Acoustic backscatter

An imaging technique which uses the intensity of acoustic waves reflected off the seafloor to indicate the grainsize of the seafloor sediment – finer sediments reflect more and therefore appear brighter in the image than coarser sediments. There is an explanation and an image of a backscatter image on this page of the CoralFISH cruise blog.

Acoustic fisheries survey

This survey determines the abundance of a target species.  It works by emitting sound waves from an transducer towed underwater by the survey vessel.  The waves are bounced back by shoals of fish or plankton, and are recorded by an echo sounder in the vessel. The results are combined with a trawl sample to identify the species involved and allow estimates of the biomass of different species.

Advection

The horizontal movement of water as in an ocean current. Advected prey has been carried along in the water.

Asexual reproduction

A form of reproduction involving only one parent. It is the primary form of reproduction for single-celled organisms such as bacteria, but many plants and fungi also reproduce asexually, and some animals (including cold water corals) have the capability to do so.

Azooxanthellate Scleractinia

A group of corals (the Scleractinia, which have external, aragonitic skeletons) that do not have symbiotic algae associated with them, and can therefore live in total darkness. (Zooxanthellate Scleractinia need light for the growth of the algae). Lophelia pertusa is an example, and one of the most important CWC in European waters

Benthic zone

The ecological region at the bottom of the water column in body of water such as a lake, sea or ocean, and comprising the sediment surface and some sub-surface layers.  Organisms that inhabit this zone are known as the benthos.

Bioeconomic model

A way of studying the dynamics of living organisms using economic models.  It can be used as a way of assessing and protecting resources such as fisheries by quantitatively examining the relationship between fishing activity and biological growth.

Biogenic

A substance produced by living substances. In the case of cold water corals, a reef may be formed from the remains of dead corals.

Biomass

The total weight of living matter in an ecosystem.  As higher levels in a food chain are reached, the biomass at that level decreases – i.e. the biomass of a food source is always more than that of the consumer, as most of the energy that comes from the food source goes to metabolic processes or is dissipated as heat.

Bottleneck traces

A population bottleneck occurs when the size of a breeding population is drastically reduced, meaning that genetic diversity is reduced as inbreeding becomes more common.  This can mean that a species is more vulnerable to e.g. environmental change or diseases.
A familiar example would be the tendency for some pure-bred dogs to suffer from diseases and ailments particular to their breed: breeders have reduced the gene pool by breeding close relatives in order to 'enhance' the looks and behaviour of the breed.

By-catch

Organisms caught ‘by accident’ as a result of fishing – e.g. corals may be caught up in fishing nets, but are not the intended target species of the fishing vessel, or birds that are caught in fishing hooks as they dive for the bait.

Clonal reproduction

See asexual reproduction

Clone

An organism genetically identical to another – see asexual reproduction

Commensalism

A relationship between two organisms in which one benefits from the relationship while the other is not significantly helped or harmed. An example from the marine environment would be the relationship between sponges and the crustaceans and worms that live in them - the worms get shelter and nutrients, while doing no harm to the sponge.

Coral garden

A diverse ecosystem with corals forming the physical structure.

Core sampling

A way of sampling the sediment, flora and fauna of the sea floor, by dropping or driving a tube into the sediment. As the tube is lifted it brings the sample with it, and the tube is sealed. The advantage of using such a sampling method is that the structure of the sediment (e.g. layering) can be preserved.
Some photographs and a diagram of the core sampling system and cores taken from the IFREMER vessel (the Pourquoi Pas?) during the BobGeo cruise in 2009 can be seen on the CoralFISH cruise blog.

CWC

Cold-water corals.  These corals, in contrast to their tropical relatives, occur between 200 and 400m, but may be found in waters as shallow as 40m, and at depths of over 1,000m.  The corals feed by filtering material from the seawater, and are usually found therefore in areas where there is a good flow of seawater.  The faster water currents will also have helped to scour sediment from the seafloor, allowing the corals to attach to a hard substrate.  For more information on CWC see www.lophelia.org

Detritus

In biology, detritus refers to particulate, non-living, organic material, and could include dead organisms or parts of organism, or fecal material.  It forms an important part of the food web

Diurnal variation

Changes between day and night. Many plankton and fish migrate vertically in the water column over the course of a day - e.g. towards the surface during the day, and to deeper water at night time.

Diversity

Also known as biodiversity. The variety of life forms in a given ecosystem.  It is generally accepted that a more diverse system is a healthier one.

Dredge

An instrument like a bucket that is dragged along the seafloor and collects sediment and fauna etc.  While it can gather larger amounts of material, it does not preserve the structures in the sediment as a corer does.

Ecological model

An ecological model uses mathematical analysis to describe ecosystems.  The model can have practical implications for the control of pollution and management of resources.

Eco-region

A geographically distinct region that contains a characteristic range of species and natural communities. In CoralFISH, there are 6 distinct eco-regions being studied: (1) Northern Norway – eastern Norwegian Sea (2) Iceland (3) Porcupine Seabight / Rockall Trough (4) Bay of Biscay (5) The Azores (6) Mediterranean: Ionian Sea. A map and short description of each of these is given on this page.

Ecosystem model

An ecosystem model uses mathematics to study the interaction of the plants, animals, micro-organisms and the environment in which they live. 

Epifauna

Organisms that live on the surface of the sediment or on other plants or animals e.g. oysters or limpets would be epifauna.

Essential habitat

An essential Habitats is an area that provides physical or biological features essential to the conservation of a species or ecosystem.

Food web

A food web shows the interaction, in terms of energy transfer (i.e. eating!), between the various members (plants and animals) of an ecosystem.  It is a more complex version of the linear food chain.  Information from a food web can be input to ecosystem models.  A food web may also be called a trophic network.
An example of a marine food web can be viewed here.

Genetic barcode

This is a classification method that uses a section of an organism’s DNA sequence to identify it as belonging to a particular species

Genetic erosion

This occurs when an already small and therefore genetically limited population loses individuals before they’ve had a chance to breed with others in the group.  The population therefore becomes even less genetically diverse.

Genetic fingerprinting

This allows individuals of the same species to be identified based on parts of their DNA.  Compare with Genetic barcoding which allows an individual to be identified as a member of a particular species.

Genetic variability

This is a measure of the tendency of individual genotypes in a population to vary from one another.  It is different from genetic diversity which is the amount of variation seen in a population.  Variability helps a population to adapt to environmental change through evolution.

Geomorphology

The study of the origin, evolution and appearance of the Earth’s surface. Geomorphologists seek to determine why a landscape looks the way it does, and may also want to predict what it will look like in the future.
The geomorphology of a region may have been shaped by wind, water, tectonic, volcanic, biological, and/or human factors, among others.

Geo-referencing

Defining something in terms of its location in physical space e.g. map reference, latitude-longitude. Essential for using GIS.

Geo-statistics

Applying statistics to geographical data e.g. where the spatial distribution of something is being investigated

Geo-visualisation

A way of communicating geographical and geospatial information in such a way that the user can ‘see’ e.g. the distribution of a species in an easily accessible manner.

Gillnet

A highly effective type of fishing net which uses a specific mesh size to catch the fish – it is of a size that the fish can get their head in through the mesh but not their body, and cannot swim back out because they are trapped by the gills. It is a method which is strictly regulated by imposing restrictions on mesh size etc. They tend to have a high by-catch of cetaceans e.g. dolphins, and their use is banned in the open ocean, but is allowed within 400km of the coast.

GIS

Geographical Information System: an information system for capturing, storing, analysing, managing and presenting data which have a geographical distribution, and are spatially referenced.

Ground-truthing

Collection of data ‘on location’ to confirm or help with the identification of data that has been collected from a distance e.g. from a satellite or geophysical survey.  In CoralFISH it could be to do with the collection of benthic fauna to confirm identifications made using video taken by a ROV.

Habitat suitability
map

A model (map) that relates various parameters of a site e.g. water depth, current, salinity, temperature, to its suitability as a habitat for a particular species or community. They are useful for planning conservation or exploitation strategies.

Hydrography

The study of the physical characteristics of water and marginal land.  Can be divided into oceanography and limnology (the study of lakes).

Impacted,
non-impacted

An impacted habitat is one which has been affected by e.g. fishing; conversely, a non-impacted habitat is in its pristine state.

In situ

In place. E.g. in situ dead corals would be still in the place where they had grown, rather than being transported.

ISO

International Organization for Standardization

Lander system

A benthic lander is an unmanned vessel that is dropped onto the seafloor to carry out observations, experiments and measurements.  At the end of its deployment, ballast is released which allows the lander to float back up to the surface for retrieval.  The advantage of a lander over e.g. a corer is that it allows almost undisturbed observation and measurement of the benthos at the correct pressure and temperature. An example of a lander being deployed in a CoralFISH cruise can be seen here.

Lipid

Any of a group of fats, oils or waxes that are insoluble in water, and are a major constituent of living cells after carbohydrates and proteins.

Long-lining

 A method of fishing which uses one long line to which many branch lines are attached. The branch lines have baited hooks at their ends.  It is especially suitable for catching high value, large fish such as tuna.  Long-lining has a relatively low rate of by-catch e.g. of turtles or sharks, but birds may get caught and drown if they dive after the bait.

Macroscale

On or at a large scale – which depends on the nature of the data being considered. Compare with Mesoscale and Microscale.

Mesoscale

On or at a medium scale – which depends on the nature of the data being considered. Compare with Macroscale and Microscale.

Metadata

Data about data – e.g. for a digital camera, the photograph is the datum, the metadata might include the date the photograph was taken, the shutter speed, aperture etc.

Microsatellite

Parts of DNA which are useful in population and kinship studies.

Microscale

On or at a small scale – which depends on the nature of the data being considered. Compare with Macroscale and Mesoscale.

Molecular
phylogenetics

The use of an organism’s molecules (e.g. DNA) to look at its evolutionary history and relationships.

MPA

Marine Protected Area. Defined by the World Conservation Union as any area of the intertidal or subtidal terrain, together with its overlying water and associated flora, fauna, historical and cultural features, which has been reserved by law or other effective means to protect part or all of the enclosed environment

Multibeam
bathymetry

A highly accurate and high-resolution method for determination of water depth using multiple echo-sounders transmitting from and recording to an underwater vessel.

Natura 2000

An ecological network of protected sites in the European Union.  www.natura.org

Octocoral

A sub-class of non-encrusting coral with 8-fold symmetry. It includes sea-pens, gorgonians, and soft corals.

OGC

Open Geospatial Consortium, Inc. (OGC) – a non-profit, international, voluntary consensus standards organization that develops standards for geospatial and location based services.
www.opengeospatial.org

Open access

No restrictions are placed on the fishing industry

OSPAR Region V

OSPAR is the mechanism by which 15 governments of the coast and catchment areas of western Europe, along with the EU, cooperate to protect the marine environment of the North-East Atlantic. Region V covers the deep waters of the NE Atlantic.
www.ospar.org

Otter-trawl

A method of trawling which uses a net kept open by ‘otter boards’ being dragged along the sea floor. There are several environmental concerns associated with the method: the damage to the benthos from the boards being dragged along the surface; the increased turbidity as sediments are disturbed; and the possible release back into the food chain of pollutants which may have been trapped in the sediments.

PANGAEA

An Open Access library (i.e. the information is available freely to anyone who wishes to use it) aimed at archiving, publishing and distributing georeferenced data from earth system research. The system guarantees long-term availability of its content through a commitment of the operating institutions.

Passive gears

A fishing method which leaves traps, lines or nets in place for a period of time before retrieval e.g. lobster pots, longlines, gillnets. Compare with active gears such as otter trawls, scallop dredges etc.

Polyp

One of two forms of individuals found in many types of cnidarians (which include corals, jellyfish and sea anemones). The two forms are the polyp and medusa, and in corals the individual is always a polyp, attached to either the substrate or to other polyps.

Preferred habitat

Living conditions that a species or community will do best in, but is not essential habitat, therefore if it is not available, the species will ‘make do’ with somewhere else.

Quota management
scheme

A system of controlling fisheries so that the catch taken in a particular time period is sustainable. The quota, or allocation, to a boat, fishing port, region or country, will be decided based on the population size and distribution of the target species so that an adequate breeding population is retained.

Renewable &
non-renewable

A renewable resource is one which is replenished naturally at a rate equal to or exceeding the rate at which it is being exploited by humans e.g. sunlight, wind power, properly managed fish stocks.
A non-renewable resource is one which is being exploited at a rate which exceeds that at which it is being replenished. Examples are oil, coal, and possibly some over-fished stocks, where the breeding adult population is too small to replenish the stock.

ROV

Remotely Operated (Underwater) Vehicle.  The umbrella term for tethered underwater robots, that can be sent down into the water to carry out various tasks such as sampling, photography etc.
The Irish ROV - Holland 1 - can be seen here as it is deployed during a CoralFISH cruise in May 2010 in the North Atlantic. Another photograph on this page shows the suction arm of the ROV being used to sample material at the seafloor.

SAC

Special Area of Conservation – an area designated under the EC’s Habitat Directive

Scientific
nomenclature

All organisms are given a two-part name: the initial letter of the first part of the name is always capitalised, and tells us the genus that the organism belongs to, the second part is the species name.  Classification of living organisms follows the sequence Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, (sub species). E.g. humans are members of the Domain Eukaryota, Kingdom Animalia, Phylum Chordata, Class Mammalia, Order Primates, Family Hominidae, Genus Homo, Species H. sapiens

Seamount

A mountain rising from the seafloor that does not reach the surface and is therefore not an island.  They have a volcanic origin, and often occur in chains.  Ecologically they are important because they provide habitats which contrast with the surrounding deep sea, and because they may cause deflection of ocean currents and e.g. upwelling of nutrient-rich waters.

Sediment dynamics

The study of the motion of sediment, its causes and effects.

Side-scan sonar

A system of analysing the seafloor using an array of sonar transmitters and receivers that send sound waves out across a wide ‘fan’ or swath of the seafloor.  The acoustic signals that are echoed back from the seafloor are analysed and stitched together to generate an image of the surface, and of any other features on the seafloor such as shipwrecks. The survey may be carried out along with studies of acoustic backscatter and multibeam bathymetry.

SME

Small & Medium Enterprises (up to 50 & 250 employees respectively)

Spatial/time closure

Banning fishing in a certain area or at a certain time of year.

Sponge

A simple animal that pumps water through its body to filter out food.  Sponges can reproduce asexually or sexually.  While sponges have different cells that carry out different tasks in the animal, these cells are not organised into tissues. Sponges have a remarkable ability to regenerate and re-organise themselves – even when broken down into individual cells.  These cells can aggregate to form a new colony.

Stable isotope

Isotopes are atoms of the same element which have the same number of electrons and protons (and therefore the same chemical characteristics) but different numbers of neutrons (and therefore different atomic masses).  Stable isotopes do not break down into other elements, unlike unstable or radioactive.  The study of stable isotopes  – particularly nitrogen, carbon, and sulphur – in living organisms can be a useful tool in identifying food web patterns.

Sub-bottom profiling

An acoustic method which allows imaging of the sediments below the water-sediment interface.  The acoustic signal used for surveying is narrower than that used in e.g. side-scan sonar, so it is a more time-consuming and costly survey to carry out.

Substrate

A surface on which an organism grows or to which it is attached.

Symbiosis

An interaction between organisms which is mutually beneficial.

Taxon

A name designating an organism or group of organisms. It could be e.g. at the genus or phylum level.

Time closure

See spatial closure

Trawling

An active fishing method which uses a towed cone-shaped net to catch fish. 

Trophic level

A description of the position of an organism within the food web, e.g. plant, herbivore, carnivore. Because energy is ‘lost’ (e.g. through heat, respiration) as a result of each food transfer, the shape of a food web tends to be in the form of a pyramid, with lots of primary producers e.g. plants, and decreasing numbers of higher-level organisms.

VMS

Vessel Monitoring System. A system which allows regulatory bodies to monitor the position and behaviour of fishing vessels, an essential part of fisheries management.  The system may also be useful for sending in catch reports, and as a safety system. Under EU law, VMS is required on vessels over 15m.

Vulnerable habitat

A habitat that is likely to be lost or degraded. CWC sites are regarded as vulnerable.

Water column

A conceptual or imaginary column of water from the surface to the bottom sediments.  Measurements within the water column can include water temperature, density, salinity.

Zonation

The tendency for species or communities to occur within reasonably definite zones in the water column or at different water depths or latitudes.

Zooplankton

Animals that drift in the water column. They can vary in size from microscopic to quite large, and include foraminifera, radiolaria, krill, juvenile fish, and jellyfish. They may be herbivores or carnivores (i.e. may be at different trophic levels in the food web) and play an important ecological role in the oceans.