Editing Coral reef (section)

===Explanations===
Around coral reefs, lagoons fill in with material eroded from the reef and the island. They become havens for marine life, providing protection from waves and storms.

Most importantly, reefs [[Biogeochemical cycle|recycle]] nutrients, which happens much less in the open ocean. In coral reefs and lagoons, producers include phytoplankton, as well as seaweed and coralline algae, especially small types called turf algae, which pass nutrients to corals.<ref name="Castro" /> The phytoplankton form the base of the food chain and are eaten by fish and crustaceans. Recycling reduces the nutrient inputs needed overall to support the community.<ref name="GuideCoralBleaching">{{cite book |author1=Marshall, Paul |author2=Schuttenberg, Heidi |year=2006 |title=A Reef Manager's Guide to Coral Bleaching |publisher=Great Barrier Reef Marine Park Authority |location=Townsville, Australia |url=http://www.coris.noaa.gov/activities/reef_managers_guide/ |isbn=978-1-876945-40-4}}</ref>

Corals also absorb nutrients, including inorganic nitrogen and phosphorus, directly from water. Many corals extend their tentacles at night to catch [[zooplankton]] that pass near. Zooplankton provide the polyp with nitrogen, and the polyp shares some of the nitrogen with the zooxanthellae, which also require this element.<ref name="Castro">Castro, Peter and Huber, Michael (2000) ''Marine Biology.'' 3rd ed. Boston: McGraw-Hill.</ref>

[[File:Multy color corals.JPG|thumb|left|The colour of corals depends on the combination of brown shades provided by their [[zooxanthellae]] and pigmented proteins (reds, blues, greens, etc.) produced by the corals themselves.]]

Sponges live in crevices in the reefs. They are efficient [[filter feeder]]s, and in the [[Red Sea]] they consume about 60% of the phytoplankton that drifts by. Sponges eventually excrete nutrients in a form that corals can use.<ref>{{cite web |url=http://news.nationalgeographic.com/news/2001/11/1107_keyholecoral.html |archive-url=https://web.archive.org/web/20011108233132/http://news.nationalgeographic.com/news/2001/11/1107_keyholecoral.html |url-status=dead |archive-date=8 November 2001 |title=Rich Coral Reefs in Nutrient-Poor Water: Paradox Explained? |first=John |last=Roach |publisher=[[National Geographic News]] |date=November 7, 2001 |access-date=April 5, 2011}}</ref>

The roughness of coral surfaces is key to coral survival in agitated waters. Normally, a boundary layer of still water surrounds a submerged object, which acts as a barrier. Waves breaking on the extremely rough edges of corals disrupt the boundary layer, allowing the corals access to passing nutrients. Turbulent water thereby promotes reef growth. Without the access to nutrients brought by rough coral surfaces, even the most effective recycling would not suffice.<ref>{{cite journal |url=https://www.newscientist.com/article/mg17523612.100-corals-play-rough-over-darwins-paradox.html |title=Corals play rough over Darwin's paradox |first=Rachel |last=Nowak |issue=2361 |journal=[[New Scientist]] |date=21 September 2002 }}</ref>

Deep nutrient-rich water entering coral reefs through isolated events may have significant effects on temperature and nutrient systems.<ref name="Leichter et al. 1996">{{cite journal|last=Leichter|first=J. |author2=Wing S. |author3=Miller S.|author4=Denny M.|title=Pulsed delivery of subthermocline water to Conch Reef (Florida Keys) by internal tidal bores|journal=Limnology and Oceanography|year=1996|volume=41 |issue=7|pages=1490–1501 |doi=10.4319/lo.1996.41.7.1490|bibcode=1996LimOc..41.1490L|doi-access=free}}</ref><ref name="Wolanski and Pickard 1983">{{Cite journal |last1=Wolanski |first1=E. |last2=Pickard |first2=G. L. |doi=10.1071/MF9830065 |title=Upwelling by internal tides and kelvin waves at the continental shelf break on the Great Barrier Reef |journal=Marine and Freshwater Research |volume=34 |page=65 |year=1983|issue=1 |bibcode=1983MFRes..34...65W }}</ref> This water movement disrupts the relatively stable thermocline that usually exists between warm shallow water and deeper colder water. Temperature regimes on coral reefs in the Bahamas and Florida are highly variable with temporal scales of minutes to seasons and spatial scales across depths.<ref>{{cite journal|last=Leichter|first=J.|author2=Helmuth B.|author3=Fischer A.|year=2006 |title=Variation beneath the surface: Quantifying complex thermal environments on coral reefs in the Caribbean, Bahamas and Florida|journal=Journal of Marine Research|volume=64|issue=4|pages=563–588 |doi=10.1357/002224006778715711|doi-broken-date=2 December 2024 }}</ref>

[[File:Polyps (PSF).png|thumb|right|{{center|Coral polyps}}]]

Water can pass through coral reefs in various ways, including current rings, surface waves, internal waves and tidal changes.<ref name="Leichter et al. 1996" /><ref name="Ezer et al. 2011">{{cite journal |last=Ezer|first=T.|author2=Heyman W.|author3=Houser C.|author4=Kjerfve B.|title=Modeling and observations of high-frequency flow variability and internal waves at a Caribbean reef spawning aggregation site|journal=Ocean Dynamics|year=2011|volume=61|issue=5|pages=581–598|doi=10.1007/s10236-010-0367-2|bibcode=2011OcDyn..61..581E|s2cid=55252988}}</ref><ref name="Fratantoni and Richardson 2006">{{cite journal|last=Fratantoni |first=D. |author2=Richardson P.|title=The Evolution and Demise of North Brazil Current Rings|journal=Journal of Physical Oceanography|year=2006|volume=36|issue=7|pages=1241–1249 |doi=10.1175/JPO2907.1 |bibcode=2006JPO....36.1241F |hdl=1912/4221|hdl-access=free |url=http://darchive.mblwhoilibrary.org/bitstream/1912/4221/1/jpo2907%252E1.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://darchive.mblwhoilibrary.org/bitstream/1912/4221/1/jpo2907%252E1.pdf |archive-date=2022-10-09 |url-status=live}}</ref><ref name="Leichter et al. 1998">{{cite journal |last=Leichter|first=J.|author2=Shellenbarger G.|author3=Genovese S.|author4=Wing S.|title=Breaking internal waves on a Florida (USA) coral reef: a plankton pump at work?|journal=Marine Ecology Progress Series|year=1998 |volume=166|pages=83–97|doi=10.3354/meps166083|bibcode=1998MEPS..166...83L|doi-access=free}}</ref>  Movement is generally created by tides and wind. As tides interact with varying bathymetry and wind mixes with surface water, internal waves are created. An internal wave is a gravity wave that moves along density stratification within the ocean. When a water parcel encounters a different density it oscillates and creates internal waves.<ref name="Talley et al. 2011">{{cite book|last=Talley|first=L.|url={{google books |plainurl=y |id=Chb14jomm08C}}|title=Descriptive Physical Oceanography: An Introduction|isbn=978-0750645522|year=2011|publisher=Elsevier Inc.|location=Oxford UK}}</ref> While internal waves generally have a lower frequency than surface waves, they often form as a single wave that breaks into multiple waves as it hits a slope and moves upward.<ref name="Helfrich 1992">{{cite journal|author1-link=Karl Helfrich|last=Helfrich|first=K.|title=Internal solitary wave breaking and run-up on a uniform slope|journal=Journal of Fluid Mechanics|year=1992|volume=243|pages=133–154|doi=10.1017/S0022112092002660|doi-broken-date=2 November 2024 |bibcode = 1992JFM...243..133H |s2cid=122915102 }}</ref> This vertical breakup of internal waves causes significant diapycnal mixing and turbulence.<ref name="Gregg 1989">{{cite journal|last=Gregg|first=M.|title=Scaling turbulent dissipation in the thermocline|journal=Journal of Geophysical Research|year=1989|volume=94|issue=C7|series=9686–9698|doi=10.1029/JC094iC07p09686|page=9686|bibcode=1989JGR....94.9686G}}</ref><ref name="Taylor 1992">{{cite journal|last=Taylor|first=J.|title=The energetics of breaking events in a resonantly forced internal wave field|journal=Journal of Fluid Mechanics|year=1992|volume=239|pages=309–340|doi=10.1017/S0022112092004427|doi-broken-date=2 November 2024 |bibcode = 1992JFM...239..309T |s2cid=121973787 }}</ref> Internal waves can act as nutrient pumps, bringing plankton and cool nutrient-rich water to the surface.<ref name="Leichter et al. 1996"/><ref name="Leichter et al. 1998"/><ref name="Andrews and Gentien 1982">{{cite journal|last=Andrews|first=J.|author2=Gentien P.|title=Upwelling as a source of nutrients for the Great Barrier Reef ecosystems: A solution to Darwin's question?|journal=Marine Ecology Progress Series|year=1982|volume=8|pages=257–269|doi=10.3354/meps008257|bibcode=1982MEPS....8..257A|doi-access=free}}</ref><ref name="Sandstrom and Elliott 1984">{{cite journal|last=Sandstrom|first=H.|author2=Elliott J.|title=Internal tide and solitons on the Scotian shelf: A nutrient pump at work|journal=Journal of Geophysical Research|year=1984|volume=89|issue=C4|pages=6415–6426|doi=10.1029/JC089iC04p06415|bibcode=1984JGR....89.6415S}}</ref><ref name="Wolanski and Hamner 1988">{{cite journal|last=Wolanski|first=E.|author2=Hamner W. |title=Topographically controlled fronts in the ocean and their biological significance|journal=Science|year=1988|volume=241|pages=177–181|doi=10.1126/science.241.4862.177|pmid=17841048|issue=4862|bibcode = 1988Sci...241..177W |s2cid=19757639}}</ref><ref name="Rougerie et al. 1992">{{cite journal|last=Rougerie|first=F.|author2=Fagerstrom J.|author3=Andrie C.|title=Geothermal endo-upwelling: A solution to the reef nutrient paradox?|journal=Continental Shelf Research|year=1992|volume=12|pages=785–798|doi=10.1016/0278-4343(92)90044-K|issue=7–8|bibcode = 1992CSR....12..785R |url=http://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_33-34/36720.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_33-34/36720.pdf |archive-date=2022-10-09 |url-status=live}}</ref><ref name="Wolanski and Delesalle 1993">{{cite journal|last=Wolanski|first=E.|author2=Delesalle B.|title=Upwelling by internal waves, Tahiti, French Polynesia|journal=Continental Shelf Research|year=1993|volume=15|pages=357–368|doi=10.1016/0278-4343(93)E0004-R|issue=2–3|bibcode = 1995CSR....15..357W }}</ref><ref name="Szmant and Forrester 1996">{{Cite journal | last1 = Szmant | first1 = A. M. | last2 = Forrester | first2 = A. | doi = 10.1007/BF01626075 | title = Water column and sediment nitrogen and phosphorus distribution patterns in the Florida Keys, USA | journal = Coral Reefs | volume = 15 | issue = 1 | pages = 21–41 | year = 1996 |bibcode = 1996CorRe..15...21S | s2cid = 42822848 }}</ref><ref name="Furnas and Mitchell 1996">{{Cite journal | last1 = Furnas | first1 = M. J. | last2 = Mitchell | first2 = A. W. | doi = 10.1016/0278-4343(95)00060-7 | title = Nutrient inputs into the central Great Barrier Reef (Australia) from subsurface intrusions of Coral Sea waters: A two-dimensional displacement model | journal = Continental Shelf Research | volume = 16 | issue = 9 | pages = 1127–1148 | year = 1996 |bibcode = 1996CSR....16.1127F }}</ref><ref name="Leichter and Miller 1999">{{cite journal|last=Leichter|first=J.|author2=Miller S.|title=Predicting high-frequency upwelling: Spatial and temporal patterns of temperature anomalies on a Florida coral reef |year=1999|volume=19|issue=7|pages=911–928|doi=10.1016/s0278-4343(99)00004-7|journal=Continental Shelf Research|bibcode=1999CSR....19..911L}}</ref><ref name="Leichter et al. 2003">{{cite journal|last=Leichter|first=J.|author2=Stewart H.|author3=Miller S.|s2cid=15125174|title=Episodic nutrient transport to Florida coral reefs|journal=Limnology and Oceanography|year=2003|volume=48|pages=1394–1407|doi=10.4319/lo.2003.48.4.1394|issue=4|bibcode=2003LimOc..48.1394L}}</ref>

[[File:Sea Cotton.jpg|thumb|left|Most coral polyps are nocturnal feeders. Here, in the dark, polyps have extended their tentacles to feed on zooplankton.]]

The irregular structure characteristic of coral reef bathymetry may enhance mixing and produce pockets of cooler water and variable nutrient content.<ref name="Leichter et al. 2005">{{cite journal |last=Leichter|first=J. |author2=Deane G.|author3=Stokes M.|title=Spatial and Temporal Variability of Internal Wave Forcing on a Coral Reef|journal=Journal of Physical Oceanography|year=2005|volume=35 |issue=11|pages=1945–1962|doi=10.1175/JPO2808.1 |bibcode=2005JPO....35.1945L |s2cid=52498621 |url=https://cloudfront.escholarship.org/dist/prd/content/qt3c97637x/qt3c97637x.pdf |archive-url=https://ghostarchive.org/archive/20221009/https://cloudfront.escholarship.org/dist/prd/content/qt3c97637x/qt3c97637x.pdf |archive-date=2022-10-09 |url-status=live}}</ref> Arrival of cool, nutrient-rich water from depths due to internal waves and tidal bores has been linked to growth rates of suspension feeders and benthic algae<ref name="Leichter et al. 1998" /><ref name="Leichter et al. 2003" /><ref name="Smith et al. 2004">{{cite journal|last=Smith|first=J.|author2=Smith C.|author3=Vroom P.|author4=Beach K.|author5=Miller S.|title=Nutrient and growth dynamics of Halimeda tuna on Conch Reef, Florida Keys: Possible influence of internal tides on nutrient status and physiology|journal=Limnology and Oceanography|year=2004|volume=49|issue=6|pages=1923–1936|doi=10.4319/lo.2004.49.6.1923 |bibcode=2004LimOc..49.1923S|doi-access=free}}</ref>  as well as plankton and larval organisms.<ref name="Leichter et al. 1998" /><ref name="Pineda 1994">{{cite journal|last=Pineda|first=J.|title=Internal tidal bores in the nearshore: Warm-water fronts, seaward gravity currents and the onshore transport of neustonic larvae|journal=[[Journal of Marine Research]]|year=1994|volume=52|issue=3|pages=427–458 |doi=10.1357/0022240943077046}}</ref> The seaweed [[Codium|''Codium isthmocladum'']] reacts to deep water nutrient sources because their tissues have different concentrations of nutrients dependent upon depth.<ref name="Leichter et al. 2003" /> Aggregations of eggs, larval organisms and plankton on reefs respond to deep water intrusions.<ref name="Wolanski and Hamner 1988" /> Similarly, as internal waves and bores move vertically, surface-dwelling larval organisms are carried toward the shore.<ref name="Pineda 1994" /> This has significant biological importance to cascading effects of food chains in coral reef ecosystems and may provide yet another key to unlocking the paradox.

[[Cyanobacteria]] provide soluble [[nitrate]]s via [[nitrogen fixation]].<ref>{{cite journal | last1 = Wilson | first1 = E | year = 2004 | title = Coral's Symbiotic Bacteria Fluoresce, Fix Nitrogen | url = http://pubs.acs.org/cen/news/8233/8233notw7.html | journal = Chemical and Engineering News | volume = 82 | issue = 33| page = 7 | doi = 10.1021/cen-v082n033.p007a }}</ref>

Coral reefs often depend on surrounding habitats, such as [[seagrass meadow]]s and [[mangrove forest]]s, for nutrients. Seagrass and mangroves supply dead plants and animals that are rich in nitrogen and serve to feed fish and animals from the reef by supplying wood and vegetation. Reefs, in turn, protect mangroves and seagrass from waves and produce [[sediment]] in which the mangroves and seagrass can root.<ref name="Greenpeace">{{cite book |url={{google books |plainurl=y |id=Pik3MQAACAAJ}}|title=Greenpeace Book of Coral Reefs |first1=Sue |last1=Wells |first2=Nick |last2=Hanna | publisher=Sterling Publishing Company |year=1992 | isbn=978-0-8069-8795-8 }}</ref>

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