mucus is used primarily for protection against silting (layers are sloughed off regularly) and against

Coral Reef Biodiversity in the Face of Climatic Changes 95

Drastic changes in the "regular" holobiont microbiodiversity, gradual loss of physiological functions and cell/tissue damage beyond recovery, are generally regarded as an aggravation of naturally existing challenges of the holobiont system, due to an unfavorable

Research now focuses on how ocean warming and acidification can lead to rapid coral mortality and affect biodiversity quantitatively and qualitatively, especially in humanimpacted areas. Coral bleaching, i.e. loss of the symbiotic microalgal partner, skeletal demineralization, and also effects on larval and juvenile stages and disease susceptibility to pathogens, are the central themes of most of the reef-building coral literature published since 1998. Parallel to stress and mortality studies, investigators report examples of species, communities, habitats or geographical areas that actually resist or acclimatize to e.g.

Bleaching (discoloration) is due to the rupture of the resident *Symbiodinium* algae with their coral host, due to mortality, loss of pigments or expulsion (Brown, 1997). Decrease in uptake and endodermal sequestration of photosymbionts may be a response to mutual perception of toxic levels of reactive oxygen species (ROS) during enhanced light-induced photosynthesis (Vidal-Dupiol et al., 2009). Coral holobiont resilience to thermal stress was extensively discussed by Coles & Brown (2003) in the light of twenty years of worldwide short- and long-term observations on various types of corals. Reef organisms are stenotolerant to heat, with tolerance limits usually not exceeding 31-32°C for branched acroporids before significant mortality occurs (Berkelmans & Willis, 1999), a range similar to that of sponge tolerance limits in the same locality of the Australian Great Barrier Reef (Webster et al., 2008). Other localities have selected for coral communities that are adapted to their climatic regime. In the Red Sea and the Arabian Gulf, the ambient summer seawater temperature reaches 34-36°C. In general, increases of 1-3°C above mean long-term annual

Recovery is very much species-specific in shallow water scleractinians. Skeletal drillings of hundreds of years old massive forms (e.g. *Porites*) provide records of severe climatic events which colonies have survived (Cleveland et al., 2004). Physiological and cytological adjustments concern the protection of the light-harvesting complex from solar photosynthesis-active radiation (PAR) and ultraviolet radiation (UVA and UVB), and against overheating. Excessive PAR over-stimulates photosynthesis with production of cytotoxic reactive oxygen species (ROS), and UV radiations are genotoxic, while infrared

Mechanisms allowing acclimatization to elevated seawater temperatures include activation of the xanthophyll cycle as a photoprotective defence (dissipation of PAR as heat), induction of heat-shock proteins and antioxidant enzymes, and the production of mycosporin-like amino acid sunscreens. The photoprotective role of GFP-like fluorescent pigments in scleractinian polyps has been established both in the visible light range (dissipation of PAR through fluorescence and light diffraction), and in the UV range (transformation of UVA radiation into longer-range non actinic fluorescence), in order to protect the algal symbiont chlorophyll and peridin from photo-oxidative damage (Salih et al., 2000). The peroxidasemediated production of reactive oxygenated species (ROS) is an initial response against abiotic stress and microbial pathogens, also observed in corals. Palmer et al. (2010) have

biogeochemical evolution of the environment.

**5.5.1 Scleractinians and thermal stress** 

radiations (IR) cause thermal stress.

repeated bleaching, whether generated by biotic or abiotic factors.

maximum temperature have consistently induced coral bleaching.

dessication at low tide, as well as acting as natural sunscreens since they concentrate UVabsorbing mycosporin-like amino acids (MAAs) produced by the zooxanthellae (Dunlap & Schick, 1998). Mucus is also used to entrap food particles (plankton and POM) which are then drawn into the endodermal sac by the tentacles. Mucus is also an obvious source of carbon to many bacteria that degrade it and use it as a dispersion vector, somewhat like bacterial biofilm streamers (Allers et al., 2008). Solitary corals (e.g. *Fungia*) may even asphyxiate and poison their competitors by emitting thick mucus layers that cover neighboring colonies. A comprehensive review on the nature and multiple roles of coral mucus has been proposed by Brown & Bythell (2005), who hypothesize that the intraspecific composition of coral mucus is not homogenous and that different types of mucus may be produced according to needs and environmental stressors. Chemically, coral mucus is a polysaccharide-protein-lipid complex secreted by corals at their surface (ectodermal goblet cells), and there are as many different types of mucus as there are types of corals. Carbohydrate photosynthates are produced at a fast rate as the major component of the mucus which is essential to the whole colony as an exchange medium. In addition to serving as food to polyps in oligotrophic waters, mucusassociated bacterial consortia appear to be an essential component for the recycling of waste and for the biosynthesis of molecules that are useful as osmocompatibles, ROS (reactive oxygen species) detoxicants, anti UV sunscreens, biogeochemical sulphur cycling, etc.

#### **5.4 Biomineralization in reef-building corals**

In corals and in mollusks, extracellular mineral structures develop upon a matrix derived from secretory products of calicoblastic tissues. This phosphate-rich 3-D matrix is typically made up of acidic proteins, carbohydrates and glycoproteins, and is genetically programmed to perform essential regulating and/or organizing functions that will result in the formation of composite biominerals (Weiner & Dove, 2003). The latter are formed as outer membranes release the cationic elements that are taken up intracellularly and delivered / diffused to the matrix where they may be orderly arranged with organic components (e.g. in oyster nacre). There has been some debate about the role of photosynthesis in the calcification process of corals, but light is certainly not a prerequisite for the calcification process. There is substantial evidence for a diurnal cycle in the coral calcification and skeleton-building process during which the types of crystals deposited, their distribution about the skeletal surface and the overall rate of calcification changes (Cohen & McConnaugh, 2003). Central to these changes is the bimodal functioning of the light-sensitive Ca++ - ATPase pump that has the dual role of transporting cations into the calcifying space while removing protons. On site mineralization is probably initiated at sulfated sites of exopolysaccharides, with crystal growth possibly "guided" by organic processes at the interface with the calicoblastic epithelium (Cohen & Mc Connaugh, 2003). An up-to-date treatment on the subject of cellular mechanisms of scleractinian coral calcification is provided by Reyes-Bermudez (2009).

#### **5.5 Scleractinian responses to environmental changes**

In contrast to the aforementioned "regular" and transient biotic and abiotic events that may contribute to the classical Darwinian view of evolution and biodiversity, the multifaceted consequences of the rise in atmospheric carbon dioxide (aggravated by industrialization) on coral reefs are now estimated to be the primary cause of massive losses of reef-associated biodiversity within the next decades.

dessication at low tide, as well as acting as natural sunscreens since they concentrate UVabsorbing mycosporin-like amino acids (MAAs) produced by the zooxanthellae (Dunlap & Schick, 1998). Mucus is also used to entrap food particles (plankton and POM) which are then drawn into the endodermal sac by the tentacles. Mucus is also an obvious source of carbon to many bacteria that degrade it and use it as a dispersion vector, somewhat like bacterial biofilm streamers (Allers et al., 2008). Solitary corals (e.g. *Fungia*) may even asphyxiate and poison their competitors by emitting thick mucus layers that cover neighboring colonies. A comprehensive review on the nature and multiple roles of coral mucus has been proposed by Brown & Bythell (2005), who hypothesize that the intraspecific composition of coral mucus is not homogenous and that different types of mucus may be produced according to needs and environmental stressors. Chemically, coral mucus is a polysaccharide-protein-lipid complex secreted by corals at their surface (ectodermal goblet cells), and there are as many different types of mucus as there are types of corals. Carbohydrate photosynthates are produced at a fast rate as the major component of the mucus which is essential to the whole colony as an exchange medium. In addition to serving as food to polyps in oligotrophic waters, mucusassociated bacterial consortia appear to be an essential component for the recycling of waste and for the biosynthesis of molecules that are useful as osmocompatibles, ROS (reactive

oxygen species) detoxicants, anti UV sunscreens, biogeochemical sulphur cycling, etc.

In corals and in mollusks, extracellular mineral structures develop upon a matrix derived from secretory products of calicoblastic tissues. This phosphate-rich 3-D matrix is typically made up of acidic proteins, carbohydrates and glycoproteins, and is genetically programmed to perform essential regulating and/or organizing functions that will result in the formation of composite biominerals (Weiner & Dove, 2003). The latter are formed as outer membranes release the cationic elements that are taken up intracellularly and delivered / diffused to the matrix where they may be orderly arranged with organic components (e.g. in oyster nacre). There has been some debate about the role of photosynthesis in the calcification process of corals, but light is certainly not a prerequisite for the calcification process. There is substantial evidence for a diurnal cycle in the coral calcification and skeleton-building process during which the types of crystals deposited, their distribution about the skeletal surface and the overall rate of calcification changes (Cohen & McConnaugh, 2003). Central to these changes is the bimodal functioning of the light-sensitive Ca++ - ATPase pump that has the dual role of transporting cations into the calcifying space while removing protons. On site mineralization is probably initiated at sulfated sites of exopolysaccharides, with crystal growth possibly "guided" by organic processes at the interface with the calicoblastic epithelium (Cohen & Mc Connaugh, 2003). An up-to-date treatment on the subject of cellular mechanisms of scleractinian coral

In contrast to the aforementioned "regular" and transient biotic and abiotic events that may contribute to the classical Darwinian view of evolution and biodiversity, the multifaceted consequences of the rise in atmospheric carbon dioxide (aggravated by industrialization) on coral reefs are now estimated to be the primary cause of massive losses of reef-associated

**5.4 Biomineralization in reef-building corals** 

calcification is provided by Reyes-Bermudez (2009).

biodiversity within the next decades.

**5.5 Scleractinian responses to environmental changes** 

Drastic changes in the "regular" holobiont microbiodiversity, gradual loss of physiological functions and cell/tissue damage beyond recovery, are generally regarded as an aggravation of naturally existing challenges of the holobiont system, due to an unfavorable biogeochemical evolution of the environment.

Research now focuses on how ocean warming and acidification can lead to rapid coral mortality and affect biodiversity quantitatively and qualitatively, especially in humanimpacted areas. Coral bleaching, i.e. loss of the symbiotic microalgal partner, skeletal demineralization, and also effects on larval and juvenile stages and disease susceptibility to pathogens, are the central themes of most of the reef-building coral literature published since 1998. Parallel to stress and mortality studies, investigators report examples of species, communities, habitats or geographical areas that actually resist or acclimatize to e.g. repeated bleaching, whether generated by biotic or abiotic factors.

#### **5.5.1 Scleractinians and thermal stress**

Bleaching (discoloration) is due to the rupture of the resident *Symbiodinium* algae with their coral host, due to mortality, loss of pigments or expulsion (Brown, 1997). Decrease in uptake and endodermal sequestration of photosymbionts may be a response to mutual perception of toxic levels of reactive oxygen species (ROS) during enhanced light-induced photosynthesis (Vidal-Dupiol et al., 2009). Coral holobiont resilience to thermal stress was extensively discussed by Coles & Brown (2003) in the light of twenty years of worldwide short- and long-term observations on various types of corals. Reef organisms are stenotolerant to heat, with tolerance limits usually not exceeding 31-32°C for branched acroporids before significant mortality occurs (Berkelmans & Willis, 1999), a range similar to that of sponge tolerance limits in the same locality of the Australian Great Barrier Reef (Webster et al., 2008). Other localities have selected for coral communities that are adapted to their climatic regime. In the Red Sea and the Arabian Gulf, the ambient summer seawater temperature reaches 34-36°C. In general, increases of 1-3°C above mean long-term annual maximum temperature have consistently induced coral bleaching.

Recovery is very much species-specific in shallow water scleractinians. Skeletal drillings of hundreds of years old massive forms (e.g. *Porites*) provide records of severe climatic events which colonies have survived (Cleveland et al., 2004). Physiological and cytological adjustments concern the protection of the light-harvesting complex from solar photosynthesis-active radiation (PAR) and ultraviolet radiation (UVA and UVB), and against overheating. Excessive PAR over-stimulates photosynthesis with production of cytotoxic reactive oxygen species (ROS), and UV radiations are genotoxic, while infrared radiations (IR) cause thermal stress.

Mechanisms allowing acclimatization to elevated seawater temperatures include activation of the xanthophyll cycle as a photoprotective defence (dissipation of PAR as heat), induction of heat-shock proteins and antioxidant enzymes, and the production of mycosporin-like amino acid sunscreens. The photoprotective role of GFP-like fluorescent pigments in scleractinian polyps has been established both in the visible light range (dissipation of PAR through fluorescence and light diffraction), and in the UV range (transformation of UVA radiation into longer-range non actinic fluorescence), in order to protect the algal symbiont chlorophyll and peridin from photo-oxidative damage (Salih et al., 2000). The peroxidasemediated production of reactive oxygenated species (ROS) is an initial response against abiotic stress and microbial pathogens, also observed in corals. Palmer et al. (2010) have

Coral Reef Biodiversity in the Face of Climatic Changes 97

pathogenic and restricted. Webster & Hill (2007) have reviewed ways into which the microbial life of the Great Barrier Reef ecosystems may be impacted by global warming. Along these lines, Ainsworth et al. (2009) have predicted a "microbial perspective" for coral reefs in the next decades, and proposed the addition of a metagenomic component in

Since mild episodes of adverse climatic and biotic conditions regularly occur, it can be assumed that coral reefs are quite resilient with respect to biodiversity losses. Today, human activities are having a steadily increasing impact on climate (global warming) and on biodiversity (overexploitation and toxic waste) and although accurate predictions cannot be made, it is assumed that massive losses of marine biodiversity associated with coral reefs will occur within the next decades. The capacity of organisms to acclimatize and that of communities to maintain their biodiversities is largely unknown, and estimates are based on isolated laboratory experiments in which tolerance limits to individual stressors are measured. The spread of microbial diseases from the shallow (0-30 m) to the mesophotic (30 – 200 m) zones has been discussed by Olson & Kellogg (2010) who prompt investigations on the algal, sponge and coral holobionts from the hitherto neglected deeper reef communities. At the holobiont level, it is important to detect early signs of stress (e.g. coral bleaching due to loss of zooxanthellae) and to identify the critical stages beyond which permanent damage results (e.g. tissue necrosis, various *band diseases* due to microbial pathogens). Intraspecific variations in the profiles of bacterial communities associated with corals may show up between distant localities (Littman et al., 2009), suggesting that environmental conditions may significantly influence the dominance profiles of a few strains, possibly reflecting on the health status of the host species. At the community and ecosystem levels, it is important to evaluate the extent of damage and whether recolonization is possible if the primary cause can be removed (e.g. by classifying an impacted area as a protected zone). Along the same lines, it should now be possible to devise molecular-based methods that can accurately estimate a shift in bacterial biodiversity from standard to pathogenic in a given sample, to estimate stress levels, or to compare metabolomic signatures between unaffected and impacted specimens. Comparable methods already exist in medical microbiology, and in cancerology in which specific markers are sought in addition to metabolomic profiling of

building predictive models.

biological fluids.

**6. Conclusion: Towards an integrative approach** 

**6.1 The common fate of biodiversity and chemodiversity** 

Biodiversity emerged as the first unicellular forms of life appeared, presumably as chemoautotrophs in hydrogeothermal environments. The original biogeochemistry was quite different to what it is today, and different mineral-water-air equilibria must have been attained several times since the emergence of life, e.g. basic Precambrian vs. acidic modern ocean (David & Alm, 2011). As biodiversity and chemodiversity increased, their influence on global biogeochemistry gradually increased (Falkowski et al., 2008). Cyanobacteria are thought to have enriched the atmosphere in oxygen to the point that through various endosymbiosis scenarios a "compromise" was reached that allowed living entities to use oxygen generated by photosynthesis for respiration while controlling its toxicity. Taming the generation of highly reactive radical oxygen species by using oxidative stresses as useful

shown that components of the immune system of corals respond to oxidative stress by activating phenoloxidases (PO) and laccase activities on-site, with the production of melanin (in addition to GFP-like pigments). Akin to algal phlorotannins, melanin and other putative antioxidants play a role in wound healing and oxidative stress mitigation, as well as pathogen encapsulation (Mydlarz & Palmer, 2011). Indeed, PO activity levels, melanin abundance and distribution and GFP-like pigments may serve as useful descriptors of susceptibility to environmental changes in shallow water scleractinian corals (Palmer et al. 2010). Overall, long-lived massive coral growth forms appear better equipped to withstand transient stress than short-lived and more delicate branched forms (Palmer et al., 2011).

A shift in the composition of resident *Symbiodinium microadriaticum* zooxanthellae from stenotolerant to thermoteolerant clades may occur following short bleaching episodes. Indeed, this "upgrading" is the basis of the adaptive bleaching hypothesis or ABH (Kinzie et al., 2001), according to which the bleached basibiont can select a clade better suited to a momentary environmental disturbance.

Another strategy against bleaching is to increase heterotrophy as a source of food energy to compensate for loss of light-derived photosynthates, in species equipped with functional food capture devices.

#### **5.5.2 Scleractinians corals and seawater acidification**

The increase in pCO2 in the water column leads to an increase in total dissolved CO2 at the expense of carbonate ions [CO32−]. The reduction in the latter, at constant seawater calcium concentration [Ca2+], consequently results in the decrease of the saturation state of aragonite (Ωarag), the polymorph of CaCO3 produced by coral calcification (Wild et al., 2011). Aragonite super-saturation is necessary for efficient accretion in most scleractinians, and a lowered external Ωarag will impede the calcification rate in internal fluids and crystal formation at the calicoblastic/seawater interface, translating into weaker skeletons and general deterioration in reef habitat construction. By the year 2100, Ωarag is expected to decrease from an average value of 4 (necessary for calcium accretion) to less than 3 (insufficient for most shallow-water branching corals). Together with natural bioerosion, decalcification may breakdown entire reef constructions in time. Along with decalcification, the lowering of seawater pH causes a shift in the bacterial microbiodiversity, in favor of the most resilient strains, some of which are typically associated with stressed and diseased corals, e.g. Vibrionaceae and Alteromonadaceae (Meron et al., 2011).

#### **5.5.3 Scleractinian corals, anoxia and eutrophication**

Shallow water colonial corals thrive in pristine oligotrophic waters, with a finely tuned carbon and nitrogen metabolism as long as the associated microalgal and bacterial flora remains unaffected.

Nutrient enrichment generally occurs close to human settlements and is therefore likely to first affect fringing reefs. Experiments using media artificially enriched with inorganic ions (PO4- and NO3 -) have shown that the release of dissolved organic carbon and of dissolved organic nitrogen actually decreased relative to tissue surface area in the test species *Montipora digitata* thus affecting not only the efficiency of the photobiosis, but also the mucus-feeding bacteria (Tanaka et al., 2010). However, the counterbalancing combination of eutrophication and seawater warming generates stress to the coral colony, setting the stage for a change in the metagenomic profile of bacteria from functional and diverse to

shown that components of the immune system of corals respond to oxidative stress by activating phenoloxidases (PO) and laccase activities on-site, with the production of melanin (in addition to GFP-like pigments). Akin to algal phlorotannins, melanin and other putative antioxidants play a role in wound healing and oxidative stress mitigation, as well as pathogen encapsulation (Mydlarz & Palmer, 2011). Indeed, PO activity levels, melanin abundance and distribution and GFP-like pigments may serve as useful descriptors of susceptibility to environmental changes in shallow water scleractinian corals (Palmer et al. 2010). Overall, long-lived massive coral growth forms appear better equipped to withstand transient stress than short-lived and more delicate branched forms (Palmer et al., 2011). A shift in the composition of resident *Symbiodinium microadriaticum* zooxanthellae from stenotolerant to thermoteolerant clades may occur following short bleaching episodes. Indeed, this "upgrading" is the basis of the adaptive bleaching hypothesis or ABH (Kinzie et al., 2001), according to which the bleached basibiont can select a clade better suited to a

Another strategy against bleaching is to increase heterotrophy as a source of food energy to compensate for loss of light-derived photosynthates, in species equipped with functional

The increase in pCO2 in the water column leads to an increase in total dissolved CO2 at the expense of carbonate ions [CO32−]. The reduction in the latter, at constant seawater calcium concentration [Ca2+], consequently results in the decrease of the saturation state of aragonite (Ωarag), the polymorph of CaCO3 produced by coral calcification (Wild et al., 2011). Aragonite super-saturation is necessary for efficient accretion in most scleractinians, and a lowered external Ωarag will impede the calcification rate in internal fluids and crystal formation at the calicoblastic/seawater interface, translating into weaker skeletons and general deterioration in reef habitat construction. By the year 2100, Ωarag is expected to decrease from an average value of 4 (necessary for calcium accretion) to less than 3 (insufficient for most shallow-water branching corals). Together with natural bioerosion, decalcification may breakdown entire reef constructions in time. Along with decalcification, the lowering of seawater pH causes a shift in the bacterial microbiodiversity, in favor of the most resilient strains, some of which are typically associated with stressed and diseased

Shallow water colonial corals thrive in pristine oligotrophic waters, with a finely tuned carbon and nitrogen metabolism as long as the associated microalgal and bacterial flora

Nutrient enrichment generally occurs close to human settlements and is therefore likely to first affect fringing reefs. Experiments using media artificially enriched with inorganic ions

organic nitrogen actually decreased relative to tissue surface area in the test species *Montipora digitata* thus affecting not only the efficiency of the photobiosis, but also the mucus-feeding bacteria (Tanaka et al., 2010). However, the counterbalancing combination of eutrophication and seawater warming generates stress to the coral colony, setting the stage for a change in the metagenomic profile of bacteria from functional and diverse to


momentary environmental disturbance.

**5.5.2 Scleractinians corals and seawater acidification** 

corals, e.g. Vibrionaceae and Alteromonadaceae (Meron et al., 2011).

**5.5.3 Scleractinian corals, anoxia and eutrophication** 

food capture devices.

remains unaffected.

(PO4- and NO3

pathogenic and restricted. Webster & Hill (2007) have reviewed ways into which the microbial life of the Great Barrier Reef ecosystems may be impacted by global warming. Along these lines, Ainsworth et al. (2009) have predicted a "microbial perspective" for coral reefs in the next decades, and proposed the addition of a metagenomic component in building predictive models.
