Environment and development
in coastal regions and in small islands

Coastal management sourcebooks 3
Part 3
Habitat Classification and Mapping 

11 Mapping Coral Reefs and Macroalgae Part B

Field survey methods  


The subject of sampling coral reefs is vast. Methods for describing coral reefs have been developed for decades and it remains an active area of research even today. Like any sampling problem, the choice of method is intrinsically linked to the spatial and/or temporal scales of the sampling objective. For example, methods for measuring fluctuations in living coral cover are far more intense than those for describing the main characteristics of reef along a continental shelf. A full description of sampling methodologies is beyond the scope of this Handbook and readers are referred to existing texts for a more thorough treatment of the subject (e.g. Stoddart and Johannes 1978, English et al. 1997, Rogers et al. 1994).

This section will provide a general overview of reef sampling methods and comment on their suitability for use in a remote sensing context. The chapter ends with a brief section on statistical issues such as determining the number of samples required.  

Survey methods for broad-scale characterisation of coral reefs  

If the mapping objective focuses on reef geomorphology and/or major habitat types, then the survey methods should be simple, quick and able to cover large areas. Given that the descriptive resolution of satellite imagery is confined to this type of general information on coral reefs, these techniques are probably best suited to most satellite remote sensing operations.

Broad-scale characterisation of coral reefs often makes use of an ordinal abundance (cover) scale of reef categories which are assigned by a diver or snorkeller. The survey is conducted by being towed behind a vessel (the manta tow technique) or simply swimming across the reef profile (plotless belt transects).  

The manta tow technique  

The manta tow method has been widely used in Micronesia and the Great Barrier Reef for assessing broad-scale changes in reef cover due to cyclone damage, coral bleaching and outbreaks of the Crown-of-thorns starfish, Acanthaster plancii. A good synopsis of the method is given in English et al. (1997) which forms the basis of the following description.

The manta board (Figure 11.9) is attached to a motor boat with a 17 m length of rope which has buoys placed at distances of 6 m and 12 m from the board. A snorkeller grips the board and is towed for approximately 2 minutes, at the end of which the boat pauses to allow the surveyor to record data (usually on water-resistant paper). The coverage of bottom features may be recorded on a percentage scale (for an example, see Figure 11.10) or on a scale of 1–5, where 5 indicates the greatest cover and 0 is used for absence. However, a scale of 1–5 does have the short-coming that observers may be tempted to place a disproportionately large number of values in the middle category (i.e. 3),thus creating observer bias. If possible, a scale of 1–6 or 1–4 is more desirable (see Kenchington 1978). 

Figure 11.9 Detail of the manta board and associated
equipment. It is recommended that the board be made 
from marine ply and painted white. Two indented handgrips
are positioned towards both front corners of the board and 
a single handhold is located centrally on the back of the board. 
Redrawn from: English, S., Wilkinson, C., and Baker, V., 1997, 
Survey Manual for Tropical Marine Resources, 2nd Edition. 
(Townsville: Australian Institute 
of Marine Science).  

Estimating percent cover

Figure 11.10 Estimating percent cover on the benthos using a metre-square quadrat with string or fishing line strung across at 10 cm intervals. In each example, shaded regions represent different types of substratum that are included collectively in the total percent cover estimate. Based on a drawing in: Rogers, C., Garrison, G., Grober, R., Hillis, Z-M., and Franke, M.A., 1994, Coral Reef Monitoring Manual for the Caribbean and Western Atlantic. (St. John: National Park Service, Virgin Islands National Park).  

Features which should be amenable to this type of survey include:

Living biotic features Substrata Others
live hard corals
soft corals
dead coral


 Plotless belt transects  

The principle of plotless belt transects is similar to the manta tow, the main difference being that observers are not towed behind a boat. This affords a useful means of independence allowing the use of scuba and permitting very shallow areas to be surveyed safely. Since the observer can get much closer to the sea bed, it is possible to record more detailed data on bottom features. In the species-rich Indo-Pacific, this may include coral and algal lifeforms (for examples, see English et al. 1997) and species or genera in the Caribbean.

Like the manta tow method, the logistical requirements for surveys are fairly simple and given adequate training, useful data can be collected by relatively inexperienced individuals. The UK-based organisation, Coral Cay Conservation has successfully adopted this principle to conduct surveys of reef habitat throughout Belize and the Philippines. After seven days intensive training, volunteer divers were able to conduct species-level surveys of Belizean coral reefs with a moderate degree of accuracy and precision (Mumby et al. 1995b) which is probably all that is required for most habitat mapping purposes.

Surveys are conducted along profiles which tend to run either parallel or perpendicular to the reef crest. The former approach is useful for describing individual reef habitats (zones) and the latter provides data on habitat zonation. Surveys are directed using a compass bearing. The width of the surveyed area (i.e. the belt width) is estimated visually but should not exceed 4 – 5 m beyond which, recognition of benthic cover becomes difficult. Distances along the survey can be estimated by counting fin strokes and multiplying these by the average distance travelled per kick cycle. However, it is easier and more accurate to use a 10 m line and survey in short ‘hops’.

Survey teams of 2 – 4 divers are used for safety reasons and to delegate survey responsibilities (e.g. into corals and macroalgae). Plotless belt transects and manta tow methods may use the same recording scales.  

Additional data to record  

  1. Location: The start and end locations of surveys should be located with a global positioning system (preferably with a differential capability, see Chapter 4).

  2. Water visibility: Visibility of the water should be noted because it may influence the interpretation of imagery and help explain areas which prove difficult to map. Visibility can be estimated in the horizontal plane by noting the visibility of buoys along the manta tow line or by holding a Secchi disc 0.5 m below the surface and seeing at what horizontal distance it remains visible.

  3. Date and time: Recording the date and time allows data to be catalogued and tidal heights to be compensated for (e.g. in bathymetry studies, Chapter 15).

  4. Depth: Depth can be measured using a weighted plumb-line (cheap approach) or an echo sounder (more expensive option). A number of manufacturers (e.g. Scubapro) produce cheap hand-held sounders which give accuracies within about 0.10 m (see equipment costs, Chapter 19).  

Survey methods for estimating coral and macroalgal cover  

For more detailed habitat mapping where habitats need to be described quantitatively, a suite of methods are available. These are more likely to be appropriate for high resolution imagery such as CASI or aerial photography. With adequate replication, most of these methods can also be used to monitor changes in bottom cover. The methods are all fairly time-consuming and the most accurate and precise methods tend to take longer. As such, quantitative sampling regimes are usually limited to smaller areas. There are four principal groups of methods for measuring coral and macroalgal cover; quadrats, photo-quadrats, line intercept transects, and video. These will be considered in turn.  


Quadrats are extensively used for sampling in all branches of ecology and many approaches are available (reviewed by Greig-Smith 1983). For coral reef assessment, quadrats usually have a minimum area of 1 m2 and are divided into a uniform grid of 100 segments (i.e. if the quadrat has a side of 1 m, each cell in the grid has dimensions of 10 x 10 cm). Every cell represents 1% coverage in the sampling unit (see Figure 11.10 and Figure 11.11, Plate 14). Quadrat size can be reduced to (say) 0.25 m2 if the main sampling objective is to estimate the cover of macroalgae.

Compared to most other quantitative sampling techniques, quadrats have the advantage that data are acquired relatively rapidly and cheaply in the field. The main disadvantages of quadrat sampling are (i) quadrats cannot be used to measure spatial relief (rugosity),(ii) large branching corals such as elkhorn coral (Acropora palmata) are difficult to sample, and (iii) quadrats only provide data on a two-dimensional surface thus underestimating coverage of features which have a predominant orientation in the vertical plane (e.g. soft corals). However, although the latter limitation is pertinent to ecological assessment, it may in fact be advantageous in the context of remote sensing where the sensor also samples a two-dimensional (flat) surface.  


Photo-quadrats are good for coral monitoring programmes but are not recommended for the purposes of field survey. Although they can provide accurate information on reef cover (particularly if taken in stereo pairs), analysis of photographs can be time consuming. Readers interested in the technique should refer to Rogers et al. (1994).  

Line intercept transects  

Like quadrats, line intercept transects are fairly rapid to deploy in the field. A fibreglass tape measure is laid close to the reef contour and the length (cover) of each reef category is recorded. A faster variant is the point intercept transect in which only the type of reef category is noted at equidistant points along the line (e.g. every 20 cm). The cover of each category is calculated by the ratio of number of points per category to the total number of points. The main limitation with line and point intercept transects is that they tend to under-sample heterogeneous areas with low cover of reef categories (e.g. areas of scattered corals).  

Video transects  

Underwater video is well-suited to field survey because large areas can be covered fairly quickly and the method can be used without extensive training. It also has the additional advantage of producing a permanent visual record of the data. A variety of methods exist for using video; the following description is taken from Carleton and Done (1995) who have used the method for monitoring coral reefs of the Great Barrier Reef.

A National video camcorder (Model NV-MC5A) with an in-water depth of field ranging from a few centimetres to infinity is used with VHS C-format video tapes. The camera is mounted in a ‘Video Sea’ underwater housing which is attached to a manta board for ease of use by scuba divers. The video is pointed directly at the seabed and held between 1 m and 1.5 m from the substratum. Diver and video are towed on a 30 m line behind a boat at ~ 1 m.s-1.

Data are analysed using the software ‘VIPS’ (Video Point Sampling) which allows the operator to pause the tape at random or evenly spaced intervals and place points at random or fixed locations of the monitor. To improve image quality, the output from the video can be ‘gen-locked’ (paused) with an Amiga Commodore 500 computer. Carleton and Done (1995) found that, for 200 m transects, the optimal processing method was five sub-samples of 110 random points or one subsample of 550 points.

The main drawbacks of video are the cost of equipment and processing facilities. It should also be borne in mind that species recognition is not usually possible with video. Most interpreters might expect to identify taxa to life-form, family or possibly genus levels.  

Survey methods for measuring macroalgal biomass  

Macroalgal biomass may show marked natural variation over a reef and seasonally. However, a dramatic increase in macro a l gal biomass may be indicative of increased levels of nutrients in the water (e. g. from sewage effluent) or reduced grazing pressure by overfishing of herbivorous fish (e. g. parrot fish).

Average macroalgal biomass can be estimated by collecting and weighing algae in a random sample of 15 or more 0.25 m2 quadrats (Rogers et al. 1994). For most purposes, wet weight is sufficient.  

Determining sample size  

A pilot study should be used to determine the number of replicates required to sample each of the main habitats adequately. This phase can be avoided if relevant details are available in the literature. Calculating the desired sample size depends on the objective of the sampling. If the aim is simply to represent the presence of most benthic features and species, a species area curve can be plotted (Figure 11.12) from a preliminary sample of (say) 20 quadrats. Samples are selected at random and the cumulative number of species (and substrata if necessary) plotted against quadrat number. The asymptote (levelling off) marks the required number of samples to represent most of the species of interest. Species area curves can also be used to determine the required length for line transects (in which case, cumulative species number is plotted against number of metres of transect traversed).

Figure 11.12 Species area curve for 20 
quadrats showing the minimal sampling 
area to represent all species.  

While being useful for general guidance, species area curves do not describe the accuracy or precision with which reef parameters are estimated from the samples. For example, sampling might be used to estimate the percentage cover of coral on a reef. The confidence of the estimate would be expected to grow as more of the reef is sampled (i.e. as sample size increases). In many cases, the required confidence is specified before undertaking sampling. Precision refers to the degree of concordance among a number of measurements for the same population (Andrew and Mapstone 1987). Precision depends on the variability of the item(s) being sampled and the degree of confidence required (Type I error). There are several equations available to calculate sample size based on these criteria and an example is given in Box 11.1


Estimation of sample size needed to achieve a stated precision in estimating a population mean (modified from Zar, 1996)

An estimate of population variance (s2) is required which can be obtained from a pilot study or the literature. The method requires access to basic statistical tables and uses an iterative approach:


where n is the sample size, s2 is sample variance (calculated with v = n -  1 degrees of freedom), is the two-tailed critical value of Student’s t with v = n - 1 degrees of freedom and d is the half-width of the desired confidence interval.

Worked example (adapted from Zar 1996): suppose we wish to estimate the density of soft corals with a 95% confidence interval no wider than 0.5 m-2, then d = 0.25 m-2, and suppose the variance (s2) of soft coral density was found to be 0.4008.

We begin by guessing that a sample size of 40 is necessary in which

We estimate n to be:

Next we estimate n to be 27, for which giving:  

Since the output agrees with our suggested sample size, we conclude that an adequate sample size is 27.  

If sampling is being planned with a specific hypothesis in mind, the pilot study is extremely important. Such a consideration often arises in a monitoring context where (say) coral cover is being compared over time or between sites. In this case, the investigator may wish to know the sample size required to test for a specified change in the parameter being measured and with a desired level of confidence in doing so correctly. For example, one might ask: ‘How many quadrats must I sample to have a 95% chance of correctly detecting a 10% change in coral cover between two reefs?’ This type of question is addressed using ‘power analysis’ and depends on the power of the statistical test being proposed, the variability in the data, the size of change being detected and the confidence of avoiding a Type I error. Since this is unlikely to be an issue in remote sensing, readers are directed to Zar (1996) for further discussions and methods.  


Satellite sensors seem to be capable of mapping the geo-morphology of coral reefs but poor at mapping ecological habitats including assemblages of reef-dwelling species and macroalgal beds. Infra-red aerial photography can be used to assess coral and macroalgal cover in shallow water environments (< 1 m depth) such as reef flats. However, to achieve such detail, the aircraft must fly at low altitude and this technique is best-suited to small areas (e.g. individual reefs).

Compared to infra-red film, true-colour aerial photography has a much greater penetration of water (up to approximately 25 m in clear water) and can be used for habitat mapping. If habitats are being defined in detail, such aerial photography appears to permit more accurate mapping than satellite sensors. However, for more general habitat mapping, multispectral classification of satellite imagery and visual interpretation of true-colour aerial photography achieve similar accuracies. In which case, satellite imagery is likely to be more cost-effective because multispectral classification of digital data is a much faster method of habitat mapping than visual interpretation of photographs. In addition, satellite imagery is much cheaper than the acquisition of new aerial photography. Even if habitat maps must be created using visual interpretation of imagery (e.g. if image processing facilities are unavailable),satellite imagery would be more appropriate than aerial photography for coarse and medium-detail habitat mapping. Although map accuracies are similar for both image types, satellite images cover a much larger are a than individual aerial photographs, thus increasing the availability of ground control points and facilitating geometric correction of the map .

The airborne digital sensor, CASI, provides significantly more accurate habitat maps than satellite sensors and is at least as accurate as aerial photography. With the exception of infra-red aerial photography of shallow waters, CASI is the only method discussed here that achieves high accuracies (> 80%) for coral and macroalgal habitats, and habitat spectra can be recorded to a depth of at least 18 m.

Field survey methods for coral reefs and macroalgae correspond to the scale of remotely sensed imagery. For general-purpose habitat mapping with imagery of medium to coarse spatial resolution such as Landsat TM, SPOT XS or Landsat MSS, broad-scale survey methods such as manta tow or plotless belt-transects are appropriate. The cover of benthic features is usually recorded on a categorical scale. Imagery with greater spatial resolution, such as CASI, warrants more intensive sampling methods such as quadrats, line intercept transects or underwater video.  


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