STANDARDISED SURVEY PROCEDURES

FOR MONITORING SHALLOW TEMPERATE

ROCKY REEF COMMUNITIES
TABLE OF CONTENTS

INTRODUCTION 3
SURVEY EQUIPMENT 7
BEFORE THE SURVEY 8
SITE AND SURVEY DETAILS 9
METHOD DETAILS 15
THE FISH SURVEY (M1) 15
THE INVERTEBRATE SURVEY (M2) 19
IN SITU QUADRATS (M3) 24
ADDITIONAL METHODS 26
DATA ENTRY 33
APPENDIX 1 - INVERTEBRATE/CRYPTIC FISH FAMILIES 36
APPENDIX 2 - METHOD 3 CATEGORICAL GROUPINGS 38
APPENDIX 3 - SURVEYS IN SPECIAL CIRCUMSTANCES 41
REFERENCES 45

2
 INTRODUCTION

This manual describes the Underwater Visual Census (UVC) methods for estimating densities of fishes, large
macroinvertebrates, sessile invertebrates, and seaweeds on rocky reefs adopted by the Australian Temperate Reef
Collaboration (ATRC, https://atrc.org.au/). This survey technique was established by Graham Edgar and Neville Barrett,
has been utilised for annual surveys of Marine Protected Areas since 1992, undertaken by University of Tasmania staff in
collaboration with government conservation and fishery agencies in Tasmania, Victoria, New South Wales, South Australia
and Western Australia. Over 680 sites have now been surveyed using the ATRC methods (Edgar & Barrett 1997, 1999,
Barrett & Buxton 2002), some with more than 30 years of annual replicate data. The data continues to inform government
reporting and research regarding Marine Protected Areas, long-term changes in biodiversity, reef health, and key species
with respect to climate change, fishing, and other anthropogenic impacts (Stuart-Smith et. al, 2017, Edgar et. al, 2020).
Compatible methods are now applied globally by Reef Life Survey, a non-profit citizen science program
(https://reeflifesurvey.com/) and data from both programs are collated by the National Reef Monitoring Network (NRMN),
providing the most extensive and comprehensive marine species dataset of this kind in the world.

3
 INTRODUCTION

Underwater Visual Census (UVC) techniques provide an effective, non-destructive way to monitor species at shallow-
water sites because large amounts of data on a broad range of species can be collected within a short dive period, with
little post-processing time required. The broad taxonomic range covered allows detection of human impacts affecting
different levels of the food web, making these methods ideal for assessing and monitoring the effectiveness of
management actions such as the declaration of Marine Protected Areas (MPAs), or the ecological consequences of
localised pollution or ocean warming.
Monitoring programs associated with marine protected areas (MPAs), such as this one, need to cover a range of taxa
because, in addition to heavily exploited species that are predicted to recover in new sanctuary zones, significant flow on
effects of fishing associated with increased predator numbers may occur that would otherwise go undetected. For MPAs,
the same sites should be investigated during different survey periods, with sampling repeated whenever possible in the
same month in different years to minimise seasonal effects.

4
INTRODUCTION
These survey methods were designed to maximise
the amount of ecological information related to all
conspicuous taxa that can be obtained during a dive
with a single tank of air, based on a 2 - 4 person
dive team.

Typically, sites are surveyed at 5m and/or 10m

contour depths. At core sites, visited every 1-2
years, the same depth(s) are surveyed every time,
starting from the same GPS point. For MPAs there
will be number of sites within protected zones and
some nearby where fishing is permitted.

A trained dive team usually surveys three sites per

day comfortably, depending on the biological
complexity of the sites and the weather conditions.
Tasks are divided between divers based on
biological knowledge of the area, survey skills and
experience.

5
INTRODUCTION

The basic unit monitored at each site is a 200 m long transect line, subdivided into four 50 m lengths, that is set along a
defined depth contour. Along the transect line three core survey methods are applied, each focusing on different major
taxonomic groupings (Method 1 for fish, Method 2 for macro-invertebrates and cryptic fish, and Method 3 for sessile
invertebrates and seaweeds). The width of survey area is different for Method 1 and Method 2, and Method 3.
Because data can vary with relatively slight modifications to protocols (e.g. with different transect band-width or diver
swimming speed for fishes), it is important that these methods are consistently applied. Data generated are most usefully
applied in a relative sense (i.e. for comparing sites or times when data are collected using the same methods). Data
collected by different divers on a field trip should be compared for consistency between divers as soon as possible,
particularly during early surveys.

6
SURVEY EQUIPMENT

➢ 2 x 100 m lead core transect line (better for sites with surge),
or 4x50 m fibreglass transect lines, marked with distance
measures

➢ 2 quadrats, 50 x 50 cm with 7 stainless wires each direction

➢ Calipers (plus spare) for measuring abalone and lobster sizes

➢ Camera for identification/reference photos

➢ Either catch bag or clips on BC to hold slate & transect line.

(It is very important to be able to clip your slate onto your BC to
allow the use of two hands during the invertebrate/cryptic fish
survey when surveying in kelp).

➢ Slate, pencil (and a spare pencil) and waterproof paper.

➢ GPS to record site position.

➢ Marker float for GPS position when not anchoring on site.

7
 BEFORE THE SURVEY
Prior to all surveys, dive teams need to be clear on dive safety procedures, both to minimize the risk of problems
developing, and so that participants all know what actions are required if an accident does occur. Safety margins should
be factored into all dive plans, and buddy checks completed before entering the water. Each diver must be certain of
what they are doing and where they are going.

It is essential that all members of the group collaborate and record the same general site details on each datasheet,
and that datasheets of buddy pairs have all survey details exactly matching (i.e. Site Name, Site Number, Latitude,
Longitude, date, Depth, and Direction). If this information is not recorded before the dive, then it must happen directly
after the dive.

For example:
• Assess the site for conditions needed for a successful survey i.e. swell, visibility, diver safety. Complete relevant on-site Assessment and
Hazard Checklist.
• Dive briefing: ensure team members are aware of the dive plan, tasks, risks associated, and clear on the relevant dive safety procedures.
• Ensure the field team and trip plan has been lodged and approved by relevant safety officers, and that all staff and volunteers are aptly
qualified and able, and that the appropriate equipment is available prior to leaving.
• Be sure that all relevant site information (i.e. date, depth, site name, site code, time, GPS, transect direction, buddy, is recorded on each
diver’s data sheet).
• Conduct relevant dive safety checks, as per protocol, including buddy systems and risk mitigation/safety margins relevant to the dive.

8
SURVEYING A NEW SITE

Transects should be positioned on hard substratum (patches of sand or silt are acceptable, but aim for at least 90%
hard substratum).

Select reefs that extend for at least 200 m along a given depth contour, usually 5 or 10 metres however other
depths may be chosen due to reef structure or exposure to prevailing swell conditions. Anchor, or place a surface
marker buoy, in the middle of the reef (or midpoint of where you want the transect to run).

Record the position where the transect line is to start in decimal degrees to 5 decimal places using WGS 84. [Note:
a boat at anchor will sit away from the anchor], and a local site name based on geographical features.

A hand drawn “mud map” can be useful, indicating reference points in relation to the shore and the layout of the
transect line where the reef contour is convoluted. If relevant, it is important that the direction of the lines from the
midpoint or the GPS point is recorded so that if the transect is resurveyed at a later date then the line will be placed
in the same direction.

9
RE-SURVEYING AN EXISTING SITE
Most ATRC surveys resurvey an existing site, in order to gather data to compare over time. If resurveying an
existing site, the site code and name and the GPS coordinates should be obtained from the program data officer.

If conducting a re-survey of an existing site it is crucial to go to the EXACT GPS coordinates associated with that
site. If safe to do so anchor on it. If it is not safe to do so, leave a weighted marker float at the GPS point. If the
GPS coordinates are incorrect and the site location is adjusted, record new coordinates on the dive data sheet for
that site. Consider any large tidal variations when assessing the depth of the site, as compared to the original
surveys.

10
 SURVEY METHODS

A single complete 50 m survey consists of the following

components:

➢ METHOD 1: Fishes are surveyed in two 5 m wide by 5

m high bands or (“blocks”), parallel with each 50 m transect
length.

➢ METHOD 2: Invertebrates and cryptic fishes are

surveyed in a 1 m wide by 2 m high band on one side of the
transect line.

➢ METHOD 3: Sessile invertebrates and

macroaglae are surveyed in-situ using 50x50cm
quadrats, completed at 10m intervals along the transect
line (i.e. 5 per transect)

11
SURVEYING A SITE – Recording data

Record the following header information: date, depth of transect, diver name, site name, time, direction, buddy, and
visibility (measure this out along the line during dive)

Four 50m transects, laid end to end along a depth contour, are surveyed at each site. As well as dividing the data into
transects, the fish data are separated into blocks either side of the line. It is important to ensure both buddies have the
appropriate transect number and block number next to their recorded data, and that all transects and blocks are
accounted for. Record what method, transect (T1, T2, T3, T4) and block (B1, B2) you are working on and make a clear
distinction (draw a line) between data for different transects and blocks.

If you have only done part of a transect make a clear note about where you are up to and who (if anyone) has done the
rest. Add the extra data for the transect from the other persons sheet as soon as you get into the boat if possible.

Land

Fish survey area

Invertebrate survey area
Algae quadrats

5m

1m T4, B2 T3, B2 T2 , B2 T1, B2

100 m 50 m 0m 50 m 100 m

T4, B1 T3, B1 T2 , B1 T1, B1

12
SURVEYING A SITE – Laying the transect
Lay the transect along the reef contour, as close as possible to the agreed depth (note most divers swim approximately
1 m off the bottom when laying the line, so the depth gauge of the diver should read 1 m less than the desired depth or
the transect will end up too deep). On steep surfaces, to hold the line in position you may have to wrap the transect line
around an algal holdfast or rock in some places. This is particularly important where there is a wall or drop off.

If you run into extensive sand or soft sediment then change direction, following inside the reef edge (keeping 2.5 m
inside the reef edge if possible so that the full width searched for fish remains over reef substratum). In these
circumstances avoid sharp angles and if the line ends up parallel to itself make sure there is a least a 6 m gap. In some
cases the reef edge will become progressively shallower, in which case it is best to stay inside the reef rather than
extend the transect over sand. The actual depth range of the transect should then be recorded on data sheets (e.g. 3.8-
5.0 m rather than 5 m).

If the reef is very flat it may be necessary to take a bearing of the coastline before descending from the surface, or take
notice of the sun angle. Check the depth and then lay the transect line along the bearing, in order to avoid
inadvertently swimming in an arch or circle

13
SURVEYING A SITE – Division of labour

Workload is divided between members of

the dive team in a way that optimises
efficiency.

Division of tasks thus depends largely on

the size of the team, who is skilled in what
disciplines, depth and survey location
(some locations take longer for particular
taxa). It is also optimal to avoid only one
person collecting the data for a method at a
site, to minimise any diver-bias.

Figure 2 show a possible division of labour

for a four person dive team with 2 people
competent at surveying macroalgae and
sessile invertebrates (M3) and fish (M1),
and 2 divers competent at surveying fish
(M1) and invertebrates and cryptic fish
(M2).

Figure 2: Possible division of labour for a 4 person dive team.

14
METHOD 1 – FISH SURVEYS (M1)

TARGET GROUP: All fishes and other large swimming animals (e.g. squid, octopus, jellyfish, seals, turtles, whales etc.)

During the fish survey, the number and estimated size-category of all fishes sighted within 5 m blocks either side of the
transect line, and within a 5 m high ceiling (and 5 m deep floor if applicable, see section on methods for surveying walls
in appendix 2 ) is recorded as the divers swim slowly along the block. The deeper side of the line is referred to as “Block
1” or “B1”, and the shallower side, “B2”. Data for the two blocks are collected and recorded separately whether done by
one or two divers.

Size-classes of total fish length (from snout to tip of tail, or longest distance, including for stingrays) used are 2.5, 5.0,
7.5, 10.0, 12.5, 15.0, 20.0, 25.0, 30.0, 35.0, 40.0, 50.0, 62.5 cm, and above. Lengths of fish larger than 62.5 cm should
be estimated to the nearest 12.5 cm and individually recorded.

Fish species sighted outside of the 5 m blocks, or at a time other than during the fish swim should be recorded
separately—particularly if they are rare or may be outside of their usual distributional range. These species when seen
“off-line” should be recorded as “method 0” (see page 20).

15
METHOD 1 - TECHNIQUE

Visualise a 5 m wide and high “tunnel” (bordered along

one edge by the transect line). Divers swim along the
middle of this about 1 metre from the seabed, but can
move to the right or left to search the entrances to caves
and under ledges (see figure 2). [As a reference, the
distance of 2.5 m is approximately the length of a tall diver
with arm outstretched in front from fin tip to finger tip, but
you should measure this on yourself to become familiar
with this distance]. Divers should practise estimating
distances underwater under varying visibilities.

Figure 2. Stylised representation of method 1 survey technique

Record the size and number of individuals of all fish species seen within the block.

If identification is not possible, then take a photograph, draw a picture, and/or write a descriptive note (the more
information the better). Be sure to ask others/check books at the end of the dive. Do NOT ignore unidentified species.
Make a record of any fish you see that you can’t identify but are sure is different from other species recorded. It is much
better to include (e.g. as unidentified member of a particular genus or family) than make no record at all – it is still
important species richness information.

16
 METHOD 1 - TECHNIQUE

• Where fish are schooling, estimate abundance by counting a subset and then multiplying by the number of similar subsets
you would estimate to fit into the school.

• Don’t count fish that overtake you.

• If you recognise the same fish that has been recorded in the other block (i.e. see a fish that has obviously moved across
the transect line), still record this animal (this balances out other fish that moved across the line in the opposite direction,
and were not counted), but don’t re-record one that you know you have already counted within the same block.

• As best as possible, avoid counting fish when there are other divers in close proximity as this can affect fish counts (plan
dives so fish counts can be done with minimal disturbance). If sea lions or other large marine mammals are around, then
make sure that their presence is noted on data sheets since this can greatly affect the fish survey.

17
METHOD 1 – HOW TO DEAL WITH HIGH DIVERSITY AREAS

Surveys of high diversity areas, such coral reefs, requires substantially more survey experience,
preparation and attention to detail. In such areas, when it is impossible to record counts for all
fishes seen, there is a defined order of priority for accuracy of information.

➢ Priority (1): get an accurate species list; i.e. record the names of every new species seen before worrying
about anything else

➢ Priority (2): individually record the abundance and size of large or rare species

➢ Priority (3): estimate of abundance of other species

➢ Priority (4): partition abundance estimates among estimated size classes for other species

Note that all of these components must still be undertaken by the end of the fish survey (before starting Method 2),
but that they should be done in this order, often with the last two priorities done at intervals along the line or at the
end of the line if necessary.

18
METHOD 2 – MACROINVERTEBRATE & CRYPTIC FISH SURVEYS (M2)

TARGET GROUP: Mobile invertebrates and fishes in families likely to be overlooked

in M1 (see next slide for details on the target group)

Large macro-invertebrates (large molluscs, echinoderms and crustaceans) and cryptic

fishes (i.e. inconspicuous species closely associated with the seabed) are censused
along the same transect lines set for fish surveys. During M2 searches, divers swim
along the bottom, counting all mobile macro-invertebrates within 1 m horizontal
distance of the line, to a maximum of 2 m height above or below the line on steeply-
sloping reefs. Data for the two blocks (either side of the line) are recorded separately.

A mental tally of the number of the most common two or three species can be kept to
KHVT
minimise the number of times you need to stop to make a record on the slate, but at
locations where large numbers of macro-invertebrates (particularly sea urchins) are
present, divers should write down data on the underwater slate at least each 5 m
along the transect line.

Size information is not required for invertebrate species, with the exception of lobsters
and abalone, for which the carapace length and shell width should be estimated,
respectively.

Record size information for all cryptic fish.

The invertebrate and cryptic fish data are analysed separately from the fish survey, so
any cryptic fishes that may have already been recorded on the M1 fish survey should
still be re-recorded in M2.

19
 METHOD 2 – MACROINVERTEBRATE & CRYPTIC FISH SURVEYS (M2)

Target group details (also see Appendix 1)

➢ ‘Large’ invertebrates refers to those that are more than 2.5 cm (approximately 1 thumb tip) when mature.

➢ Invertebrates counted include large molluscs (e.g. nudibranchs, abalone and whelks, giant clams, scallops), echinoderms
(e.g. feather stars, sea cucumbers, sea stars, sea urchins) and crustaceans (e.g. lobsters, large crabs and hermit crabs).

➢ Cryptic fishes are those closely associated with seaweeds or the seabed such as gobies, blennies, triplefins, cardinal
fishes, scorpionfishes, frogfishes (anglerfishes), cat sharks, rays, and moray eels. All families considered cryptic and to
include in M2 are listed in Appendix 1.

➢ Fishes not regarded as cryptic, hence not generally counted in M2, include wrasses and damselfishes, for which method 1
provides better density estimates. If such species are seen during M2, but were not recorded during M1, they can be
recorded as “Method 0” (see slide 20) – but never added to M1 datasheets afterwards.

➢ Invertebrates not counted include any species permanently attached to the seabed other than scallops, pearl oysters or
giant clams. Thus, edible oysters, mussels, sponges, anemones (other than the large ‘swimming’ anemones), barnacles
and corals are not counted. Small (<2.5 cm) molluscs also are not counted, as these can occur in very high abundance
and take up too much dive time. Small abundant shrimps (<2.5 cm) are also not counted, nor are brittlestars and chitons,
even if they grow larger than 2.5 cm.

20
METHOD 2 - TECHNIQUE

➢ Stay close to the bottom and push aside any seaweeds to reveal the substratum. If large seaweeds are present, it
usually helps to clip your slate off to your BC and use both arms in a “breaststroke” fashion to part the seaweed for this
(this also helps ensure that the full 1 m width can be effectively searched). In coral dominated areas, care should be
exercised to maintain good buoyancy to stay as close to the bottom without touching it and breaking the coral (and
likewise avoid any gear dangling and breaking coral).

➢ Some urchins and gatropods live curled up in seaweeds and can be felt as the seaweeds are moved aside. These
should be counted.

➢ Record abundance and size of all invertebrates and cryptic fishes on all surfaces of the substrate in 2 m high and 1 m
wide bands on each side of the transect line (see figure 3). This includes the top and bottom of some overhangs, or at
least the portion of them within 1 m of the line. Search all crevices, cracks and walls for animals visible from the entrance
but do not turn over rocks or boulders.

Figure 3. Stylised representation of method 2 survey technique

21
METHOD 2 - TECHNIQUE

➢ Rock lobsters and abalone need to be counted and also measured vernier callipers to at least 5mm accuracy. If
you cannot catch the animal, estimate the size as best you can and note that you have made an estimate on
your data sheet by writing an E after the size. Abalone size is measured across the widest part of the shell and
rock lobster size is measured from the antennal horns to the rear edge of the carapace.

➢ Estimate and record size of cryptic fishes using the same size categories as for M1

➢ Some programs require divers to also measure all other M2 invertebrates using the same size categories as for
M1, except for lobsters and abalone. Starfish sizes are estimated from the centre to the tip of the arm (radius),
urchins are estimated by the widest part of the test (excluding spines), gastropods by shell length, and crabs
are measured using carapace width.

➢ Only measure the first 20 of each species per 50 m transect but make sure to count the abundance of all
thereafter.

22
METHOD 2 - TECHNIQUE
➢ It is easy to accidentally “narrow” your focus and search a band less than 1 m wide when in dense kelp.
Conversely, it is also easy to accidentally “broaden” your focus to wider than 1 m when in areas of bare rock or
coral and when not swimming close enough to the substrate. To avoid this, using the transect markings as a
ruler, measure where on your body 1 m reaches from fingertips across your outstretched arm and chest. Then,
whilst searching, regularly reach out to the tape to calibrate the outer boundary of the band. This is particularly
important when deciding whether to count an animal that is close to 1 m away from the tape.

➢ Where numbers of large macroinvertebrates are extremely dense, such as beds of screw shells or turbo shells,
numbers can be estimated in a patch by counting a subset and multiplying by the estimated area along the
transect line (in the 1m search-band).

➢ If identification is not possible, take a photograph (of both the upper and lower views for molluscs) and make a
note on your data sheet.

Count “swimming anemones” Photograph both sides of unknown gastropods Non-sessile bivalves can be counted

23
METHOD 3: In Situ quadrats
TARGET GROUP: All algae, sessile invertebrates (including corals) and substratum categories (e.g. sand).

TECHNIQUE:
➢ Five quadrats are sampled per 50 m transect segment, making 20 per site

➢ Quadrats are placed at 10 m intervals, marked on the transect line.

➢ Record how many contact points the algae (inverts or substratum) has with the 50 quadrat points. Contact points
consists of the 49 quadrat intersection points plus one corner

Count everything that

occurs directly under
these 49 intersection
points plus 1 corner.

Figure 4. Diagram of quadrat used in algae surveys.

24
METHOD 3: In Situ quadrats

TECHNIQUE Continued:

➢ Count all layers of algae. This is done by counting the canopy species, then brushing these aside to count what is
underneath, keep going through the layers until you reach the substratum, then finally record the composition of
the substratum layer. NOTE: the lowest layer recorded is often a mixture of substrate, encrusting or turf forming
species.

➢ Try to identify algae to species, if not possible then to genus, or accepted categories as per the tables in Appendix
2. Sponges, ascidians and others sessile invertebrates are often lumped into broad categories such as:
“encrusting sponge”, “massive sponge” etc.

➢ If identification to species or genus is not possible while underwater then make a note on your data sheet, take a
sample (try and get an entire plant) and/or photo and ask others/check books at the end of the dive. You may also
press the alga for future reference. Ensure you have marked on your data sheet the result of your queries by the
end of the trip so that it may be entered affectively into the database.
➢ Urchin barren identifiers are recorded, where the quadrat is situated on more than 75% urchin barren. This is done
by recording 50 points of the code for barrens, “BRB”. In addition to this, the normal quadrat procedure is
conducted, including scoring all points of bare rock in the substratum under the normal code for bare rock “BRN”.

25
ADDITIONAL METHODS
METHOD 4 – Macrocystis M4

TARGET GROUP: Macrocystis pyrifera plants

TECHNIQUE:
➢ In areas where Macrocystis occurs we
add an additional survey count. This is
done by counting the number of
Macrocystis plants that are taller than 1m
in a 2 m wide swathe (1 m on either side
of the line) in 10 m long blocks. Count
each 10 m block while swimming
between successive algal quadrats. A
total of 20 counts per site. If you are
using this method be sure to make a
clear note on your data sheet.

26
ADDITIONAL METHODS
METHOD “0” - M0
This method is not a defined part of an ATRC transect, but rather a way of recording species that were not included
within the time and space boundaries of M1 and M2.

This can be done at any stage of the dive and for any species, and serves two main purposes:
1. To allow a mechanism for recording the presence of species which were not recorded in M1 or M2 (this is
particularly important for rare species, or those that are outside of their usual distributional range, or a large
school of pelagic fish off-transect).
2. To allow people to record more species without ‘cheating’ by including those only seen beyond the 5 m or 1 m
boundary for M1 or M2, or during a part of the dive in which they were not specifically undertaking the method
designed to record those species (e.g. if a non-cryptic fish species, like a wrasse, was not seen during the fish
survey (M1), but is seen whilst doing the invertebrate survey (M2)).

➢ It is critical not to include such species in M1 or M2 as this will bias results.

M0 observations can be recorded at any time, and on any part of the datasheet, provided it is clear that these are
separate from the remainder of the data (usually the bottom of the page is best if there is space).

27
ADDITIONAL METHODS
METHOD 5 – Limpet counts

TARGET GROUP: Limpets

TECHNIQUE:
➢ In NSW additional counts of turban shells
(Astralium tentoriformis and
A.squamiferum) and limpets (Scutellastra
chapmani) as a total count under each
quadrat. Again if you are using this
method make a clear note on your data
sheet saying what you have done. Other,
difficult to identify limpets are recorded
as “unidentified limpets” and still counted.

Unidentified limpets

Scutellastra chapmani

Astralium tentoriformis

28
ADDITIONAL METHODS
PHOTOQUADRATS (PQs)

SK

TARGET GROUP: All algae, sessile invertebrates (including corals) and substratum categories (e.g. sand).

In instances where a lack of resources dictate that Method 3 cannot be completed, this method can be replaced with
photoquadrats. The percentage cover of different macroalgal, coral, sponge and other attached invertebrate species in
photoquadrats is later assessed using specialised computer software and is thus not part of the survey.

Digital photoquadrats are taken directly downwards from approximately 50 cm above the seabed (usually sufficient to
encompass an area of approximately 0.3 m x 0.3 m).

29
ADDITIONAL METHODS
PHOTOQUADRATS (PQs) - TECHNIQUE
Using a digital camera, 20 quadrats are photographed along each 50 m transect, at distances of 2.5, 5, 7.5, 10, 12.5,
15, 17.5 m, and so on up to 45m, then at 47.5 and 49 m positions as marked on the transect line.

A photo showing the divers depth gauge or dive computer should be taken at the start and end of the photo-quadrat
run along each transect (to ‘bookmark the photo-quadrats), and a single shot should also be taken at the start of the
line, looking along the line to show the general habitat (unless experienced with wide-angle photography, it is best to
turn the flash off for this shot, but then turn it back on for the PQs).

Photo-quadrats are usually centred on the transect line, with the line running across the shortest axis of the picture
(see examples below).

If the survey tape is not lying on the bottom, don’t worry about trying to get the tape in the photo, and instead lower the
camera to 50 cm from the bottom to ensure a clear photo of the substrate.

GOOD – In focus and sufficiently lit. NOT SO GOOD – Seaweed in BAD – Too much back-scatter,
focus, but large dark areas. seaweeds not easily identifiable
Transect line vertical across shortest axis

30
ADDITIONAL METHODS
PHOTO QUADRATS (PQs) - TECHNIQUE
A flash should generally be used. If a separate strobe is not
available and the camera’s in-built flash is used, a closer shot that
encompasses a smaller area of the seabed, but more clearly
shows the seabed, is preferred over a larger quadrat in which the
substratum is unclear due to turbidity or backscatter.

The exact area photographed is not critical because information is

calculated from each image as a percentage, not total density. It is
more important to take a sharp image without dark areas or too
much backscatter than to worry too much about the size of image.
If you need to go closer to take good clear images, then increase
the number of photos taken (for example, take 40 pictures if they
are only 15 cm x 15 cm each).

Use wide angle lens or zoom at widest angle when available. Use
highest digital resolution and largest recorded image size possible.
Save images in highest resolution .jpg rather than raw.

PQs should be downloaded and labelled as soon as possible,

following the naming convention on the next page.

PQs can be sent to RLS via email, Dropbox, or post.

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ADDITIONAL METHODS
LABELLING PHOTO QUADRATS
PQs should be labelled consistently to include all of the following 5 bits of information:
➢ Site code (e.g. NSW12)
➢ The initials of the photographer/RLS diver who is submitting the PQs.
➢ Transect depth (followed by ‘m’ for metres)
➢ Date (6 digits, e.g. 021108 for 2 November 2008)
➢ Site name (this can be abbreviated, but should be easily identifiable)

Underscores can be used to separate numbers from two of these naming components.
e.g. for PQs taken by Rick Stuart-Smith at site number NSW12 at 7 m depth on 25 January 2010 at Bushranger Bay, Bass
Point, the labels would be:

NSW12_RSS7m250110BushrangerBay

Photo-quadrats should be labelled as a batch for each transect, using the rename function if you use Windows. This
involves highlighting all photos for one transect, leaving the cursor on the first of these highlighted quadrats, right-clicking
and going down the bottom of the scroll list to the rename function. This highlights the title of the first photo-quadrat and
details should then be typed in. The rename function will apply this code to all PQs for that transect followed by (1), (2) etc.

It is very important that the details in the PQ labels match the details for that survey in the datasheet exactly to allow these
two parts to be matched up in the RLS database – so cross check depth and site codes in particular, to ensure they match
what you have entered into excel and what your buddy has entered.

All images for each transect should be put in a folder for that transect, with the folder labelled with the same format.

32
DATA ENTRY
Data should be entered onto specifically-designed ATRC Excel templates, which can be obtained from the data officer.
Numerous surveys can be entered onto these templates, one below another, but be careful to ensure the appropriate
site numbers, depths etc. are changed when new transects are started.

On data entry the four 50m transects from a site will use the same depth integer, but will differentiated by their depth’s
decimal values (i.e for a five-metre site transect 2 will have a depth of 5.2m, and transect 1 will have a depth of 5.1 m);
this is because in the NRMN database it is the site code x depth x date combination that distinguishes different 50 m
surveys.

Figure 4. Example of how underwater data sheets relate to the Excel data entry template .

33
TIPS FOR ACCURATE TRANSCRIPTION OF SURVEY DATA

➢ When underwater, write words on the underwater data sheets as clearly as possible with printed letters. Don’t
forget that others may need to read your entries down the track to crosscheck.

➢ Record which block you are working on and make a clear distinction (draw a line) between data belonging to
different blocks and between data from methods 1 & 2.

➢ Record abundance information as either a written number or by using tally lines in groups of 5. Always
distinguish between groups of numbers with commas or by underlining (e.g. avoid 32 being interpreted as a
3+2) and take particular care with written 11 (eleven) as this looks identical to two tally strokes.

➢ Try and use recognised names for animals (preferably scientific but common names are fine) underwater. It is
o.k. to make up your own naming conventions or codes for species but consistency is key and correct names
must be added clearly in PEN (preferably red so it stands out) at the end of the line after the data sheet is dry.

➢ Data should be entered onto the template as soon as possible after the dive to improve accuracy and prevent
loss of important information (i.e. before memory becomes fuzzy!) see figure 4.

➢ Method 0 observations should be given a value of “0” in the block column of the data entry template as they
don’t relate to a specific survey component.

➢ If a survey is done, but no species were in that block (sometimes happens for fish), enter the blocks method,
block number and the species “No species found” with a total of “0”

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 HOW TO DEAL WITH UNIDENTIFIED SPECIES

In some cases, you may come across species which aren’t in any identification book and you just can’t identify it to species
level. If this happens:

1.) Email a photo of the unknown species - if you don’t have a photo then it is probably most accurate to record it to genus
level if known ( i.e. Genus spp.), or even family level if genus is unknown (i.e. Family spp.)

2.) If a species level identification cannot be provided then the photo should be labelled according to the following syntax:

Scenario a.) Genus ?species

This naming convention is used when you are sure of the genus and you believe your species may be a form or
variant or another described species. E.g. Pomacentrus ?coelestis would be a Pomacentrus species which may
be coelestis or an undescribed species closely resembling P. coelestis

Scenario b.) Genus species [?]

This is for when you are unsure of both the genus and the species but you believe your species may be a form
or variant or a particular described species. E.g. Pomacentrus coelestis [?] would be used for a damselfish
which you believed may be a variant of Pomacentrus coelestis but could still possibly belong to a different
genus. This is the same as the general scientific protocol of adding preceding the genus name with the question
mark (but is easier to sort and search)

Scenario c.) Genus sp. [identifying character]

When you are sure of the genus (or family) but the species can’t be determined with confidence, a qualifier can
be placed in the square brackets. E.g. Pomacentrus sp. [blue ear spot]

It is critical that the photo of the unknown species receives the same naming convention and that the photo is sent
in at the same time as the data.

35
 APPENDIX 1. – GROUPS OF INVERTEBRATES & FISH FAMILIES
COUNTED IN METHOD 2

Table 1. Invertebrate groups counted in the Method 2 search

PHYLA/GROUPS ORDER/SUB-GROUPS RULES/EXCEPTIONS
Echinoderms Echinoids Count all
Crinoids Count all
Holothurians Count all
Asteroids Count all
Ophiuroids ONLY count basket stars (because they are exposed)
Crustaceans Crabs & hermit crabs Count only if they grow bigger than 2.5cm
Lobsters Count all and size (to nearest 0.5cm) first 20 in each 50m transect
Shrimps Cleaner shrimps only (Don’t count small shrimps such as hinge-beak shrimps).
Barnacles DON'T count any
All others Count only if: (1) grow bigger than 2.5cm
Count only if: (1) mobile, AND (2) grow bigger than 2.5cm. Also NOT Patellidae,
Molluscs Gastropods Polyplacophora
Count giant clams (e.g. Tridacna spp.), razor clams (e.g. Pinna spp.), scallops (e.g. Pecten spp.)
Bivalves and pearl oysters (e.g. Pinctada spp.). Don’t count other bivalves including edible oysters.
Abalone Count all and size (to nearest 0.5cm) first 20 in each 50m transect
Cephalopods Count all

All others Count only if: (1) mobile, AND (2) grow bigger than 2.5cm
Worms (including Polychaetes) All DON'T count any
Sessile groups Ascidians DON'T count any
Sponges DON'T count any
Bryozoans DON'T count any
Hydroids DON'T count any

36
Table 2. Families considered to be cryptic and should be recorded if found during a method 2 swim.

FAMILY COMMON NAME FAMILY COMMON NAME FAMILY COMMON NAME

Agonidae Poachers Cyclopteridae Lumpsucker Pempheridae Bullseye
Ambassidae Glassfishes Cynoglossidae Tonguefish Pholidae Gunnels
Anarhichadidae Wolf eels Dasyatidae Stingrays Pinguipedidae Grubfishes
Antennariidae Anglerfishes Diodontidae Porcupinefish Platycephalidae Flatheads
Aploactinidae Velvetfishes Eleotridae Gudgeons *Plesiopidae – excluding Trachinops Longfins
Apogonidae Cardinalfishes Gnathanacanthidae Red velvetfish Pleuronectidae Righteye flounder
Ariidae Catfishes Gobiesocidae Clingfishes Plotosidae Catfishes
Aulopidae Sergeant bakers Gobiidae Gobies Priacanthidae Bigeyes
Bathymasteridae Ronquils Grammistidae Soapfishes Pseudochromidae Dottybacks
Batrachoididae Frogfishes Hemiscylliidae Longtail carpet sharks Psychrolutidae Fatheads
Blenniidae Blennies Heterodontidae Bullhead sharks Rajidae Skates
Bothidae Lefteye flounder Holocentridae Squirrel and soldier fishes Rhinobatidae Shovelnose rays
Bovichtidae Thornfish Hypnidae Coffin rays Scorpaenidae Scorpionfish, orbicular velvetfish
*Serranidae - excluding “Anthias”,
Brachaeluridae Blind sharks Labrisomidae Tropical blennies Rockcods & Seaperches
Caesioperca, and Lepidoperca
Brachionichthyidae Handfishes Leptoscopidae Pygmy stargazers Scyliorhinidae Catsharks
Bythitidae Blindfishes and cuskeels Liparidae Snailfishes Soleidae Soles
Callionymidae Dragonets Lotidae Burbots Solenostomidae Ghostpipefishes
Caracanthidae Crouchers Monocentridae Pineapplefishes Stichaeidae Prickleback
Carapidae Pearlfish Moridae Beardies Synanceiidae Stonefish
Centriscidae Razorfish Muraenidae Moray eels Syngnathidae Pipefish & Seahorses
Chaenopsidae Tubeblennies, flagblennies Nototheniidae Icefishes Synodontidae Lizardfishes and Sauries
Chironemidae Kelpfishes Ophichthidae Snake and worm eels Tetrabrachiidae Anglerfishes
Cirrhitidae Hawkfishes Ophidiidae Lings Tetrarogidae Waspfishes
Clinidae Weedfishes Opistognathidae Jawfishes Torpedinidae Numbfish
Congridae Conger eels Orectolobidae Wobbegongs Trachichthyidae Roughies
Congrogadidae Eel blennies Paralichthyidae Large-tooth flounder Tripterygiidae Threefins
Cottidae Sculpins Parascylliidae Catsharks Uranoscopidae Stargazers
Creediidae Sand divers Pataecidae Prowfishes Urolophidae Stingarees
Cryptacanthodidae Wrymouths Pegasidae Seamoths Zaproridae Prowfish
Zoarcidae Eelpouts

37
APPENDIX 2. – METHOD 3 GROUPINGS TO BE USED FOR
SUBSTRATUM, ALGAE AND SESSILE INVERTEBRATES

Substratum categories Description

Urchin barrens - rocks grazed bare of macroalgae and most invertebrates,
Bare rock
large numbers of urchins present.
Bare rock cleared by action other than urchin grazing: possibilities include
Bare rock - barrens
waterflow, wave action, sand scour.
Loose rock from 80mm to 200mm in diameter or measured across the
Cobble
longest axis.
Loose rock from 25mm to 80mm in diameter or measured across the
Pebbles
longest axis.
Loose rock from 5mm to 25mm in diameter or measured across the
Gravel
longest axis.
Sand Sand, shell grit, sediment or silt less than 5mm in diameter.
Sand, shell grit, sediment or silt less than 5mm in diameter that rests on a
Silt on reef
hard substratum, silt depth less than 5cm.

38
APPENDIX 2. – METHOD 3 GROUPINGS TO BE USED FOR
SUBSTRATUM, ALGAE AND SESSILE INVERTEBRATES
Algae categories Description
Browns
Long chains, threads, or filaments of brown algae. These filaments often
Filamentous browns
intertwine forming a mat.
Foliose browns Flat leafy brown algae that cannot be identified to genus or species
Encrusting algae
Green rhizomes forming random 'net' like structure over substratum;
Caulerpa rhizomes when obvious, Caulerpa flexilis is generally responsible, so if that species
is present best to use species name
Crustose coralline algae Calcareous pink encrusting algae; “pink paint”
Encrusting brown algae Unidentified brown algae that adhere closely to substratum
Encrusting green algae Unidentified green algae that adhere closely to substratum
Medium to dark red brown to purplish 3-80cm across, tightly bound to
Hildenbrandia spp.
substratum, smooth to warty or knobby surface, with very fine felt of hairs
Peyssonnelia flat Hard red rubbery encrusting algae
Greens
Long chains, threads, or filaments of green algae. These filaments often
Filamentous greens
intertwine forming a mat.
Foliose greens Flat leafy red algae that cannot be identified to genus or species
Other
Drift Unattached algae of any type, sometimes common in depressions on reef.
Reds
Long chains, threads, or filaments of red algae. These filaments often
Filamentous red algae
intertwine forming a mat.
Foliose reds Flat leafy red algae that cannot be identified to genus or species
Turf
Dense unidentified brown algae that attain a canopy height of only 1 to 10
Brown Turf
mm.
Green Turf Dense unidentified green algae that attain a height of only 1 to 10 mm.
Dense unidentified red algae that attain a canopy height of only 1 to 10
Red turf
mm.
Matrix formed by organic sessile structures that trap sand, shell grit,
Turf/sand/sediment matrix sediment or silt into a matrix on a hard substratum, usually less than 5mm
deep.

39
APPENDIX 2. – METHOD 3 GROUPINGS TO BE USED FOR
SUBSTRATUM, ALGAE AND SESSILE INVERTEBRATES
Invertebrates Description
Ascidians
Encrusting ascidians Ascidians that adhere to substratum closely.
Ascidians Ascidians that do not adhere to substratum closely
Bryozoans
Encrusting bryozoans Bryozoans that adhere to substratum closely
Hard bryozoans Bryozoans that are erect but do not bend if touched.
Soft bryozoa Bryozoans that are erect but do bend if touched.
Coral
Encrusting soft coral Soft coral that adheres closely to substratum.
Soft coral species Soft coral that does not adhere to substratum closely
Brain coral Brain coral
Bramble coral Bramble coral
Plate coral Plate coral
Coral (other than plate) Hard coral that does not form plate structure
Sponges
Erect sponges Erect or plate like sponges that do not adhere to substratum closely
Sponge (encrusting) Sponges that adhere to substratum closely.

40
APPENDIX 3. – SURVEYS IN SPECIAL CIRCUMSTANCES

SURVEYING WALLS

Vertical walls can be surveyed using the RLS methodology, but extra consideration needs to be paid to how the
survey works, given that the methodology requires fishes to be surveyed in 5 m wide bands out horizontally from the
transect line. A ceiling of 5 m should be applied to all transects (see fish survey methods above), but for wall
surveys a floor of 5 m below the transect line should also be applied. For the invertebrate survey, the standard
vertical height limits of 2 m above (for block 2) and below (for block 1) apply.

A number of scenarios exist, depending on whether the wall reaches the surface and where on the wall the transect
line is laid (see the diagrams in the following pages). If the wall does not reach the surface (or very close to it), and
the line is in a depth of 5 m or less, then the survey can go ahead using the standard method, with a maximum of 5
m vertical distance of wall below the transect line surveyed for fishes in B1, and 5 m out from the transect in both B1
and B2. If the wall does reach the surface, or the transect line is laid more than 5 m deeper than the top of the wall,
then the “wall method” needs to be used for fishes.

41
THE WALL METHOD

For near vertical surfaces, B1 encompasses all fishes below a plane extending 5 m out from the transect line to a
maximum depth of 5 m below the transect line, while all fishes within 5 m above it are in B2. This is essentially the
same as the standard method, but with blocks placed one on top of the other instead of side by side. It is essential
to always follow one or the other method, with no intermediate configuration, although switching between methods
on a single transect will be necessary in some cases (i.e. when a wall is only present along part of the transect).

5m 5m
B2 B2

5m
B1

5m
Transect line
Max 5m

Transect line

5m
B1

Figure 5. Representation of standard method on a Figure 6. Representation of wall method for walls
wall that doesn’t reach the surface. that reach the surface, or when transect line is set >
5 m below the top of a wall.

42
THE WALL METHOD

5m 5m
B2 B2

5m
B1

5m

B1

Transect line Transect line

5m
5m

a.) Standard Method b.) Wall Method

Figure 7. When to use wall method. A decision needs to made as to when to switch to the wall method. Generally, somewhere
between these two scenarios would be most appropriate, before the area covered in B2 becomes too small using the standard
method. In Figure a.) the standard method can still be used but in Figure b.) The Wall methodology would need to be adopted.
Divers need to be consistent with their decisions for using the wall methodology.

43
SURVEYING NARROW REEF

A survey may still be undertaken on a wall that reaches the surface, but is less than 10 m high above sand (and is
thus too short for the wall method to be applied), as is the case for many breakwaters or shallow rocky shores. In
this case, only one block should be surveyed along the line (for both fishes and invertebrates/cryptic fishes). A
second line should then be subsequently set, so that two blocks are still surveyed, “end on end” (N.B. please ensure
they are still labeled as “block 1’ and ‘block 2’ in the data entry). Photo-quadrats should be taken on both lines. If you
have any queries regarding the application of this method, please feel free to contact RLS organisers for
clarification.

5m

5m
No reef (sand)
Transect line

Figure 8. Reef less than 10 m wide and/or wall less than 10 m high (e.g. groyne).
Only 1 block is surveyed and a second line should be surveyed on one end in the
same manner.

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REFERENCES

➢ Barrett NS, Buxton CD (2002) Examining underwater visual census techniques for the assessment of population structure and
biodiversity in temperate coastal marine protected areas. Tasmanian Aquaculture and Fisheries Technical Report Series 11:1-114
➢ Edgar, G.J., Cooper, A., Baker, S.C., Barker, W., Barrett, N.S., Becerro, M.A., Bates, A.E., et al. (2020). Establishing the ecological
basis for conservation of shallow marine life using Reef Life Survey. Biological Conservation, 252: 108855.
➢ Edgar GJ, Banks S, Fariña JM, Calvopiña M, Martínez C (2004a) Regional biogeography of shallow reef fish and macro-invertebrate
communities in the Galapagos Archipelago. Journal of Biogeography 31:1107–1124
➢ Edgar, G. J. and R. D. Stuart-Smith (2009). "Ecological effects of marine protected areas on rocky reef communities: a continental-
scale analysis." Marine Ecology Progress Series 388: 51-62
➢ Edgar GJ, Barrett NS (1997) Short term monitoring of biotic change in Tasmanian marine reserves. Journal of Experimental Marine
Biology and Ecology 213:261-279
➢ Edgar GJ, Barrett NS (1999) Effects of the declaration of marine reserves on Tasmanian reef fishes, invertebrates and plants. Journal
of Experimental Marine Biology and Ecology 242:107-144
➢ Edgar GJ, Barrett NS, Morton AJ (2004b) Biases associated with the use of underwater visual census techniques to quantify the
density and size-structure of fish populations. Journal of Experimental Marine Biology and Ecology 308:269-290
➢ Edmunds M, Hart S (2003) Parks Victoria Standard Operating Procedure. Biological Monitoring of Subtidal Reefs. Parks Victoria
Technical Series 9:1-48
➢ Stuart-Smith, R.D., Edgar, G.J., Barrett, N.S., Bates, A.E., Baker, S.C., Bax, N.J., Becerro, M.A., Berkhout, J., et al., 2017. Assessing
national biodiversity trends for rocky and coral reefs through the integration of citizen science and scientific monitoring programs.
Bioscience, 67(2), pp.134-146.

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