UP Marine Science Institute

BI 194 Biology Practicum

Antoni Andreu M. Martija

Progress Report 1
April 23 to April 29, 2012

Background of the Institution

The Marine Science Institute (MSI) of the University of the Philippines Diliman is a
research institution dedicated to the marine sciences, particularly Marine Biology, Marine
Physical Science, and Marine Biotechnology. As a center of excellence for the marine sciences,
the Institute has the following primary objectives: generation of basic and applied information
regarding proper management and conservation of the marine environment, marine science
education through M.Sc. and Ph.D. degree programs, and development of marine-based
technologies for sustainable use of the countrys marine resources. MSI has a marine laboratory
located on the northwestern shore of the Lingayen Gulf, Pangasinan: the Bolinao Marine
Laboratory (BML). The BML complex serves as the Institutes marine station for ecological
field studies and mariculture. The main building houses several laboratories for various fields of
study including coral reef ecology, invertebrate biology and seagrass biology. BML also has an
outdoor hatchery for the rearing of corals, seaweeds, sea cucumbers, and other marine
organisms. Also, housing is available for resident and transient researchers, research assistants
and interns.

Supervisor

Ronald D. Villanueva, Ph.D. is the resident scientist of the Bolinao Marine Laboratory.
He specializes in coral reef restoration and ecology, having published a number of ISI journals
on the said field. Dr. Villanueva may be contacted through the BML administrative office (c/o
Ms. Charina C. Caalim, Administrative Officer) at 542-8022 loc. 102 or through
villanuevr@yahoo.com.

Nature of Work

Internship at the Bolinao Marine Laboratory consists primarily of the following tasks:
assisting in coral reef restoration projects and conducting a mini-study on the seagrass
community in Bolinao, Pangasinan. The first task involves the following: collection of coral egg
bundles during spawning season, counting of coral larvae, estimation of coral larvae population
and rate of gamete fertilization, and counting of recently settled coral juveniles on both natural
and artificial substrates. Coral reef restoration projects also involve assisting and observing Dr.
Villanueva and his research team in field works such as gravid coral collection and in situ coral
juvenile seeding in various study sites in Bolinao, Pangasinan.

The second phase of the practicum work at BML is the mini-study on seagrass
distribution along water quality gradients as influenced by fish farm effluents in Bolinao,
Pangasinan. This research work entails the estimation of seagrass cover and diversity and the
evaluation of water quality in six different study sites. Correlation between seagrass cover and
water quality as influenced by fish cage proximity were analyzed afterwards.

Expectations

Practicum at the Bolinao Marine Laboratory is expected to involve the learning of proper
research methods in coral reef restoration and ecology. This includes methods in coral egg
bundle collection, coral larvae counting (discrimination between fertilized and unfertilized eggs,
computations of fertilization rates) and in situ seeding. Laboratory work is projected to have an
indefinite schedule due to the uncertainty of coral spawning. Intensive diving activity around
Santiago Island, Pangasinan, is also anticipated due to the nature of the research projects of Dr.
Ronald Villanueva. Learning the proper use of laboratory and field equipments such as tetrapods,
underwater cameras, light meters, and multi-parameter water quality sensors is also expected.
This also includes learning the use of various computer software that are used to process data
from field monitoring.

Week One (April 23 to April 29, 2012)

The first week of internship at the Bolinao Marine Laboratory consists of introduction to
the BML complex, initial exposures to potential study sites, refining of research proposal and
assisting Mr. Dexter Dela Cruz, M.Sc., Dr. Villanuevas research assistant, on his choice
experiment on coral settlement. On the first day, Dr. Villanueva toured us around the BML main
building and outdoor hatchery. He showed us several rooms that can be used for research inside
the BML main building. These rooms include the GEF lounge, Instruments Room, Computer
Room, Library and the Coral Reef Restoration and Ecology Room (BML 109). The GEF lounge
and the Computer Room are mostly for data processing and analysis. Meanwhile, the BML
library contains a rich catalogue of journals, books and other marine science literature. The
Instruments Room and coral reef restoration and ecology room contains all the equipment
necessary for laboratory and fieldwork, respectively. Dr. Villanueva also showed us the BML
dive locker room, where most of the diving gears are located.


Figure 1. BML Dive Locker Room

The BML outdoor hatchery contains the facilities for mariculture. Corals, sea cucumbers,
giant clams, seaweeds and the like are being reared in the hatchery for both restoration and
research purposes. Mr. Dexter Dela Cruz also showed us the containers with juvenile corals that
settled in both dead coral and artificial tile substrates. This is for his ongoing experiment
regarding the substrate preference of several juvenile coral species. The said experiment is being
conducted in collaboration with several Australian researchers.


Figure 2. Tanks and containers containing seaweed and juvenile coral specimens,
respectively

The following day, Dr. Villanueva allowed us to join his M.Sc. students in their field
class. This is to expose us to potential sites for our proposed studies. We went snorkeling in the
Lucero MPA (marine protected area), where we surveyed the coral reefs. Afterwards, we
returned to the outdoor hatchery to assist Mr. Dela Cruz in the counting of juvenile corals. He
also gave a short lecture on coral larvae settlement and on the discrimination between living and
dead juvenile corals. A total of three tiles were surveyed for the presence of juvenile corals.
Counting of juvenile corals involve laying a mini-quadrat above the tile, and consequently
observing the tile under a stereomicroscope. The number of juvenile corals located on both sides
of the tiles were then recorded in the data sheet provided by Mr. Dela Cruz.


Figure 3. Counting of juvenile corals under a stereomicroscope

The next few days consisted of several consultations with Dr. Villanueva regarding the
mini-study to be conducted in Bolinao. The final proposal approved by Dr. Villanueva was the
research on seagrass distribution along water quality gradients
as influenced by fish farm effluents in Bolinao. After the
approval, we then practiced the use of several field
equipments that we will be using for our study, including the
tetrapod and the underwater camera, in the BML front
(Guiguiwanin, Bolinao, Pangasinan). Knowing how to use the
underwater camera attached to a tetrapod is essential because
most field surveys use such methods for documentation. The 1
m x 1 m tetrapod is usually laid above the quadrat being
surveyed. The camera will then capture the whole area
covered by the quadrat. Aside from practicing the use of such
equipments, a survey of the BML front, Guiguiwanin shore
was also performed. The BML front was selected to be one of
the preliminary study sites due to the presence of seagrass
meadows and also because of its relative proximity to the fish
cages located in Riripayan Point. Figure 4. A 1 m x 1 m tetrapod

Aside from these, Dr. Villanueva also provided us several computer programs for data
analysis. We practiced using Vidana 1.2.1 and Coral Point Count with Excel Extensions (CPCe),
which are used for the computation of percentage cover of various marine organisms, including
corals and seagrasses. The first software allows the user to highlight the area covered by the
organism of interest. The program will then compute the percentage cover and actual area cover
of the organism based on the selected scale and on the highlighted area. Meanwhile, CPCe
allows the user to define the identity of a number of random points in the plot. The program will
consequently compute for the percentage cover of the organism of interest based on the
percentage of the number of points occupied by the said organism. For example, if 25 of the 50
random points on the plot are identified as seagrass, then CPCe will calculate that the quadrat is
roughly 50% covered by seagrass. These computer programs are a more accurate and efficient
measure of percentage cover, compared to the traditional Saito-Atobe method, which often takes
more time and provides general estimates of percentage cover only.














Figure 4. Vidana 1.2.1 software

UP Marine Science Institute
BI 194 Biology Practicum
Antoni Andreu M. Martija

Progress Report 2
April 30 to May 6, 2012

Week Two (April 30 to May 6, 2012)

On the morning of April 30, 2012, the remaining five potential study sites around
Santiago Island, Bolinao, Pangasinan, were surveyed for the presence of extensive seagrass
meadows. The extent of the seagrass meadows were evaluated by laying a 100 m transect line
parallel to the shore in each of the sites. Aside from the presence of seagrass, site selection was
also based upon the establishment of a water quality gradient as influenced by fish farming
activity as recommended by Dr. Villanueva. The five additional study sites surveyed were the
following: Riripayan Point, Siapar Island, Lucero, Ducoy and the Seagrass Reserve near Benew.
The reserve was intended to serve as the control of the experiment, while all the other sites were
selected in order to establish the water quality gradient. Kuya Andrew of BML served as the
boatman of the GEF boat during the survey.


Figure 1. Map showing the preliminary study sites around Santiago Island, Bolinao,
Pangasinan.

After the site survey, reservations for the equipment necessary for the study were made
through Maam Shiela of BML. The following equipment were reserved: YSI multi-parameter
water quality sensor, a Global Positioning System (GPS) device, and the pH meter of the
Instruments Room. Permission to use the permanent quadrats of Dr. Villanuevas projects was
also acquired.

On the morning of May 1, 2012, we performed the first environmental sampling in BML
front. A 100 m transect line was again laid parallel to the shore, and the first quadrat was laid on
the 0 m mark. Documentation of the plot was performed. Also, a water sample from the first
zone was taken. However, we encountered some problems regarding the use of the YSI multi-
parameter water quality sensor and the counting of seagrass individuals. The sensor kept on
disconnecting from the logger; also, due to the high tide and unavailability of a boat, we had
difficulty in keeping the logger from being wet by the wave action. Moreover, we were also not
able to count the seagrass individuals properly because we did not have diving gears during that
time. We initially thought that it would be easy to go skin diving at a depth of less than a meter
to count the seagrass; physical constraints including shortness of breath, however, kept us from
doing so. We then decided to postpone the water quality sampling and seagrass counting and
plan the necessary adjustments instead.

After the planning phase, we then proceeded to practice the use of the pH meter in the
Instruments Room. The pH meter, however, was not calibrated properly. The calibration buffer
solutions inside the laboratory were expired already and Maam Shiela told us that it would take
time to acquire the new solutions, so we decided to measure the pH of our water samples when
we return to Manila after the practicum.

The following day, May 2, 2012, we accompanied Dr. Villanueva and his research team
in their field monitoring in Cangaluyan and RDB, Pangasinan. They went to collect gravid coral
colonies for the full moon was nearing; it meant that these coral colonies are nearing the
spawning stage. We went snorkeling and skin diving at an average depth of 20 feet in
Cangaluyan to observe Dr. Villanueva and his team collect the colonies. By the time we went to
RDB, we already assisted Dr. Villanueva and his research assistants in the collection of gravid
Acropora tenuis colonies. The collected colonies were placed in a container full of seawater and
were eventually transferred to the outdoor hatchery.


Figure 2. Collected gravid colonies of Acropora tenuis

On May 3, 2012, we went to Lucero and Ducoy, Pangasinan to perform our first official
field work on our study on seagrass. One of Dr. Villanuevas research assistants, Mr. Fernando
Castrence, also known as Sir Jun, accompanied us during the sampling. Kuya Andrew again
served as our boatman during the trip. Sir Jun assisted us in the laying of the 100 m transect line.
We then performed the following in each of the three zones in both areas (0, 50 and 100 m
marks): plot documentation, seagrass counting, water sample collection and measurement of
water quality parameters using the YSI multi-parameter sensor. All data, including the GPS
location of each of the zones, were recorded on a slate. These data were then transferred,
analyzed and processed in the computers inside the GEF lounge. Data analysis involved
computation of percentage cover using Vidana 1.2.1. and biodiversity using the Shannon-Wiener
index. Water samples also were put in a freezer for future analysis.


Figure 3. YSI multi-parameter water quality sensor













UP Marine Science Institute
BI 194 Biology Practicum
Antoni Andreu M. Martija

Progress Report 3
May 7 to May 15, 2012

Week Three (May 7 to May 15, 2012)

On May 7, 2012, we went to Riripayan Point and Siapar Island to continue the data
collection process for our study on seagrass distribution. Sir Jun and Kuya Alfon served as our
research assistant and boatman, respectively. After the transect line was laid parallel to the shore
in Riripayan, we began counting the number of Cymodocea rotundata individuals in the first
zone (0 m mark) in Riripayan Point. We also recorded the water quality parameters and GPS
location of plot. The next two zones (50 and 100 m mark) were barren; we only evaluated water
quality and took underwater pictures of the zones for documentation. Dr. Villanueva also
dropped by Riripayan to observe the data collection process. He then suggested measuring light
penetration as an additional variable, since light, aside from water quality, also significantly
affects seagrass distribution. We then returned to BML to get the Li-Cor light meter from Dr.
Villanuevas project room. Afterwards, we went to Siapar Island to perform another set of data
collection. Seagrass cover in Siapar Island is not as extensive as the cover in Lucero and Ducoy;
the last two zones consisted of few Enhalus acoroides and Thalassia hemprichii individuals
only. After the fieldwork in Siapar Island, we went back to the BML dive locker room to rinse
the materials we used. It was necessary to rinse the water quality sensor, light meter and
underwater camera case to prevent the accumulation of salt, thus preserving them in good
condition. Data collection in the GEF lounge followed afterwards.


















Figure 1. Mr. Fernando Castrence, research assistant, and Ivy Uy, colleague, during
the fieldwork in Siapar Island
The following day, May 8, 2012, we again accompanied Dr. Villanueva and his research
team in their fieldwork in Silaki Island, Pangasinan. By this time, some of the collected gravid
coral colonies have already spawned; thus, fieldwork consisted of in situ seeding of juvenile
corals, which meant the release of coral larvae in their natural substrate. Mr. Dexter Dela Cruz
and Mr. Marcos Ponce (Sir Macoy), research assistants of Dr. Villanueva, primarily conducted
the release of larvae. Sir Jun also showed us some of the Acropora tenuis colonies they have
transplanted approximately two to three years ago. These colonies are still very young, as
indicated by their relatively small sizes compared to the corals we saw in Cangaluyan and RDB.














Figure 2. (L) Sir Macoy releasing some of the coral larvae and (R) Acropora tenuis colonies
in the waters of Silaki Island, Pangasinan

Aside from this work on corals, we also released a pawikan named Punggay near the
waters of Silaki Island, Pangasinan. The sea turtle was approximately two years old and was
released away from the site of intensive fishing activity to ensure that poachers or irresponsible
fishermen will not catch it.














Figure 3. (L) Punggay, the two-year old pawikan, in a container in the hatchery and (R) Ivy
Uy releasing Punggay in the open sea

After the fieldwork, Dr. Villanueva took us to the giant clam nursery. We went
snorkeling to observe many Tridacna gigas individuals in the said area. The nursery is also near
Silaki Island and is protected by the municipality of Pangasinan.


















Figure 4. Tridacna gigas individuals in the giant clam nursery in Silaki Island, Pangasinan

On May 10, 2012, we again computed for the seagrass cover in Lucero, Ducoy, Riripayan
Point and Siapar Island using the Coral Point Count with Excel Extensions (CPCe) software. Dr.
Villanueva recommended using the said software instead of Vidana 1.2.1. for faster data
analysis. Using the CPCe software only involves the designation of the identity of the random
data points; for our plots, we chose to have 50 random points. Once the identities of the points
are established, CPCe will then automatically compute for percentage cover using Microsoft
Excel.















Figure 5. Coral Point Count with Excel Extensions (CPCe) computer software
On the night of May 18, 2012, some of the gravid Acropora and Favites colonies in the
hatchery underwent spawning. I, together with Ivy Uy and Mr. Dexter Dela Cruz collected the
coral egg bundles. The Acropora colonies spawned earlier at around 6:30 PM, while the Favites
colonies spawned around 8:30 PM. Coral egg bundles were transferred from the main containers
to a 14 L bucket. Spawning of the Acropora corals were also documented using the underwater
camera.























Figure 6. (L) Spawning of Acropora tenuis
colonies and (R) Collection of coral egg
bundles

After the collection of coral egg bundles, three samples were collected for coral larvae
counting. The 14 L bucket containing the egg bundles were mixed homogenously; once
homogenous, three 60 mL tube containers for each of the species were dipped underwater to
collect the larvae. These tubes were then transferred to the Instruments Room where counting
was performed. All of the larvae in each tube were transferred into a disc plate; the plate was
then viewed under a stereomicroscope. A counter was used to easily count the larvae. Both
fertilized (cells in the 2- or 4-cell stage) and unfertilized (one-celled) eggs were counted.
Dividing the number of fertilized eggs by the total number of eggs and multiplying the answer by
100 gave the fertilization rates for both species. The actual number of coral larvae collected in
the 14 L bucket was also estimated through dimensional analysis: the total number of coral
larvae inside the tubes was divided by 60 mL and subsequently multiplied to 14,000 mL (14 L),
thus giving the estimated number of collected coral larvae. The same mathematical computation
was used to determine the actual number of unfertilized eggs in the 14 L container.














Figure 7. (L) Unfertilized eggs of Acropora tenuis as viewed under the
stereomicroscope and (R) Disc plate containing the coral larvae collected

Lastly, we conducted the final set of data collection on May 14 and May 15 in Silaki
Island and in the Seagrass Reserve, respectively. We decided to use Silaki Island as the fifth
experimental site instead of the BML front, due to the high amount of seagrass diversity in the
area as reported by the journals we found in the BML Library. The standard protocol was
performed for both areas: plot documentation, water quality evaluation, measurement of light
penetration, collection of water samples and seagrass counting. Kuya Alfon served as our
boatman during both trips. Data processing and analysis for seagrass cover and diversity were
conducted in the GEF lounge after the fieldwork.


















Figure 8. Survey of seagrass cover and diversity in the Seagrass Reserve near
Benew, Pangasinan

Insights

My internship at the Bolinao Marine Laboratory made me realize how far the Philippines
is still from becoming the leading center of marine science research in the world. As a tropical
archipelago blessed with vast amounts of marine resources, the country should have, as of this
moment, a significant number of researchers and research facilities in the said field. It is a pity
that most of the students of the life sciences go into an already crowded postgraduate course,
medicine, without even realizing the wealth and significance of the knowledge that they can
unearth while doing research underwater. Also, in the words of Mr. Dexter Dela Cruz, it is
humiliating that there are only few marine stations in the country, notably UP-MSI and the
marine stations of De La Salle University and Siliman University. The efforts of these
institutions clearly have not gone to waste, but there is still a lot of progress that needs to be
reached by the country in terms of becoming the leading marine research center in the globe.
Support through proper funding by the government and other institutions and igniting the interest
of life sciences majors for the marine sciences are some of the key solutions to this problem.

Acknowledgments

I would like to thank the following people for making my practicum a worthwhile
experience and for making our research on seagrass possible:

Ronald Villanueva, Ph.D., for guiding us throughout the course of our research work and
for teaching us how rewarding it is to work with the countrys marine resources,

Dexter Dela Cruz, M.Sc., for the jokes and for the laboratory methods we learned during
the course,

Sir Jun and Kuya Alfon, for accompanying us during fieldwork and for assuring that we
get to our study sites safely,

Maam Sheila, for the patience and for allowing us to borrow her multi-parameter water
quality sensor again and again,

Ate Marife, for always cooking our packed lunch during fieldworks,

And Mr. Ronald Cruz, M.Sc. and the Department of Biology, for giving us this great
opportunity to experience marine science research.