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Benthic species are those that live in or on the sea bed. Most environmental monitoring uses benthic invertebrates, which include a wide range of polychaete worms, gastropod molluscs, bivalve molluscs, and various crustaceans. Collectively these are termed the benthos.

Infaunal species are those animals that live in the sediment, whilst epifaunal species are those that live on the surface. many epifaunal species are active and may move considerable distances. For this reason environmental monitoring often targets the infauna, as their presence at a site means that conditions are suitable for them over long periods.

Benthic surveys are one of the main ways that scientists assess the health of our estuaries and coastal waters. Samples are usually taken using a grab. Commonly used grabs include the Smith-McIntyre and Day grab. These sample 0.1 of a square metre of seabed, to a depth of 15-20 cm. At each sampling site it is usual to take replicate samples to provide a more accurate estimate of densities of the invertebrates and to ensure that most of the rarer invertebrates present are collected. Benthic macrofauna are defined as those animals that are retained by a 1 mm mesh, but juveniles of a species will be smaller and will pass through this mesh. Samples are usually sieved through a 0.5 mm mesh, although sometimes 1 mm or 2 mm meshes are used if most of the sediment is too coarse to pass through a 0.5 mm sieve. The material retained on the sieve is carefully transferred to a labelled plastic container, and buffered formaldehyde is added to preserve the sample. A tightly fitting lid is placed on the container (formaldehyde is carcinogenic). The most commonly used buffer is borax. This prevents the shells of molluscs from dissolving in the formaldehyde.

When the sample is returned to the laboratory the formaldehyde solution is removed by washing the sample with tap water in a fume cupboard. The sample is then processed by re-sieving, sometimes through a stack of sieves if a large range of different particle sizes are present. It is also helpful to separate light fractions, which contain detritus and most of the soft-bodied species such as worms, from the dense fraction, which contains sand, gravel and larger molluscs and crustaceans.

The sample is then examined in minute detail under a binocular microscope in order to remove any invertebrates present. These are identified and counted by skilled biologists. When all the data from the survey sites has been collated it is normal to carry out a range of statistical tests to determine relationships between the sites. These tests include univariate measures such as the number of taxa (species), number of individuals, diversity and evenness indices. Multivariate statistical tests include cluster analysis and multi-dimensional scaling (MDS).

The final report highlights any rare or scarce species that have been found in the survey and provides an interpretation of the distribution patterns and their relationship to natural factors (eg salinity, sediment type, depth) and human influences (eg sewage or industrial discharges). It is possible to accurately map the area of influence of any polluting discharge using this method.

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