I. Importance of coral reefs
    A. High biodiversity –
    B. Store CO2 (to produce CaCO3)
    C. High productivity
    D. Indicator of stresses on marine ecosystems
    E. Human economy
        1. tourism
        2. food
        3. medicine
    F. Basic biological and paleontological questions
II. Reef distribution and limiting factors
    A. Structure of corals
        1. reef is built entirely by biological activity
            a. reef-building corals – Phylum Cnidaria, Class Anthozoa, Order Scleractinia
            b. calcareous algae and a few other organisms also contribute
        2. hermatypic corals
            a. reef-producing corals
            b. found only in the tropics
            c. possess zooxanthellae in their tissues (symbiotic algae – dinoflagellate)
            d. most are colonial
                (1) individual coral animals (polyps) sit in corallites
                (2) each polyp is a 3 layered animal --
                        outer epidermis, middle mesoglea, inner gastrodermis – contains the zooxanthellae
                (3) tentacles have nematocysts (stinging cells) for capturing zooplankton
            e. reproduction
                (1) polyps can bud off new polyps asexually
                (2) new colonies can form asexually from fragmented colonies
                (3) sexual reproduction produces a planula larvae that disperses and settles
        3. ahermatypic corals
            a. do not form reefs
            b. distributed worldwide
    B. Distribution of reefs –limiting factors
        1. temperature
            a. Minimum
            b. Optimum
            c. bleaching
        2. depth/light
            a. do not grow deeper than about 50-70 m; generally <25 m
            b. requirement for light
        3. salinity
            a. hermatypic corals are intolerant of variations in salinity
            b. areas of freshwater input
            c. areas of high salinity

        4. sedimentation rate

        5. wave action

        6. exposure to air -- tidal extension

III. Types and composition of reefs
    A. Three general categories of reefs
        1. atolls –  ring of reef surrounding a lagoon, in deep water far from land

        2. fringing reefs
            a. simplest and most common - grow in band close to shore
            b. is a continuum between fringing and barrier reefs
        3. barrier reefs
            a. adjacent to, but separated from a landmass
            b. lagoon lies between reef and shore – more protected area with soft bottom
    B. How reefs form
        1. Atolls –
            How could reefs develop in deep water, miles from shore, when reef-building corals can't live deeper than 50-70 m?
            a. subsidence (compensation) hypothesis  (proposed by Darwin)
                (1) atolls are created as fringing reefs on the shores of new volcanic islands; as the islands subside slowly,
                reef growth keeps up with the subsidence; in the center there is quiet water with high sedimentation that prevents
                vigorous coral growth -- results in a lagoon
                (2) tested >100 years later

        2. Fringing and barrier reefs

    C. Common Biota on Reefs
        1. stony corals (Phylum Cnidaria, Class Anthozoa, Order Scleractinia)
        2. Gorgonians (Phylum Cnidaria, Class Anthozoa, Order Gorgonacea)
            a. sea fans and sea whips
            b. common in Atlantic reefs
        3. soft corals (6 different orders of Cnidarian; subclass Octocorallia)
            a. common in Indo-Pacific and rare in Atlantic
            b. don’t contribute to reef formation
        4. hydrocorals (Phyllum Cnidaria, Class Hydrozoa, Order Hydrocorallina)
            a. include fire coral, Millepora
            b. can build reefs
            c. do have a medusa stage

        5. coralline algae
            a. red algae (Rhodophyta)
            b. precipitate CaCO3
            c. cements the reef together
            d. form the algal ridge
        6. calcareous green algae
        7. mollusks
            a. giant clams
            b. gastropods abundant but inconspicuous
        8. echinoderms (e.g., urchins, sea cucumbers, starfish, feather stars)
        9. sponges --
            a. common
            b. minor role in modern reef formation
            c. sclerosponges on deep slopes
            d. can have cyanobacterial symbionts that increase productivity
        10. fishes -- can be hundreds or thousands of species
    D. Have been reefs throughout geologic history
        1. modern scleractinian reefs developed in the mid-Triassic (235 mybp)
        2. earlier reefs dominated by algae, sponges, clams (rudists), extinct corals
        3. geological mass extinctions, followed by new reef communities
IV. Reef Zonation and Biogeography
    A. Indo-Pacific has ~10X more species of coral than does the Atlantic Ocean
    B. Few species at the edges of the range
    C. Physical structure is complex
    D. Zonation patterns generally the result of physical factors; atoll example
        1. windward side
            a. outer seaward slope
            b. ~15 m - is often a terrace; area of most severe wave action; poorly studied
            c. windward reef margin -- at surface
            d. buttress zone (spur and grove zone) coral alternates with deep surge channels;
                optimal conditions here - fastest growth
            e. algal ridge (lithothamnion ridge) -- coral free area with coralline algae

            f. reef flat – shallow, strong gradients, good conditions for growth
            g. seaward beach of the island -- corals become less abundant
        2. lagoon side of the island
            a. narrow beach
            b. lagoon (generally <50 m)
                (1) lagoon reefs
                (2) lagoon floor
        3. leeward side
            a. boulder zone -- area of poor coral growth
            b. leeward reef flat -- narrower than windward side
            c. leeward reef margin --
                (1) algal ridge is only poorly developed;
                (2) no surge channels or buttresses;
                (3) down to 15-20 m coral is abundant and diverse
            d. leeward reef slope -- similar to windward slope; sparse corals
        4. fringing and barrier reefs have similar zonations
    E. Small scale patchiness

    F. Differences between Atlantic (Atl) and Indo-Pacific (IP) Reefs
        1. Differences in coral species
        2. IP reefs also have more sponges, mollusks, crustaceans, cnidarians, and fishes
        3. Some taxa are more common in Atlantic
            a. gorgonians (sea fans and whips)
            b. sponge biomass 2-10X higher (but few have photosynthetic symbionts)
        4. Taxa less common or absent in Atlantic
            a. no true anemone fishes, although some fish do associate with anemones
            b. no giant clams; few octocorals other than gorgonians
            c. no crab and shrimp guarders of corals
            d. no coral eating starfish, like Acanthaster planci
        5. Dominance
            a. Atlantic dominated by Acropora palmata (elkhorn coral) and Millepora complanata (a hydrocoral)
            b. IP not have any reefs dominated by Millepora
            c. Dominant Atlantic grazers are echinoids; dominant IP grazers are fishes
        6. Diurnal rhythms
            a. Atlantic corals mostly nocturnal
            b. IP corals also can be diurnal
        7. IP and Atl also differ in reef age and shape –
            a. Atlantic reefs are usually on shallow banks or platforms
            b. In Atlantic corals often grow deeper
            c. In Atlantic corals usually cover 60% of the reef area; IP they cover 80-90%
            d. IP reefs are older
V. Reef Productivity ('oases in a watery desert')
    A. 1,500-5,000 g C/m2/yr – about 100X more productive than tropical open ocean systems (18-50 g C/m2/yr)
    B. Production by zooxanthellae, algae, and phytoplankton
    C. Some nitrogen fixation from cyanobacteria – some free-living and some symbiotic
    D. Reef systems hold and recycle nutrients efficiently --
        1. filter oceanic productivity
        2. many primary producers
        3. symbioses
        4. large bacterial populations -- efficient recycling
VII. Biology of Hermatypic Corals
    A. Nutrition
        1. Corals are predatory; nematocysts to capture plankton; 10% of requirements
        2. Corals also secrete mucus that entraps small organisms
        3. Zooxanthellae live in coral polyps --  most of the energy for the corals
        4. DOC from the water can be utilized by coral directly
        5. Corals have an interconnected gastrovascular cavity – excess food transported from one region of the colony to
            another region that is receiving less food
    B. Growth and Calcification
        1. zooxanthellae are important in calcification
        2. Hard to measure growth rates
    C. Reproduction
        1. asexual – budding (binary fission); fragmentation
        2. sexual – planula larvae that establish new colonies when they settle
        3. some corals can produce planulae asexually
        4. mature at 7-10 years of age
        5. most are broadcast spawners (some simultaneous), but some brood;
    D. Recruitment
        1. virtually all reef fishes and 85% of corals have a planktonic larval stage
        2. recruitment lower in the Caribbean than in the Great Barrier Reef
        3. may affect recovery from catastrophic events
        4. mortality of new colonies appears to be high
VIII. Species interactions and ecology of reefs
    A. Competition
        1. space in short supply
        2. corals and algae compete for space
        3. exploitative competition 

        4. How can slower growing corals exist?
                a. interference competition (direct interactions)
                b. shade-tolerance; depth zonation

                c. some soft corals have water-borne chemicals -- cause tissue damage and growth inhibition in hard corals

       5. corals must also compete for space with other encrusting invertebrates
                a. sponges
                b. fast-growing algae
    B. Predation
        1. cryptofauna – (hidden animals) if exposed, they are consumed by fishes
        2. predators grazing on the reef itself – gastropods, polychaetes, starfish (Acanthaster planci), fish
            a. predation on coral often resembles grazing -- whole colony not killed

            b. corallivorous fish consume pieces of the coral skeleton to eat the polyps 

            c. physical disturbance (hurricanes; temperature change) may kill corals and concentrate predators on the few remaining corals

            e. Acanthaster planci, crown of thorns starfish
    C. Grazing – without grazing, many corals would be overgrown with algae
        1. herbivorous fish and urchins
            a. can remove 50-100% of total algal production
            b. prefer fleshy filamentous algae
            c. cause increased growth of coralline algae
        2. algal defenses
        3. die-off of the grazing urchin, Diadema, in the Caribbean in the early 1980's
                (effects compounded by overfishing)
        4. urchins are unselective and can also destroy young coral colonies while grazing
        5. damselfish (Pomacentridae) are territorial and graze and ‘farm’ the algae in their territory

    D. Bacteria in Reef Systems
        1. are abundant
        2. some cyanobacteria may erode reefs and cause reef diseases
    E. Algae in Reef Systems
        1. Can have high productivity -- eaten by herbivores
        2. Red coralline algae cement the reef
        3. green calcareous algae (Halimeda) contribute to sand in reefs and lagoons
        4. Some algae bore into coral skeletons

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