The Menjangan Island Reef Project, Bali, Indonesia
The Menjangan Island Reef Project, Bali, Indonesia:
Preserving ocean biodiversity & ecosystem integrity through Marine
Protected Areas: defining Indonesian coral reef tipping points
Final Report to the Royal Geographical Society (with IBG)
Ralph Brown Expedition Award for 2011
Phillip Dustan RGS, FLS1,2*, Orla Doherty RGS1, Carol Milner1, and Abigail Alling FLS 1
P.O. Box 808
Big Pine, CA 93513 USA
Department of Biology2
College of Charleston
Charleston, SC 29424 USA
Phillip Dustan Ph.D., RGS, FLS
Department of Biology
College of Charleston
Charleston, S.C. USA 29424
The Biosphere Foundation, with funding from the Royal Geographical Society’s Ralph G. Brown
Award carried out a four month expedition to Bali, Indonesia to assess the vitality of Menjangan
Island’s coral reefs. The team completed over 3300 meters of underwater transects at 11 sites testing
the hypothesis that digital rugosity, a new method for estimating coral reef structural complexity, could
be used as estimator of ecological integrity. We found that while digital rugosity does provide an
estimate of structural complexity, the biological diversity of corals themselves is also an important
correlative of coral reef fish community structure. Thus, both physical and biological complexity are
significant components of coral reef vitality.
The Biosphere Foundation Expedition to Bali Barat National Park focused on assessing and conserving
the health and vitality of coral reefs within the Coral Triangle. Almost 35 years ago, the Indonesian
Park Authority established Menjangan Island as a marine protected area within Bali Barat National
Park. The reef system is a top-rated dive destination in Indonesia with large areas of well-developed
shallow reef and extremely luxuriant deeper wall communities. It is considered the most spectacular of
the Balinese reef systems and receives an estimated 50-100 plus divers per day. The fishers were
persuaded to switch from fishing to ferrying and today business is booming with over 100 boats
working out of two ports. Today, Menjangan Island boasts some of the most beautiful reefs in Bali in
large part to this economic community-based shift.
Before the region came under protection the reefs were chronically abused. Blast fishing was
common, areas were mined for cement production, and cyanide was commonly employed for tropical
fish collecting. Furthermore, climate change induced bleaching and crown of thorns starfish invasions
have decimated some beautiful inshore reefs in the area. Our goal was to survey reefs habitats in an
effort to understand the relationship between the physical structure of the reef and its fish and coral
populations. Additionally, our study sites were aligned with earlier research surveys to provide
information on the efficacy of the Bali Barat National Park Marine Protected Area designation for
S/V Mir, the Biosphere Foundation‘s recently renovated 35 meter 1910 classic yacht departed
Singapore for Bali on February 14, 2011. Her first stop was Jakarta, for customs and immigration, then
on to the Port of Benoa on Bali’s south coast for more paperwork. Finally, on March 9th Mir,
navigating through the swift currents of the Bali Strait, dropping anchor in Tanjung Gelap
Banyuwedang, a beautiful bay sheltered on three sides by mangroves and mountains.
Mir is an extraordinary vessel. She was built in Holland and spent much of her life sailing the
Mediterranean Sea. In 2008 she underwent a refit including replacing the engine and generator, fitting
in a new SCUBA compressor, water maker, and new interior with its superb galley, the heart and soul
of any ship. Our expedition would not have gotten off the ground were it not for the tireless support of
Mir’s captain, Mark van Thillo, and all her volunteer crew.
Mir at anchor in Tanjung Gelap, Bali Barat National Park
Our Biosphere Foundation in-water research group: Orla Doherty, Carol Milner, Abigail Alling, and
the author were joined by expert fish biologist Tasrif Kartawijaya from Wildlife Conservation Society
Indonesia. We surveyed eleven sites ranging from areas where the reef had completely collapsed under
the combined weight of all the human and natural pressures to seemingly intact reefs with the most
beautiful fish and reef life imaginable. At each site we surveyed three 50 meter transects at each of 2-4
and 6-8 meters depths. We counted fish, measured coral abundance, condition, and measured the
topographical complexity with a newly developing technique we have named Digital Reef Rugosity. It
has been long known that more physically complex ecosystems support more species through
increased niche dimensionality. The same appears to be true for coral reefs, but precise measurements
of habitat complexity have eluded researchers. Our new technique enables a diver to quickly and
accurately measure reef topographical complexity at the centimeter scale using a high precision,
relatively inexpensive, limnological submersible level gauge. In forty nine dives with a combined
bottom time exceeding 200 hours we amassed a data set totaling over 3300 meters of transect
Study sites ranged from near intact habitat to virtually destroyed reefs that resembled parking lot pavements.
Orla Doherty surveys reef for damage
Coral entangled in fishing net was common.
We employed local boats from the local association for diving. These converted fishing boats were sea
kindly and expertly piloted. Their low freeboard and open space provided ample room for our diving
operations. One day, our boatman told us how he and some friends had stayed out at Menjangan
overnight to ward off fishers from Java who came to blast fish during a local religious holiday, Nyepi,
on which the Balinese stay at home to pray and meditate. They had to chase the poachers away to
protect the reef because in his words he said “If there is no reef I have no job”.
Local boats operate out of two service pools at Labuan Lalang and Banyumandi, much like taxi cabs
waiting in line for customers. Their low freeboard, sun shades, and expert operators made them efficient
and comfortable dive boats.
Study Site: Menjangan Island Coral Reef Ecosystem, NW Bali, Indonesia
Menjangan Island lies off the northwest corner of Bali, Indonesia, within the Coral Triangle, a 2.3
million square mile area of ocean containing over 75% of known reef-coral species and 40% of fish
species. The Coral Triangle sustains over 120 million humans (1).
Menjangan Island lies within the boundaries of the Bali Barat National Park, which encompasses an
area of 300 square miles, constituting 10% of Bali’s total area. Brief surveys of Bali have reported the
occurrence of 53 of 61 scleractinian genera in this western region of Bali (2,3). The reef system is a
top-rated dive destination in Indonesia with large areas of well-developed shallow reef and extremely
luxuriant deeper wall communities. It is considered the most spectacular of the Balinese reef systems.
The Menjangan Island corals suffer mostly from blast fishing (reduced but ongoing, with impact
craters observed as recently as 2012), overfishing in what has been nominally declared a utilization
zone only meaning fishing is only allowed for personal consumption, bleaching from elevated seawater
temperature (1998, 2009 and 2010), severe Acanthaster planci infestation (1997), ongoing anchor
damage,, and chronic plastic debris. Reefs situated along the Bali coastline have additional pressures
from land based sources of pollution such as nutrient and sediment runoff, as well as greatly increased
fishing pressures over Menjangan Island. All of these sources of disturbance highlight the need for
improved conservation and ecosystem-based management.
The general morphology of northwest Bali coastal reefs consists of a very shallow reef flat with a short
drop to a terrace at 4-6 meters depth which transitions into a fore reef with a relatively steep,
sometimes vertical, reef wall face beginning at 6-10m (4). Reef development is often more luxuriant at
the edge of the break in slope, as evidenced by the formation of small sill reefs at the top of the wall.
In places, blast fishing and/or coral mining have leveled the coral community to the substrate, but in
most sites we visited on Menjangan Island such extensive physical damage was slight and the reef
coral cover and diversity were high. We visited eleven sites with four on Menjangan Island and seven
along the NW coastline of Bali proper. A comparison of sites is the subject of a separate report (5,
Doherty, et. al in prep, appended).
Site ID Site Name Latitude S Longitude E 4 Batu Togog Garden Eels 08° 07.127' 08° 07.127' 114° 35.712' 114° 35.712' 5 Teluk Kelor 6 Kisik 1 7 Kisik 2 8 9 Kotal Labuan Lalang 11 Pos 1 12 Pos 2 13 Pura Tanjung Gelap 08°05.809' 08° 06.720' 08° 06.767' 08° 06.767' 08° 06.767' 08° 06.767' 08° 06.767' 08° 06.767' 114°31.652' 114° 36.309' 114° 36.862' 114° 36.862' 114° 36.862' 114° 36.862' 114° 36.862' 114° 36.862' 08°08.066' 114°33.540' 2 16 Facing direction Tourism, diving Exposed/ Sheltered N N E sand and rubble patches with coral patches and bommies between N T E reef slope with high coral cover N N E N N E Patchy reef, soft coral, with sand and rubble between mix of live and dead coral patches with sand and rubble between N N E mostly dead coral rubble and sand E T S Bommies and sand N N S Lots of sediment, sand, with patches of reef SW T S close to the edge of the reef as it fell to rubble and sand. SE T S mixed reef sparse cover of hard coral NE T E extensive soft coral and sand NE T S Mostly Porites fingers bushes Reef description Site location details
Study sites marked on a Google Earth image. Refer to Table 1 for names and GPS locations.
Our field studies were conducted in March-April 2011 in mostly calm seas. At each site two sets of
three 50 meter transects were set parallel to the general reef zonation, approximately perpendicular to
swell direction so that we were working along bathymetric contours and within, rather than across,
habitat zones. The transects were set end-to-end in shallow (2-6m) and deeper (6-10m). The end of
each transect was spaced approximately 5 meters from the next covering an approximate 160 meter
length of reef.
Fish populations were visually censused by divers along transects in general accordance with Wildlife
Conservation Society protocol (6). Fish biomass, abundance and species were recorded by divers
along a belt 2 meters wide for fish under 10 cm long and a 5 m wide belt along the centerline for fish
over 10 cm long. Estimates of fish abundance and size were converted to biomass using published
length-weight relationships at four organization levels: species, genera, families and morphological
groups (7,8). Observers made multiple passes on each transect to capture large and as well as smaller
Substrate cover was estimated using point intercept at 50 cm intervals generating 100 pts per transect.
Coral colonies (live and dead if still discernable) were identified to genus and their condition noted. A
second observer swam a 2 meter belt along each transect tabulating coral condition including physical
damage, disease, fishing gear, bleaching, and crown of thorns starfish.
Calculations of diversity (Shanon Index H’ =∑ pi Log pi) for fish diversity were based on either counts
of fish (H’abundance) or the aggregate species biomass (H’biomass) of each species. Estimates of coral
biodiversity are based on colony point intercept at a generic level of identification and are thus
constitute a very conservative estimate of coral biodiversity.
Reef rugosity was parameterized by fine scale pressure measurements recorded with a digital level
gauge, an instrument normally used to track subtle changes in groundwater or stream levels and
temperature (Onset Computer Company #U21_001-02). The ceramic pressure transducer has a
nominal operating depth range of 0-30 meters with a resolution of 0.41cm and an accuracy of +/- 1.5
cm over its depth range. The instrument has the capacity to record 42,400 individual data points at
intervals as fine as one second, equaling almost 6 hours of data collection for pressure and temperature.
It can be programmed to begin recording at a predetermined time to alleviate the necessity of bringing
a computer into the field. The instrument also logs detailed temperature (0-40C, 12-bit resolution
with ±0.37°C accuracy) enabling a diver to profile temperature in the water column and to explore the
fine scale distribution of temperature with great precision.
Data recording, at one second intervals, began on the surface to estimate barometric pressure in air at
the sea level. Then the instrument was given a few minutes at the surface to equilibrate in seawater to
ensure an accurate temperature descent profile. DRR transects were begun by resting the instrument on
the substrate surface at the transect start point for 2-4 minutes to mark the beginning and to gain an
estimate of the influence of wave height variability. The start of a transect was marked by raising the
probe up above the reef quickly one to three times to mark the data file with recognizable spikes. The
diver then carefully and slowly swam along the transect line with the probe as close as possible to the
reef contour without bumping the bottom. The probe was quickly raised 1-2 times at each five meter
transect mark for distance calibration. Swimming speed was such that data sampling rate approximated
10cm/sec along the taught linear transect tape. The end was delineated with multiple such spikes and
then resting the probe on the bottom for 1-2 minutes. The whole procedure for a fifty meter transect
took approximately 10-15 minutes or about 40 minutes for a set of three.
Transect tapes were marked in centimeters which helped to calibrate swimming speed during a run.
Most of the transects were swum at a speed that yielded between 9 and 11 points per meter, about 10
cm/point. Marking each five meters with a vertical depth spike allowed us to examine the variability
of swimming speed. We found it easier to control the height of the instrument above the substrate and
to regulate swimming speed and direction by swimming into rather than with a current. Very often we
would find ourselves swimming diagonally across the transect line as we crabbed into the current to
keep the level gauge on its straight path.
Topside, the raw data were downloaded, corrected for pressure, converted into depth (meters), and
parsed into individual transects. The distant marks were marked the data file and used to examine the
rate of travel (points/meter) for consistency. The contour of the reef along each transect was calculated
by subtracting the deepest point from all other depths (relative depth). At this juncture we are using
calculations of standard deviation (std) as an estimate of transect variabilty (i.e. rugosity). The use of
other measures including fractal anaylsis and Fast Fourrier Transform is under study.
The data we collected are voluminous and a deep analysis is a work-in-progress with a number of
collaborators. In this report we focus on the results of our preliminary analysis of rugosity and its
bearing on fish and coral community structure across all sites. Previous research had suggested that
this measure of topographical complexity is an indicator of ecological integrity and the principal
purpose of our proposal to RGS was to address this hypothesis in greater detail.
Results and Interpretation:
Our survey extended over a wide range of reefs across a wide spectrum of ecological vitality. Some of
these reefs were nearly intact while others seemed to be near ecological collapse. Live coral cover
varied greatly between sites as the reefs ranged from nearly intact to heavily damaged. Reefs with less
than 10% coral cover seemed to have lost their ecological integrity and were dominated by large areas
of brownish-green benthic algal mats.
Mean live coral cover at eleven study sites off N.W. Bali, Indonesia. Digital rugosity was not measured at Site 7.
Both Fish abundance and biomass varied over two orders of magnitude across the eleven sites we
Mean fish population densities and biomass estimates at eleven study sites off N.W. Bali, Indonesia.
Thus our study sites provided a broad range of communities for testing the utility of digital rugosity as
an indicator of community-level ecological integrity. That said, like most real-world ecological
situations, the data, are high data are highly variable because nature in the field is not always as clear
cut as we would like. We must always remember that we are observing nature, not some carefully
designed laboratory experiment. Thus, even though it was “messy”, examining digital rugosity over
this wide spectrum of community states provided a window into the relationship between reef fish and
the physical and biological aspects of coral communities under environmental stress.
Surprisingly, even though reef coral are the structural members of a reef, there was no significant
correlation between digital reef rugosity (DRRstd) and living coral cover across all sites (below).
However, when recently dead coral was added to living coral cover the relationship became
Relationship between coral community cover and digital reef rugosity
The implications of this are that both live and recently dead coral form the physical structure of the
reef that contributes to rugosity. Simply measuring live coral leaves out those colonies that have
recently perished from disease, bleaching, cyanide poisoning, or soft tissue predation (i.e. crown of
thorns). However, if the ratio of live to dead coral shifts in favor of dead coral, rugosity will decrease
over time as the dead skeletons degrade due to reef flattening due to bioerosion and storms (8).
The data revealed a positive correlation of fish abundance and biomass estimates with (DRRstd) as
depicted in the data plots below:
Relationship between fish community abundance and digital reef rugosity
The obvious implication here is that more reef fish live in structurally complex habitats. While the
correlation is not strong, only explaining about 10 to 20% of the variation it is highly significant. Reef
habitat degradation generally reduces the structural complexity through physical means (bombing,
mining, etc) or indirect stressors such as severe bleaching, disease, algal overgrowth, or reduced water
quality, which will have a cascading effect on the luxuriance of the fish community (9-13). This has
been observed as a common fate for many coral reef fisheries (8,14).
Coral reefs are among the most complex communities on Earth. One measure of their biological
complexity is biodiversity (species diversity) while rugosity describes aspects of their structural
complexity. Community species diversity encompasses two aspects of community structure: species
richness and the proportion of species, termed evenness. A community that has more species (higher S)
will be considered more diverse. Evenness describes the relative proportion of individuals of each
species in the community. An even community will have approximately the same number of
individuals of each species while an uneven community will be dominated by a few very common
(numerous) species with many more rare species. Ecologists commonly characterize community
structure using the Shannon and Weaver index of Diversity (H’ for diversity) and Evenness (J’) as the
ratio of H’/H’maximum (15). Highly diverse communities that possess high evenness are thought to be
biologically accommodated/regulated assemblages. Species-species interactions such as competition
and predation are thought to carry a lot of importance in determining community structure. In contrast,
uneven communities are thought to be more physically controlled and are generally characterized by a
few species that have adapted to strong physical forcing functions. As a general rule-of-thumb, tropical
communities, forests and reefs, tend to show high species diversity (H’) as well as high evenness (J’)
as opposed to higher latitude communities (i.e. temperate zone forests) due to the intense species
packing resulting from top down forcing functions and interspecific competition.
Coral reef fish species diversity was positively correlated with coral biological diversity suggesting
that the species composition of the fish community is responding to different types of coral and not just
the amount of coral. This conclusion makes sense as niche specialization has been widely described in
the coral reef fish literature with many fish showing close affinities to coral species or habitat zones
(16). Our finding that the evenness of the fish community is positively correlated with fish species
diversity adds reinforcement to our argument that species-specific interactions are important elements
regulating niche packing on the reef.
Reef fish community diversity is positively correlated with coral diversity while Fish community evenness
increases with fish species diversity.
In contrast, fish community diversity based on biomass (H’biomass) was not correlated with rugosity.
Furthermore, fish diversity based on abundance of individuals (H’abundance) demonstrated a highly
significant negative correlation with rugosity. Thus while structural complexity does not appear to be
a determinant of fish diversity, more fish live in more structurally complex habitats. The negative
relationship between fish species diversity based on abundance (H’ abundance) and rugosity is perplexing.
It may result from a disproportionate increase of smaller fish as physical complexity increases or may
be related to habitat degradation but a conclusion must await further analysis.
Reef fish community diversity based on abundance is not significantly correlated with digital rugosity while fish
diversity based on the number of individuals shows a significant correlation with rugosity.
In summary, the data are consistent with the hypothesis that biological and physical habitat complexity
are both significant components of coral reef fish community structure. While other work has
demonstrated that rugosity is an important component of fish species diversity (9-11), this is probably
the first work that has revealed the importance of both coral biological diversity and physical
complexity across such broad spectrum of reef degradation. Fish community abundance appears to
respond to physical complexity (increased rugosity) by increasing abundance, while increased species
diversity is a correlative of increased coral diversity. An explanation for this might center on structural
complexity providing increased living space while biological diversity allows for more specialized
species niche packing. The inescapable conclusion is that both biological and physical complexity are
co-requisite components of a healthy coral reef ecosystem. The yield of some degraded fishing
grounds might be improved by artificially increasing rugosity but this will probably not restore the fish
community to its previous community structure. Improving rugosity may promote increased fish
abundance; it may not be as effective by itself to restore species diversity. In many ways this is
analogous to the differences between the biodiversity of tree farms or urban landscapes and natural
forests. All provide structural complexity but natural forests support much greater species diversity of
birds, insect, and mammals due to the increased biological diversity of the trees and woody plants that
have coevolved complex species interactions with their associated fauna. There is every reason to
expect coral reefs follow similar patterns of community assembly as the highly diverse Indo-Pacific
reefs possess a relatively high degree of endemism and co-evolution between species. Our data are
consistent with the vision of a coral reef community being highly co-evolved system with multiple
layers of species-specific interactions comprising the community matrix.
Friends of Menjangan: A community conservation initiative
Given the expressed interest in protecting Menjangan reef by the community, Biosphere Foundation
initiated a project called “Friends of Menjangan” with its local NGO partner based in BBNP, Yayasan
Dwi Asih Sejahtera. The aim of the Friends of Menjangan project is to bring together all interested
stakeholders to work together and make a difference for the future of Menjangan Island and its reef.
The management of the project is local, the funds to support the conservation initiatives are local and
international, and the membership includes everyone who visits the land or reef of Menjangan Island.
This concept was embraced with enthusiasm by the community and its inaugural event was held on
May 6th and 7th at Labuan Lalang and Menjangan Island. Members of all stakeholders were present
including fishermen, central government, local government, temple priests, schools, local NGOs,
international NGOs, resorts, dive operators, tour-guides, tourists and the media.
The overall objective of Friends of Menjangan is to coordinate a comprehensive community-based
conservation program involving everyone who cares about Menjangan and its reef.
Its near-term objectives include:
Setting up grade school, high school and Graduate school educational programs for local
and international students about reef conservation and waste management.
Implementation of a regional waste management program for NW Bali.
Eradicating destructive fishing by implementing educational outreach programs and co-operative
patrols between local government, central government and the fishermen at Menjangan Island.
Designing and implementing a maintenance program for the Menjangan Island mooring buoy
system and installation of additional buoys.
Facilitating educational programs for the boat divers, tour guides and tourists about reef
maintenance and protection.
Implementing regular beach and reef clean-ups.
Involvement by the priests and community to remove all garbage from the temples after each
Development of sustainable projects that will provide the community with income.
To prepare Menjangan Island and Labuan Lalang for the May 6th and 7th event to launch Friends of
Menjangan, and in order to improve communications to visitors and alleviate pressure on the island,
several conservation initiatives were carried out.
Three new signboards to welcome visitors to Menjangan Island were placed on the island: one
at Pos1, one at Pos2 and one at Temple Jetty. These boards give three clear and simple
instructions in English and Bahasa Indonesia: ‘Don’t break the reef’, ‘Take your trash home’
and ‘Don’t use an anchor’.
Two more of these signboards were placed at Labuan Lalang and Banyumandi, the two
gateways to Menjangan Island.
Small versions of these signs were placed in each of the 78 boats at Banyumandi and the 45
boats at Labuan Lalang which take visitors to the island.
They were also posted at eight dive shops in Pejarakan, Sumber Klampok and Pemuteran.
Four mooring buoys were restored to alleviate the pressure on dive sites around Menjangan
Mark van Thillo with a BBNP Officer installing a signboard at Pos1 on Menjangan Island (left)
Students gather at Pos1 on Menjangan Island to start a trash cleanup (right)
Mir departs Singapore
Mir arrives Jakarta
Mir departs Jakarta
Mir arrives Benoa Marina, south Bali
Mir departs Benoa Marina
Mir arrives Menjangan Island, Bali
Field Studies begin
Field studies completed
mooring buoy project begins
Friends of Menjangan launched at Bali Barat National Park
Educational programme piloted at Menjangan Island
Mir departs for Singapore
Biosphere Foundation Bali 2011 Expedition Timeline
College of Charleston
Wildlife Conservation Society
Global Coral Bank
Biosphere Foundation Bali 2011 Expedition Personnel
On the last day of diving in April 2011 we came upon a section of reef on the seaward (north) coast of
Menjangan Island that was as perfect and beautiful a reef as any of us had ever seen. We named it
Symphony Reef because the reef was a symphony of color, corals and fish with a magical beauty. In
June 2012, we revisited the reef to find large parts of it completely destroyed from crest to drop off.
Much of the area was smashed into mere fragments of what had been delicate foliose leaves of stony
coral colonies. Deeper, debris from the shallows continued to damage the benthos as it cascaded
downslope. Local fishermen blamed anchoring by dive boats while others suggested that blast fishing
might have also contributed to the destruction. In the year between our visits, we found that many of
the moorings we had installed around Menjangan Island were no longer active. Mooring lines that
broke had not been repaired. Other mooring blocks designed for one or two boats had been drug
through the reef when they were asked to hold more than 5 or ten boats. Biosfir Indonesia is now
endeavoring to obtain the equipment necessary to install more robust moorings that are anchored into
the reef substrate as well as instituting a program of mooring repair to insure reliable mooring for the
burgeoning dive industry of Menjangan Island.
Symphony Reef, Menjangan Island: Left frames taken April 2011, Right frames taken June 2012
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Menjangan Island sign erected by Biosphere Foundation