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Glossary of Terminology: S

The glossary is organized alphabetically by page -- A through Z. Literature sources are listed on the References Page.

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Number of records found : 441


S phase - the cell cycle phase during which the DNA doubles with replication of the chromosomes

sabellid worm - a marine polychaete worm in the family Sabellidae which lives in flexible tubes constructed of sand grains embedded in mucus

saccate - sac-like

safety stop - on ascending from a dive, a safety stop is a specified time spent by a scuba diver at a specific depth, for nitrogen off-gassing. While not mandatory during a no-decompression dive, it is a sound safety practice. A safety stop may be 3-5 minutes at 10-15 ft below the surface

sagittal - relating to the sagittal plane, which extends through the midline of a bilateral animal, dividing it into two equal halves

sagittal section - a section sliced parallel to the longitudinal axis of the animal or structure examined

sagittiform - arrow-shaped

Saharan dust - large quantities of dust, originating in the Sahara desert of Africa, are blown across the Atlantic Ocean each summer, and may be a contributing factor for the declining health of Caribbean coral reefs. The dust may modify clouds and rainfall both in Africa and across the tropical North Atlantic as far away as Barbados. Other studies suggest that the dust may play a role in determining the frequency and intensity of hurricanes formed in the eastern Atlantic Ocean

salinity - a measure of the salt concentration of water

Image of salt marsh

A salt marsh. (Photo: NOAA)


salt marsh - a marsh periodically flooded by marine water

sampling - the probabilistic, systematic, or judgmental selection of a sub-element from a larger population, with the aim of approximating a representative picture of the whole

sampling bias - the tendency of a sample to exclude some members of the sampling universe and over-represent others

sampling error - the variability of a statistic from sample to sample due to chance

sampling unit - the sub-element of the total population selected for sampling

sampling universe - the largest entity to be described, of which the sample is a part

Image of sand and seagrass

Tidal current patterns in the sand and sea grass at low tide.


sand - coarse sediment typically found in areas exposed to currents and wave energy

Image of sand flat with patch reef

A patch reef surrounded by sand flats. (Photo: http://www.biosbcc.net)


sand flat - sandy areas found in depressions and gullies in a coral reef, or between patch reefs, or in deeper areas below or beyond the reef. Seemingly near barren during the day, at night sand flats teem with biological activity; also a sandy tidal flat barren of vegetation. A tidal flat is an extensive, nearly horizontal, marshy or barren tract of land that is alternately covered and uncovered by the tide. It consists of unconsolidated sediment (mostly mud and sand)

sandflat - a flat expanse of sand on the coast or in an estuary

sanguivore - an animal that obtains its nourishment primarily as blood

sanguivore - an organism feeding principally on blood

saprophyte - any plant that lives and feeds on dead organic matter

saprotroph - an organism which feeds on dead and decaying organisms, allowing the nutrients to be recycled into the ecosystem. Fungi and bacteria are two groups with saprophytic members

sasi - a generic name for an indigenous and historic family of Indonesian cultures, institutions, laws, and ritual practices that regulate access to natural resources, including coral reefs and other ecological systems. During recent years, a movement has developed to support indigenous Indonesian cultural communities, Indonesian NGOs, and the Ministry of the Environment by promoting sasi as an environmental institution and body of customary law promoting sustainable development, conservation, and social equity.

satellite - a small celestial body orbiting a larger one; a man-made object designed to orbit a celestial body

satellite colony - a colony that develops within the tissue of a parent colony and which has its own unattached skeleton

GOES-8 image of airborne dust

GOES-8 (May 1999) image of airborne dust over the Caribbean Sea. This dust originated in the Sahara Desert where it was carried off the coast by strong winds.


satellite imagery - a representation of the measurement of energy emitted or reflected by the Earth in a variety of wavelengths. Earth observation imagery takes a number of forms, of which the most traditional are optical and near-infrared radiation, from about 0.4 (blue) to 2.0 (IR) micrometers. Apart from visual and near-infrared, other bands of the spectrum commonly used include thermal infrared (heat) and microwave (radar). Each of these has its own applications

satellite mapping - digital maps derived from satellite images

saturation - in diving, the degree to which a gas is dissolved in the blood or other tissues. Full saturation occurs when the pressure of gas dissolved in the blood or tissues is the same as the ambient pressure of that gas

saturation diving - the situation where a diver is at a depth or pressure for a long enough period of time (12 hours or longer) to have the partial pressures of the dissolved gases in the body at equilibrium with the partial pressure of the gases in the surrounding environment. Scientists are able to live in and work around underwater habitats for extended periods without the risk of developing decompression sickness (the bends). Divers breathe compressed air mixed with light, inert gases, such as helium. When the diver's blood becomes saturated with helium, the time required for decompression, even if the diver returns to the surface after a period of weeks, is no greater than that required after a dive lasting just a few hours

saxitoxin - a powerful biotoxin produced by bacteria in certain marine dinoflagellates. Saxitoxin may be concentrated in the tissues of filter feeding shellfish, and results in shellfish poisoning when ingested by humans; also known as mytilotoxin

scale - the degree of resolution at which ecological processes, structures, and changes across space and time are observed and measured

scale-like corallites - corallites that form a pattern which resembles fish scales

Example of scatter diagram

A scatter diagram.


scatter diagram - a two-dimensional histogram showing the joint probability density of two variables within a data sample; it is used to interpret data by graphically displaying the relationship between two variables

Image of feeding falcon

A scavenger feeding on a dead aquatic animal.


scavenger - an animal that feeds on dead or decaying organic matter

schizocoelous - the mesoderm and coelom initially develop from a solid block of mesodermal tissue in an embryo that subsequently develops a split down the middle.The cavity thus formed is the coelom. Schizocoelous development of the coelom occurs in protostomes

Image of school of reef fish

A school of smallmouth grunt with elkhorn coral in the background. (Photo: Paige Gill, Florida Keys NMS)


school - a social group of fishes (and some other aquatic animals), usually of the same species, which tends to orient and move in the same direction

schreckreaktion - an alarm response in some fishes as a result of an alarm substance (schreckstoff), or alarm pheromone being introduced into the water via rupture of specialized dermal club cells. Presumably a fish attacked by a predator releases schreckstoff into the water, resulting in the conspecifics making a variety of coordinated escape or fright actions

schreckstoff - a chemical alarm substance (a pheromone) produced by the skin of some groups of fishes when injured. It stimulates conspecifics and perhaps some other fishes to exhibit fright and escape movements

science - a method of learning about the physical universe by applying the principles of the scientific method, which includes making empirical observations, proposing hypotheses to explain those observations, and testing those hypotheses in valid and reliable ways; also refers to the organized body of knowledge that results from scientific study

scientific law - a statement of a scientific fact or phenomenon that is invariable under given conditions. A law may be either quantitative (including measurement) or qualitative (general characteristics). It must describe evidence that has been gathered using acceptable scientific standards of reproducibility. Examples of scientific laws: Faraday’s Law of electromagnetic induction, Coulomb’s Law of electrostatic attraction, Dalton’s Law of partial pressures, and Boyle’s Gas Law

scientific name - the Linnaean binomial. A name of a species composed of two words: the genus (or generic) name and the species (or trivial) name, e.g., Acropora palmata. The scientific name is always written in italics. The first letter of the generic name is always capitalized; that of the species name is never capitalized

sciophilous - thriving in conditions of low light intensity

Image of elkhorn coral

A scleractinian - elkhorn coral (Acropora sp.)


Scleractinia - an order of Cnidaria, usually producing calcareous skeletons with hexameral symmetry

sclerite - a skeletal element in octocorals. Sclerites are composed of calcite spicules; also, a hard plate or element of the exoskeleton of some arthropods

scleroblast - a cell that produces a sclerite

sclerocyte - a cell in sponges that produces spongin or spicules

sclerodermite - the basic unit of coral skeletal microstructure. A center of calcification from which bundles of acicular aragonite crystals radiate outward; the hard integument of Crustacea.

scleroseptum - one of many radiating calcareous partitions in the skeletal cup (corallite) of stony corals

Image of tapeworm scolex

The scolex of the tapeworm, Taenia solium. (Photo: Center for Disease Control)


scolex - the knoblike anterior end of a tapeworm, having suckers and/or hooklets that, in the adult stage, serve as organs of attachment to the host organism

scorpionfish - any of about nearly 400 species of bony fishes in the family Scorpaenidae. Scorpionfishes have large, heavily ridged and spined heads.They possess venomous spines on their dorsal fins, each with a groove and venom sac. Scorpionfishes are well camouflaged to blend in with their environment with fleshy projections and background coloration. Some can change their color to better match their surroundings. The most venemous fish in the world, the reef stonefish (Synanceia verrucosa), is disguised to look like a encrusted rock or lump of coral. This species is widely distributed throughout tropical, marine waters of the Indo-Pacific. Most species of scorpionfishes are demersal, living on or near the bottom. They are carnivorous ambush predators feeding on crustaceans, cephalopods and fishes

scotoscope - an instrument for detecting objects in darkness

Image of SCUBA diver

Diver training with a full face mask and underwater communications.


SCUBA (Self-Contained Underwater Breathing Apparatus) - a diving mode independent of surface air supply in which the diver uses open circuit self-contained underwater breathing apparatus which supplies air or breathing gases at ambient pressure

Image of a sea turtle

Sea turtle with shell comprised of hard, platelike scutes.


scute - an external horny, chitinous or bony plate or scale, such as those on the shell of a turtle

scutiform - shield-shaped

sea - a subdivision of an ocean

Image of two manatees

The West Indian Manatee, Trichechus manatus, in Florida bay. (Photo: Copyright Laurel Canty-Ehrlich, NOAA)


sea cow - a large, herbivorous aquatic mammal of the order Sirenia that contains two Recent families: Dugongidae for the genera Dugong (dugong, one species) and Hydrodamalis (Steller's sea cow, one species hunted to extinction); and Trichechidae for the single genus Trichechus (manatees, three species). The dugong inhabits coastal regions in the tropical parts of the Old World, and some individuals go into estuaries and rivers. Steller's sea cow inhabited the Bering Sea, and was the only Recent member of this order adapted to cold waters. Manatees live along the coast and in coastal rivers in the southeastern United States, Central America, the West Indies, northern South America, and western Africa

sea cucumber - an echinoderm in the class Holothuroidea. Sea cucumbers possess a flexible, elongated body and leathery skin, and tentacles surrounding the mouth. Although they don't superficially resemble other members of the phylum Echinodermata, they retain pentameral (five-rayed) symmetry, with five rows of tube feet running from the mouth down along the sides of the body. Sea cucumbers are an abundant and diverse group that are found in nearly every marine environment, but are most diverse on tropical, shallow-water coral reefs.They are economically important in two main ways. They produce chemical compounds that are of interest to pharmaceutical firms, and as a food item in Asia, they form the basis of a multimillion-dollar industry that processes the body wall for sale as beche-de-mer or trepang

sea pansy - a soft coral in the order Pennatulacea and subclass Alcyonaria. A sea pansy is a colony of polyps having different forms and functions. A single, leaf-like, giant primary polyp up to two inches in diameter forms the anchoring stem (peduncle). This peduncle can be distended to better anchor the colony in the substrate.The primary polyp possesses secondary polyps, autozooids (feeding polyps) and siphonozooids (serve as intakes for water, which circulates within the colony and helps keep it upright) on the upper surface.The sea pansy is bioluminescent when disturbed, due to Green Fluorescent Protein.

sea pen - a soft coral in the order Pennatulacea and subclass Alcyonaria. Sea pens are colonial octocorals which exhibits polyp dimorphism. One polyp grows very large, loses its tentacles and forms a central axis. The base of this primary polyp forms a bulb which may be expanded or contracted. The bulb is used to anchor the colony. Branching off this primary polyp are various secondary polyps. Some, called autozooids, are typical feeding polyps. Others, called siphonozooids, serve as intakes for water, which circulates within the colony and helps keep it upright. Calcareous spicules and frequently a central axial rod of calcium carbonate also provide support. One group of sea pens have secondary polyps grouped into "polyp leaves," giving these species a feather-like appearance, from which we get the common name as they look something like old-fashioned quill pens. Most species, however, do not have polyp leaves, and look more like clubs, umbrellas, or pinwheels

Image of a sea snake

This sea snake was photographed and released during a 1998 cruise of the NOAA ship McARTHUR to South America.


sea snake - a member of the family Hydophiidae. Sea snakes are common in the Indo-Pacific. Related to cobras, these live-bearing reptiles are highly venomous but not aggressive by nature

sea star - an echinoderm characterized by radial symmetry, and usually with five arms (rays) radiating from a central body. Minute pincer-like structures on the arms, called pedicellaria, ensure that the surface of the arms stay free from algae. There are a few sea stars that have 6 or 7 arms, and some with even more. Injuries will also cause more arms to grow. The majority of sea stars are carnivorous and feed on sponges, bryozoans, ascidians and mollusks. Other are detritus feeders or scavengers. Some sea stars, for example the crown-of-thorns that feeds on coral polyps, are specialized feeders; also called "starfish"

Image of fishing boat in rough seas

Fishing vessel battles through rough conditions (sea state). (Photo: NOAA/National Weather Service/Ocean Prediction Center)


sea state - a description of the sea surface with regard to wave action

Sea Surface Temperature (SST) - the temperature of the layer of seawater (approximately 0.5 m deep) nearest the atmosphere

sea urchin - sea urchins are echinoderms in the class Echinoidea, that possess a hard calcareous shell (test) armed with spines, which may be long and pointed, or short and pointed, or dull. The spines are used for locomotion (along with tube feet), protection, and for trapping drifting food particulates, such as algae. Most sea urchins are algal grazers but some feed on sponges, ectoprocts and ascidians, and others on detritus. Sea urchins help to keep corals free of overgrowing algae

seabed - the ocean floor

Seaflower Biosphere Reserve - This reserve is locatred at the Archipelago of San Andrés, Providencia and Santa Catalina, at the southwestern Caribbean, off the East coast of Nicaragua, halfway between Colombia and Jamaica. As a marine biosphere reserve, it covers approximately 10% of the Caribbean sea, with three main islands, surrounded by coastal mangroves swamps and highly intact and productive associated coral reef ecosystems. The old Providence barrier reef alone is 32 km long and covers an area of 255 Km2 making it one of the largest coral reefs in the Americas. It is identified as a major site of coral and fish diversity and is considered a biodiversity “hotspot”

Image of seagrass bed

Seagrass bed.


seagrass - a flowering plant, complete with leaves, a rhizome (an underground, usually horizontally-oriented stem) and a root system. They are found in marine or estuarine waters. Most seagrass species are located in soft sediments. However, some species are attached directly to rocks with root hair adhesion. Seagrasses tend to develop extensive underwater meadows

SeaGrass Net - a worldwide monitoring program that investigates and documents the status of seagrass resources and the threats to this important and imperiled marine ecosystem. The program started in 2001 in the Western Pacific and now includes 110 sites in 30 countries with a global monitoring protocol and web-based data reporting system

Seagrass Watch - a community-based monitoring program developed by Queensland's Department of Primary Industries and Fisheries (QDPI&F) in conjunction with community groups. Seagrass-Watch collects data about the condition and trend of near-shore seagrasses throughout Queensland and provides an early warning of major changes in seagrass abundance, distribution and species composition

Image of C-MAN Station

Coastal-Marine Automated Network (C-MAN) Station.


SEAKEYS - NOAA and the Florida Institute of Oceanography (FIO) supply daily and historical enhanced Coastal-Marine Automated Network (C-MAN) data via the SEAKEYS program. Since 1992, SEAKEYS has provided hourly data from up to seven meteorological and oceanographic monitoring stations situated throughout the Florida Keys National Marine Sanctuary and Florida Bay. These stations measure the usual C-MAN meteorological parameters, such as wind speed, gusts and barometric pressure, but are enhanced with oceanographic instruments measuring salinity, sea temperature, fluorometry and turbidity These data are collected and presented via email and the Web daily, and are supplied through a historical database on the Web. Unique software developed for SEAKEYS data operates in near real-time and provides alerts as to conditions conducive to natural events such as coral bleaching (Coral Reef Early Warning System [CREWS]), larval conch survival, and in the future, harmful algal blooms

seamount - a submarine mountain, usually conical in shape and volcanic in origin, that rises 1000 meters or more above the sea floor. Some definitions of seamounts do not include the height criterion

seasonal monogamy - a pair-bond normally maintained throughout one breeding season

seawall - a massive structure built along the shore to prevent erosion and damage by wave action

seaward slope - the area of a barrier reef or atoll from the reef crest. It includes spurs, grooves, terraces, reef walls, etc.

SeaWiFS - Sea-viewing Wide Field-of-view Sensor carried on the SeaStar satellite

Secchi depth - the depth at which a Secchi disk disappears from view as it is lowered in water Secchi disk a white disk 20-30 cm in diameter, used as a qualitative way of measuring water clarity. It is lowered from a vessel and viewed from above the surface in full solar illumination to estimate the light attenuation in the water column. This is done empirically by relating the depth at which the disk disappears to the attenuation of light

Second Law of Thermodynamics - each time energy is converted from one form to another, some of the energy is always degraded to a lower-quality, more dispersed, less useful form; no system can convert energy from one form to another useful form with 100 percent efficiency; energy cannot be transferred spontaneously from a cold body to a hot body. As a result of this fact, natural processes that involve energy transfer must have one direction, and all natural processes are irreversible. This law also predicts that the entropy of an isolated system always increases with time

Image of NOAA diver

The second stage regulator is contained in this NOAA diver's mouthpiece. (Photo: NOAA/National Undersea Research Program)


second stage regulator - in scuba breathing equipment, the second stage regulator, which is attached to the mouthpiece, reduces the intermediate pressure from the first stage regulator (attached to the air tank) to that needed for comfortable breathing at depth

secondary male - a male derived through sex change from a protogynous female in which there is a regression of the ovaries and a proliferation of testicular tissues

secondary male or female - a male or female that is the result of sex change. A secondary male would be derived from a protogynous female, while a secondary female would be derived from a protandrous male

secondary polyp - polymorphic polyps which grow as branches from the supporting primary polyp in colonial octocorals. These secondary polyps are specialized for feeding or water circulation within the colony

secondary production - the production of living material per unit area (or volume) per unit time by herbivores. It is usually expressed as grams carbon per meter square per year

secondary septum - partial plates/partitions that separate mesenteries within a mesenterial pair

secretion - the passage of a molecule from the inside of a cell through the cell membrane into the periplasmic or interstitial space, or the extracellular medium; the organic process of synthesizing and releasing some substance from the body of an organism

secretory product - a functionally specialized substance, not a waste product, released from a gland or cell. Hormones, for example, are secretory products

section - see "microscopic section"

sedentary - not moving. Many organisms, both plants and animals, spend the majority of their lives in one place

sediments - soil, sand, and minerals washed from land into water, usually after rain. They pile up in reservoirs, rivers, harbors, and coastal areas destroying habitats, and clouding the water so that sunlight cannot reach aquatic plants. Careless farming, mining, and building activities expose sediment materials, allowing them to wash off the land after rainfall

seep - a small area where water that may be of a different temperature and density flows from below the seafloor and rises slowly into the ocean; a spot where water that is flowing below the earth’s surface slowly oozes out to form a small pool or a spring abov

seepage - the movement of water through a porous medium

segmentation - in many animals, the body is divided into repeated subunits called segments, such as those in centipedes, insects, and annelid worms. Segmentation is the state of having or developing this type of body plan

seine - a fish net that hangs vertically, with floats at the top and weights at the bottom

selective pressure - forces acting on populations that determine that some individuals are more reproductively successful or genetically fit than others, and contribute more descendants (or genes) to subsequent generations

self-fertilization - when a sperm cell and ovum from the same organism fuse and form a zygote

semelparity - the reproductive condition where individuals reproduce only once during their lifetime

seminal receptacle - a sac that stores spermatozoa (sperm cells) prior to fertilization of an egg

semipermeable membrane - a thin membranous barrier that permits passage of particles up to a certain size or of a special nature; also referred to as a 'differentially permeable membrane'

senior homonym - in taxonomy, the older, or earliest established taxonomic name

senior synonym - in taxonomy, the older name of two synonyms

sens. lat. - in the broad sense (sensu lato)

sensor - a device that receives electromagnetic radiation and converts it into a signal that can be recorded and displayed as numerical data or as an image

sensory receptor - a neurological structure specialized to respond to stimuli and changes in the internal or external environment of an organism. Sensory receptors consist of neuron endings and specialized cells in close contact with neurons

septate shell - a shell divided into smaller chambers, as in the chambered nautilus (Cephalopoda-Mollusca)

septocosta - when corallite walls are absent or indistinct, the distinction between septae and costae is lost and they become known as septocostae

septum - a thin partition

Image of coral polyp skeleton

Skeleton of a coral polyp. Notice the septa radially arranged around a central axis.


septum (pl. septa) - the skeletal plate that projects into the calyx from the theca. Septa may be subdivided into primary, secondary, and tertiary structures

sequencing - analytical procedures for the determination of the sequential order of amino acids in a polypeptide chain or nucleotides in a DNA or RNA molecule

sequential hermaphrodite - a form of hermaphroditism where individuals can change sex, but the sexes are separate

sequestration - segregation; the act of removing, separating, segregating or sequestering

sere - the series of communities that follow one another in a natural succession, as in the change from a bare field to a mature forest

serial homology - representative or repetitive relation in the segments of the same organism, as in the lobster, where the parts follow each other in a linear series; repeated structures within an organism that have similar developmental origins

serial spawning - spawning more than once in a season

series - in taxonomy, the sample available for study

serosa - a serous membrane

serous membrane - an epithelial and connective tissue membrane that lines body cavities and covers visceral organs within these cavities. Epithelial cells constituting this membrane secrete a fluid (serous fluid) to the membrane's surface, which keeps the membrane moistened; also called "serosa"

serpulid worm - a marine polychaete worm in the family Serpulidae which secretes and lives in a rigid calcareous tube

serrate - saw-like; notched

server - a computer which is designed to be accessed by many other computers. Servers can be attached to local area networks and/or be hooked up to the internet. With the proper software and connections, servers can control the distribution of email, store World Wide Web documents, and provide access to files that are shared by many users

sesquiterpene isocyanides - a class of toxic chemicals which act as defensive chemical secretions in some sea slugs

Image of sessile anemone

A sessile colonial anemone (Epizoanthus americanus) living in Gray's Reef off Sapelo Island, GA.


sessile - describes an immobile organism because of its attachment to a substrate. The term has also been applied to organisms, such as anemones, that move very slowly

seston - minute particulate material moving in water that is composed of both living organisms, such as plankton, and non-living matter such as plant debris and suspended soil particles

set - in mathematics, a collection of things without regard to their order

seta - a cuticular hair arising from the outside of the exoskeleton of an invertebrate

setiform - bristle-like; brush-like

setose - bearing setae

sewage - the total of organic waste and waste water generated by residential and commercial establishments

sex chromosome - a heteromorphic chromosome that plays a role in sex determination, such as the X and Y chromosomes, whose distribution in a zygote determines the sex of the organism; a chromosome whose DNA determines sexual characteristics in females (X)-and males (Y)

sex inversion - change of sex naturally or after steroid hormone application; also called "sex reversal"

sex ratio - the relative number of males and females in a population.

sex-linked gene - a gene coded on a sex chromosome, such as the X-chromosome-linked genes

Image of Asain dwarf gouramis

Sexual dichromatism in the freshwater southeast Asian dwarf gourami, Colisa lalia. The male is to the left of the female.


sexual dichromatism - pertaining to differences in color and color pattern between the sexes of a particular species

Image of male and female sockeye salmon

Female (above) and male (below) sockeye salmon (Oncorhynchus nerka) show extreme sexual dimorphism (color, male hump).


sexual dimorphism - pertains to systematic differences between males and females. The two sexes are markedly dissimilar in appearance

shallows - the marine environment located close to the surface where the influences of waves, wind, tides, sun and cooling are most pronounced

shearwater - any of about 25 species of medium-sized, long-winged seabirds in the family Procellariidae. Those in the genus Procellaria are usually called 'petrel'

sheen - a very thin layer of oil (less than 0.0003mm in thickness) floating on the water surface

shelf break - nearshore bathymetry characterized by rapid and substantial increases in depth that are continuous with the deeper parts of the ocean

shelf escarpment - the edge of the bank/shelf where depth increases rapidly into deep oceanic water

shelf reef - a reef that forms on the continental shelf of large land masses

shelf-edge reef - a synonym of ribbon reef

Image of a crab (dorsal side)

Edible crabs, shrimp, lobsters, crayfish, clams, mussels, scallops, and oysters are considered shellfish.


shellfish - a term that includes both molluscs, such as clams and oysters, and crustaceans, such as lobsters and shrimp

Sherwood Forest Reef - a unique coral reef within the Dry Tortugas Ecological Reserve between 60 to 130 feet deep. Sherwood forest reef, estimated to be over 9,000 years old, is an important nursery ground and spawning site for aggregating species of fishes. The reef has extensive and abundant fungiform coral colonies

shikimate pathway - the biochemical sequence employed by plants and microorganisms to generate the aromatic amino acids: phenylalanine, tyrosine, and tryptophan, and other aromatic metabolites. The pathway is thought to play a role in how algae protect itself and corals from ultraviolet (UV) radiation

shoal - a submerged expanse of coral reef, surrounded by deep water, which does not form a part of a barrier or fringing reef

shoal (biol.) - a social group of fishes of the same species that are not always similar in size or equal in social status. The shoal does not usually move in a highly coordinated fashion, as does a school. Shoals are typically found in shallow water or at the surface. Some consider shoals to be schools in shallow water

Graphic of SHOALS image

SHOALS imagery of the South Moloka'i reef tract shows the position of a distinctive channel that crosses the reef and a large hole in the reef. The large hole is shown below in oblique view. The origin of features such as this one is being investigated by USGS scientists. (Photo: U.S. Geolgical Survey)


SHOALS (Scanning Hydrographic Operational Airborne Lidar Survey) - SHOALS is a laser-based scanning LIDAR bathymeter which collects high-resolution bathymetric data in shallow, offshore areas. Map products provide a view of sea-floor topography. In areas with coral reefs, this includes not only the top surface of the reef but also associated channels and sand flats

shore bird - any of various species of bird, such as the sandpiper, plover, or snipe, that frequents the shores of coastal or inland waters

shore reef - a synonym of fringing reef

shore species - marine fishes that are always found near the shore

Image of tropical shoreline

Shoreline of Fanning Island in the South Pacific.


shoreline - the line separating land and water. It fluctuates as water rises and falls

shoreline - the intersection of the land, including man-made waterfront structures, with the water surface. The shoreline depicted on NOS maps and charts represents the line of contact between the land and a selected water elevation. In areas affected by tidal fluctuations, the shoreline is the interpreted mean high water line. In confined coastal water of diminished tidal influence, the mean water level line may be used. In non-tidal waters, the line represents the land/water interface at the time of survey. In areas where the land is obscured by marsh grass, cypress or similar marine vegetation, the actual shoreline can not be accurately represented. Instead, the outer limit line of the vegetation area is delineated (where it would appear to the mariner as the shoreline) and is referred to as the apparent shoreline

short interfering RNA (siRNA) - a 21-23 nucleotide-long RNA that mediates messenger RNA (mRNA) catalysis; used in gene suppression

short tandem repeats (str) - repetitive segments of DNA of a pattern of length from 2 to 10 bp, scattered throughout the genome in the non-coding regions between genes or within genes (introns), often used as markers for linkage analysis because of high variability in repeat number between individuals. These regions are inherently unstable and susceptible to mutations

shotgun sequencing - a DNA sequencing technique in which a large number of small fragments of a long DNA strand are generated at random, sequenced, and computationally reassembled to form a sequence of the original strand; also known as "shotgun cloning"

shower - precipitation that is intermittent in time, space or intensity

sibling species - closely-related species that are nearly morphologically indistinguishable

sic - thus

Graphic of side scan sonar "fish"

Deployment of the side scan sonar tow vehicle, also called a ‘fish’. (Photo: NOAA)


side scan sonar - sonar designed to look sideways and at a downward angle from both sides of a towed unit, called a towfish. The bottom and any objects in the water above the bottom reflect sound waves back to the towed array. An image is produced fom this information

Graphic of sigmoid curve

This sigmoid (or s-shaped) curve is characteristic of many growth situations.


sigmoid growth - a growth rate trend characterized by an elongated S–shaped, or sigmoid curve. It is typical of population growth rate trends which begin rapidly at an exponential rate but slow as limiting factors are encountered until a limit is approached asymptotically

sign - in pathology, an indication of the existence of something pathological; any objective evidence of a disease

sign stimulus - the effective part of an action or object that triggers a highly stereotyped innate behavior (or fixed action pattern) in an animal by means of a hypothetical neural pathway called the innate releasing mechanism (IRM)

signal-to-noise ratio - the difference between the source level of a sound signal from a source and the source level of the background noise

signalment - in pathology, identification of the organism whose health is being examined, by describing distinguishing peculiar, appropriate, or characteristic physical marks or signs (e.g., species name, age or stage in development, size, coloration, gross lesions) and collection site and date collected. The basic signalment is aided by including collection site information, the specific samples collected from the specimen for investigation, and other observations on the history of the specimen’s condition, to the extent known

signature sound - a unique sound that is associated with a specific sound source

significance level (level of significance) - in statistics, the probability of a false rejection of the null hypothesis in a statistical test

Sikes Act - passed in 1960, and amended several times, the Sikes Act authorizes the Secretary of Defense to develop cooperative plans for conservation and rehabilitation programs on military reservations and to establish outdoor recreation facilities. The Act also provides for the Secretaries of Agriculture and the Interior to develop cooperative plans for conservation and rehabilitation programs on public lands under their jurisdiction. Some coral reefs are affected by this Act

siliceous - composed of silicon or primarily of silicon

sill - the lowest point on a submarine ridge or saddle at a relatively shallow depth, separating a basin from an adjacent sea or another basin

sill reef - a synonym of ribbon reef

silt - sediment deposited by water

simple - not divided or branched

simultaneous hermaphrodite - a form of hermaphroditism where individuals simultaneously possess functional testes and ovaries, and can release either male or female gametes during spawning

sine - without

single nucleotide polymorphism (SNP) - a SNP (pronounced "snip") is a small genetic change, or variation, that can occur within an organism's DNA sequence. The genetic code is specified by the four nucleotides: adenine, cytosine, thymine, and guanine. SNP variation occurs when a single nucleotide, such as adenine, replaces one of the other three nucleotides. SNPs found within a coding sequence are of particular interest to researchers because they are more likely to alter the biological function of a protein. Because of the recent advances in technology, coupled with the unique ability of these genetic variations to facilitate gene identification, there has been a heightened activities of SNP discovery and detection

single-stranded - a term used to describe nucleic acid molecules consisting of only one polynucleotide chain. The genomes of certain phages are single-stranded DNA molecules; rRNA, mRNA and tRNA are all single-stranded nucleic acids

single-stranded DNA - a single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle

sinistral - left, as opposed to dextral, or right

Image of coral, sea, and island

The marine environment is a sink for many nutrients. (Photo: copyright Digital Vision Ltd.)


sink - a process or place that acts to absorb or remove energy or a substance from a system. The ocean, for example, is a sink for carbon dioxide

sink population or species - a population or species that cannot reproduce fast enough to replace themselves. Sink populations or species are present only because immigrants compensate for excess deaths in the area. Eventually, sink species will disappear from isolated areas

sinkhole - a depression formed in an area either by dissolving of the surface limestone or by collapse of underlying cavities

Graphic of sinuses in human head

The sinuses are a group of 4 pairs of air filled spaces in the head. They are called the ethmoid, maxillary, sphenoid, and frontal sinuses. They warm and humidify the air as one breathes. They also trap and filter organic and non-organic particles from the air, such as bacteria, spores, and dust. (Graphic: Cystic Fibrosis Center at Stanford University)


sinus - one of several air spaces within the skull that are in contact with ambient pressure through nasal passage openings in the posterior pharynx; a sac-like space

Image of an octopus on the move

An octopus rapidly swimming by forcibly expelling water through the tubular siphon projecting from the head. (Photo: Jeff Jeffords)


siphon - an opening in molluscs or in urochordates (tunicates) which draws water into the body cavity. In many molluscs, such as octopods and squids, the siphon may be used to forcibly expel water, providing a means of propulsion

siphonoglyph - a groove in the pharynx of some cnidarians that is lined with cilia which pump water into the animal's gastrovascular cavity.This water current inflates the body, circulates fluids, and provides a volume of water to act as a hydrostatic skeleton

siphonophore - siphonophores are "colonial jellyfish" which have swimming bells at the top, and tentacles with stinging cells below that help them to catch their prey. Each individual of the colony is specialized for a different function, such as swimming, feeding and reproduction. Some siphonophores can be more than 10 meters long. They are in the phylum Cnidaria, class Hydrozoa and order Siphonophora

siphonozooid - a specialized polyp found in colonial soft corals, such as sea pens and sea pansies, which functions as as intake for water, which circulates within the colony and helps keep it upright

siphuncle - a tubelike structure in the body of a shelled cephalopod, such as the chambered nautilus, extending through the partitions of each chamber of the septate shell; the term is also used to describe tubular structures that direct water flow, or as a feeding siphon of several different kinds of invertebrates

Sipuncula - an animal phylum that contains the peanut or starworms. They are small, non-segmented benthic animals (they are not worms), some of which live in coral crevices, empty mollusk shells or marine worm tubes. Several species bore into coralline rock

sister group - a taxon thought to be the closest relative of a given taxon, exclusive of the ancestral species of both taxa

sister taxa - two taxa that are more closely related to each other than either is to a third taxon

sixteen S rRNA (16S rRNA) - a large polynucleotide (about 1500 bases) which functions as a part of the small subunit of the ribosome of prokaryotes and from whose sequence evolutionary information can be obtained; the eukaryotic counterpart is 18S rRNA.

skeletal density - certain massive coral species (e.g. Porites) exhibit annual variations in the density of their calcium carbonate (CaCO3) skeleton, similar to tree rings. The annual density bands are revealed when slices of coral skeleton are X-rayed

skeletogenesis - the process of skeleton formation in vertebrates and invertebrates

skeleton - a supportive or protective structure or framework of an animal, a plant, or part of an animal or plant. In animals it is an external (exoskeleton) or internal (endoskeleton) support structure, against which the force of muscles acts. Vertebrates have a skeleton of bone or cartilage; arthropods have one made of chitin; corals have one of calcium carbonate: sponges have a mass of spicules; many other invertebrates use a hydrostatic skeleton, which is an incompressible fluid-filled region of their body. In plants, the skeleton may be a rigid protective covering, as in the shell of a diatom, or the vascular system of a vascular plant; in scleractinian corals, the structurally supporting matrix of aragonite crystals formed on the outside of the polyp, technically an exoskeleton, or the structural support for an octocoral

skeleton eroding band disease (SEB) - a coral disease that appears similar to black-band disease but is caused by the folliculinid ciliate protozoan, Halofolliculina corallasia

skerry - a low-lying rocky island or reef, often without terrestrial vegetation, and frequently swept by waves

Image of sea slug

Lettuce sea slug (Tridachia crispata) from the Florida Keys National Marine Sanctuary.


slug - a pulmonate or opisthobranch gastropod in which the shell is absent, or reduced and buried within the mantle

smooth - describes a surface without projections; glabrous

snapper - any species of bony fishes in the family Lutjanidae. Snappers are found in the tropical and subtropical regions of the Atlantic, Pacific, and Indian oceans. A few are estuarine to entirely freshwater. Many species are popular food and game fishes. Some ha

sneaky male - a small, non-dominant male fish which attempts to fertilize eggs by darting suddenly onto the nest site; also called "sneaker"

Image of swimmer using snorkel

This swimmer is breathing through a snorkle. (Photo: Courtesy of Cayman Islands Department of Tourism)


snorkel - a breathing device that allows a swimmer to breathe while face down in the water. It consists of a bent plastic or rubber tube fitting into a swimmer's mouth and extending above the surface

Image of fish snout being measured

Measuring the snout length of a fish.


snout - the portion of the head that is just anterior to the eyes

social behavior - any kind of interaction between two or more animals, usually between animals of the same species

social rank - in animal behavior, the position an animal holds in a social group of the same species

social resilience - the resilience of communities to adapt to and withstand institutional, environmental and economic changes in their particular geography

socioeconomics - a branch of economics that considers the relationships of social factors and the market place. For example, coral reef management decisions should identify how these essentially ecological decisions effect the coral reef dependent community

Image of soft coral

Beautiful specimen of soft coral


soft coral - common name for species of the anthozoan order Alcyonacea of the subclass Octocorallia. In contrast to the hard or stony corals, most soft corals do not possess a massive external skeleton

Graphic of snapper (side view)

The spiny dorsal (spd) and soft dorsal (sod) fin of a schoolmaster snapper. (Photo: Fishing-Florida.com)


soft dorsal - a dorsal fin containing only soft rays, or the soft-rayed hind part of the dorsal fin, if both spines and soft rays are present (as in squirrelfish)

sol - a liquid colloidal dispersion; a cytoplasmic phase (the other phase is a gel)

solar energy - electromagnetic energy from the Sun

solar radiation - the amount of radiation or energy received from the sun at any given point

solar year - the time it takes the Earth to make one orbit around the Sun; approximately 365.2422 days

soleiform - slipper-shaped

solenium - in octocorals, a small canal lined with gastrodermis penetrating the coenenchyme, forming a network, and fusing with the larger gastrovascular canals to interconnect the gastrovascular cavities of the polyps

solitary coral - coral polyps can be solitary or colonial. Solitary forms remain as a single individual polyp and one corallite

solstice - either of the two times of the year when the sun is the greatest distance from the celestial equator, occurring about June 22 and December 22

solute - the chemical substances dissolved in a solution, such as salts in seawater

solution - a liquid mixture in which the minor component, the solute, is uniformly distributed within the major component, the solvent

solvent - the liquid in which a solute is dissolved to form a solution

somatic mutation - a change in the genetic structure that can occur in any of the cells of the body except the reproductive cells, and therefore is neither inherited nor passed to offspring. Also called an 'acquired mutation'

somite - a segmental mass of mesoderm in the vertebrate embryo, occurring in pairs along the notochord, and developing into skeletal muscles and vertebrae; in some invertebrates, the term "somite" refers to a metamere

Image of bottlenose dolphins

Mother and juvenile bottlenose dolphins (Tursiops truncatus). Dolphins and whales can use echolocation to help navigate.


sonar - SONAR is an acronym for "sound navigation and ranging." Active sonar describes an apparatus that transmits high frequency sound waves in water and registers the vibrations reflected back from an object. Passive sonars listen without transmitting. They are usually military (although a few are scientific). Some marine animals, such as whales and dolphins, use echolocation systems similar to active sonar to locate predators and prey

sonic muscle - in fishes, a muscle(s) associated with the swimbladder, which when contracted against the swimbladder wall, produces sounds associated with territorial and reproductive behavior

soniferous - sound producing

Image of a sonogram

Sonograph of a crested warbler. Time is on the x-axis and frequency (pitch) is on the y-axis. The sonograph shows discrete pulses of sound over time. Loudness (amplitude) is indicated by the darkness of the pulse.


sonograph - a hard copy display of sound data generated either in real time or from recorded data. Also known as a sonogram

sorus - a group or cluster of sporangia

sound - a longitudinal pressure wave produced by the vibration of molecules in an elastic medium, which can be a liquid, solid, or gas. As the molecules are set in motion, they radiate outwards, colliding into other molecules (compression), then move apart farther than their equilibrium distance (rarefaction), travelling in this manner until they stimulate a sound receptor organ, such as an ear or tactile organ.The receptor translates the mechanical energy of the pressure wave to electrochemical energy of a nervous system, which stimulates a hearing or tactile sensation in the receiving organism; a body of water that is usually broad, elongate, and parallel to the shore between the mainland and one or more islands, e.g., Long Island Sound

source DNA - the DNA from an organism that contains a target gene. This DNA is used as starting material in a cloning experiment

source species - a species whose births exceed deaths in an area. Source species can provide individuals to populate other areas

Southern Cross - a small conspicuous constellation in the southern hemisphere in the Milky Way near Centaurus

Southern Oscillation - a large-scale atmospheric and hydrospheric fluctuation centered in the equatorial Pacific Ocean. It exhibits a nearly annual pressure anomaly, alternatively high over the Indian Ocean and high over the South Pacific. Its period is slightly variable, averaging 2.33 years. The variation in pressure is accompanied by variations in wind strengths, ocean currents, sea-surface temperatures, and precipitation in the surrounding areas. El Niño occurrences are associated with the phenomenon

sp richness - species richness; also "sp. richness" and "sprichness" (very rare)

spat - tiny single corallites that form immediately after the metamorphosis of planula larvae

spathiform - resembling a rounded pole in form

spatial data - information about the location and shape of, and relationships among, geographic features, usually stored as coordinates and topology

spatial index - the ratio of reef surface contour to linear distance. As part of a monitoring program employing a chain transect protocol, the spatial index provides a way to quantify changes in the topographical complexity of the reef

spatial index - as pertaining to coral reef ecosystems, the ratio of reef surface contour distance to linear distance. A high index indicates a surface of high rugosity

spatiotemporal - of, concerning, or existing in both space and time

spatulate - spoon or broadly blade-shaped

Image of fish spawn

Fish spawn (egg mass) deposited on a coral. (Photo: Kev Jacklin)


spawn - to produce or deposit eggs; the eggs of aquatic animals; the mass of eggs deposited by fishes, amphibians or mollusks; offspring in great numbers or masses; to give forth young in large numbers

spawning - in corals, the release of gametes into the water

Spearman's Rank Correlation Test - a statistical test for correlation (statistical dependence) between a sequence of pairs of values. Using ranks eliminates the sensitivity of the correlation test to the function linking the pairs of values. It assesses how well the relationship between two variables can be described using a monotonic function (a function that either never decreases or never increases as its independent variable increases). It is a non-parametric alternative to correlation and it is used when the data do not meet the assumptions about normality, linearity and homoscedasticity

specialist - an organism which has adopted a lifestyle or niche specific to a particular set of conditions

specialist species - species that have a relatively narrow ecological niche

speciation - the evolutionary process that gives rise to a new species

species - in sexually reproducing organisms, a species is a group of genetically related organisms, usually similar in physical appearance, that actually or potentially interbreed and are reproductively isolated from other groups. In microbiology, a species is a collection of closely related strains of organisms sufficiently different from all other strains to be recognized as a distinct unit

species aggregate - a group of species that are morphologically similar and therefore difficult to identify

species diversity - the number of different species in an area and their relative abundance

species group - a group of species considered together, often because they are difficult to differentiate without detailed examination, e.g., very similar species; a group of closely related species; a superspecies

species list - a list of species encountered in an area

species recovery plan   - a plan for restoration of an endangered species through protection, habitat management, captive breeding, disease control, or other techniques that increase populations and encourage survival

species richness - the number of species in an area or biological collection

species-area curve (SAR) - there exists a relationship between the area of a habitat and the number of species found within that area. The species-area curve plots the number of species as a function of habitat area, the size of which correlates strongly with the number of plant and animal species found in that area

specific action potential - instinctive behavior, triggered by internal chemico-physiological factors that builds to a certain level, and allows the behavior to take place. This build up is called the specific action potential. It is responsible for an animal performing one behavior in preference to other behaviors

specific epithet - the label (or designation) of a particular species in the binomial system of nomenclature . For example, "palmata" is the specific epithet of the elkhorn coral, Acropora palmata

specific name - the second name in a binomen and in a trinomen

speciose - having many species

spectrometer - an instrument for measuring wavelengths of light of a spectrum

spectrophotometer - an instrument for measuring speed of different parts of light spectrum

spectroradiometer - a radiometer that measures radiant energy as a function of wavelength

speleothem - a secondary mineral deposited in a cave by the evaporation of mineral-rich water. Stalactites, stalagmites, pillars, and columns are kinds of speleothems. Most common speleothems are composed of calcite, aragonite (calcium carbonate) or gypsum (calcium sulphate)

spermary - an organ in which male gametes are developed. In cnidarians, spermaries are located within the mesoglea of mesenteries

spermatangium - the male gamete-producing reproductive organ in certain algae

spermatium - a non-motile male gamete produced by a spermatangium in red algae

spermatocyte - a male gametocyte that develops into spermatozoa

spermatogenesis - the process of sperm cell (spermatozoa) development in male animals, in which the diploid number of chromosomes is reduced by half to the haploid number in the spermatozoa

spermatophore - a packet containing sperm cells which is produced by the male genital system for transfer to the female. This method of sperm transfer is found in some vertebrates (salamanders) as well as invertebrates

spermatozoan - a sperm cell; the male reproductive cell; the male gamete

spicule - one of the numerous small to minute calcareous or siliceous bodies occurring in and serving to stiffen and support the tissues of various invertebrates, as in the majority of sponges, alyconarians, and many radiolarians, holothurians and compound ascidians

spicule - minute, hard, needle-like or sharp-pointed processes or projections

spillover - with reference to a marine protected area, adults and juvenile animals may swim out of the MPA into adjacent areas, and planktonic stages and eggs can drift out from the MPA into the surrounding waters

spinate - spine-like or composed of spines

spine - a sharp hard bony structure on the skeleton or skin. Body spines serve as predator deterrents; a usually stiff, sharp, dermal rod which supports a fin in fishes

spiniform - spine-shaped

Image of spiny lobsters

Spiny lobsters in a seagrass bed.


spiny lobster - a crustacean of the Family Palinuridae; it lacks large claws and has a flexible, leathery tail fan

spiracle - one of the external openings communicating with the air tubes (tracheae) or book lungs of certain arthropods; a tubular opening, formed from the modified first gill cleft, communicating with the gill cavity of certain ganoid (e.g., gar pike, bowfin) and all elasmobranch fishes

spiral cleavage - a developing embryo has spiral cleavage if, as it undergoes cleavage and changes from a four-cell embryo to an eight-cell embryo, the cells divide at slight angles to one another, so that the none of the four cells in one plane of the eight-cell stage is directly over a cell in the other plane. Spiral cleavage is characteristic of protostomes

spirocyst - a type of nematocyst (stinging cell) limited to the tentacles and oral disc of cnidarians

spirocyte - a cell that produces the spirocyst in anthozoans

spit - a stretch of sand, attached to the land at one end, and extending out into the sea

splicing - the removal of introns and joining of exons to form a continuous coding sequence in RNA

split spawning - spawning occurring over consecutive nights or consecutive lunar cycles within a reef

splitter - refers to a taxonomist who focuses more on small differences among taxa, emphasizing minor variation among individuals, and who tends to recognize more taxa

Image of tube sponges with sea fans

Tube sponges (Phylum Porifera)with sea fans (gorgonia) in background.


sponge - a multicellular animal (metazoa) below the tissue grade of construction. Sponges belong to the phylum Porifera. There are approximately 5,000 living species classified in three distinct groups, the Hexactinellida (glass sponges), the Demospongia, and the Calcarea (calcareous sponges). They are important components of a coral reef ecosystem

sponge - the egg mass of a female crab, which she carries attached to long "hairs" on her pleopods

spongin - a fibrous horny protein that forms the skeletal framework of some sponges

Image of a barrel sponge

The central cavity of this sponge is the spongocoel. Note the banded shrimp in the spongocoel. (Photo: Dr. Anthony Picciolo)


spongocoel - the central body cavity of sponges, which opens to the outside by way of the osculum.

spongocyte - a cell that secretes spongin fibers in sponges

sporangium - an organ containing or producing spores in some algae and fungi

spore - a small reproductive cell produced by certain bacteria, algae, fungi and nonflowering plants. Spores contain at least one genome and are highly resistant to heat excess and dehydration

sporophyll - a fertile blade in attached brown algae

Image of three-spotted gourami

This female three-spotted gourami, Trichogaster trichopterus, gets its common name from the conspicuous spots on its flank and caudal peduncle. The third "spot" is the eye. (Photo: Miguel Pais)


spot - a circular area of pigment

spur and groove - a system of shallow ridges (spurs) separated by deep channels (grooves) oriented perpendicular to the reef crest and extending down the upper seaward slope

squall - a brief sudden and violent wind storm, often accompanied by rain or snow

squall line - any nonfrontal line or band of active thunderstorms

squamous epithelium - an epithelium consisting of one or more cell layers, the most superficial of which is composed of flat, scalelike or platelike cells

squeeze - pain or discomfort in an enclosed space (sinuses, middle ears, inside a face mask) experienced by scuba divers on descent and ascent, caused by barotrauma to the affected area

squirrelfish - a bony fish in the family Holocentridae. Squirrelfishes are small, brightly colored spiny-finned fishes, commonly found living on coral reefs. Most squirrelfishes are reddish in color mixed with silver and white. All species have large eyes. During the day they are usually found hiding in crevices or beneath ledges. They are crepuscular species, most active at low light levels and at night

stability - in ecological terms, a dynamic equilibrium among the physical and biological factors in an ecosystem or a community; relative homeostasis; unchanging with time. This can be a static state, where nothing changes or a steady state where resource flows occur

stable isotope - an isotope of a chemical element which is not spontaneously radioactive. Elements can exist in both stable and unstable (radioactive) forms. Most elements of biological interest (including C, H, O, N, and S) have two or more stable isotopes, with the lightest of these present in much greater abundance than the others. Among stable isotopes the most useful as biological tracers are the heavy isotopes of carbon and nitrogen. These two elements are found in the earth, the atmosphere, and all organisms

stakeholder - an individual or group with an interest in the success of an organization in delivering intended results and maintaining the viability of the organization's products and services. Stakeholders influence programs, products, and services

stalked eye - an eye carried on the end of a stalk or peduncle

standard deviation - a measure of the spread or dispersion of a set of data. It is calculated by taking the square root of the variance

starboard - the right side of a vessel to someone facing the bow or front

start codon - the set of three nucleotides in an mRNA molecule with which the ribosome starts the process of translation. The start codon sets the reading frame for translation. The most commonly used start codon is AUG, which is decoded as methionine in eukaryotes, and as N-formylmethionine in prokaryotes; also called 'initiator codon'

statistic - an estimate based on a sample or samples of a population, providing an indication of the true population parameter

statistical analysis - the application of probability theory to quantified descriptive data

statocyst - a sensory organ possessed by many invertebrates for the perception of gravity, thus body orientation and balance. Statocysts are found in many invertebrates. Each one has a cavity lined with sensory cells and contains a statolith

statolith - a sand grain or a calcium carbonate granule or other hard secreted substance, found in the cavity of a statocyst. Under the influence of gravity, a statolith makes contact with the lining of the cavity, thereby stimulating sensory cells that line it

status and trends analysis - a monitoring program designed to evaluate the current condition of physical and biological features found in an ecosystem and to detect changes that may occur over time.

Image of diver holding starfish

The diver is holding a stellate-shaped starfish. (Photo: Copyright Corel Corp.)


stellate - star-shaped

stem cell - an embryonic cell that can give rise to any type of differentiated cell. They can be derived from two sources: the inner cell mass from a blastocyst or the primordial germ cells (eggs and sperm) of an older embryo

stenohaline - pertaining to an aquatic organism that can withstand a narrow salinity range

stenoky, stenokous - adapted for only a few specific ecological niches

stenothermal - pertaining to an aquatic organism that can withstand a narrow temperature range

stereoblastula - a solid blastula, lacking a blastocoel

stereocilium - a specialized microvillus that superficially resembles a cilium and projects from the surface of certain cells, such as the auditory hair cells

stereogastrula - a solid gastrula, lacking a gastrocoel

stereotypical behavior - in animal behavior, any behavior that an animal repeats in the same way

stern - the rear (back) end of a vessel

sternite - the ventral plate (or sclerite) of each segment of the body of an arthropod

stewardship - related to the environment, the concept of responsible caretaking, based on the premise that we do not own resources, but are managers and are responsible to future generations for their condition; the science, art and skill of responsible and accountable management of resources

stipe - stalk or erect portion, as in some brown algae

stipitate - body mass supported by a long stalk or stipe

stochastic - random; exhibiting variability due to random events

stolon - a type of stalk that lies in contact with the substrate; in corals, a horizontal polyp outgrowth from which daughter polyps are budded

stoloniferous - a type of colony formation in which the zooids are connected by a common stolon which is in contact with the substrate, as found in ectoproctans (moss animals)

stoma - any of various small openings or pores in an animal body, especially an opening resembling a mouth in many invertebrates; also a minute pore in the epidermis of the leaf or stem of a plant; plural is 'stomata'

stomodaeum - the pharynx in anthozoans; foregut of higher animals; the anterior or oral portion of the alimentary canal of an embryo

stone canal - the section of the water vascular system in echinoderms that connects the ring canal to the madreporite

stony coral - a synonym of hard coral

stop codon - a codon in mRNA for which there is no corresponding tRNA molecule to insert an amino acid into the polypeptide chain. Protein synthesis is terminated and the completed polypeptide is released from the ribosome. Three stop codons are known: UAA, UAG, and UGA. Mutations which generate any of these three codons in a position which normally contains a codon specifying an amino acid are known as 'nonsense mutations'; also called 'nonsense codons.' A stop codon signals the end of the amino acid chain in protein synthesis

Image of storm surge

Storm surge swamps a house. (Photo: NOAA)


storm surge - a rise above normal water level on the open coast due to the action of wind stress on the water surface

strain - a group of individuals within a species having a common origin

strand - the flat area of land that borders a body of water, such as an ocean, a sea, a lake or a river bank

strategic plan - a document used by an organization to align its organization and budget structure with organizational priorities, missions, and objectives. A strategic plan should include a mission statement, a description of the agency's long-term goals and objectives, and strategies or means the agency plans to use to achieve these general goals and objectives

stratified random sample - in statistics, a sample drawn from a population divided into tiers or strata specifically relating to the study being undertaken; a sample derived by dividing the data population into a number of nonoverlapping classes or categories from which cases are selected at random, the number of cases selected from each category being proportional to the number therein

stratigraphy - the branch of geology that deals with the origin, composition, distribution and succession of strata

stream bed - the stream bottom or surface over which a stream flows

stress - how an organism, population, community or ecosystem reacts to a stressor (a stimulus that causes stress). Acute stressors have a short term effect; chronic stressors have an effect over the longer term. Environmental stress refers to physical, chemical, and biological restraints affecting the ecosystem. Stress may be caused by natural environmental factors, such as volcanic eruptions, severe storms, climate change, biological interactions, disease, etc, or by human activities which contribute to the degradagtion of the environment

stressor - a physical, chemical or biological factor that adversely affects organisms; an agent, condition or similar stimulus that causes stress to an organism

striated - marked with lines or grooves

stridulation - the process in which a biological sound is produced when one body part rubs against another

stridulation - to produce a sound by rubbing two body parts together. Some fishes make sounds by rubbing together bodily structures, especially skeletal parts

Image of Moorish idol

Distinctive striping of the Moorish Idol (Zanclus canescens). (Photo: Dr. James P. McVey, NOAA)


stripe - a straight line of pigment that can vary in width, and which can be oriented vertically, horizontally, or obliquely on the head, body, or fins of an organism

Image of strobila

The late strobila stage of the jellyfish Aurelia. This sessile stage contains numerous discs stacked on top of one another. Eventually, each of these discs will break free from the stack as free-swimming ephyra larvae. (Photo: Rick Gillis, Ph.D., Biology Dept., University of Wisconsin-La Crosse)


strobila - a stage in the jellyfish life cycle. Free-swimming scyphozoan (true jellyfishes) medusae produce gametes which give rise to small polyps called scyphistomae. After a period of growth, a scyphistoma divides transversely to become a strobila that resembles a stack of discs. Each of the "discs" becomes an ephyra larva, detaches from the strobila and swims freely in the plankton. The ephyra larva will eventually grow into an adult medusa

stromatolite - a layered, fossilized deposit, mainly of limestone, formed by photosynthesizing colonial cyanobacteria and other microbes. They are the oldest known fossils, dating back more than 3 billion years. Stromatolites are prokaryotes that thrived in warm aquatic environments and built reefs much the same way as coral does today. They were common in Precambrian time (i.e., more than 540 million years ago). Although stromatolites continue to form in certain areas of the world today, they grow in greatest abundance in Shark Bay in western Australia

stromatoporoid - a fossil calcareous sponge

structural complexity - as pertaining to coral reef ecosystems, a measure of the amount of coral surface area in relation to linear area. For example, branching coral reef habitats will have a higher structural complexity than encrusting coral reef habitats

structural gene - a DNA sequence that forms the blueprint for the synthesis of a polypeptide, such as an enzyme

structure-forming deep-sea sponge - any species of sponge generally occurring at depths below 50 m that provides vertical structure above the sea floor and can occur at a population density such that they promote the development of associated communities

Structured Query Language (SQL) - a specialized language for sending queries to databases

stygobite - a species generally restricted to subterranean groundwater

styliform - having the shape of a pointed rod

subadult - an individual similar to the adult in appearance but not yet capable of reproducing

subclass - a taxonomic group that is below a class and above an order

subduction - the process in which one lithospheric plate collides with, and is forced down under another plate

subequal - nearly, but not quite equal

subfamily - a taxonomic group that is below a family but above a genus

subgenus - a taxonomic group that is between a genus and a species

subgular - below the throat

subkingdom - a taxonomic group comprising a major division of a kingdom

sublethal - a toxic or genetic effect that does not cause death, but impairs the organism in various ways

submarine groove - a troughlike depression with vertical to overhanging walls which cut across the reef front at right angles

submersible - a small underwater vessel (submarine) which requires a support ship to transport it to and from the diving area. It is used primarily for oceanographic research. There are also some commercial submersibles that carry tourists below scuba diving depths to view coral reef walls

suborbicular - nearly circular

suborbital - an area below the eye

suborder - a taxonomic group that is a subdivision of an order

subordinate - in taxonomy, belonging to a lower or inferior taxonomic rank. For example, a genus is subordinate to the family to which it belongs

subordinate taxon - in taxonomy, a taxon at a lower rank than the taxon of the same coordinate group with which it is compared

subphylum - a taxonomic group ranking that is between a phylum and a class

subpopulation - a well-defined set of interacting individuals that compose a proportion of a larger, interbreeding population

subradular organ - a sensory organ in chitons (Polyplacophora-Mollusca) which can be protruded and pressed against the substrate in the search for food

subset - in mathematics, a subset of a given set is a collection of things that belong to the original set

subsidence - a gradual sinking of land with respect to its previous level; the slow sinking of air, usually associated wit high-pressure areas

subspecies - a taxonomic group that is a division of a species. It usually evolves as a consequence of reproductive isolation of one or more populations within a species

subspecific name - the third term of the trinomen, a subspecies

substrate - the material making up the base upon which an organism lives or to which it is attached

subterminal - located some distance away from the end

subumbrella - the lower or oral surface of a medusa or jellyfish

Image of octopus suckers

Suckers on an octopus tentacle allow the animal to adhere to almost any surface. (Photo: J'nie Woosley/National Zoological Park)


sucker - a structure, such as those at the end of tube feet of echinoderms, or on the tentacles of octopods and squids, that can produce a small vacuum and enable the animal to stick to many surfaces

sucker - any organ which has an adhesive action

sucking disk - a disk-like structure used by some fishes to attach itself to rocks or vegetation

Suess effect - dilution of the atmospheric concentrations of heavy isotopes of carbon (13C and 14C) by the admixture of large amounts of fossil fuel-derived CO2, which is depleted in 13CO2 and contains no 14CO2. The Suess effect has been used in studies of climate change

Sula Reef - a deep water Lophelia reef located on the Sula Ridge on the Mid-Norwegian shelf at depths of 200 - 300 m. A very large deep water coral reef, it is about 13 km long, 700 m wide, and up to 35 m high

Sundarbans - the world's largest mangrove forest located in Bangladesh at the edge of the delta where the Ganges, Brahmaputra and Meghna Rivers come together

superclass - a taxonomic group that is below a phylum and above a class

superfamily - a taxonomic group that is below an order but above a family

superficial cleavage - a type of cleavage, typical of centrolecithal eggs found in most arthropods, in which karyokinesis (nuclear division) occurs without cytokinesis (cytoplasmic division), resulting in a syncytium. Cleavage furrows form to separate the nuclei

supergene - a group of neighboring genes on a chromosome that tend to be inherited together and sometimes are functionally related

superior - the anatomical term for "above" (e.g., the head is superior to the shoulder)

supermale - a male which does not change sex and is the principal spawner

supernatant - the soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids

supernumerary - superfluous or extra

superorder - a taxonomic group that is above an order and below a class or subclass

supersucker - a mechanical suction device developed by the Hawai`i Marine Algae Group to remove the invasive algae Gorilla Ogo (Gracilaria salicornia) on reefs.

supporting cell - in cnidarians, a columnar epethilial cell in the epidermis or gastrodermis which may have apical specializations of microvilli, cilia or flagellae

suppressor gene - a gene that can reverse the effect of a mutation in other genes, i.e., a gene that suppresses the phenotypic expression of another gene, especially of a mutant gene

supraesophageal gangia - a nerve plexus above the esophagus in the head of malacostracan crustaceans

supraorbital - an area above the eye

suprapsammon - organisms which swim just above sand and are dependent upon it as a food source

surf - a collective term for "breakers"; the wave activity in the area between the shore line and the outermost limit of breakers. In literature, surf usually refers to the breaking waves on shore and on reefs

surface feeder - an organism, usually a fish, that takes its food from the air/water interface, or feeds just below the water surface, e.g., a needlefish

surface interval - the length of time that a scuba diver spends on the surface between two consecutive dives

surface ocean 13C Suess effect - the annual decrease in 13C caused by the addition of anthropogenic CO2 to the atmosphere

surface water - an open body of water, such as a stream, lake, reservoir or wetland

surge channel - a deep channel in the windward side of a coral reef through which water moves in and out of the reef

surgeonfish - any species of brightly colored reef-dwelling bony fishes in the family Acanthuridae which have laterally compressed bodies and possess one or more sharp erectile spines near the base of the tail; also called "tangs" and "doctorfish"

surrogate species - small number of species whose distributions and abundances are well known; used in conservation planning; assumed to reflect the distribution and abundance of the regional biota; subsumes indicators and umbrella species; also called "focal species"

survey (biology) - the systematic and usually standardized collection or inventorying, processing, and analysis of representative portions of a biological community or defined site with its habitats, to determine the community structure and function

susceptibility - the state of being susceptible; easily influenced or affected; in epidemiology, a susceptible individual is one which is at risk of becoming infected by a disease if the individual is exposed to the infectious agent

suspended organic matter - floating organic particles derived from the decomposition of dead organisms

Image of sponge with coral

Suspension-feeding sponge among corals.


suspension feeder - an organism that feeds by capturing particles suspended in the water column. A synonym of filter feeder

sustainability science - a multi-disciplinary approach to science that recognizes the limitations of traditional scientific inquiry in dealing with the complex reality of social institutions interacting with natural phenomena. Sustainability science seeks to improve on the substantial but limited understanding of nature-society interactions gained in recent decades. This has been achieved through work in the environmental sciences estimating and evaluating human impacts, and evidence from social and development studies that takes into account environmental influences on human well-being. Urgently needed is a better understanding of the complex dynamic interactions between society and nature so that the trend towards increasing vulnerability is reversed

sustainable development - those efforts to guide economic growth in an environmentally sound manner with an emphasis on natural resource conservation

sustainable yield - the number or weight of organisms in a population that can be harvested without reducing the population biomass from year to year, assuming that environmental conditions remain the same

sustained monogamy - a pair-bond normally maintained longer than one breeding season

suture - the line of union of two bones or plates

swamp - a type of wetland that is dominated by woody vegetation. When it does not, it is usually termed a marsh. Swamps may be fresh or salt water and tidal or non-tidal

sweeper polyp - a polyp that acts in an aggressive manner by stinging neighboring corals and sessile invertebrates

Image of sweeper tentacle

A hammer coral (right) thrusts out a sweeper tentacle towards a mushroom anemone (left). (Photo: Scott Brooks)


sweeper tentacle - A coral polyp tentacle that has an increased number of nematocysts and elongates in order to 'sting' neighboring corals and sessile invertebrates. A tool in the competition for space and resources

Image of an ocean swell

An ocean swell


swell - the persistence of a wind-formed wave after the wind ceases

Graphic of juvenile lobster

The arrow points to a swimmeret of a juvenile lobster. (Graphic: NOAA)


swimmeret - one of several flat, fringed, and usually bilobed, paired appendages on the ventral surface of the abdominal somites of decapod crustaceans, used for swimming and reproduction

Diagram of syconoid sponge

Anterior end of a syconoid sponge in which the body wall has been folded into a series of internal and external canals.-1= osculum; 2= spongocoel; 3= ostium; 4= radial canal; 5= incurrent canal; 6= apopyle. (Photo: Rick Gillis, Ph.D., Biology Dept., University of Wisconsin-La Crosse)


syconoid - a body form of medium complexity in sponges where the body wall has become folded and the choanocytes (flagellated collar cells) are not located along the spongocoel, but along radial canals. Water enters the sponge through a series of incurrent canals and passes through internal pores called prosopyles into the radial canals, which are lined with flagellated choanocytes.- It is the action of these choanocytes that keeps water moving through the sponge. From the radial canals, water then enters the central spongocoel through pores called apopyles, to exit to the environment through a single opening, the osculum.

Image of clownfish w. anemone

These clownfish exist in a symbiotic relationship with the sea anemone; the anemone provides protection and the clownfish feed and clean the anemone. Different clownfish species choose particular anemone species for their hosts. (Photo: Copyright Corel Corp.)


symbiont - a symbiotic organism; either of two organisms participating in a symbiotic relationship

Image of clownfish with sea anemone

A clownfish has a symbiotic relationship with a sea anemone, finding protection within the clump of stinging cell-bearing tentacles.


symbiosis - a relationship between two species of organisms in which both members benefit from the association (mutualism), or where only one member benefits but the other is not harmed (commensalism), or where one member benefits at the expense of the well-being of the other (parasitism)

sympatric species - different species that live in the same area but are prevented from successfully reproducing by a reproductive isolating mechanism

symplesiomorphy - in evolution, a shared primitive character

synapomorphy - in evolution, a shared derived character

synapse - the site where neurons communicate with each other. A synapse is a small gap that physically separates neurons. Axon terminals of a neuron sending a nervous impulse (the presynaptic neuron) release neurotransmitters into the synapse. The neurotransmitters diffuse to the other side (the postsynaptic side) where they bind to receptors on the postsynaptic neurons, thereby relaying the nervous impulse

synchronous - occurring at the same time

synchrony - the relation that exists when things occur at the same time

Image of skeletal muscle cells

Skeletal muscle cells are a multinucleate syncytium. The dark stained bodies are nuclei. (Photo: General College, University of Minnesota)


syncytium - a mass of cytoplasm containing several nuclei and enclosed in a membrane, but having no internal cell boundaries, e.g., skeletal muscle cells

syndrome - a group of symptoms or signs that are characteristic of a disease; a pattern of symptoms indicative of some disease

synecology - the branch of ecology that deals with whole communities and the interactions of the organisms within them

syngamy - the process of union of two gametes, also called fertilization. It encompasses both plasmogamy and karyogamy.

synomone - a chemical substance produced by one organism that is beneficial to both itself and a member of another species

synonym - in taxonomy, one of two or more scientific names that are spelled differently, but refer to the same organism

synonymy - in taxonomy, the relationships between different names applied to the same taxon; a chronological list of taxonomic names which have been applied to a single taxon, including authors and dates

synopsis - in taxonomy, a brief description of the main characters of a taxon

syntrophy - the relationship between the individuals of different species (especially bacterial species) in which one or both benefit nutritionally from the presence of the other. The different species may combine their nutritional metabolic capabilities to utilize, for nutrition, a substance not capable of being utilized by either one alone

syntype - in taxonomy, each specimen of a type series from which neither a holotype nor a lectotype has been designated. The syntypes collectively constitute the name-bearing type

systemic - a condition or process that affects the body as a whole, not localized to one area or system

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