Environ Monit Assess (2019) 191:633

https://doi.org/10.1007/s10661-019-7808-2

Development and application of a low-cost rapid

assessment system for coastal benthic habitats
Caryl S. Benjamin & Patrick Lawrence P. Cadeliña &
Aletta T. Yñiguez & Cesar L. Villanoy

Received: 12 March 2019 / Accepted: 8 September 2019

# Springer Nature Switzerland AG 2019

Abstract Information on community structure and spa-
tial distribution of benthic habitats are important in
marine conservation and management. Coral areas, of-
ten monitored by trained scuba divers, are of importance
for the ecosystem goods and services they provide. The
data gathered may, however, be limited due to cost and
time constraints. These restrictions and the continuing
decline in coral reef health contribute to the need to
develop rapid methods to efficiently document the dis-
tribution and status of coral reefs. A Rapid Assessment
Instrument for Coastal Benthic Habitats (ARAICoBeH)
System was developed to enable large-scale but low-
cost coastal benthic habitat characterization and map-
ping without compromising accuracy. Inquiries on com-
munity structure and status in coral-dominated areas are
also possible with the data collected using the method.
The instrument, as well as the data processing and
mapping algorithm are described in detail in this paper.
A comparative study was conducted between
ARAICoBeH and the frequently used underwater photo
transect method. Variables compared were percent coral
cover, functional group diversity, community structure
as well as time and monetary requirements. There were
C. S. Benjamin : P. L. P. Cadeliña (*) : A. T. Yñiguez :
C. L. Villanoy
Marine Science Institute, University of the Philippines, Diliman,
1101 Quezon City, Philippines
e-mail: plcadelina@msi.upd.edu.ph
C. S. Benjamin
Chair of Ecoclimatology, Technische Universität München,
Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
no significant differences in estimates of percent coral
cover and diversity of benthic functional groups for
majority of sites while estimates of community structure
were very similar. ARAICoBeH is cheaper and requires
less time to gather the same amount of data as that of the
photo transect method. The spatial distribution of coast-
al benthic habitats and community structure of coral-
dominated areas in El Nido, Palawan, Philippines, are
included to illustrate the application of the method.
Keywords Mapping . Coral assessment . Coral
monitoring . Rapid assessment . Community structure
Introduction
Corals are important coastal resources because of the
ecosystem goods and services that they provide
(Connell 1978; Moberg and Folke 1999). According to
Burke et al. (2011), approximately 850 million people or
one-eighth of the world’s population live within 100 km
of a coral reef and most probably derive some benefit
from these reefs. Majority of these people depend on
reefs for their sustenance and livelihood and come from
developing countries and island nations. Unfortunately,
there is a global trend of decline in coral reef health
(Knowlton 2001; McClanahan 2002; Pandolfi et al.
2003; Wilkinson 2008). Coral reefs are vulnerable to
local sources of stress such as terrestrial runoff
(Fabricius 2005) and eutrophication (Tomascik and
Sander 1985; Szmant 2002) as well as global stressors
such as global warming and ocean acidification (Hoegh-
 633 Page 2 of 15
Guldberg et al. 2007; Pandolfi et al. 2011). Local activ-
ities alone like overfishing and destructive fishing,
coastal development, and watershed-based or marine-
based pollution threaten more than 60% of the world’s
coral reefs (Burke et al. 2011). Documentation of the
current state of coral reefs is therefore a research priority
to provide baseline information, monitor changes due to
threats and disturbances as well as recoveries (Gardner
et al. 2005; Bruno and Selig 2007; Baker et al. 2008;
Wilkinson 2008; Wilkinson and Souter 2008).
Resource maps are excellent tools for coastal re-
source management and conservation because large
amounts of information (e.g., spatial distribution and
status of resources) can be reduced into a simple visual
representation (Tortell 1992). Coral reef habitat maps
have been produced using remote sensing for resource
assessment (Andréfouët and Riegl 2004; Gilbert et al.
2006) and conservation (Aswani and Lauer 2006).
However, the accuracy and level of detail derived from
satellite and airborne images are limited to geomorpho-
logical classes and coarse habitat discrimination (e.g.,
coral versus non-coral) because there is high variability
in accurately discerning finer taxonomic habitat classes
and density estimates using supervised classification
(Green et al. 1996; Mumby et al. 1997; Andréfouët
et al. 2006). There is a need for a method to produce
maps with more detailed information to provide insights
on indicators of reef status (Scopélitis et al. 2010).
There is a variety of existing coral survey methods
which require various levels of expertise as well as
resources (Dethier et al. 1993; Beenaerts and Berghe
2005; Lam et al. 2006; Leujak and Ormond 2007; Jokiel
et al. 2015). It is suggested that choice of method should
be based on scale, level of detail required as well as
availability of resources. Methods to gather fine-scale
and detailed data are ideal for scientific research while
large-scale but less detailed data collection are more
practical for management decisions (Hill and
Wilkinson 2004).
Earlier methods for coral census required in situ data
acquisition. The manta tow method involved a snorkeler
being towed by a boat running at constant speeds.
Estimates of benthic cover were recorded during regular
stops. The method can be used to survey large areas in a
short period of time but has a tendency to underestimate
abundance and is ideally combined with benthic moni-
toring methods involving scuba diving (Hill and
Wilkinson 2004). Other commonly used underwater
survey methods are the transect and quadrat methods.
Environ Monit Assess (2019) 191:633
Transect methods are often preferred in studies
assessing environmental impacts in medium scales
while quadrats are suited for fine-scale surveys
(Beenaerts and Berghe 2007). These methods give good
estimates of percent coral cover and diversity but require
extensive time underwater as well as expertise in both
scuba diving and identification of benthic components
(Hill and Wilkinson 2004).
Advancements in technology have led to the exten-
sive use of digital video surveys and underwater pho-
tography to collect photo quadrats (PQs) as an alterna-
tive to in situ methods (Lam et al. 2006; Leujak and
Ormond 2007). PQs are collected along transects and
percent cover of the different benthic components are
estimated from points superimposed over the PQs using
an image analysis software (English et al. 1997; Houk
and Van Woesik 2006; Kohler and Gill 2006). Advan-
tages over the in situ methods include reduction in time
spent underwater and creation of permanent records
(Leujak and Ormond 2007). Previous studies have also
established the superiority of these methods in terms of
efficiency and precision in detecting differences in coral
communities between sites and over time (Weinberg
1981; Murdoch and Aronson 1999; Ninio et al. 2003;
Brown et al. 2004; Lam et al. 2006; Leujak and Ormond
2007).
These scuba-based methods, however, have limita-
tions in terms of underwater time, sensitivity to weather
conditions as well as access to scuba facilities. These are
also often used at a narrow range of depths and are
therefore limited to only a fraction of a benthic zone.
To address these limitations, methodologies using re-
motely operated vehicles (ROVs), towed cameras, or
drop cameras to remotely collect photos or videos have
been developed (Mitchell and Coggan 2007; Grizzle
et al. 2008). All three have both advantages and disad-
vantages. ROVs have been widely used for prolonged
deep reef surveys (Williams and Mahon 2004; Lam
et al. 2006; Lirman et al. 2007), but these can be bulky,
difficult to deploy and control, and are expensive.
Towed cameras are usually housed in sledges dragged
across the seafloor and are therefore not ideal for hard
substrates and have the tendency to damage fragile
benthic species (Service and Golding 2001). Converse-
ly, drop cameras are convenient, affordable, and can be
deployed in areas where towed and ROV systems can-
not be deployed, such as rocky or high-energy environ-
ments (e.g., Cole et al. 2001). All three can be used to
survey large spatial scales. However, most studies
Environ Monit Assess (2019) 191:633
utilizing these methods focus either on visualization of
sublittoral communities (Jones et al. 2000; Bates et al.
2004) or on ground-truthing data in acoustic studies
(Beaman and Harris 2005; Roberts et al. 2005). Only a
few studies utilize remote photo/videography for habitat
assessment in shallow areas (Schneider et al. 1987;
Dunbabin et al. 2005; Pacunski et al. 2008; Walcott
et al. 2014).
A Rapid Assessment Instrument for Coastal Benthic
Habitats (ARAICoBeH) is a drop camera system that
was developed as an alternative to scuba-based coral
reef and shallow-water benthic habitat survey methods.
Cost of the system is lower than ROVs because it takes
advantage of the low cost of action cameras, which are
compact, rugged, and waterproof. Unlike scuba-based
methods, ARAICoBeH System includes positional data
(latitude and longitude) for each PQ collected in the
field. The spatial distribution and status of benthic hab-
itats (e.g., percent live coral cover) can therefore be
generated as an output. The method significantly re-
duced the time necessary to survey larger areas due to
the elimination of scuba diving and the development of
an algorithm to automate time-intensive and repetitive
post-survey processing tasks.
The objectives of this study are to develop, test, and
apply a low-cost rapid monitoring system to assess
coastal benthic habitats. This is an end-to-end system
from the instrument to the data processing and mapping
algorithm. A comparative study between the
ARAICoBeH System and the frequently used underwa-
ter photo transect method in terms of estimates of coral
reef health as well as time and cost requirements are
presented. The spatial distribution of coastal benthic
habitats and community structure of coral-dominated
areas in El Nido, Palawan, Philippines, are included to
illustrate the application of the method.
Materials and methods
ARAICoBeH system
Instrument design and operation
ARAICoBeH System is composed of three compo-
nents: underwater photography, acquisition of location
information, and depth monitoring. Pictures are taken
underwater at a 2-s interval using an underwater action
camera (GoPro Hero 3 Silver with waterproof housing),
Page 3 of 15 633
and a makeshift fin that acts as a rudder is attached to a
half meter metal pole (Fig. 1a). A 3-kg lead weight is
attached to the pole with a sturdy rope at 0.75 m from
the camera. The instrument is lowered and towed from
the boat using a calibrated rope (Fig. 1b). Depth and
location are continuously measured per second and are
recorded by a single beam echo sounder transducer
(Garmin Airmar Tilted™ Element, and P19–20°) and a
GPS/transducer viewer (GPSMap 421s), respectively.
This GPS/transducer viewer is powered by a portable
lithium 33,000-mAh power bank. A handheld GPS
(optional) is used to easily mark the starting point of
each transect. The GPS attached to the transducer may
also be used for this purpose.
Sampling using the ARAICoBeH System can be
done using a small boat manned by three individuals.
One person takes note of the start and end time for each
transect. The same person determines the starting points
of transects based on distances between transects mea-
sured using the GPS. The second person deploys the
instrument according to the current depth less 1 m to
prevent disturbance and damage of benthic communi-
ties. The third person is responsible for directing the
course of the boat and for keeping the speed at a mini-
mum (0.5 knots) to optimize quality of pictures. Each
transect extends from a depth of 3 to 15 m and is
perpendicular to the shore.
The camera time should be synchronized with the
GPS time. The GoPro Hero 3 Silver camera displays the
current time only as hours and minutes, but these values
are corrected to achieve accuracy to the second on the
time a picture was taken. This is done by taking a few
pictures of the GPS time at the start of each sampling
day. The correction of the difference in seconds between
the GPS time and the time the picture was taken is
included in the data processing script. Data collected
during a field survey include pictures or PQs, start and
end times for each transect, GPS tracks, and echo sound-
er depths.
Data processing algorithm
Thousands of pictures of benthic habitats or PQs can be
collected within a few days of field sampling using
ARAICoBeH. Selection of photos, geotagging, picture
file organization, data management, and finally map-
ping are simplified with the development of an algo-
rithm written in the R language (R Core Team 2015) to
automate these tasks.
 633 Page 4 of 15
Fig. 1 a ARAICoBeH
instrument, b during deployment
(a)
showing its components: (1) un-
derwater camera attached to a (2)
20-cm metal pole with (3) acrylic
1
fin to serve as a rudder. (4) A 25-
cm rope attaches the pole to (5) a
3-kg weight which acts as stabi-
lizer. All these are tethered to the
boat via (6) a calibrated 20-m
mountaineering rope
Management and processing of a large quantity
of picture files often require long periods of time
and/or computing resources. To address this, the
algorithm works with the picture information and
not the actual picture files during the initial stages
of data processing. The Exchangeable Image File
Format (EXIF) information from all the pictures
collected from the field, specifically the filename
as well as date and time taken, is first extracted
and saved into a single data frame. The total space
and computer power, required to process this data
frame, is lower by several magnitudes as compared
to that of thousands of picture files. Geographic
coordinates are added to each picture information
by matching the time the picture was taken and
time recorded from the GPS. A subset of pictures
to be used for analysis and mapping is then se-
lected according to a user-specified spatial interval.
An interval of 2 m measured from the geographic
coordinates associated with each picture was used
in this study. The selected pictures are then copied
to a new folder. A map of the locations of these
pictures may be generated to visualize extent of
survey.
Image analysis to quantify the different components
of the benthic ecosystem to percent cover is done using
Environ Monit Assess (2019) 191:633
(b)
6
4
3
the Coral Point Count with Excel Extension (CPCe)
software (Kohler and Gill 2006). Stratified random
method is employed wherein each PQ is divided into
five rows and two columns, with a single point random-
ly overlaid in each cell. This method is used in order to
reduce the chance of points clumping in each image
(Kohler and Gill 2006). The benthic component under
each point is then identified manually by an observer
using a key (Table 1) modified from English et al.
(1997). The key focused on coral life forms (e.g.,
Acropora branching, coral massive), other benthic func-
tional groups (i.e., other invertebrates, macroalgae,
seagrasses), and abiotic factors (i.e., sand, rubble).
CPCe generates the results in several spreadsheets
but the merging into a single file is automated in the
data-processing algorithm. Geographic coordinates are
then reattached to each quantified PQ. Some PQs may
be rejected and excluded during image analysis due to
image quality. A complete datasheet with geographic
coordinates and cover of biotic and abiotic components
is generated for further statistical analysis. The same
data is used to generate maps to visualize the spatial
variability of live hard coral cover. The relative compo-
sition in terms of major benthic categories in different
areas of the surveyed site may also be compared through
pie charts. The data processing algorithm is
Environ Monit Assess (2019) 191:633 Page 5 of 15 633

Table 1 Identification key of functional groups modified from Comparison of ARAICoBeH to underwater photo
English et al. (1997) used to quantify benthic components using
transect method
the software Coral Point Count with Excel extension (CPCe,
Kohler and Gill 2006)
Estimates of reef health
Key Functional/abiotic group

ACB Acropora branching

The comparative study was undertaken in three different
locations in the Philippines (Fig. 2). These were among
ACD Acropora digitate
several coral reef areas assessed under research pro-
ACE Acropora encrusting
grams funded by the Philippine government: The Na-
ACS Acropora branching
tional Assessment of Coral Reef Environments
ACT Acropora tabulate
(NACRE) program of the Department of Science and
CB Coral branching
Technology and the Coral Reef Visualization (CoRVA)
CE Coral encrusting
program of the Department of Environment and Natural
CF Coral foliose
Resources. Field surveys were conducted in January,
CM Coral massive
March, and June 2015 for VIP, Sablayan, and El Nido,
CMR Coral mushroom
respectively.
CS Coral submassive Following the sampling strategy for ecological field
CHL Blue coral methods by van Woesik et al. (2009) for the underwater
CME Fire coral photo transect, three sites were chosen per location with
CTU Organ-pipe coral two stations per site. Figure 2 shows the three sites per
SC Soft coral location: VIP (13.773° N, 120.875° E)—site 1: Ligpo,
AN Anemones site 2: Dive and Trek, site 3: Twin Rocks; Sablayan
ASC Ascidians (12.827 N, 120.767° E)—site 1: North Pandan Island,
GOR Gorgonians site 2: South Pandan Island, site 3: mainland Mindoro;
OIV Other invertebrates and El Nido (11.127° N, 119.320° E)—site 1: Miniloc,
SP Sponges site 2: Shimizu-Inatula, and site 3: Pangulasian. Four
ZO Zoanthids 50-m transects were laid following different depth con-
AA Algal assemblage tours: 15, 10, 7, and 5 m. The data from site 2: South
HA Halimeda Pandan Island in Sablayan, Mindoro was limited to the
MA Macroalgae 5-m depth due to the steepness of the slope. Pictures
TA Turf algae were taken at 1-m intervals along the transect line. The
SG Seagrasses distance between the camera and the seafloor is kept
CA Coraline algae constant at 1.3 m using a PVC frame which allows
DC Dead coral coverage of at least 1 m2. The frame includes a 1-m
DCA Dead coral with algae PVC base used for scaling.
R Rubble ARAICoBeH surveys were done at the same
RCK Rock study sites immediately after completing the un-
S Sand derwater photo transect method. Three transect
SI Silt tows were conducted per station, with at least
W Water 50-m intervals between transects. These were per-
TWS Tape, wand, shadow
pendicular to the shore and targeted depths from 3
U Unknown
to 15 m. The length of each transect varied de-
pending on the bathymetry of the site.
Estimates of live hard coral cover, functional group
diversity, and community structure were compared be-
tween the two methods in the different field locations.
conveniently saved as two R scripts: pre-CPCe and Functional group diversity was used as an alternative to
post-CPCe and is maintained and accessible upon re- species diversity because finer-resolution taxonomic
quest at https://github.com/biome-upmsi. classification is very difficult based on photographs.
 633 Page 6 of 15 Environ Monit Assess (2019) 191:633

Fig. 2 Map for the comparative a) VIP 1

study showing three sites in red
2
box for each location. a Verde 117 E 120 123 126
Island Passage—site 1; Ligpo, 21
site 2: Dive and Trek, site 3: N
Twin Rocks b Sablayan, Occi-
dental Mindoro—site 1: North
Pandan,
18
site 2: South Pandan, 0 2.5 km
site 3: mainland Mindoro c El 3
Nido, Palawan—site 1: Miniloc,
site 2: Shimizu-Inatula, b) Sablayan
1
site 3: Pangulasian 15

A 2

B
12

C
0 2.5 km
3

9
c) El Nido

1
6 2

0 2.5 km
3

Data were analyzed at the site level to compare the
methods at a finer spatial scale with the objective of
minimizing the sources of variation. A location level
analysis would introduce more variation due to differ-
ences between sites. Data for live hard coral cover and
diversity were tested for normality (Shapiro-Wilk test)
and homogeneity of variances (Levene’s test). Two-way
ANOVA with method (ARAICoBeH System or Under-
water photo transect) and site (1,2, or 3) as factors were
used for data that satisfied assumptions of normality and
homogeneity of variances and the non-parametric
Kruskal-Wallis test for data that did not satisfy the
assumptions. Non-metric multidimensional scaling
(nMDS) on untransformed data based on Bray-Curtis
similarities and analysis of similarities (ANOSIM;
Clarke and Warwick 1994) were used to compare esti-
mates of community structure. The R statistic in
ANOSIM indicates that communities are well separated
when R > 0.75, overlapping but clearly different when
R > 0.50 and barely separable when R < 0.25. All statis-
tical analyses were done in R (R Core Team 2015).
Time and monetary costs
The time and monetary costs of data collection and
analysis are also compared in this study. Comparison
of required time was estimated for 50 PQs. Field survey
time included the collection time of PQs using the
ARAICoBeH System and the underwater photo transect
method. Post-survey data processing components in-
cluded time needed to download data from the camera,
selection of photos for analysis, geotagging, and analy-
sis in CPCe as well as mapping.
Monetary costs were divided into the one-time ex-
pense for necessary equipment and total amount to
cover all expenses (e.g., boat and scuba tank rental, daily
wages, etc.) for collecting 400 PQs. This is equivalent to
data from one site with two stations each and four
transects for each station obtained by one diver for the
underwater photo transect which is a standard sampling
strategy as suggested by van Woesik et al. (2009). The
monetary cost for the ARAICoBeH System was esti-
mated also for 400 PQs.
Environ Monit Assess (2019) 191:633
Application of ARAICoBeH system
In order to test and illustrate the efficacy of
ARAICoBeH System as a method for large-scale as-
sessment, a more extensive field survey was conducted
in the town of El Nido, Palawan, on November 2015.
This survey was independent of the survey done in three
locations in El Nido for method comparison (June 2015).
El Nido is a protected area in the Philippines as part of
the National Integrated Protected Areas System. The
town center lies next to Bacuit Bay, which is a 150-
km2 bay opening to the West Philippine Sea and consists
of 45 islands. Marine resources in Bacuit Bay are said to
be diverse; with estimated 910 fish species, more than
400 coral species, 8 seagrass species, 3 species of en-
dangered sea turtles and presence of large marine verte-
brates (e.g., sharks, whales, and rays; CCRES 2014).
Two of the primary livelihoods of the El Nido commu-
nity are derived from coral reefs: fishing and tourism
(Cesar 2000; Cola et al. 2005).
The boat-based ARAICoBeH transects were made at
least 1 km apart targeting areas that have coral reefs
present based on the 2010 Global Distributions of Coral
Reefs from United Nations Environment Program–
World Conservation Monitoring Centre (UNEP-
WCMC 2010). The data analysis and visualization al-
gorithms were then applied to the data gathered in the
field survey.
Results and discussion
Comparison of coral reef indicators derived
from ARAICoBeH and underwater photo transect
method
The feasibility of using ARAICoBeH System as an
alternative to the commonly used underwater photo
transect method was assessed. The criteria used for
comparison were three common indicators of coral reef
health: live hard coral cover, functional group diversity,
and community structure. On the average, the three
study locations differed in terms of these indicators
relative to each other. Coral cover is lower in VIP
relative to Sablayan and El Nido while diversity is
higher in El Nido and Sablayan relative to VIP. Live
hard coral cover showed that estimates using the
ARAICoBeH system and the underwater photo transect
method were mostly similar. There were no significant
Page 7 of 15 633
differences in estimates of live hard coral cover in two
out of three sites in all three study locations (Fig. 3).
Live hard coral cover estimates for VIP yielded no
significant differences in sites 2 (p value = 0.618) and
3 (p value = 0.096). For Sablayan, there were no signif-
icant differences between the methods in sites 1 (p
value = 0.326) and 3 (p value = 0.753), while for El
Nido, no significant differences were found in sites 1
(p value = 0.460) and 2 (p value = 0.140). The differ-
ences in 1 out of three sites in each study location were
artifacts of the site and survey conditions. The direction
of the wind, when the survey was done in site 1 in VIP,
was towards the shore which led to difficulty in maneu-
vering the boat. This created a problem specifically for a
method comparison study wherein a complete overlap
in the area sampled was necessary. The differences in
site 2 in Sablayan could be due to the bathymetry of the
area. Underwater transect data was reduced to only one
depth (5 m) because the area beyond that depth was a
wall. In contrast, ARAICoBeH still covered a depth
gradient starting at 3 m. The differences in El Nido site
3 can also be attributed to abrupt changes in bathymetry.
These changes led to problems in keeping the distance
of the camera from the reef constant. Quality of some
pictures is affected and is therefore discarded from
analysis.
In terms of functional group diversity between the
two methods, there were also no significant differences
in majority of the study sites (Fig. 4). There was no
significant difference in site 3 (p value = 0.085) in VIP.
The same was observed in all sites in Sablayan: site 1 (p
value = 0.894), site 2 (p value = 0.328), and site 3 (p
value = 0.354). Differences were also not significant in
sites 2 (p value = 0.068) and 3 (p value = 0.967) in El
Nido, Palawan. The comparison of functional diversity
highlighted the higher standard error in the
ARAICoBeH estimates relative to that of the underwa-
ter photo transects. This can be expected because it
covers a continuous depth gradient, while underwater
photo transects were laid at discrete depths only.
ARAICoBeH therefore captures the variability expected
in a coral reef at a depth gradient of 3 m to 15 m.
For community structure, the two methods also
yielded highly similar results in most sites. Non-metric
multidimensional scaling (nMDS) plots of community
structures for all the sites quantified from PQs collected
using the two methods are compared in Fig. 5. The
yellow and blue polygons represent the two datasets
derived from ARAICoBeH System and Underwater
 633 Page 8 of 15 Environ Monit Assess (2019) 191:633

Fig. 3 Comparison of live hard a) Verde Island b) Sablayan, c) El Nido,

coral cover. Error bars are Passage Mindoro Palawan
standard errors of the mean 100

Hard coral cover (%)

75

50

25

1 2 3 1 2 3 1 2 3

Site

ARAICoBeH System Underwater photo transects

photo transects, respectively. These large overlaps in the
colored polygons suggest that community structure data
were highly similar for three sites in VIP and two for
Sablayan (1 and 3) and El Nido (2 and 3). These visual
results from nMDS for all sites in the three study loca-
tions were consistent with the results of ANOSIM,
showing that the community structures estimated by
the two methods were barely separable (R < 0.25) in
majority of the sites. The R values of these sites are as
follows: VIP (site 1: R = 0.074, p = 0.001; site 2: R =
0.028, p = 0.2; site 3: R = 0.13, p = 0.001), Sablayan
(site 1: R = 0.13, p = 0.001; site 3: R = 0.011, p =
0.001), and El Nido (site 2: R = 0.19, p = 0.001; site 3:
R = 0.011, p = 0.066). Exceptions are sites 1 in El Nido
(R = 0.28, p = 0.003) and 2 (R = 0.33, p = 0.001) in
Sablayan with slightly higher R values but still with
clear overlaps. This is consistent with the results for
coral cover (Fig. 3) wherein there was a significant
difference in site 2 in Sablayan and a higher standard
error for ARAICoBeH in site 1 El Nido. Both can be due
to the rapid changes in the bathymetries of the sites.
The three metrics analyzed here, namely live hard
coral cover, functional diversity, and community struc-
ture, are the typical parameters used to evaluate the
condition of coral reefs (van Woesik et al. 2009;
Licuanan and Aliño 2014). Based on our results, the

Fig. 4 Comparison of Shannon a) Verde Island b) Sablayan, c) El Nido,

diversity. Error bars are standard Passage Mindoro Palawan
errors of the mean 1.50
Shannon Diversity index

1.25

1.00

0.75

0.50

1 2 3 1 2 3 1 2 3

Site

ARAICoBeH System Underwater photo transects

Environ Monit Assess (2019) 191:633
Fig. 5 Non-metric multidimensional scaling (nMDS) ordination
based on Bray-Curtis similarities characterizing community struc-
ture gathered using ARAICoBeH System (yellow) and underwater
photo transect (blue) for each site within the three study locations.
ARAICoBeH system can provide realistic estimates for
these measurements without the need for scuba divers
with a few exemptions in terms of bathymetry of the
area.
Time and monetary cost analysis
A comparison of time and monetary cost for sampling
and analysis are summarized in Tables 2 and 3, respec-
tively. Overall, the time needed for a coastal benthic
habitat analysis with 50 PQs from field survey to gen-
eration of results is shorter with ARAICoBeH by
13 min. Field survey time for ARAICoBeH for 50
PQs takes an average of 7 min while the survey time
using the underwater photo transect method takes about
25 min. The need to set up scuba diving gear and lay
transects before the PQs are collected in the scuba-based
Page 9 of 15 633
Each point is a composition (functional group percent cover) of
one photoquadrat. Stress values for all sites are < 0.3 which
indicates a relatively good representation but needs careful inter-
pretation (Clarke 1993)
method requires much longer time for the field survey.
Selection of photos collected using ARAICoBeH for
analysis and geotagging which involves running a pre-
written script in R takes about 5 min. On the other hand,
the diver in the underwater photo transect method takes
a picture of the benthic habitat at specified intervals and
these pictures are ready for the next step which is the
analysis using the CPCe software. The manual classifi-
cation benthic groups from photos using CPCe are
common for both methods and thus require the same
amount of time. Visualization of results using the
ARAICoBeH method involves running a pre-written
script. Results include maps of live hard coral cover as
well as general benthic composition. All results are in a
single datasheet which is a convenient start to statistical
analysis. Visualization of results from an underwater
photo transect survey would require more time when
 633 Page 10 of 15 Environ Monit Assess (2019) 191:633

Table 2 Comparison of average time required to collect and process 50 photoquadrats using ARAICoBeH and the underwater photo
transect method

Activity Time needed (min)

ARAICoBeH System Underwater photo transect

Field survey 7 25
Selection of photos for analysis and geotagging 5 0
Photo analysis using CPCe 50 50
Visualization of results 5 5
Total time 67 80

starting a monitoring or assessment program because the however, assumed that a plotting script is already avail-
researcher would need to write script for this or run a able, and a similar amount of time was identified for
series of procedures in plotting software. It was, visualization of results for both methods.

Table 3 Comparison of monetary cost to collect and process 400 photoquadrats using ARAICoBeH and the underwater photo transect
method. Amounts are in US dollars and based on prices and salaries in the Philippines in 2015

ARAICoBeH System Underwater photo transect

Unit cost Quantity Total cost Unit cost Quantity Total cost

I. Equipment
GoPro Hero 3 Silver with underwater case 300.00 1 300.00 300.00 1 300.00
Metal pole 2.20 1 2.20 – – –
Marine rope 160.80 1 160.80 – – –
1-m kernmantle rope 10.80 1 10.80 – – –
3-kg lead weight 65.00 1 65.00 – – –
GPS/transducer viewer 440.00 1 440.00 – – –
Single beam transducer 150.00 1 150.00 – – –
Power bank 107.00 1 107.00
Makeshift fin 3.00 1 3.00 – – –
Handheld GPS – – – 283.50 1 283.50
Dive computer – – – 278.80 2 557.60
50-m transect tape – – – 21.45 4 85.80
PVC camera frame – – – 16.00 1 16.00
Full SCUBA set, excluding tank – – – 750.70 2 1501.40
Total 1238.80 2744.30
II. Expenses per site
Scuba tank rental – – – 6.50 4 26.00
Boat rental 65.00 1 small boat × 0.5 day 32.50 110.00 1 big boat × 1 day 110.00
Gasoline 10.00 0.5 gal × 0.5 day 5.00 20.00 1 gal × 1 day 20.00
Salary: boat operator/s 10.00 1 person × 0.5 day 5.00 10.00 2 persons × 1 day 20.00
Salary: researchers 20.00 2 persons × 0.5 day 20.00 20.00 2 persons × 1 day 40.00
Total 62.50 216.00
Grand total 1301.30 2960.30
Environ Monit Assess (2019) 191:633 Page 11 of 15 633

Fig. 6 Live hard coral cover (%)

map of El Nido, Palawan, in the
Philippines during the 2014
survey. Inset of map in red box
shows coral cover variability at
a finer scale

Monetary costs were also evaluated and compared the underwater photo transect survey method requires
for both methods (Table 3). Equipment costs for the an initial equipment expense of USD 2744.30. The
ARAICoBeH System amount to USD 1238.80 while difference is mainly due to the expensive cost of scuba

Fig. 7 Community structure map

of benthic habitats of El Nido,
Palawan, in the Philippines
during the 2014 survey. Red
boxes indicate boundaries of the
clustering of transects
 633 Page 12 of 15
diving equipment. Sampling a site with two stations
each takes less time when using the ARAICoBeH meth-
od. This translates to savings in terms of boat rental
expenses, gasoline as well as salary for both boat oper-
ators and researchers. Total boat rental costs inclusive of
gasoline and boat operators for sampling using
ARAICoBeH are USD 62.5 per day while it costs about
USD 216.00 for the underwater photo transect surveys.
The difference in cost is also due to the need for a bigger
boat for transport of dive equipment. The big diving
boats are usually manned by two people and consume
more gasoline. Tank rentals are cheap, but services may
not be readily available in remote areas. Additional costs
may be incurred for transport of scuba diving tanks and
in some cases an air compressor to the survey location.
Distribution and composition of benthic habitats in El
Nido, Palawan
A more extensive survey independent of the method
comparison was conducted in the town of El Nido,
Palawan, to illustrate the application of the method.
The survey covered an approximate total length of
72 km of coastal waters in more than 10 islands and
was completed within a period of 4 days. These results
were based on a subsample of 1676 PQs from a total of
27,299 pictures, using the pre-processing ARAICoBeH
algorithm which ran for 30 min. Manual scoring of PQs
was conducted over a period of 3 days, while the data
merging and mapping step were carried out for about
20 min using the post-processing algorithm. Overall, it
took about 8 days to complete, from data collection to
visualization. The application of ARAICoBeH System
to assess the benthic habitats of El Nido highlighted the
capacity of the system to detect trends and differences at
different scales. The output maps can be used to focus
on a benthic category of interest such as live hard coral
cover and to visually show differences at finer scales
(e.g., transect level, Fig. 6, red box). The distance be-
tween PQs for this study was set to 2 m, but the resolu-
tion of the survey can still be improved by decreasing
the distance since pictures are available at two-second
intervals. This level of detail can be used as a decision-
support tool for managers working at smaller scales
such as village leaders and people’s organizations.
Figure 7 illustrates presentation of results at a differ-
ent scale and can be used to highlight differences be-
tween sites. The transects were clustered into six sites
according to location. The western-most cluster is
Environ Monit Assess (2019) 191:633
Guntao while the transects in the central islands of
Miniloc, Shimizu, Entalula, and Pangulasian are pooled
together. There are two clusters in the north, and these
are transects from the north and south of the island of
Cadlao. Two more clusters were created from the tran-
sects surveyed inside the bay: Bay north and Bay south.
The sites with the highest live coral cover are found in
Guntao and the central islands, while the lowest are
found in the clusters of the inner Bacuit Bay: Bay north
and Bay south. Live hard corals were the most dominant
in these two island clusters while the rest of the clusters
were dominated by sand and other abiotic components.
The highest algal cover was found in Bay north and Bay
south.
Results of the ARAICoBeH survey agree with the
previous rapid ecological assessment conducted by
Turak and Devantier (2010), wherein similar sites in
Miniloc island and Guntao have coral covers that are
higher than the average for all sites sampled in El Nido,
while other sites monitored (e.g., inner Bacuit Bay,
Cadlao) were found to have significantly lower coral
cover. Average score of live hard coral cover for El Nido
was 34.48%, considering all the sites surveyed.
Disregarding all ‘sandy’ areas within El Nido, which
comprised about 30% of all analyzed PQs, the average
score increases the average to 47.48%. This was similar
to the initial findings of the recent national reef assess-
ment in the Philippines wherein El Nido was catego-
rized as ‘excellent’, with a hard coral cover score of over
44% which was twice the national average (Licuanan
et al. 2017).
Licuanan and Gomez (1988) previously established
that the fringing reefs in El Nido are consistent with
Miyadi’s Embayment Principle (1944, cited by
Horikoshi 1988), which states that the variability in
coral community structure is a function of the relative
position within a bay. This is due to the different envi-
ronmental gradients prevalent in the area or the degree
of exposure of benthic communities in the bay. One
important environmental factor that influences the El
Nido coral communities is sedimentation rate
(Quibilan and Aliño 2006). Higher sedimentation rates
may be observed inside the bay relative to the other
areas as a result of river input. Sedimentation is known
to be detrimental to coral health (Fabricius 2005). The
increased sediment output from Manlag River in the
1980s has been shown to affect coral health with ob-
served decreases in coral cover, diversity, and colony
sizes particularly in sites within Bacuit Bay (Hodgson
Environ Monit Assess (2019) 191:633
and Dixon 2000). Higher algal cover and a higher
percentage of the abiotic components in the clusters in
the inner bay drive the difference from the Guntao and
central island clusters which are dominated by hard
corals.
This survey demonstrates the effectiveness of
using ARAICoBeH System as a survey tool to
rapidly collect data over large spatial scales, as
well as to hasten the analysis work using its com-
panion pre- and post-processing algorithms. This
system would be helpful in developing countries
like the Philippines where monitoring to inform
coral reef resource management is limited by man-
power and certified scuba divers.
Conclusions
The assessment of ARAICoBeH as an alternative to the
underwater photo transect method showed that it
yielded estimates of common indicators of reef health,
such as hard coral cover and functional diversity, that are
very similar to the results from the scuba-based method
across different levels of reef health and diversity. This
shows that the ARAICoBeH System can be used to
assess and monitor the state of shallow marine benthic
habitats without compromising accuracy. It should,
however, be noted that there are some limitations. The
method is not applicable to sites with a steep slope (e.g.,
reef wall) and with sudden changes in bathymetry. En-
vironmental conditions, such as water turbulence, sedi-
mentation, current, and wind velocities during survey
times, should also be considered as these would defi-
nitely affect quality of images taken. It is also not
possible to identify corals and coral associated organ-
isms to higher taxonomic detail. Sizes of areas covered
in each PQ differ due to the variability in distance of the
camera from the substrate. Units are therefore presently
limited to percent cover but means to scale the photos
are currently being undertaken.
Most coral reefs are found in less-developed coun-
tries where monitoring and research programs are often
limited by availability of resources. The lower time and
monetary cost of using ARAICoBeH would allow re-
source managers and researchers to increase the spatial
and temporal scale of their assessments. The method
presented here can be applied to other areas to gather
spatially explicit ecological data necessary for the con-
servation and management of marine benthic habitats.
Page 13 of 15 633
Acknowledgements Special thanks to the Philippine Associa-
tion of Marine Sciences (PAMS) for the opportunity to present this
paper.
Funding information This study was funded by the National
Assessment of Coral Reef Environments (NACRE) research pro-
gram of the Department of Science and Technology (DOST) and
the Coral Reef Visualization and Assessment (CoRVA) research
program of the Department of Natural and Environmental Re-
sources (DENR). Patrick Lawrence P. Cadeliña was also supported
by an Outright Research Grant through the University of the
Philippines Diliman Office of the Vice-Chancellor for Research
and Development (UP-OVCRD) during the revision and fine-
tuning of this paper.
Compliance with ethical standards
Conflict of interest The authors declare that they have no con-
flict of interest.
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