Reef Glossary

What does that term mean?



Acclimation: The process of making aquatic animals become accustomed to a different aquatic system.

Adductor muscle: the muscle found in bivalves used to hold each shell half together.

Aerobic: Utilizes oxygen for life processes.


Alkalinity: A measure of buffering capacity of water, also describes a state of high pH.

Allelopathy: Chemical warfare between some plants and aquatic animals.

Ambulacral: One of the five radial areas of the undersurface of the sea stars and echinoderms, from which the tube feet are protruded and withdrawn.

Ambulatory: Able to move around.

Anaerobic: Cannot function in the presence of oxygen.

Anoxic: In the presence of no oxygen.

Aperture: An opening, such as a hole, gap, or slit.



Aragonite: Calcareous sand or substrate.


Asexual: Having no sex, neither male nor female. A form of reproduction that requires neither male nor female sperm or eggs.

Atmospheres: A unit of pressure equal to the air pressure at sea level. It equals the amount of pressure that will support a column of mercury 760 millimeters high at 0 degrees Celsius under standard gravity, or 14.7 pounds per square inch (1.01325 × 105 pascals).

Atrium: A body cavity or chamber, especially either of the upper chambers of the heart that receives blood from the veins and forces it into a ventricle. Also called auricle.

Autotomy: The spontaneous casting off of a limb or other body part, such as the tail of certain lizards or the claw of a lobster, especially when the organism is injured or under attack.

Autotrophic: An organism capable of synthesizing its own food from inorganic substances, using light or chemical energy.

Axenic: Sterile.



Benthic: In association with sea-floor, describes flora and fauna found attached to or in association with the sea-floor.

Bioassay: Determination of the strength or biological activity of a substance, such as a drug or hormone, by comparing its effects with those of a standard preparation on a culture of living cells or a test organism. A test used to determine such strength or activity.

Bioluminescent: Describes animals and microbes that can produce their own light via chemical processes.

Biomass: The total mass of living matter within a given unit of environmental area.


Bleaching: A process by which those photosynthetic animals that contain zooxanthellae within their tissues will expel them, thus leading to a lack of pigmentation.

Blue Green Algae: See “Cyanobacteria”.

Budding: An asexual reproductive structure, as in yeast or a hydra, that consists of an outgrowth capable of developing into a new individual. To reproduce asexually by forming a bud.

Byssal: A mass of strong, silky filaments by which certain bivalve mollusks, such as mussels, attach themselves to rocks and other fixed surfaces.

Byssus: Opening that byssus threads are issued from to attach the living shell to the substrate.


Calcareous: (kal-KAR-ree-us) Formed of calcium.

Calcification: Impregnation with calcium or calcium salts, as with calcium carbonate. Hardening, as of tissue, by such impregnation.

Calcite: A common crystalline form of natural calcium carbonate, CaCO3, that is the basic constituent of limestone, marble, and chalk. Also called calcspar.

Calyces: A plural of calyx: a cuplike structure or organ, such as one of the cuplike divisions of the pelvis or of the kidney.

Carapace: A hard bony or chitinous outer covering, such as the fused dorsal plates of a turtle or the portion of the exoskeleton covering the head and thorax of a crustacean.

Cephala(o): From the Greek: kephale “head”, and meaning head, skull, or brain.



Chitinous: Substance that is formed of chitin.

Choanocytes: One of a layer of flagellated cells lining the body cavity of a sponge and characterized by a collar of cytoplasm surrounding the flagellum. Also called collar cell (as in sponges).

Chordates: That which possesses a spinal chord.

Chromatophores: Pigmented, voluntarily controlled cells by which many cephalopods are able to change their coloration for camouflage, to exhibit fright, anger, sexual receptiveness, et al.

Cilia: small, hairlike structures.

Ciliary feeder: That which utilizes cilia for feeding strategies.

Circumtropical: Around all tropical or equatorial areas.

Cirri: A tendril or similar part. A slender flexible appendage, such as the fused cilia of certain protozoans.



Cloaca: The common cavity into which the intestinal, genital, and urinary tracts open in vertebrates such as fish, reptiles, birds, and some primitive mammals.

Clonal: A cell, group of cells, or organism that are descended from and genetically identical to a single common ancestor, such as a bacterial colony whose members arose from a single original cell. An organism descended asexually from a single ancestor, such as a plant produced by layering or a polyp produced by budding.

Coelom: The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. Also called body cavity.

Collar cells (in sponges): See choanocytes.

Commensal: Of, relating to, or characterized by a symbiotic relationship in which one species is benefited while the other is unaffected.

Cometary fission:

Conotoxin: Toxin found within the venom utilized by the Cone Snail.

Corallimorphs: Coral-like animals, such as “mushrooms”.

Coralline algae: An encrusting microalgae that utilizes calcium to grow, often found in pleasing colors of red, purple, and others.

Crepuscular: Active during twilight and predawn hours.

Cryptic: Animals “in disguise”, describes flora and fauna that blends into its background.

Ctenida: Gills found in bivalves.

Cyanoacrylate: Superglue.

Cyanobacteria: A photosynthetic bacterium of the class Coccogoneae or Hormogoneae, generally blue-green in color and in some species capable of nitrogen fixation. Cyanobacteria were once thought to be algae; also called blue-green algae.


Demersal: Dwelling at or near the bottom of a body of water. Sinking to or deposited near the bottom of a body of water.

Detritus: Accumulated material.

Detritivores: Flora and fauna (more usually fauna) that consume detritus.

Diatom: Microscopic one-celled or colonial algae having cell walls of silica.

Digitate: Having digits or fingerlike projections.

Dinoflagellate: Any of numerous minute, chiefly marine protozoans of the order Dinoflagellata, characteristically having two flagella and a cellulose covering and forming one of the chief constituents of plankton.

Dioecious: Separate sexes.

Diurnal: Active during daylight hours.

DOC: Dissolved Organic Compounds.

Drip acclimation: Method for slow, even acclimation of aquatic specimens


Ecdysis: The shedding of an outer integument or layer of skin, as by insects, crustaceans, and snakes; molting.

En masse spawn: An event where all or many local creatures are stimulated to spawn at once.

Endoperoxide synthetase:


Epiphytes: A plant, such as a tropical orchid or a staghorn fern, that grows on another plant upon which it depends for mechanical support but not for nutrients.

Epipodium: One of the lateral lobes of the foot in certain gastropods.


Estuary: The part of the wide lower course of a river where its current is met by the tides. An arm of the sea that extends inland to meet the mouth of a river.

Excurrent: Outflow.

Exhalent: An organ, such as the siphon of a clam, that is used for exhalation.

Extant: Still in existence; not destroyed, lost, or extinct.

Exudation: The act or an instance of oozing forth. An exudate.


Fallow: To let lie quiet, in aquaristics it is to allow a tank to run with no life, more often specifically with no vertebrate life.

Family: A taxonomic category of related organisms ranking below an order and above a genus.

Fileclams: scallops.

Filter Feeder: An animal whose feeding strategy is to filter out particulate matter, including planktonic life forms, from the water column.

Fission: Division. An asexual reproductive strategy.

Flagella: A long, threadlike appendage, especially a whiplike extension of certain cells or unicellular organisms that functions as an organ of locomotion.



Fragmentation: A means of artificial reproduction by which sections or segments of a cnidarian (corals) is divided, cut, or broken into pieces from which a new colony is grown.

Frags: Refers to fragments taken from (largely) stony corals that are then used to propagate more coral colonies.


Gametes: A reproductive cell having the haploid number of chromosomes, especially a mature sperm or egg capable of fusing with a gamete of the opposite sex to produce the fertilized egg.

Ganglia: A brain-like assemblage of nerve cells found in cephalopods.

Genus: A taxonomic category ranking below a family and above a species and generally consisting of a group of species exhibiting similar characteristics.

Glitter lines:

Gonads: Sexual organs.

Gratis: Without charge.



Hemophilia: A state in which the blood fails to clot.

Hermaphrodite: That which possesses both male and female sexual organs.


Heterotrophic: An organism that cannot synthesize its own food and is dependent on complex organic substances for nutrition; heterotroph.



Hydrogen peroxide: H2O2

Hyponome: Modified “tentacle” found within the mantles of cephalopods by which they draw in and expel water forcibly to create propulsion.


Infauna: Aquatic animals that live in the substrate of a body of water, especially in a soft sea bottom.

Intertidal: Of or being the region between the high tide mark and the low tide mark.

Incurrent: Affording passage to an inflowing current






Labial palps: An elongated, often segmented appendage usually found near the mouth in invertebrate organisms such as mollusks, crustaceans, and insects, the functions of which include sensation, locomotion, and feeding. Also called palpus. Of or relating to the lips or labia.

Laminar: A thin scalelike or platelike structure, as one of the thin layers of sensitive vascular tissue in the hoof of a horse.

LPS: Large Polyp Stony coral.





Mantle: The flesh/tissue of mollusks.


Maxilliped: One of the three pairs of crustacean head appendages located just posterior to the maxillae and used in feeding.


Meroplankton: Any of various organisms that spend part of their life cycle, usually the larval or egg stages, as plankton.

Mesenterial filaments:

Metabolites: A substance produced by metabolism. A substance necessary for or taking part in a particular metabolic process.

Microalgae: Algal form only visible with a microscope.


Midden: Trash pile.


Morphology: The branch of biology that deals with the form and structure of organisms without consideration of function. The form and structure of an organism or one of its parts: the morphology of a cell; the morphology of vertebrates.

Motile: Mobile, movable. Moving or having the power to move spontaneously.

Mutualism: An association between organisms of two different species in which each member benefits.


Nanoplankton: Very small plankton. Plankton of minute size, especially plankton composed of organisms measuring from 2 to 20 micrometers

Necrosis: The process of tissue die-off. Death of cells or tissues through injury or disease, especially in a localized area of the body

Necrotic: Dead or dying tissue.

Nekton: The collection of marine and freshwater organisms that can swim freely and are generally independent of currents, ranging in size from microscopic organisms to whales.

Nematocysts: A capsule within specialized cells of certain coelenterates, such as jellyfish, containing a barbed, threadlike tube that delivers a paralyzing sting when propelled into attackers and prey. Also called stinging cell.


NSW: Near Sea Water (in regards to water quality parameters).

Nori: A type of prepared Japanese seaweed used to wrap sushi. Also spelled noori.


Obligate: Able to exist or survive only in a particular environment or by assuming a particular role: an obligate parasite; an obligate anaerobe.

Ocellated: having one or more pairs of eyespots. Theorized to be used to confuse any possible predators.


Oolitic: Rock, usually limestone, composed of oolites. A small round calcareous grain found, for example, in limestones.

Operculum: A platelike covering, for gills in vertebrate fishes, or as found in snails.

Oral disc:

Order: A taxonomic category of organisms ranking above a family and below a class.

Organic dyes:

Oscula: The mouthlike opening in a sponge, used to expel water. Also called the osculum.

Osmoregulation: Maintenance of an optimal, constant osmotic pressure in the body of a living organism.

Osmosis: Diffusion of fluid through a semipermeable membrane from a solution with a low solute concentration to a solution with a higher solute concentration until there is an equal concentration of fluid on both sides of the membrane.

Osmotic shock:

Ossicles: Small bones.

Ostia: A small opening or orifice, as in a body organ or passage. Any of the small openings or pores in a sponge.

Ovary: The usually paired female or hermaphroditic reproductive organ that produces ova and, in vertebrates, estrogen and progesterone.




Pathogen: An agent that causes disease, especially a living microorganism such as a bacterium or fungus

Pelagic: Of, relating to, or living in open oceans or seas, ocean-going.

Photic zone:


Photocells: Light sensitive cells that function almost like eyes.


Photosynthetic: That which uses the process of photosynthesis to live and gain energy through utilization of sunlight.

Phragmocone: The chambers of a Nautilus’ shell, further divided into partitions by septa.

Phylum: A primary division of a kingdom, as of the animal kingdom, ranking next above a class in size.

Phytoplankton: Minute, free-floating aquatic plants.

Photosynthesis: The process in green plants and certain other organisms by which carbohydrates are synthesized from carbon dioxide and water using light as an energy source. Most forms of photosynthesis release oxygen as a byproduct.

Pinnules: A featherlike or plumelike organ or part, such as a small fin, or one of the appendages of a crinoid.

Piscine: Fish-like, or fish. Of, relating to, or characteristic of a fish or fishes.

Planktivorous: Plankton-eating, as in carnivorous (meat-eating).

Plankton: The collection of small or microscopic organisms, including algae and protozoans, that float or drift in great numbers in fresh or salt water, especially at or near the surface, and serve as food for fish and other larger organisms.

Plankton reactor:

Planulae: The flat, free-swimming, ciliated larva of a coelenterate.


Podia: Structure resembling or functioning as a foot.

Polymorphic: The occurrence of different forms, stages, or types in individual organisms or in organisms of the same species, independent of sexual variations.


Positively Rheotactic: From rheotaxis– Movement of an organism in response to a current of water or air.

Predation: The capturing of prey as a means of maintaining life.

Propagation: Multiplication or increase, as by natural reproduction, or fragmentation.

Prostaglandin: Any of a group of potent hormonelike substances that are produced in various (usually mammalian) tissues, are derived from arachidonic acid, and mediate a wide range of physiological functions, such as control of blood pressure, contraction of smooth muscle, and modulation of inflammation.

Protein skimming: A.k.a. foam fractionation–a form of chemical and particulate filtration by which super-fine bubbles are created in a reaction chamber. Dissolved organic compounds then attach their hydrophobic ends onto the air bubbles and are carried up the chamber into a collection cup.

Proteinaceous: Contained or composed of protein molecules. In feeding, meaning meaty foods.

PVC: Polyvinyl chloride.


Quarantine/QT: A condition of enforced isolation.


Radula: A flexible tonguelike organ in certain mollusks, having rows of horny teeth on the surface.

Random turbulent:


Redox: Oxidation-reduction.

Refugia: An area that provides a suitable habitat for species.


Regenerate: To regrow.

Respiratory pores:

Respiratory trees:


Saturation point:

Scute: A horny, chitinous, or bony external plate or scale, as on the shell of a turtle or the underside of a snake. Also called scutum.

Sedentary: Remaining or living in one area, as certain birds; not migratory. Attached to a surface and not moving freely, as a barnacle.

Sedimentation: The act or process of depositing sediment.

Senescence: The process or state of growing old; the onset of old age.

Sepia: The liquid exuded by squid or octopus (usually when fleeing) called “ink”. A highly concentrated solution of the pigment melanin and mucus and tyrosinase.

Septa: The partitions found within a Nautilus’ chambers (phragmocone).

Septum: A thin partition or membrane that divides two cavities or soft masses of tissue in an organism

Sessile: Permanently attached or fixed; not free-moving.

Setae: A stiff hair, bristle, or bristlelike process or part on an organism.

Siltation: To fill, cover, or obstruct with silt, the process of.

Siliceous: Containing, resembling, relating to, or consisting of silica.

Siphon: A tubular organ, especially of aquatic invertebrates such as squids or clams, by which water is taken in or expelled.

Siphuncle: The tube that passes through all chambers of the shell of Nautilus, which is used to control the flow of internal water and gas to maintain and control buoyancy.

Slough: To shed.


Spicules: A small needlelike structure or part, such as one of the silicate or calcium carbonate processes supporting the soft tissue of certain invertebrates, especially sponges.

Spirulina: A microalgae.

Spongin: A horny, sulfur-containing protein related to keratin that forms the skeletal structure of certain classes of sponges.

SPS: Small Polyp Stony coral

Subclass: A taxonomic category of related organisms ranking between a class and an order.

Substrate: A surface on which an organism grows or is attached. An underlying layer; a substratum.

Subtidal: Unaffected by tidal changes; residing in areas that do not experience periods of exposure due to changes in tide.

Sump: A low-lying place, such as a pit (or in this case anything that holds water), that receives drainage.

Surge flow:

Symbiotic: A close, prolonged association between two or more different organisms of different species that may, but does not necessarily, benefit each member. Symbiosis.

Symptomatically: Of, relating to, or based on symptoms.


Taxa: Plural of taxon. A taxonomic category or group, such as a phylum, order, family, genus, or species.

Taxonomy: The classification of organisms in an ordered system that indicates natural relationships.

Trochophore: The small, free-swimming, ciliated aquatic larva of various invertebrates, including certain mollusks and annelids.

Trophic level:

Turbidity: Relating to the visibility within a body of water. Having sediment or foreign particles stirred up or suspended

Turbulent flow:

Turf algae:

Turgid: Swollen or distended, as from a fluid; bloated.



Vacuolations: From vacuole: A small cavity in the cytoplasm of a cell, bound by a single membrane and containing water, food, or metabolic waste.

Vascular: Of, characterized by, or containing vessels that carry or circulate fluids, such as blood, lymph, or sap, through the body of an animal or plant.

Veliger: A larval stage of a mollusk characterized by the presence of a velum.

Velum: A ciliated swimming organ that develops in certain larval stages of most marine gastropod mollusks. A covering or partition of thin membranous tissue, such as the veil of a mushroom or a membrane of the brain.


Water column:




Zooplankton: Plankton that consists of animals, including the corals, rotifers, sea anemones, and jellyfish.

Zooxanthellae: Any of various yellow-green algae that live symbiotically within the cells of other organisms, such as those of certain radiolarians and marine invertebrates.