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

Ahermatypic: Corals that do not build reefs

Alkalinity: A measure of buffering capacity of water

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the five radial areas of the undersurface of the sea stars and echinoderms, from which the tube feet are protruded and withdrawn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: Living in the absence of both free and bound oxygen

Anoxic: An absence of free oxygen

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

Aposymbiotic: When symbiotic organisms live apart from one another (for example, a clownfish living independently of a sea anemone)

Aquaristic: A curator, collector, or ichthyologist associated with an aquarium

Aragonite: Calcareous sand or substrate

Asexual: A type of reproduction that does not involve the fusion of gametes or change in the number of chromosomes. The offspring that arise by asexual reproduction inherit the full set of genes of their single parent

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: 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

Azooxanthellate: A coral that lacks symbiotic zooxanthellae


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

Bio-minerals: Biominerals are natural composite materials based upon biomolecules (such as proteins) and minerals produced by living organisms via processes known as biomineralization, yielding materials such as bones, shells and teeth

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:<?strong> Several species of bacteria that produce blue-green colored pigments. They grow in salt water and some large fresh water lakes

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


Calcareous: 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

Cephalotoxins: A poison, believed to be a protein, found in the salivary glands of cephalopods

Chitin: A polysaccharide which is a primary component of cell walls in fungi, the exoskeletons of arthropods, such as crustaceans and insects, the radulae of molluscs, cephalopod beaks, and the scales of fish

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: Animals having a notochord, as the lancelets and tunicates, as well as all the true vertebrates, including fish, amphibians, reptiles, birds, and mammals

Chromatophores: Cells that produce color, of which many types are pigment-containing cells, or groups of cells, found in a wide range of animals including amphibians, fish, reptiles, crustaceans and cephalopods

Cilia: Small, hairlike structures

Ciliary feeder: That which utilizes cilia for feeding strategies

Circumtropical: Around tropical or equatorial areas

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

CITES: The Convention on International Trade in Endangered Species of Wild Fauna and Flora, a multilateral treaty to protect endangered plants and animals

Chelipeds: One of the pair of legs that bears the large chelae (claw or pincher) in decapod crustaceans

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. Also called body cavity

Collar cells: A flagellated endodermal cell that lines the cavity of a sponge and has a contractile protoplasmic cup surrounding the flagellum. Also called choanocyte

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

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 blend into their backgrounds

Ctenida: Respitory organ or 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

Endosymbiotic: A symbiotic association in which one or more organisms live inside another, such as single-cell algae inside reef-building corals

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

Errantiate: A class of Polychaetous Annelids. Characteristics include numerous, similar segments, well-developed lateral processes. Have definitive “heads” with a pharynx with jaws or teeth. Include swimming, crawling, burrowing and tube-dwelling members

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


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

Flocculant: A substance added to a suspension to enhance aggregation of the suspended particles

Filtrants: The liquid or solution that has passed through a filter, and which has been separated from the filtride

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: Glitter lines are caused by focusing and de-focusing of light by ‘lensing’ (both concave and convex) action of water surface waves, and add a nice effect to any reef aquarium

Gonads: Sexual organs

Gratis: Without charge

Greenwater: Aquarium water that turns green due to green algae


Hemophilia: A state in which the blood fails to clot

Hermaphrodite: That which possesses both male and female sexual organs

Hermatypic: Hermatypic corals are those corals in the order Scleractinia which build reefs by depositing hard calcareous material for their skeletons, forming the stony framework of the reef

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

Holdfast: A root-like structure that anchors aquatic sessile organisms, such as seaweed, other sessile algae, stalked crinoids, benthic cnidarians, and sponges, to the substrate

HUFA: Highly unsaturated fatty acids

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



Kalkwasser:Kalkwasser is German for limewater. Limewater, AKA kalk, is a highly concentrated solution of calcium hydroxide Ca (OH)

Kelvin:The SI base unit of thermodynamic temperature (equivalent in size to the degree Celsius), first introduced as the unit used in the Kelvin scale


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

Laminar: Flow where fluid particles follow smooth paths in layers

LPS: Large Polyp Stony coral


MACNA:The Marine Aquarium Conference of North America, an annual event

Macroalgae:Macroalgae is a large, plant-like form of algae. Another name for macroalgae is seaweed. Like the nuisance algae, macroalgae feeds off the nutrients in the water

Macrophagous:feeding on relatively large particulate matter

Mantle:a significant part of the anatomy of molluscs: it is the dorsal body wall which covers the visceral mass and usually protrudes in the form of flaps well beyond the visceral mass itself

MASNA:a non-profit organization composed of marine aquarium clubs, individual hobbyists, and industry partners from North America and abroad, totaling several thousand individuals

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

Meiofauna:Small benthic invertebrates that live in both marine and fresh water environments. The term meiofauna loosely defines a group of organisms by their size, larger than microfauna but smaller than macrofauna, rather than a taxonomic grouping

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

Mesenterial filaments:String-like extensions of the mesenteries—the internal folds of tissue which create structure within a coral polyp’s body. They are typically bright white and full of nematocysts—specialized stinging cells that corals use to capture and kill prey, and to sting their competitors

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

Microphagous:feeding on minute particles or microorganisms

Midden: Trash pile

Mixotrophic:An organism that can use a mix of different sources of energy and carbon, instead of having a single trophic mode

Morphology: The branch of biology that deals with the form and structure of organisms without consideration of function

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: 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

Nitrate: A polyatomic ion with the chemical formula NO−3. Salts containing this ion are called nitrates

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

Nori: A type of prepared Japanese seaweed used to wrap sushi


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

Octocoral: A subclass of Anthozoa comprising around 3,000 species of water-based organisms formed of colonial polyps with 8-fold symmetry

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: The more or less flattened upper or free end of the body bearing the mouth in its center and tentacles near or at its border in most polyps

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

Oscula: The mouthlike opening in a sponge, used to expel water and waste

Osmoregulation: Maintenance of an optimal, constant osmotic pressure in the body of a living organism to maintain the homeostasis of the organism’s water content; that is, it maintains the fluid balance and the concentration of electrolytes

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: Physiologic dysfunction caused by a sudden change in the solute concentration around a cell, which causes a rapid change in the movement of water across its cell membrane. Under conditions of high concentrations of either salts, substrates or any solute in the supernatant, water is drawn out of the cells through osmosis

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


Papillations: Small fleshy projections

P.A.R.:Photosynthetic Active Radiation (PAR) is a term used within the reef tank community when talking about lighting

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

Photic zone: The uppermost layer of a body of water that receives sunlight, allowing phytoplankton to perform photosynthesis

Photoadaptation: Adaptation of an organism to the changing amount of light in its environment

Photocells: Light sensitive cells that function almost like eyes

Photoinhibition: Light-induced reduction in the photosynthetic capacity of a plant, alga, or cyanobacterium

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: A simple system for producing plankton in a natural food chain. Within the plankton light reactor, micro-algae are produced with light, fertilizer and CO2

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

Plenum: In aquarium filtration, an open space under a layer of gravel or sand

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

Porocytes: Tubular cells which make up the pores of a sponge known as ostia

Positively Rheotactic: The ability to orient into currents

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. PVC comes in two basic forms: rigid (sometimes abbreviated as RPVC) and flexible. The rigid form of PVC is used in construction for pipe and in profile applications such as doors and windows


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: A fluid motion with particle trajectories varying randomly in time, in which irregular fluctuations of velocity, pressure and other parameters arise

Redox:  A type of chemical reaction in which the oxidation states of atoms are changed. Redox reactions are characterized by the actual or formal transfer of electrons between chemical species

Refugia: An area that provides a suitable habitat for species

Refugium: A typical refugium setup includes a bed of fine sugar sand or miracle mud for beneficial bacteria, a macroalgae like chaeto, and some small live rock. A refugium light supports the macroalgae, which sucks up nutrients to prevent nuisance algae

Regenerate: To regrow

Respiratory pores: A part of the respiratory system of gastropods

Respiratory trees: Also known as the tracheobronchial tree, branches at the bottom of the trachea, at a forked membrane called the carina


Saturation point: The point at which a substance will receive no more of another substance in solution, chemical combination, etc

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

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 bristle-like 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

Slurried: A mixture of solids denser than water suspended in liquid, usually water

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:/strong> 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: A transient flow event that occurs in internal flow systems such as flow in piping systems or flow in compressors

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

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: The trophic level of an organism is the position it occupies in a food web

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

Turbulent flow: Flow in which the fluid undergoes irregular fluctuations, or mixing, in contrast to laminar flow, in which the fluid moves in smooth paths or layers. In turbulent flow the speed of the fluid at a point is continuously undergoing changes in both magnitude and direction

Turf algae: A somewhat broad category consisting of many different forms, i.e., finely branched delicate structures; short and stubby tubular forms; thick grass-like mats; and, both low and/or tall growing forms consisting of leafy lettuce or cabbage-like structures

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



Vacuolations: 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: The final larval stage of certain mollusks, having two ciliated flaps for swimming and feeding

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: Conceptual column of water from the surface to the bottom of a body of water




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