**2.2.2 Man has colonized most reef environments, denaturing them in the process**

Human influence on coral reefs is enormous, multifaceted and expanding at a fast rate. Apart from the generation of gases producing the greenhouse effect, "contact" influences result from (i) natural landscape remodeling, (ii) industrial dumping, and (iii) household pollution. All have direct and readily observable effects on marine biota, with alien molecules killing sensitive species and microbial pathogens plaguing entire populations to extinction.

#### **2.3 Bleaching of shallow water photosymbiotic systems**

Bleaching has been defined as the loss of integrity of the photosymbiont – host relationship (hermatypic corals and some sponges) or the loss of photosynthetic pigments by the photosymbiont (zooxanthellae). Following the first large-scale bleaching events, Brown (1997) classified the causes of bleaching in corals as (i) elevated/decreased seawater temperature, (ii) solar irradiation, (iii) reduced salinity, and (iv) microbial infection. Longterm bleaching leading to mortality of entire expanses of shallow-water reefs was clearly identified as pathological in contrast to short-term episodes of occasional bleaching that allow corals to renew their resident zooxanthellae with better adapted *clades* (Suggett & Smith, 2011), some of which, e.g. *Symbiodinium* clade D may be regarded as indicators of habitat degradation more than agents of adaptation to warming (Stat & Gates, 2011). Research over the last decade has benefited from two major analytical developments: (i) functional genomics and transcriptomics that allow exploration of stress responses at cellular and whole-organism levels (Reitzel et al., 2008), and (ii) microbial metagenomics that allow culture-independent comparative analyses of bacterial and viral (Vega Thurber et al., 2008) profiles of impacted vs. healthy organisms (Vega Thurber et al., 2009), based on robust database on the former (e.g. Wegley et al., 2007). Various scenarios have been proposed to account for coral bleaching, leading to debate as to the respective importance of causative factors of mortality of corals (Bourne et al., 2009; Leggatt et al., 2007; Rosenberg et al., 2007; Rosenberg et al. 2007b), while the functional importance of bacteria in essential coral life processes is emerging from multiple examples (Mouchka et al., 2010) that also reveal their evolutionary significance (Fraune et al., 2010).

#### **2.4 Decalcification of reef-structuring biomineralizers**

Decalcification is the decrease or loss of the ability of marine invertebrates and of calcifying algae and plankton to perform accretion of calcium into adapted and functional skeletal

Coral Reef Biodiversity in the Face of Climatic Changes 79

Open ocean life forms such as nanoplankton represent a considerable biomass of calcifying organisms with very short generation times, and are thus particularly susceptible to acidification and are potential bio-indicators of the progress of decalcification. Coccolith fossil records indicate that responses to past volcanism-related seawater acidification included malformations and dwarfism, and that carbonate recovery is a very long process

Bioavailability of calcium and bicarbonate ions in seawater is therefore central to the question of calcification by corals, coralline algae and other biomineralizers, and to the success of their larvae or spores in metamorphosing into viable adults. A progressive lowering of the pH of seawater (acidification) occurring as a result of greenhouse effects would tend to keep divalent cations, e.g. calcium and magnesium, in soluble form in sea water, thus requiring an ever increasing metabolic effort on behalf of the organisms or of

Pluteus larvae of sea-urchins from various latitudes subjected to different pH levels (6.0 to ambient) suffer from reduced size and survival time, some also showing degradation of fine skeletal structures (Clark et al., 2009). Knowing the importance of urchins (e.g. *Diadema*) in regulating algal proliferation on coral reefs, imbalances between trophic fluxes are to be expected if key grazers are eradicated. An interesting question is that of the effects acidification will have on settling larvae of calcifying benthic organisms that often rely on a combination or a sequence of physical, chemical and contact cues to initiate their establishment and induce cementation. Barnacle larval proteome responds to ambient acidification by producing unique protein signatures, an expression considered of adaptive value by Wong et al (2011, in press). Little is known about the conditions in which calcification inducing genes are activated in settling coral planulae. The physiological mechanisms of the responses of adult coral colonies to the direct effects of CO2 or to changes

concentration have been investigated (Marubini et al., 2008), the net effect being a

decrease in the calcification of coral skeletons. The development and survival of mollusks has been considerably affected since preindustrial CO2 concentrations of 250 ppm, and the survival of commercially important species will be compromised in year 2100 with CO2

Loss of benthic diversity will occur as soon as biomineralizing organisms (essentially corals and coralline algae, foraminiferans and other benthos to a lesser extent) will no longer be able to adequately turn dissolved cations into insoluble cement, meaning their larvae may no longer be able to settle, metamorphose and build a strong mineral matrix upon a steadily cemented holdfast. Solid substratum being one of most important resources in shallow marine habitats (Jackson & Buss, 1975; Connell, 1978), biodiversity on coral reefs will inevitably be affected by the non-replacement of disaggregating limestone structures, dwarfism or crooked shells. Gradual seawater acidification may lead to a new mass extinction of marine species, this time as a result of human interference rather than of cataclysmic events at planetary scale (Veron, 2008). There is an urgent need for studying the effects of climatic changes on sensitive species that may act as bioindicators (Sammarco & Strychar, 2009), and to have coordinated environmental policy-making and management

When the soil-fixing coastal vegetation is destroyed, the physico-chemistry of lagoon waters is upset with negative impacts on all stages of the adult and plankton instars of marine

levels expected to reach 750 ppm (Talmage & Glober, 2010).

their larvae or spores to achieve an acceptable level of calcification for their needs.

(Erba et al., 2010).

in HCO3-

(Sammarco et al., 2007).

**2.5 Human exploitation of coral reefs** 

structures, due to increasing seawater protonation. Biomineralization is a finely-tuned process requiring proper equilibrium between external (seawater) and internal (body fluid) chemistries. Individual susceptibilities to seawater acidification vary between organisms.

#### **2.4.1 Coral reefs as contributors or sinks to atmospheric CO2**

There has been controversy as to whether the global impact on atmospheric CO2 by coral reefs is positive or negative. Coral respiration produces carbon dioxide and so does calcification on a mole-to-mole basis (Gattuso et al., 1995), a fact that tends to place corals as net contributors to atmospheric carbon dioxide. On the other hand, communities dominated by coralline algae in temperate seas may act as carbon sinks (Bensoussan & Gattuso, 2007), an important consideration in estimating carbon dioxide fluxes in reef systems with high algal biomass. Furthermore, factors such as the influence of land runoff on inshore reefs may explain that in some areas, coral communities act as carbon dioxide sinks rather than sources (Chisholm & Barnes, 1998). The debate on carbon cycling in coastal marine environments is now taking a new dimension with consideration of functional interactions of marine microorganisms with their hosts. Useful information about calcification and ocean acidification is found in pages of the website of the European EPOCA project (http://epoca-project.eu/) and of the Woods Hole Oceanographic Institute website (http://www.whoi.edu /OCB-OA/FAQs/).

#### **2.4.2 Key parameters in marine biomineralization**

Biomineralization is widespread in marine eukaryotes and in all marine ecosystems. Carbonates, phosphates, oxides, silicates, etc. are produced by marine organisms to form tissue supporting, defensive or protective structures such as shells, spicules, skeletons, tests, or teeth in invertebrates (e.g. Bentov et al., 2009). Calcification in the form of carbonates is the most widespread form of biomineralization, and calcite (coralline red algae and foraminifers) and aragonite (corals and green calcifying algae) represent the most important contributors to the hard substrata and lagoon sand of coral reefs. Biomineralization results from a finely controlled interfacial chemistry between the organisms and seawater. Basically, the carbonate system in seawater is defined by four master variables, total or dissolved inorganic carbon (DIC), total alkalinity (TA), the partial pressure of CO2 in water (pCO2w), and pH (Blackford, 2010). Knowledge of any two of these along with basic physical properties is sufficient to derive the other two and the carbonate saturation state omega (Ω), bicarbonate ion concentration ([HCO3−]) and carbonate ion concentration ([CO32−]). Marine calcifiers do not all respond in the same way to Ω thresholds, and acidification will most strongly affect species and their larvae that are the most susceptible to lowering carbonate saturation state.

#### **2.4.3 Biomineralization and short and long term consequences on coral reefs**

Biomineralization of CaCO3 (calcification) in the oceans, undertaken by planktonic eukaryotes in the photic zone of open oceans and numerous plants, invertebrates and protists in coastal zones, is one of the major processes that control the global carbon cycle.

The atmospheric partial pressure of carbon dioxide (pCO2) will almost certainly be double that of pre-industrial levels by the year 2100 and will be considerably higher than at any time during the past few million years. The oceans are a principal sink for anthropogenic CO2 with an estimated 30% increase in surface water protonation since the early 1900s and with a projected drop in seawater pH of up to 0.5 units by 2100 (Hall-Spencer et al., 2008), i.e. down to 7.6 to 7.8 in 100 years time (Clark et al., 2009).

structures, due to increasing seawater protonation. Biomineralization is a finely-tuned process requiring proper equilibrium between external (seawater) and internal (body fluid) chemistries. Individual susceptibilities to seawater acidification vary between organisms.

There has been controversy as to whether the global impact on atmospheric CO2 by coral reefs is positive or negative. Coral respiration produces carbon dioxide and so does calcification on a mole-to-mole basis (Gattuso et al., 1995), a fact that tends to place corals as net contributors to atmospheric carbon dioxide. On the other hand, communities dominated by coralline algae in temperate seas may act as carbon sinks (Bensoussan & Gattuso, 2007), an important consideration in estimating carbon dioxide fluxes in reef systems with high algal biomass. Furthermore, factors such as the influence of land runoff on inshore reefs may explain that in some areas, coral communities act as carbon dioxide sinks rather than sources (Chisholm & Barnes, 1998). The debate on carbon cycling in coastal marine environments is now taking a new dimension with consideration of functional interactions of marine microorganisms with their hosts. Useful information about calcification and ocean acidification is found in pages of the website of the European EPOCA project (http://epoca-project.eu/) and of the Woods Hole

Biomineralization is widespread in marine eukaryotes and in all marine ecosystems. Carbonates, phosphates, oxides, silicates, etc. are produced by marine organisms to form tissue supporting, defensive or protective structures such as shells, spicules, skeletons, tests, or teeth in invertebrates (e.g. Bentov et al., 2009). Calcification in the form of carbonates is the most widespread form of biomineralization, and calcite (coralline red algae and foraminifers) and aragonite (corals and green calcifying algae) represent the most important contributors to the hard substrata and lagoon sand of coral reefs. Biomineralization results from a finely controlled interfacial chemistry between the organisms and seawater. Basically, the carbonate system in seawater is defined by four master variables, total or dissolved inorganic carbon (DIC), total alkalinity (TA), the partial pressure of CO2 in water (pCO2w), and pH (Blackford, 2010). Knowledge of any two of these along with basic physical properties is sufficient to derive the other two and the carbonate saturation state omega (Ω), bicarbonate ion concentration ([HCO3−]) and carbonate ion concentration ([CO32−]). Marine calcifiers do not all respond in the same way to Ω thresholds, and acidification will most strongly affect species and their larvae that are the most susceptible

**2.4.3 Biomineralization and short and long term consequences on coral reefs** 

Biomineralization of CaCO3 (calcification) in the oceans, undertaken by planktonic eukaryotes in the photic zone of open oceans and numerous plants, invertebrates and protists in coastal zones, is one of the major processes that control the global carbon cycle. The atmospheric partial pressure of carbon dioxide (pCO2) will almost certainly be double that of pre-industrial levels by the year 2100 and will be considerably higher than at any time during the past few million years. The oceans are a principal sink for anthropogenic CO2 with an estimated 30% increase in surface water protonation since the early 1900s and with a projected drop in seawater pH of up to 0.5 units by 2100 (Hall-Spencer et al., 2008),

**2.4.1 Coral reefs as contributors or sinks to atmospheric CO2** 

Oceanographic Institute website (http://www.whoi.edu /OCB-OA/FAQs/).

**2.4.2 Key parameters in marine biomineralization** 

to lowering carbonate saturation state.

i.e. down to 7.6 to 7.8 in 100 years time (Clark et al., 2009).

Open ocean life forms such as nanoplankton represent a considerable biomass of calcifying organisms with very short generation times, and are thus particularly susceptible to acidification and are potential bio-indicators of the progress of decalcification. Coccolith fossil records indicate that responses to past volcanism-related seawater acidification included malformations and dwarfism, and that carbonate recovery is a very long process (Erba et al., 2010).

Bioavailability of calcium and bicarbonate ions in seawater is therefore central to the question of calcification by corals, coralline algae and other biomineralizers, and to the success of their larvae or spores in metamorphosing into viable adults. A progressive lowering of the pH of seawater (acidification) occurring as a result of greenhouse effects would tend to keep divalent cations, e.g. calcium and magnesium, in soluble form in sea water, thus requiring an ever increasing metabolic effort on behalf of the organisms or of their larvae or spores to achieve an acceptable level of calcification for their needs.

Pluteus larvae of sea-urchins from various latitudes subjected to different pH levels (6.0 to ambient) suffer from reduced size and survival time, some also showing degradation of fine skeletal structures (Clark et al., 2009). Knowing the importance of urchins (e.g. *Diadema*) in regulating algal proliferation on coral reefs, imbalances between trophic fluxes are to be expected if key grazers are eradicated. An interesting question is that of the effects acidification will have on settling larvae of calcifying benthic organisms that often rely on a combination or a sequence of physical, chemical and contact cues to initiate their establishment and induce cementation. Barnacle larval proteome responds to ambient acidification by producing unique protein signatures, an expression considered of adaptive value by Wong et al (2011, in press). Little is known about the conditions in which calcification inducing genes are activated in settling coral planulae. The physiological mechanisms of the responses of adult coral colonies to the direct effects of CO2 or to changes in HCO3 concentration have been investigated (Marubini et al., 2008), the net effect being a decrease in the calcification of coral skeletons. The development and survival of mollusks has been considerably affected since preindustrial CO2 concentrations of 250 ppm, and the survival of commercially important species will be compromised in year 2100 with CO2 levels expected to reach 750 ppm (Talmage & Glober, 2010).

Loss of benthic diversity will occur as soon as biomineralizing organisms (essentially corals and coralline algae, foraminiferans and other benthos to a lesser extent) will no longer be able to adequately turn dissolved cations into insoluble cement, meaning their larvae may no longer be able to settle, metamorphose and build a strong mineral matrix upon a steadily cemented holdfast. Solid substratum being one of most important resources in shallow marine habitats (Jackson & Buss, 1975; Connell, 1978), biodiversity on coral reefs will inevitably be affected by the non-replacement of disaggregating limestone structures, dwarfism or crooked shells. Gradual seawater acidification may lead to a new mass extinction of marine species, this time as a result of human interference rather than of cataclysmic events at planetary scale (Veron, 2008). There is an urgent need for studying the effects of climatic changes on sensitive species that may act as bioindicators (Sammarco & Strychar, 2009), and to have coordinated environmental policy-making and management (Sammarco et al., 2007).

#### **2.5 Human exploitation of coral reefs**

When the soil-fixing coastal vegetation is destroyed, the physico-chemistry of lagoon waters is upset with negative impacts on all stages of the adult and plankton instars of marine

Coral Reef Biodiversity in the Face of Climatic Changes 81

sponges (Carballo & Avilla, 2004). Several CCA metabolites have been identified as potential inducers, e.g. 11-deoxyfistularin-3, a bromotyrosine derivative which stimulates settlement of coral planulae in the presence of algal carotenoids (Kitamura et al., 2007), aminovaleric acid and other salts which induce competent abalone larvae (Stewart et al., 2008), and dibromomethane which induces sea-urchins and the invasive slipper limpet *Crepidula fornicata* (Taris et al., 2010). Bacterial consortia which form specific biofilm-like CCA-associated assemblages, and/or their products have also been shown to act as inducers (Johnson et al., 1991) in the settlement and metamorphosis of larvae (reviewed by Hadfield, 2011). Coralline algae do not grow in sediment-rich coastal waters. Organisms with larvae that specialize in settling on CCA are naturally excluded from zones that are unsuitable for the growth of their host (Fabricius & De'ath 2001). This is a possible explanation for the lower species abundance and community composition of CCAs in coastal environments receiving sediments from rivers or from heavy rainfall washing unstabilized top soil (e.g. mining sites), in addition to insufficient bioavailability of calcium for calcification. Increasing metabolic cost associated with global climate change may offset the advantages of calcification, and recent increases in disease may indicate that oceans are becoming a more stressful environment for calcified algae. Dessication, temperature and light are capable of inducing 50% pigment loss within 24 minutes of emersion in the model species *Calliarthron tuberculosum*, and predictionoriented models based on the combined effects of these parameters are being developed to evaluate the effects of progressive climatic changes (Martone et al., 2010). Taking *Neogoniolithon fosliei* (a primary reef-builder) as a case study, Webster et al. (2010a) demonstrated a strong correlation between elevated sea water temperature (32°C) and (i) de-pigmentation, (ii) a large shift in the structure of microbial communities associated with CCAs, (iii) development of chlorophytic endophytes, and (iv) a dramatic decrease in the ability to induce metamorphosis of coral planulae, i.e. loss of bacterial surface flora. Physiological experiments have recently shown that temperature stress induced bleaching of the coralline alga *Corallina officinalis* was the result of pigment loss following an oxidative burst, i.e. an increase in production of H2O2 and other reactive oxygen species

and decrease in quenching capacity of the haloperoxidase system (Latham, 2008).

**3.2.1 Algae are phylogenetically ancient and have coevolved in association with** 

Macrophytic algae belong to three distinct lineages that diverged early in the history of eukaryotic evolution. Red and green algae (including plants) arose from a common ancestor (Keeling, 2010) through primary endosymbiosis, i.e. engulfing of a cyanobacterium by an aerobic eukaryote, the former becoming the original plastid. Fossils as old as 1 to 1.2 billion years (mid-Proterozoic) indicate the existence of filamentous forms of both red and green algae at the root of present day plants (Javaux et al., 2004). Brown algae (stramenopiles) evolved much later as a consequence of secondary endosymbiosis (engulfing of a unicellular red alga by an aerobic eukaryote). Analysis of the genome of the filamentous brown alga *Ectocarpus siliculosus* (Cock et al, 2010) has provided evidence of the independent evolution of multicellularity within the stramenopile lineage which also includes diatoms. All three lineages have since developed into thousands of different forms with sizes ranging from microscopic (e.g. endophytes) to gigantic (e.g. brown kelp *Macrocystis*) and adaptation to most known aquatic ecosystems. Their capacity to survive eons of biotic and abiotic stresses

**3.2 The phycosphere and its associated microbiome** 

**microbes** 

biota. When mangroves are removed, the nutrient cycling efficiency needed to maintain biodiversity along a seaward gradient is overproductive for heterotrophic microorganisms and underproductive for eukaryotic consumers. Biodiversity loss in coastal waters is the result of ever-increasing activity of sea farming, fishing and tourism in tropical countries. Poor household waste management and the use of fertilizers cause oxygen depletion of seawater with suffocation of reef invertebrates and fish. In the longer term, nutrient enrichment, by favoring algal growth, will cause a strong imbalance between trophic compartments of coral reefs, to the detriment of coral survival.
