National Committee on Marine Sciences (NCMS)
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- The complete mitochondrial genome of a wild-collected Kappaphycus malesianus (Solieriaceae, Rhodophyta)Crisostomo, Bea A.; Dumilag, Richard V.; Roleda, Michael Y.; Lluisma, Arturo O. (Taylor & Francis, 2023-03-04)Kappaphycus malesianus is a red seaweed farmed primarily for its carrageenan, a polysaccharide important in the food and pharmaceutical industries. Among the commercially cultivated Kappaphycus species, only K. malesianus has no mitogenome data available. Here, we assembled the mitochondrial genome of K. malesianus from next-generation sequencing data. The circular mitogenome consisted of 25,250 base pairs (bp) with a GC content of 30.25%. These values were comparable to previously sequenced solieriacean mitogenomes. Structural features, such as the stem-loop and hairpin, which were previously reported in other rhodophytes mitochondrial DNA, were also identified. The annotated genes (24 protein-coding genes, 24 tRNA genes, and 2 rRNA genes) were arranged in an order similar to the other available solieriacean mitogenomes. Lastly, phylogenetic analysis using 23 predicted protein domains showed the sister relationship of K. malesianus with other Kappaphycus species.The authors are grateful to Z.-Z. Aguinaldo, S. Damsik, and J. Turong for aiding during laboratory and field works. The authors also acknowledge the LGU of Sitangkai, Tawi-Tawi for granting permission for the collection activities. This is contribution no. 495 from the University of the Philippines the Marine Science Institute (UPMSI), Diliman, Quezon City.
- Strong genetic structure and limited gene flow among populations of the tropical seagrass Thalassia hemprichii in the PhilippinesNakajima, Yuichi; Matsuki, Yu; Fortes, Miguel D.; Uy, Wilfredo H.; Campos, Wilfredo L.; Nadaoka, Kazuo; Lian, Chunlan (MDPI AG, 2023-02-05)Seagrasses are marine angiosperms, and seagrass beds maintain the species diversity of tropical and subtropical coastal ecosystems. For proper understanding, management and conservation of coastal ecosystems, it is essential to understand seagrass population dynamics. Population genetic studies can cover large geographic scales and contribute to a comprehensive understanding of reproductive dynamics and potential dispersal among locations. The clonal and genetic diversity and genetic connectivity of Thalassia hemprichii in the Philippines were estimated by a population genetics approach. The geographic scale of this study has a direct distance of approximately 1600 km. Although high clonal diversity was found in some sites (R = 0.07–1.00), both sexual and asexual reproduction generally maintains separate populations. Genetic diversity is not definitely correlated with latitude, and genetic differentiation is significant in all pairs of sites (FST = 0.026–0.744). Complex genetic structure was found in some regions, even at a fine geographic scale. The migration of fruits and seedlings was elucidated as an infrequent and stochastic event. These results suggest the necessity for the conservation of this species due to a deficiency in migrants from external regions.We thank members of CECAM project.
- Emerging pharmaceutical contaminants in key aquatic environments of the PhilippinesMariano, Shyrill Mae F.; Angeles, Luisa F.; Aga, Diana S.; Villanoy, Cesar L.; Jaraula, Caroline Marie B. (Frontiers Media SA, 2023-09-13)Pharmaceuticals in natural waters are considered emerging pollutants due to their low concentrations and the negative effects they pose to the environment. Common sources of such pollutants include untreated wastewater from hospitals, residential, industrial, and agricultural sources. Many wastewater treatment methods only remove a subset of all pharmaceuticals from the wastewater; remaining pharmaceuticals are discharged into natural waters, and ultimately drain into coastal areas. Regions without proper wastewater treatment are especially susceptible to such contamination. This study deals with the distribution, sources, and seasonal variability of pharmaceuticals in key aquatic systems in the Philippines. Two watershed continuums (Davao Gulf, Davao City; Macajalar Bay, Cagayan de Oro City); two tourist areas (Boracay Island, Aklan; Mabini, Batangas); and one pristine atoll (Tubbataha Reefs, Palawan)—all with varied prevailing human population pressures—were studied. Samples of hospital wastewater as well as groundwater, surface and bottom water samples from rivers and coastal seas collected during dry and wet seasons were analyzed using solid-phase extraction and liquid chromatography-tandem mass spectrometry. Thirty-four target pharmaceutical residues and antibiotics were extracted and quantified. Acetaminophen was detected at concentrations of up to 289.17 ppb in freshwater samples, and at concentrations of up to 253.39 ppb in seawater samples. Ubiquitous to all the sites was caffeine, reaching 1848.57 ppb. Sulfamethazine, a commonly used veterinary antibiotic, was detected at 764.91 ppb in a river site in Cagayan de Oro. Untreated hospital wastewater contained metformin, iopamidol, sulfamethoxazole, acetylsulfamethoxazole, ciprofloxacin, and azithromycin, but these pharmaceuticals were not detected in other river and coastal waters. Samples collected during the dry season exhibited higher concentrations than those from the wet season, which appears to be related to increase in transient populations from tourism activities as well as dilution. The presence of pharmaceutical residues and antibiotics in these areas and the potential impact on the environment indicate the need for stricter wastewater management measures, particularly in communities located near water bodies. As the results of this study show, such measures might be most beneficial and effective if imposed during dry season and in areas open to tourism.We thank the crew and researchers aboard M/Y Panata expedition PA0421 to Tubbataha in October 2019 and cruise to Boracay December 2019. Our gratitude to Mary Antoinette Limen, Mishel Valery Rañada, Gio Ferson Bautista, and Ernest Guiller Pineda for helping us in the field, and to Lahiruni Halwatura for assisting in the creation of a standard calibration curve for saltwater.
- 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.
- Reproductive biology and early life history of the solitary coral Heliofungia actiniformis from Singapore and the PhilippinesSayco, Sherry Lyn G; Prasetia, Rian; Todd, Peter A.; Loya, Yossi; Valencia, Brian; Calle, Lala Grace; Cabaitan, Patrick C. (Springer, 2024-01-13)Reproduction and early life history are central to understanding the biology and ecology of organisms, however such information is limited for solitary corals. Here, we compared the reproductive traits of the solitary coral Heliofungia actiniformis from different latitudinal locations (Singapore, 1°N and the Philippines, 16°N) and examined their early life development, settlement competency, and juvenile growth and survival. A total of 32 corals from Pulau Hantu reefs in Singapore and 102 corals from Bolinao and Anda reefs in the Philippines were studied between 2019 and 2022. Heliofungia actiniformis broadcasts spawned gametes during several nights, generally between 22:00 and 01:00, before and after full moon, from February to May in Singapore and from March to June in the Philippines. Spawning within a month occurred for up to 16 nights in Singapore and 10 nights in the Philippines. Sex change in two individuals between years was observed in the Philippines. The average egg size was smaller in Singapore than that in the Philippines. We determined that eggs were fertilized within 2 h after sperm addition, and developed into swimming larvae within 64 h, which began to settle after 24 h. Larval survival after three mo of culture was 1.72 ± 1.0% and juvenile diameter ranged from 0.33 to 1.30 mm. Asexual buds were first observed in 15 mo old juveniles that were at least 8 mm in diameter. 24 mo old juveniles were observed to detach from their stalk and the empty stalk regenerated polyps. Our results highlight the latitudinal variability in the reproductive traits of solitary corals, serve as a baseline for their early life history, and advance our understanding of their population dynamics.
- Submerged reef features in Apo and Tubbataha Reefs, Philippines, revealed paleo sea-level history during the last deglaciationMunar, Jeffrey C.; Aurelio, Mario A.; Dumalagan, Edwin E.; Tinacba, Erin Joy C.; Doctor, Ma. Angelique A.; Siringan, Fernando P. (Springer, 2024-02-27)The morphology of coral reefs provides an effective benchmark of past sea levels because of their limited vertical range of formation and good geologic preservation. In this study, we analyze the seafloor morphology around two atolls in the Philippines: Tubbataha Reef, in Palawan, and Apo Reef, in Occidental Mindoro. High-resolution multibeam bathymetry to a depth of 200 m reveals seafloor features including reef ridges and staircase-like terraces and scarps. Depth profiles across the reefs show terraces formed within six and seven depth ranges in Tubbataha Reef and in Apo Reef, respectively. These were further observed through a remotely operated vehicle. The terraces and scarps are interpreted as backstepping reefs that were drowned during an overall rise in sea level from the Last Glacial Maximum (LGM). Terraces are used as indicators of paleo sea level and the separation between terraces as the magnitude of sea-level rises coeval with meltwater pulse events during the last deglaciation. The pattern for both Apo and Tubbataha reefs indicates subsidence, consistent with the absence of Holocene emergent features and their atoll morphologies. Subsidence of up to 17 m since the LGM in Apo Reef is mainly attributed to the downbowing of the crust toward Manila Trench. In Tubbataha Reef, subsidence of up to 14 m is attributed to the continuous cooling of the volcanic crust underlying the atoll. These can be used to fill gaps in the tectonic history of the study sites from the last deglaciation.This study was funded by the Department of Science and Technology–Philippine Council for Agriculture, Aquatic and Natural Resources Research Development (DOST-PCARRD) Geophysical Coral Mapping Project and Acquisition of Detailed Bathymetry for Coastal Erosion Management Project both under F. P. Siringan, and National Assessment of Coral Reef Environment (NACRE) Project under Hazel Arceo. We would like to mention, in particular, Dominic Jone Cabactulan, Timothy Quimpo, Ronald Olavides, Mary Ann Calleja, Patrick Cabaitan, and Cesar Villanoy who were members of the project team. We thank the Tubbataha Management Office, Sablayan Local Government Unit, and Department of Environment and Natural Resources for the work permits and logistical help during the surveys.
- Short-term exposure to independent and combined acidification and warming elicits differential responses from two tropical seagrass-associated invertebrate grazersBaure, Jerwin G.; Roleda, Michael Y.; Juinio-Meñez, Marie Antonette (Springer, 2023-08-10)Ocean acidification and warming could affect animal physiology, key trophic interactions and ecosystem functioning in the long term. This study investigates the effects of four pH−temperature combination treatments simulating ocean acidification (OA), ocean warming (OW) and combined OA and OW conditions (FUTURE) relative to ambient present-day conditions (PRESENT) on the grazing of the juveniles of two seagrass-associated invertebrates namely the sea cucumber Stichopus cf. horrens and topshell Trochus maculatus over a 5-day exposure period. Diel and feeding activity of both species increased under OW and FUTURE to some extent, while the nighttime activity of Trochus but not Stichopus decreased under OA relative to PRESENT during the first 2 days. Fecal production of Stichopus did not differ among treatments, while the lowest fecal production of Trochus was observed under OA during the first 24 h of grazing. These responses suggest that Trochus may be initially more sensitive to OA compared with Stichopus. Interestingly, fecal production of Trochus in FUTURE was significantly higher than OA, suggesting that warming may ameliorate the negative effect of acidification. Diel activity, feeding and fecal production after 5 days did not differ among treatments for both species, suggesting acclimation to the acute changes in temperature and pH after a few days, although Stichopus acclimated rapidly than Trochus. The ability of the two juvenile invertebrate grazers to rapidly acclimate to increased temperature and lowered pH conditions after short-term exposure may favor their survival under projected changes in ocean conditions.This work was supported by the Department of Science and Technology–Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development under Grant QMSR-MRRD-MEC-295-1449. The authors would like to thank Dr. Ian Enochs for his invaluable help in improving this paper. We also thank Tirso Catbagan, Garry Bucol, Rona Soy and Tomilyn Jan Garpa for their assistance during the conduct of this study. We would also like to thank the Marine Biogeochemistry Laboratory of the UP Marine Science Institute for their assistance in analyzing our water samples as well as the DNA Barcoding Laboratory of the UP Institute of Biology for the species identification of our animals.
- Genetic diversity of Kappaphycus malesianus (Solieriaceae, Rhodophyta) from the PhilippinesDumilag, Richard V.; Crisostomo, Bea A.; Aguinaldo, Zae-Zae A.; Lluisma, Arturo O.; Gachon, Claire M.M.; Roleda, Michael Y. (Elsevier, 2023-07)Kappaphycus farming for carrageenan production is characterized by a strong selective pressure at the genetic level. Traits of agronomic importance are compromised due to domestication bottlenecks and the subsequent events of possible selective breeding of founding cultivars. Kappaphycus malesianus is farmed in Malaysia and the Philippines, and is distributed within the Malesian region. While the majority of genetically characterized specimens of this species are from Malaysia, those from the Philippines are poorly explored. Here, we assessed the genetic diversity of K. malesianus from the Philippines based on cox1 sequences. Of the 15 identified haplotypes, 14 specimens represent three novel haplotypes (wild specimens) that form a group distinct from the main clade comprising most K. malesianus haplotypes known to date. An additional haplotype from a cultivated specimen was identical to that of the most widely distributed haplotype. Our findings demonstrate that the K. malesianus is genetically more diverse than previously recognized. It is expected that higher genetic diversity may be revealed through additional sampling from a wider geographic range and careful application of integrative approaches. Future selective breeding programs in Kappaphycus would benefit from the incorporation of the genetic resources, as provided in this study.
- Multi-scale coral reef and seascape habitat variables combine to influence reef fish assemblagesSievers, Katie T.; McClure, Eva C.; Abesamis, Rene A.; Russ, Garry R. (MDPI, 2024-04-15)While benthic characteristics of coral reef habitats are a major driver of the structure of coral reef fish assemblages, non-reef habitats adjacent to coral reefs (e.g., mangroves, seagrass beds, and macroalgal beds) can affect reef fish assemblages. Here, we investigate how reef fish assemblages respond to local-scale benthic habitats within a coral reef and larger-scale adjacent seascape features (habitats within 500 m of coral reefs) on Siquijor Island in the Philippines. We examined an abundance of species for the entire reef fish assemblage and within the assemblages of parrotfishes (subfamily Scarinae) and wrasses (family Labridae). Five distinct habitat types were identified in a cluster analysis, which incorporated benthic characteristics within coral reefs and habitats adjacent to coral reefs. We found that the diversity and structure of coral reef fish assemblages were affected by benthic characteristics within coral reefs and also by benthic habitat types adjacent to coral reefs. Individual species responses and juveniles of certain species demonstrated uniquely high abundances in habitat clusters characterized by the non-reef habitats surrounding coral reefs. Considering coral reef habitats and adjacent non-reef habitats as a holistic, interconnected seascape will provide better estimations of the drivers of the structures of coral reef fish assemblages.This work would not have been possible without the invaluable contributions of the late Angel Alcala. His groundbreaking work paved the way for research in the Philippines, and his lifelong dedication to exploring and protecting the natural ecosystems of his country granted us access to crucial research sites. He also provided essential logistical and administrative support, significantly enhancing the feasibility of this project.
- Reproductive consequences of thermal stress-induced bleaching in the giant clam Tridacna croceaSayco, Sherry Lyn G.; Alabort Pomares, Ana; Cabaitan, Patrick C.; Kurihara, Haruko (Elsevier, 2024-01)Reproduction is a fundamental process necessary for maintaining a population. However, reproductive processes are sensitive to thermal stress which can cause bleaching in reef organisms such as corals and giant clams. Here we examined the phototrophic and physiological performances, particularly the reproductive processes, in Tridacna crocea during bleaching and recovery periods. Giant clam individuals were induced to bleach at heated treatment (32-33 °C) for 16 days and allowed to recover at 28-29 °C for 35 days. The control giant clams were kept at 28-29 °C. Heated giant clams showed lower phototrophic performances (Fv/Fm and photosynthesis), but their respiration and survival were similar to control giant clams. The gonadosomatic index (GSI) was lower, and the proportion of regressive eggs (i.e., eggs that are no longer viable) was higher in heated than in control giant clams. However, heated giant clams were able to maintain their egg size. In addition, T. crocea showed recovery of phototrophic potential and color of mantle but not of their reproductive output after a month of recovery. Our results indicate that bleaching reduces the reproductive output in giant clams by disrupting their gametogenesis, such as through egg resorption, but giant clams showed potential reproductive strategy, through maintenance of their egg size, to ensure the quality of their offspring. Furthermore, one month of recovery is not sufficient to restore the normal reproductive processes in T. crocea, which may delay their population recovery after a bleaching disturbance.