Where sea water is shallow or very clear we can see the submarine topography and some large organisms moving about. In small streams, coastal rock pools and freshwater pools, we can also wade into the water and lift out pieces of the substratum to view its structure and investigate the community of animals and plants that grow there. This can also be done from the banks or margins and thus create minimal disturbance. Many of us had our introduction to aquatic biology by playing in rock pools during summer holidays, although our enthusiastic collecting after turning over stones probably had a deleterious effect on the habitat.

One of the problems of looking into the water comes from light reflected at the surface and this is overcome by using buckets with transparent bases or their larger equivalent, the use of glass-bottomed boats. The latter are operated in some large, spring-fed rivers and also over coral reefs so that visitors gain an uninterrupted view of the corals, reef fish and invertebrates. The glass-bottomed bucket is a valued tool for aquatic biologists [3.1.] and can be used in conjunction with a long, clawed pole to capture animals. Not surprisingly, several of the techniques used to study the biology of organisms in water derive from practices evolved to acquire food.

In tropical coastal waters there is a well-developed tradition of diving for food, pearl-containing bivalves, and other decorative materials. Diving to depths of tens of metres on one lungful of air is commonplace, with the most practised divers remaining submerged for more than one minute. Snorkels allow swimming at the water surface while the head is submerged and snorkelling has become an important recreational means of observing reefs and other warm-water habitats. It is essentially similar to the use of glass-bottomed boats except that the observer is able to dive down for a short time to take a closer look at something of interest.

Diving using an external air source began with suits having air pumped from the surface, a valve ensuring that exhaled air vented from the helmet [3.2.]. This type of suit is used today as it affords protection for those working on undersea construction, but the most significant advance in diving for aquatic biologists came with the development of self-contained underwater breathing apparatus (SCUBA) [3.3.]. SCUBA diving with tanks of compressed air allows free dives of much longer duration than those allowed by one lungful of air and the diver is therefore independent of the surface for breathing. There are problems in diving at depths of more than a few tens of meters unless care is taken to ascend slowly through the water column. Rapid ascent results in the "bends", where nitrogen that has dissolved in the blood at depth is released in small bubbles as pressure on the diver decreases. Providing ascent is controlled, with pauses to alleviate the effects of pressure, divers can descend over a hundred metres. Although it is not much fun to dive in the cold, turbid waters often characteristic of temperate regions, the advent of SCUBA has brought the exploration of shallow seas and lakes to a wide public as well as to scientists. SCUBA has also made cave diving possible and we have learned a lot about subterranean aquatic systems from explorations mounted by cave divers.

Television, film and video are used to record lake and submarine topography, organisms of the substratum, and the macrobiota of the water column. The underwater films of Hans Hass and Jacques Cousteau have been an education for those watching television over the past forty years. These pioneers have been joined by many other programme makers, so that popular knowledge of the seas has been enhanced many fold in the latter half of the twentieth century. Films on the underwater world of lakes and rivers are less common.

Aquatic science also uses film and videorecording techniques and these may be from the photic zone or from any part of a water column if illumination is used. Cameras may be manipulated on site by free divers or aquanauts in submersibles and they may also be used in remotely operated vehicles (ROVs), responding to directions given from the surface [3.4.].

The earliest manned diving bells were connected to the surface with ropes and had attached air lines down which air had to be pumped. These devices appeared surprisingly early in the exploration of the sea but have now been replaced by sophisticated submersibles, like the pioneering ALVIN [3.5.], that can descend to great depths. On-board crews are protected within a pressure chamber and they manipulate arms, collecting devices and cameras. Some submersibles have satellite vehicles that are controlled from the parent craft and similar vehicles are lowered to the ocean bed from ships, being driven remotely from shipboard control rooms.

The use of submersibles is not confined to oceans and recent discoveries in deep freshwater lakes have been aided by the use of these vehicles. Obviously, the current velocity and shallow depth of rivers prevent submersibles being used to investigate these waters and slow-flowing rivers are often highly turbid.

There is increasing use of remote sensing using satellite images, enhanced by techniques developed for military purposes. GIS (Geographic Information Systems) allow investigation of the surface of water bodies, extending down into the superficial part of the photic zone. Combining satellite images with recordings at the water surface, and with closer aerial photography from aeroplanes, provides a powerful tool for recording large-scale changes in physico-chemical factors. It is this technology that allows us to measure changes in sea surface temperature and thus monitor El Niño events, or changes that result from global climate change. Use of GIS is not confined to the study of oceans. Analysis of colour patterns within many different types of water body also gives much information on the growth of algal blooms and the drying of lakes and rivers can be monitored. Satellites thus allow remote monitoring of environmental change.

In addition to its use with GIS technology, temperature is recorded in situ using thermistors and thermographs. There are also a large number of portable meters to measure pH, conductivity, oxygen tension and many other factors needed in studies within aquatic habitats. Current velocity is measured using flow meters and discharge by gauging weirs, for example. Dyes are used to follow the passage of water in rivers and they are also a means of recording patterns of flow in water.

Given the volume of water bodies, it is clear that we cannot measure the total number of organisms, or the total amount of other matter that is present. It is therefore necessary to take samples. It has been said that each study requires its own sampling strategy or sampling device. Nevertheless, we can group sampling methods into those used to investigate: the water column (for analysis of physico-chemical factors, microbiology, particles in suspension [both living and dead], and larger organisms of the pelagic); benthic sediments and the organisms they contain; and benthic solid substrata and organisms living on them.

The simplest way to obtain water samples in by means of bottles or buckets plunged into the water. There are many variants on this general theme, depending on the requirements of each study and the degree of precision required. Water bottle samplers, sometimes with attached thermometers, are in standard use for obtaining small water samples at known depth [3.6.]. The largest water samplers are automated and take samples in series under the remote control of shipboard scientists, the whole device being lowered from large derricks necessary to support its weight [3.7.]. The smallest and simplest water samplers are bottles submerged into a pond, using a thumb to cover their opening.

On occasions, samples are needed of the air-water interface and the surface microlayers that accumulate there. The simplest method is to use a sheet of glass, dipped into the water at an angle and slowly withdrawn. Hydrophobic materials adhere to the glass and are collected easily by scarping the glass with a wiper blade. Other approaches use Teflon strips and even model boats equipped with Teflon drums rotating past a scraper to collect materials into a small container.

The commonest method for sampling organisms within the pelagic of lakes and oceans, or within the water column of streams, is to use nets. The size of mesh of the netting depends on the size of the organisms under investigation. Commercial fishing nets and trawls [3.8.] are used to capture large organisms with decreasing fineness of mesh for the smaller plankton (the very smallest planktonic organisms being examined from water samples). The finer the mesh of the net the greater the resistance to its movement through the water, so too high a speed causes damming at the mouth of the net and potential failure of the net by tearing. If sampling is to be quantitative, a means of measuring the velocity of water through the net is an option as it allows the volume of water entering the net to be estimated.

Of necessity, plankton netting is conducted over small distances but various methods have evolved for looking at oceanic plankton using special samplers towed behind commercial ships. Their design must cope with problems presented by the speeds of these vessels and it is essential that the mouth of the sampler is parallel to the ocean surface. Several samplers meet these requirements but they do not give quantitative samples, rather a record of large-scale patchiness of plankton along line transects.

Sometimes we need to investigate the dynamics of processes within the water column, e.g., the sedimentation of particles or movements of plankton over time. Bottles and nets can be used for each approach but we can also monitor changes in situ using sediment traps or sonar. Sediment traps [3.9.] are usually tubular and should have a high aspect ratio (i.e., with height : diameter preferably > 5). They are anchored on to lines suspended from the surface and provide a region of still water within the trap into which particles sediment and from which they cannot be removed by currents or other disturbances within the water column. When traps are sealed and returned to the surface their contents represent an integration of the total number of particles sedimenting at the depth of the trap in the time period used. In addition, sediment traps are located into the bed of oceans, lakes and rivers to record the numbers and type of particles reaching the substratum. When used in this way, sediment traps contain some particles that have become re-suspended and care is needed in analysing data from traps in beds.

Sonar allows movements of organisms to be monitored within the water column [3.10.]. Modified from military origins, sonar provides an important method of tracking fish and is used both by commercial fishermen and by recreational boat anglers. Sonar has also been used to track vertical movements of plankton (when they are found in sufficiently high numbers to give a sonar trace) and is even used by those looking for large dinosaur-like reptiles said to lurk in the depths of some lakes.

Sampling the sea bed for large organisms is carried out using trawls and dredges that are towed by ships [3.11.]. At abyssal depths this becomes impossible as the mass of the towing cables is too great and submersibles must then be used. Trawls and dredges developed for commercial catching of fish and shellfish are brought onto the deck of the towing ship and the catch released for counting and measurement.

Smaller-scale catches are made using grabs, small dredges and cores. Grabs vary in size from very small devices that take a bite of a few cm² from muddy substrata up to large ship-borne marine grabs that take a bite of over 1 m². Small grabs only work effectively when the substratum consists of fine mineral grains, larger particles causing much reduced efficiency as they prevent correct closure of the jaws. If quantitative samples are required this problem needs to be borne carefully in mind, especially as the operation of grabs is not seen in situ in lakes and the sea and their efficiency is often assumed. Like their larger commercial relatives, small dredges are towed over the substratum and bite into it to remove a strip. Just like grabs, their efficiency varies with type of substratum, their mass, and the ease with which they can be deflected. Cores are usually taken in shallow water as most corers are hand held. They take a vertical section of substratum and are useful for looking at laminated deposits and the remains of organisms contained within them. In deeper water, corers must be lowered from ships or piers [3.12.] and a considerable weight is required to drive them into sediments.

Benthic organisms on solid substrata usually need to be dislodged. The solid substratum of streams and low-order rivers frequently consists of stones and pebbles under which animals shelter from the current. As the water is flowing, it is possible to disturb these organisms into a net or screen [3.13.]. The disturbance may be by kicking into the substratum with a boot ten times, or by manual removal and washing of stones within a quadrat of known size. The water current sweeps organisms into the net and the lower limit of size is then met by the net mesh size. Care must be taken to remove organisms that are attached to stones and the method loses efficiency when current velocity is slow as motile organs then easily escape. In this case, sweeping the net through disturbed sediments aids collection.

Quadrats of various sizes are used to record plant density, and scrapings of stone surfaces used to investigate the microbial community. This technique is also used to obtain estimates of the numbers of organisms on rocky marine and lake shores, especially as some organisms have attachment devices that make them difficult to dislodge, and thus collect, by other means.

Measurements of physical factors such as temperature, pressure, etc. are taken at the sampling site, and samples from the water column can then be analysed for chemical contents, e.g. for carbon, nitrogen, dissolved free amino acids, or many other inorganic and organic chemicals. Conductivity, pH and biochemical oxygen demand (BOD) may also be recorded. A subsample of the whole sample is sometimes used or the sample may be filtered or centrifuged, further analysis being carried out after fractionation. There is a large literature on methods of chemical analysis of water and suites of analytical techniques are used according to need.

Particles are analysed according their chemical constituents, or categorised as being organic or inorganic. Some of the organic particles are living or recently dead organisms that can be identified keys and the binomial system of classification. Micro-organisms are frequently identified after culture, but not all can be cultured in this way. Viruses are not living particles but they do replicate and they are now estimated in some studies.

It is important to note that many organisms can only be counted after they have been removed from particulate material in collections. The "picking" of organisms is often a laborious process. Sorting is speeded up by flotation in a liquid that supports organisms but not mineral particles, or by the use of subsampling. The accuracy of each subsampler must be known if quantitative estimates are required.

3.1. http://www.gofishing.co.uk/upload/24098/images/aquascope-2.jpg
3.2. http://brassgoggles.co.uk/images/LeonLyons.jpg
3.3. http://oceanexplorer.noaa.gov/explorations/02sab/background/products/media/natprod1.html
3.4. http://www.eca-robotics.com/photo/ecatalogue/593-1.jpg
3.5. http://oceanexplorer.noaa.gov/technology/subs/alvin/alvin.html
3.6. http://www.oktopus-mari-tech.de/wpn-e.html
3.7. http://www.seabird.com/products/spec_sheets/32data.htm
3.8. http://isiria.files.wordpress.com/2009/03/bottom-trawling.jpg
3.9. http://www.whoi.edu/cms/images/oceanus/2006/2/trap_diagram_19735.jpg
3.10. http://www.washington.edu/news/2009/03/18/deimos-joins-mars-and-its-satellite-of-instruments-on-seafloor/
3.11. http://www.photolib.noaa.gov/fish/
3.12. http://paleomag.uqar.ca/spip.php?article56
3.13. http://www.epa.gov/region1/lab/reportsdocuments/wadeable/equipment/macro.html