Journal Articles - UP - MSI
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- C30 — A simple, rapid, scientifically valid, and low-cost method for citizen-scientists to monitor coral reefsLicuanan, Wilfredo Y.; Mordeno, Princess Zyrlyn B.; Go, Marco V. (Elsevier, 2021-09)The extent and speed of recent changes in reef coral abundances due to ocean warming and human impacts require more widespread capability to map and measure these changes, especially in countries like the Philippines. We present “C30”, a simple, rapid, scientifically valid, and low-cost method for skin divers or freedivers to take random photo-quadrat images within predefined stations on the upper reef slope. C30 yields coral cover data similar to those collected using the more intensive C5 method and can be as powerful in detecting small differences in reef cover. Less time is also needed for training personnel and sampling. However, more photo-quadrat images, better cameras, and closer collaboration with local scientists are required if higher precision data and estimates of coral diversity are needed from C30. C30 is a valuable tool for participatory, community-based citizen science monitoring of coral reefs.We thank the Department of Science and TechnologyPhilippine Council for Agriculture, Aquatic and Natural Resources Research and Development (QMSR-MRRD-COR-0-1209 and PCAARRD-GIA 4478), and the Department of Environment and Natural Resources Coral Reef Visualization and Assessment, The Philippines Project for funding some of the fieldwork. The initial research on citizen-science monitoring was undertaken with funding from Oscar M. Lopez Center for Climate Change Adaptation and Disaster Risk Management Foundation, Inc., The Philippines (Grant number OMLC RG 2017-18). We also thank the DLSU Innovation and Technology Office for the patent application for the C30 monopod in the Intellectual Property Office of the Philippines. The comments and suggestions of the reviewers are acknowledged and are very much appreciated. WY Licuanan is the holder of the Br H Alfred Shields FSC Professorial Chair in Biology and Br Cresentius Richard Duerr FSC Professorial Chair in Biochemistry.
- Characterization of Alexandrium tamutum (Dinophyceae) isolated from Philippine waters, with the rare detection of paralytic shellfish toxinBenico, Garry; Azanza, Rhodora (Association of Systematic Biologists of the Philippines, 2022-04-01)Alexandrium tamutum M.Montressor, A.Beran & U.John is a non-toxic, bloom-forming dinoflagellate species commonly reported in temperate waters. In this study, 8 cultures of A. tamutum established from Bolinao Channel and Manila Bay, Philippines were characterized in terms of their morphology, phylogeny and toxicity. Cells were roundish, measuring 25.5 –29.84 µm long and 26.2–28.45 µm wide. The nucleus is equatorially elongated and located at the center of the cell. The chloroplasts are numerous, golden brown in color and radially arranged. Thecal tabulation is typical of Alexandrium: APC, 4', 6'', 6c, 6s, 5''', 2''''. Shape of the taxonomically informative thecal plates such as sixth precingular plate (6'') and posterior sulcal plate (sp) was similar to A. tamutum, which confirms the species identity. However, the presence of anterior and posterior attachment pores observed in our cultured isolates is the first case in this species. Molecular phylogeny inferred from LSU rDNA and ITS supports our identification by forming a well-supported clade composed of A. tamutum strains from other geographic regions. HPLC analysis showed that A. tamutum is generally non-toxic except for strain ATC9 which has low amount of decarbamoylsaxitoxin (dcSTX), resulting to a toxicity of 0.07 fmole STX eq per cell. The present study reports the first verified occurrence of Philippine A. tamutum with reliable morphological and molecular information, including the first record in Manila Bay and first detection of PST in one strain at a certain culture period.We acknowledge the Department of Science and Technology Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST PCAARRD) and the University of the Philippines-The Marine Science Institute (UP-MSI) for the funding support. We are grateful for the assistance of Joshua Vacarizas, Keith Pinto and Jenelyn Mendoza for the molecular and toxicity analyses of the cultures. We also acknowledge Estrelita Flores, Emelita Eugenio and Jayson Orpeza for their assistance during the fieldwork and other logistical support.
- Effect of the Intensified Sub‐Thermocline Eddy on strengthening the Mindanao undercurrent in 2019Azminuddin, Fuad; Lee, Jae Hak; Jeon, Dongchull; Shin, Chang‐Woong; Villanoy, Cesar; Lee, Seok; Min, Hong Sik; Kim, Dong Guk (American Geophysical Union, 2022-02)The northward-flowing Mindanao Undercurrent (MUC) was directly measured by acoustic Doppler current profilers from a subsurface mooring at about 8°N, 127°E during 2 years (November 2017–December 2019). Its depth covers a range from 400 m to deeper than 1,000 m with its core appearing at around 900 m. The mean velocity of MUC's core was approximately 5.8 cm s−1 with a maximum speed of about 47.6 cm s−1. The MUC was observed as a quasi-permanent current with strong intraseasonal variability (ISV) with a period of 70–80 days. Further analyses with an eddy-resolving circulation model output suggest that the ISV is closely related to sub-thermocline eddies (SEs). In this study, two types of SEs near the Philippine coast are disclosed: the westward propagating SE (SE-1) and the quasi-stational SE southeast of Mindanao Island (SE-2). The SE-1 has both cyclonic and anticyclonic polarities with the propagation speed of 7–8 cm s−1, while the SE-2 is an anticyclonic eddy that moves erratically within 4–8°N, 127–130°E with the mean translation speed of about 11 cm s−1. Even though the SE-1 plays an important role in modulating the MUC, our results show that the observed strong MUC event (May–July 2019) is evidently induced by the intensified SE-2 that moves northwestward. This study emphasizes that the SE-2 when intensified, receives more energy from the strengthened New Guinea Coastal Undercurrent and loses the energy northward along the Philippine coast by intensifying the MUC.This study was part of the project entitled “study on air–sea interaction and process of rapidly intensifying Typhoon in the northwestern Pacific” (PM61670) funded by the Ministry of Oceans and Fisheries, Rep. of Korea. This study was also partly supported by the project entitled “Influences of the Northwest Pacific circulation and climate variability on the Korean water changes and material cycle I—The role of Jeju warm current and its variability” (PEA0011) funded by Korea Institute of Ocean Science and Technology (KIOST). The mooring data used in this study were provided by KIOST and are available from the KIOST live access server (http://las.kiost.ac.kr/data_adcp/). The model data are freely available from Mercator Ocean (https://resources.marine.copernicus.eu/?option=com_csw&view=details&product_id=GLOBAL_ANALYSIS_FORECAST_PHY_001_024).
- Through the boundaries: Environmental factors affecting reef benthic cover in marine protected areas in the PhilippinesPanga, Fleurdeliz M.; Anticamara, Jonathan A.; Quibilan, Miledel Christine C.; Atrigenio, Michael P.; Aliño, Porfirio M. (Frontiers Media SA, 2021-08-18)Philippine coral reefs have been on the decline since the 1970s, and this degradation has posed a risk to biodiversity, food security, and livelihood in the country. In an effort to arrest this degradation, marine protected areas (MPAs) were established across the country. MPAs are known to improve fish biomass, but their effect on live coral cover and other benthos is not yet well documented and understood. In this study, 28 MPAs across the Philippines were surveyed comparing benthic cover and indices between protected reefs and adjacent unprotected reefs. No consistent differences were found between reefs inside and outside MPAs through all the benthic categories and reef health indices considered that are indicative of protection effects or recovery within MPAs. However, there were notable site-specific differences in benthic cover across the study MPAs-suggesting that factors other than protection play important roles in influencing benthic cover inside and outside of MPAs. Storm frequency and proximity to rivers, as a proxy for siltation, were the strongest negative correlates to live coral cover. Also, high coastal population, a proxy for pollution, and occurrence of blast and poison fishing positively correlated with high dead coral cover. The lack of significant difference in benthic cover between reefs inside and outside MPAs suggests that protection does not necessarily guarantee immediate improvement in benthic condition. Correlations between benthic condition and storm frequency, siltation, and pollution suggest that it is necessary to augment MPAs with other management strategies that will address the multiple stressors that are usually indiscriminate of MPA boundaries. Supplementing long-term and systematic monitoring of benthic cover and biodiversity inside and outside of MPAs with data on other important environmental and human impact variables will help improve understanding of benthic cover and biodiversity dynamics inside and outside of MPA boundaries.We would like to thank RARE Philippines and USAID, in collaboration with the Marine Environment and Resources Foundation (MERF), for research funding, coordination, and support in the execution of this research. We would also like to thank the RARE Conservation Fellows and Local Government Units for logistical support and coordination on all of the MPAs studied. We would also like to thank the Fisheries team of the MSI Community Laboratory for the municipal profile data, and the MSI Physical Oceanography Laboratory for the storm frequency and relative exposure index used in the environmental correlation. We would also like to thank the rest of the MERF-RARE Team/MSI Community Ecology Laboratory who joined and supported the many months of data gathering, encoding, and data analysis.
- Survival and sexual maturity of sexually propagated Acropora verweyi corals 4 years after outplantationLigson, Charlon A.; Cabaitan, Patrick C. (Wiley, 2021-04-19)Most coral reef restoration efforts are carried out over 1–2 years, and few have assessed long-term (over 3 years) outcomes. Although studies of outplantation of sexually propagated corals have reported promising initial results, few studies have followed outplanted corals to maturity. Here, we monitored sexually propagated Acropora verweyi corals for 4 years post-outplantation to determine their survival and sexual maturity. These corals were outplanted when 4 months old in two size classes (small = 0.3–0.5 cm; large = 1.0–1.5 cm) at two sites in the northwestern Philippines. Four years after outplantation, the 240 colonies of A. verweyi exhibited 17.9% survival, with mean diameters ranging from 7.48–26.8 cm. Most of the surviving outplants were gravid (81.4% of the 43 colonies) with mean diameters of at least 11.8 cm. Higher survivorship was detected in the initial large size class outplants than in the small ones at the natal site, but not at the other site. However, 4 years after outplantation, there was no significant difference in terms of geometric mean diameter between the initial size classes or between the sites. Results show that 4-month-old outplants of sexually propagated corals can survive until sexual maturity and are already capable of contributing gametes for the potential recovery of degraded coral communities at age 4 years.The authors are grateful to Ronald de Guzman, Francis Kenith Adolfo,and Renato Adolfo for the field and hatchery assistance.This study was supported by a grant from the Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development of the Department of Science and Technology to PCC. The authors are also grateful to Prof. Peter Harrison for providing CAL a research assistantship opportunity and for additional logistical support through an Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development.
- Characterizing the vertical phytoplankton distribution in the Philippine Sea off the northeastern coast of LuzonCordero-Bailey, Kristina; Bollozos, Iris Salud F.; Palermo, Joseph Dominic H.; Silvano, Kathleen M.; Escobar, Ma. Teresa L.; Jacinto, Gil S.; San Diego-McGlone, Maria Lourdes; David, Laura T.; Yñiguez, Aletta T. (Elsevier BV, 2021-06)The vertical distribution of phytoplankton in the open ocean shows an increase in biomass at a depth referred to as the Subsurface Chlorophyll Maximum (SCM) that contributes significantly to the primary production of the water column. Hence, it is important to understand the dynamics that lead its formation and maintenance. This study examines the SCM in the Philippine Sea off the northeast coast of Luzon, utilizing bio-optical and empirical phytoplankton data from two oceanographic cruises conducted northeast of the island of Luzon in May/June 2011 and April/May 2012. Chlorophyll (Chl) profiles were converted to smoothed chlorophyll functions by using a b-spline basis. In 2011, the mean SCM depth was 97.24 m ± 22.33 m with mean SCM concentration of 0.43 μg/L ± 0.09 μg/L while in 2012, mean SCM was deeper at 115.45 m ± 24.25 m and mean SCM concentration of 0.31 ± 0.09 μg/L. Functional principal component analysis showed that the first principal component (PC) explained variability in the SCM depth, the second PC showed variability in the magnitude of the SCM concentration while the third PC accounted for the presence of multiple peaks. K-means clustering using the principal components resulted in three clusters which represented the offshore stations with the deepest SCM, stations within an observed cyclonic eddy with intermediate SCM and stations with coastal and shelf waters showing shallow SCM. Correlation analyses between Chl and physico-chemical and bio-optical parameters showed that Chl was positively correlated to beam attenuation, a bio-optical property that has been used as an alternative proxy for phytoplankton. This suggests that the observed SCMs represent actual increase in phytoplankton biomass. When the influence of the Kuroshio recirculation gyre was dominant in 2011, cooler temperature in surface waters was seen to significantly increase surface Chl. In 2012, highly saline waters from the tropical North Equatorial Current (NEC) waters appeared to lower the Chl distribution, particularly at the SCM. Phytoplankton abundance was recorded to be higher at the SCM than the surface in both years. In 2011, different species of diatoms dominated all clusters, except at the SCM of the coastal and shelf cluster wherein the dinoflagellate Gyrodinium grossestriatum was dominant. Most dominant species from 2011 were conspicuously absent in 2012 and there was a shift to the diatoms Fragilariopsis (surface), Thalassiosira and Rhizosolenia spp. in all clusters. These provide new insights on the phytoplankton community in relation to the changes in the oceanic circulation from subtropical North Pacific water in 2011 to tropical NEC water in 2012.This work is Marine Science Institute contribution number 482. We would like to acknowledge Dr. Cesar Villanoy and Dr. Olivia Cabrera and the anonymous reviewers who provided invaluable inputs for the development and improvement of the paper.
- Zooxanthellae diversity and coral-symbiont associations in the Philippine archipelago: specificity and adaptability across thermal gradientsTorres, Andrew F.; Valino, Darryl Anthony M.; Ravago-Gotanco, Rachel (Frontiers Media SA, 2021-10-20)Prolonged thermal stress and high levels of solar irradiance can disrupt the coral-algal symbiosis and cause bleaching and lowered overall fitness that lead to the likely death of the cnidarian host. Adaptive bleaching and acclimatization of corals, which posits bleaching as an opportunity for the coral host to switch its currently susceptible endosymbionts to more stress-tolerant taxa, offers hope for survival of reefs amid rapidly warming oceans. In this study, we explored the diversity and distribution of coral-zooxanthellae associations in the context of geospatial patterns of sea surface temperature (SST) and thermal anomalies across the Philippine archipelago. Thermal clusters based on annual sea surface temperature means and each site’s frequency of exposure to heat stress were described using three-decade (1985–2018) remotely sensed data. Haphazard sampling of 628 coral fragments was conducted in 14 reef sites over 3 years (2015–2018). Using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and sequencing of the zooxanthellae ITS2 region, we characterized endosymbiont diversity within four reef-building coral families across archipelagic thermal regimes. Consistency in dominant Symbiodiniaceae taxon was observed in Acropora spp., Porites spp., and Heliopora coerulea. In contrast, the family Pocilloporidae (Pocillopora spp., Seriatopora spp., and Stylophora pistillata) exhibited biogeographic variability in zooxanthellae composition, concordant with inferred occurrences of sustained thermal stress. Multivariate analyses identify two broad Pocilloporidae clusters that correspond with mean SST ranges and frequency of exposure to bleaching-level thermal stress which are largely supported by ANOSIM. Differences in zooxanthellae assemblages may reflect host-specific responses to ecological or environmental gradients across biogeographic regions. Such patterns of variability provide insight and support for the adaptability and potential resilience of coral communities in geographically and oceanographically complex regions, especially amidst the increasing severity of global and local-scale stressors.This paper is dedicated to the late Ronald D. Villanueva whose contribution to the project during its inception has been invaluable. The authors thank Patrick R. Pata and the reviewers LE and RC-T for their helpful comments and suggestions, and acknowledge Hazel O. Arceo, Cesar L. Villanoy, and Maria Lourdes San Diego-McGlone for their support of this study. Eileen Peñaflor and Mariana Soppa shared key knowledge in processing satellite products. Mikhael Tañedo, Romer Albino, Emmeline Jamodiong, David Siquioco, Lovely Heyres, Rhea Luciano, Joey Cabasan, Frederico Sabban, Geminne Manzano, Clairecynth Yu, Joyce Velos, Joseph Garcia, Robert Casauay, Maryjune Cabiguin, Macy A onuevo-Arcega, Ariel Loja, Jerome Genilan, Amabelle Go, Jamie Dichaves, Elaine Saniel, and Miledel Quibilan assisted with field collections. Supporting hard coral data were provided by the DOST-PCAARRD NACRE Program and the DENR-BMB WPS and SECURE Philippine Rise Projects. This is MSI contribution number 486.
- Estimation of the vertical phytoplankton distribution in the Philippine Sea: Influence of turbulence following passage of typhoonsCordero-Bailey, Kristina S.A.; Almo, Aldwin T.; David, Laura T.; Yñiguez, Aletta T. (Elsevier, 2022-11)The subsurface chlorophyll-a maximum (SCM) is a phenomenon that contributes significantly to the total primary production of the open ocean but it is not observable from remote sensing, thus primary production based on satellite information is highly underestimated. In a highly dynamic region such as the Philippine Sea, turbulence caused by tropical storms may exert significant impact on the SCM feature. In this study, we attempt to estimate the vertical phytoplankton profile in the Philippine Sea from remote sensing images by applying a generic quantitative approach. Generalized Additive Models (GAM) followed by Generalized Linear Models (GLMs) were used create predictive equations between response variables (Chl-a profile parameters) and predictor variables (RS parameters). GAM was able to predict integrated Chl-a biomass using photosynthetic active radiation (PAR), wind speed and wind stress, the depth of the Chl-a peak using surface Chl-a, wind speed and wind stress, and the baseline Chl-a concentration using sea surface temperature, sea surface salinity and PAR. GLM found wind stress and wind speed as significant predictors for integrated Chl-a biomass, while surface Chl-a, wind speed and wind stress were significant predictors for depth of the Chl-a peak. When the predictive equations were applied to 2020 monthly satellite images, they were seen to adequately estimate the offshore spatial distribution of the two Chl-a parameters. Increased turbulence due to high wind speed and wind stress during passage of tropical storms was seen to result in shallowing of the SCM and subsequent increase in Chl-a within the water column. These equations could be refined if long-term observational data was available. The capacity to estimate vertical distribution of primary productivity in the Philippines provides a means to better understand fisheries productivity and biogeochemical cycling in the region.
- Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery managementLal, Monal M.; Macahig, Deo A. S.; Juinio-Meñez, Marie A.; Altamirano, Jon P.; Noran-Baylon, Roselyn; de la Torre-de la Cruz, Margarita; Villamor, Janine L.; Gacura, Jonh Rey L.; Uy, Wilfredo H.; Mira-Honghong, Hanzel; Southgate, Paul C.; Ravago-Gotanco, Rachel (Frontiers Media SA, 2024-06-04)The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean Fst=0.016), with greater separation evident between geographically distant sites (Fst range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.
- Local tide and geoid corrections significantly improve coastal retracked Jason sea surface heights in the PhilippinesFlores, Paul Caesar; Reyes, Rosalie; Amedo-Repollo, Charina Lyn; Rediang, Abegail; Alfante, Rey Mark; Bauzon, Ma. Divina Angela; Pasaje, Nikki; Bringas, Dennis (Science and Technology Information Institute, 2022-11-08)Retracking algorithms increase the accuracy of coastal sea surface height (SSH) measurements. However, it is still important to validate these retracking estimates with tide gauge (SSHtg) observations. We downloaded the freely available Jason altimeter SSH processed using the XTRACK-ALES algorithm, then detided the SSH using different tide models. The first model is the default tidal correction based on Finite Element Solution 2014 (SSHfes), and the second model is the T_Tide harmonic analysis of the nearest tide gauge (SSHaltimeter). SSHfes showed a very poor correlation (< 0.31) and very high root mean square error (RMSE, > 29 cm). In contrast, SSHaltimeter generally showed a very high correlation (> 0.91) and low RMSE (< 17.4 cm). A further quality check based on the average and standard deviation of the difference between the SSH readings (SSHfes – SSHtg and SSHaltimeter – SSHtg) also showed the superior performance of SSHaltimeter,which scored < 9.3 and < 16.5 cm, respectively; compared to SSHfes, which scored < 9.3 cm and > 27 cm for the same parameters. The poor performance from the SSHfes likely comes from the complex bathymetry and coastal geomorphology of the country, which is not accounted for in the FES. The Philippines generally has a narrow shelf, and the FES tide corrections may be related to deep-water tides rather than the shallow-water tides observed from tide gauges. Despite the high correlation and agreement between the SSHaltimeter and SSHtg, the rate of sea level rise from the SSHaltimeter in some sites is more than twice the rate from SSHtg, which indicates the possible influence of the vertical land movement.This study was supported by grants to R.B. Reyes by the Department of Science and Technology–Philippine Council for Industry, Energy, and Emerging Technology Research and Development through the Coastal Sea Level Rise Philippines Project. We also thank the anonymous reviewers for their feedback on how to improve the manuscript.