Challenge 07: Expand the Global Ocean Observing System

Permanent URI for this collectionhttps://repository.unesco.gov.ph/handle/123456789/28

Ocean Decade

Challenge 07:
Expand the Global Ocean Observing System

Ensure a sustainable and sustained ocean observing system across all ocean basins that delivers accessible, timely and actionable data and information to all users.

Browse

Now showing 1 - 20 of 21

Indo-West Pacific affinities of Philippine seagrasses
Fortes, M. D. (Walter de Gruyter, 1988)
A dendrograph was developed to depict the mutual relationships among 27 Indo-Pacific countries with similar seagrass floras. Hierarchical (cluster) analysis of the resulting affinities provides strong evidence that the countries could be partitioned into seven discrete provinces. The genus Halophila represents a major connection between most of these provinces, strongly influencing the clustering of the Seagrasses. The degree of species overlap (9.5 — 46.2%) between Province A (where Philippines belongs) and Province G (Western, Southern, and Southeastern portions of Australia) favors vicariance as an explanation. The separation of Kampuchea as a discrete unit within Province A appears to be an artifact of collection rather than a reflection of the true floral affinities in the region. The lack of sufficient basic floristic information remains as the most serious limitation in any attempt to describe the phytogeographic affinities of seagrasses in the Indo-Pacific region.
Fisheries Administrative Order No. 266: Series of 2020. Rules and regulations on the implementations of Vessel Monitoring Measures (VMM) and Electronic Reporting System (ERS) for commercial Philippine flagged fishing vessels amending FAO 260 Series of 2018.
(Department of Agriculture, 2020-10-12)
The objectives of this Order include: a. To enhance monitoring of fishing operations for fisheries management through the implementation of vessel monitoring measures. b. To enhance law enforcement to regulate the capture fisheries sector towards achieving long term resource sustainability. c. To implement vessel monitoring measures to track fishing behavior for scientific research and data. d. To establish a system that will facilitate law enforcement and aid in case building and prosecution of fisheries law violations. e. To gather data on fishing effort and catch data by means of an electronic reporting system which will serve as basis for fisheries management measures. f. To aid in the seafood traceability and catch documentary requirements of the government. g. To ensure safety for fishers thru a tracking device that would monitor the vessels' location during accidents and disasters. h. To implement policies embodied in Republic Act 8550, as amended by RA 10654 and its implementing rules and regulations, relating to the vessel monitoring requirements of fishing vessels. The Text consists of 26 Sections divided into 5 Chapters: General Provisions; lmpJementation of Vessel Monitoring Measures; Operational Requirements for Vessel Monitoring Measures; Penalties; Miscellaneous Provisions. All commercial catcher fishing vessels operating in Philippine waters and all fishing vessels in distant waters shall not engage in fishing activity without the vessel monitoring measures as established in FAO 260 and herein. The VMS shall apply to all licensed Philippine flagged commercial fishing vessels authorized by the Bureau of Fisheries and Aquatic Resources (BFAR) to operate in the high seas and those fishing vessels with access rights to fish in other countries' exclusive economic zones. All catcher vessels 30 GT and above operating either in the high seas or with access rights to fish in other coastal states and/or fishing in the Philippine EEZ shall have an installed Electronic Reporting System which can connect to the VMS transceiver to send fishery information to BFAR. For all other vessels, a combination of onboard and port ERS systems shall be implemented to electronically capture and report catch information. As a prerequisite for registration or license renewal, all commercial fishing vessels must secure a certification confirming that: a. An accredited ALC has been installed and verified as fully operational by the Department of Agriculture- Bureau of Fisheries and Aquatic Resources (DA-BFAR). b. The ALC unit deployed has been accredited and certified as meeting the minimum standards set by the DA-BFAR. The Order further make provisions for: the main center for monitoring and gathering data for the purpose of this Order; data access; vessel monitoring measures in marine protected areas; minimum data requirements; accreditation of data systems and service provider; frequency of reporting: offences and penalties; etc.
Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta
Matriano, Danielle M.; Alegado, Rosanna A.; Conaco, Cecilia (Springer, 2021-03-16)
Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome—evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.
We thank Joshua Dizon and Francis Tablizo of the Philippine Genome Center Core Facility for Bioinformatics for assistance with scripts and database construction. We thank Becca Lensing (University of Hawai’i), Cheryl Andam (University of New Hampshire), Deo Onda and Ron Leonard Dy (University of the Philippines) for insightful comments and suggestions on the analysis and interpretation of the data. This work was supported by thesis grants from the Department of Science and Technology Accelerated Science and Technology Human Resource Development Program-National Science Consortium (DOST-ASTHRDP-NSC) and the University of the Philippines Marine Science Institute to DM.
Thecal tabulation, body scale morphology and phylogeny of Heterocapsa philippinensis sp. nov. (Peridiniales, Dinophyceae) from the Philippines
Benico, Garry; Lum, Wai Mun; Takahashi, Kazuya; Yñiguez, Aletta T.; Iwataki, Mitsunori (Elsevier, 2021-08)
The thecal tabulation and body scale structure of the marine armoured dinoflagellate Heterocapsa, isolated from Philippines, were examined using LM, SEM and TEM, and its phylogenetic position was inferred from ITS and LSU rDNA sequences. Cells were ovoid and the plate tabulation (Po, cp, X, 5′, 3a, 7′′, 6c, 5s, 5′′′, 2′′′′) was consistent with most Heterocapsa species. The second anterior intercalary plate (2a) had a circular pattern with a thick marginal border free of pores. The nucleus was longitudinally elongated and curved, and located at the dorsal side of the cell. Discoid lobes of brownish chloroplast were peripherally distributed, and a pyrenoid was positioned at the centre. The triradiate body scales, measuring 250–300 nm in diameter, consisted of a roundish basal plate with six radiating ridges, nine peripheral uprights/spines, and three radiating spines. These components were identical to those of H. pseudotriquetra and H. steinii, except for the roundish outline of basal plate. Molecular phylogeny showed that the species clustered with H. pseudotriquetra and H. steinii. This species was differentiated from all other Heterocapsa species in the sausage-shaped nucleus and circular pattern on the 2a plate. This study proposed a novel species Heterocapsa philippinensis sp. nov. for the isolate.
Nitrite regeneration in the oligotrophic Atlantic Ocean
Clark, Darren R.; Rees, Andrew P.; Ferrera, Charissa M.; Al-Moosawi, Lisa; Somerfield, Paul J.; Harris, Carolyn; Quartly, Graham D.; Goult, Stephen; Tarran, Glen; Lessin, Gennadi (Copernicus GmbH, 2022-03-07)
The recycling of scarce nutrient resources in the sunlit open ocean is crucial to ecosystem function. Nitrification directs ammonium (NH4+) derived from organic matter decomposition towards the regeneration of nitrate (NO3-), an important resource for photosynthetic primary producers. However, the technical challenge of making nitrification rate measurements in oligotrophic conditions combined with the remote nature of these environments means that data availability, and the understanding that provides, is limited. This study reports nitrite (NO2-) regeneration rate (RNO2 – the first product of nitrification derived from NH4+ oxidation) over a 13 000 km transect within the photic zone of the Atlantic Ocean. These measurements, at relatively high resolution (order 300 km), permit the examination of interactions between RNO2 and environmental conditions that may warrant explicit development in model descriptions. At all locations we report measurable RNO2 with significant variability between and within Atlantic provinces. Statistical analysis indicated significant correlative structure between RNO2 and ecosystem variables, explaining ∼65 % of the data variability. Differences between sampling depths were of the same magnitude as or greater than horizontally resolved differences, identifying distinct biogeochemical niches between depth horizons. The best overall match between RNO2 and environmental variables combined chlorophyll-a concentration, light-phase duration, and silicate concentration (representing a short-term tracer of water column physical instability). On this basis we hypothesize that RNO2 is related to the short-term autotrophic production and heterotrophic decomposition of dissolved organic nitrogen (DON), which regenerates NH4+ and supports NH4+ oxidation. However, this did not explain the observation that RNO2 in the deep euphotic zone was significantly greater in the Southern Hemisphere compared to the Northern Hemisphere. We present the complimentary hypothesis that observations reflect the difference in DON concentration supplied by lateral transport into the gyre interior from the Atlantic's eastern boundary upwelling ecosystems.
We thank the crew of the AMT19 cruise. MSLA data were obtained and analysed through the NERC Earth Observation Data Acquisition and Analysis Service (NEODAAS), and further data were provided by the European Space Agency's Sea Level CCI. This is contribution number 320 of the AMT program supported by UKRI through the National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science program and further from the Natural Environment Research Council funded Microbial Carbon Pump project. We would like to thank Dennis Hansell and two anonymous reviewers for constructive and insightful comments.
Asterocladon ednae sp. nov. (Asterocladales, Phaeophyceae) from the Philippines
Sasagawa, Eriko; Santiañez, Wilfred John E.; Kogame, Kazuhiro (Wiley, 2022-06-21)
Members of the brown algal order Asterocladales are characterized by stellate arrangement of its chloroplasts, in which a stellate configuration has a protruding central pyrenoid complex. The order is represented by the genus Asterocladon, which consists of only three species so far. Similar to other small and filamentous seaweeds, studies on Asterocladon remain scant and their diversity poorly understood. To fill this gap, we conducted molecular-assisted taxonomic studies on Asterocladon based on seven culture isolates collected from Okinawa Prefecture, Japan and Cebu, the Philippines. One culture isolate from the Philippines was revealed to be a new species of Asterocladon based on morpho-anatomical and molecular analyses using rbcL and psaA genes and is described here as Asterocladon ednae. The other isolates were attributed to A. rhodochortonoides. A. ednae was most closely related to A. rhodochortonoides in morphology and molecular phylogeny but was distinguished from the latter by its elongately ellipsoid plurilocular sporangia. This is the first report of the genus and species A. ednae in the Philippines, further increasing the diversity of seaweeds in the country.
Manzaea minuta gen. & comb. nov. (Scytosiphonaceae, Phaeophyceae) from the tropical Northwestern Pacific Ocean
Santiañez, Wilfred John E.; Kogame, Kazuhiro (Philippine Journal of Systematic Biology, 2022-07-11)
Recent molecular-assisted taxonomic studies on the brown algal genus Hydroclathrus has resulted in discoveries of new taxa in the family Scytosiphonaceae, both at the genus and species level. However, phylogenetic studies on Hydroclathrus based on wide geographical sampling also suggested that the genus is not monophyletic. That is, one of the recently described species Hydroclathrus minutus is consistently segregated from the Hydroclathrus main clade. We propose here to segregate H. minutus from the brown algal genus Hydroclathrus and establish the new monotypic genus Manzaea (i.e., Manzaea minuta gen. & comb. nov.) based on information on molecular phylogenetics and morpho-anatomy. Morphologically, M. minuta is similar to Hydroclathrus and Tronoella in having clathrate (net-like) and spreading thalli but is differentiated from the latter two genera in having membranous thalli that are sometimes interadhesive resulting in portions of the thallus forming amorphous clumps. Additionally, Manzaea is distinguished from both clathrate genera in having thick-walled medullary cells and short closely arranged quadriseriate plurangia. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on single (plastidial psaA and rbcL genes) and concatenated (cox3 + psaA + rbcL) genes showed that M. minuta is consistently segregated from the highly supported clade of Hydroclathrus species and often clustering with Tronoella and/or Rosenvingea. Our proposal further increases the diversity of monotypic genera in the Scytosiphonaceae and underscores the need to conduct further studies on tropical seaweed biodiversity.
WJES thanks Dr. Gavino C. Trono, Jr. and Dr. Edna T. Ganzon-Fortes for the inspiration and encouragement to conduct seaweed biodiversity and systematics research. WJES is funded by the University of the Philippines through the Balik PhD Program of the Office of the Vice President for Academic Affairs (OVPAA-BPhD-2018-05), the University of the Philippines Diliman through the In-house research grant of the Marine Science Institute, and the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of the Government of Japan under the Monbukagakusho Scholarship Grant. WJES also acknowledges the support of the Department of Science and Technology (DOST)-Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (PCAARRD) of the Government of the Philippines through the DOST Balik Scientist Program.
Survival and growth of coral recruits in varying group sizes
Ligson, Charlon A.; Cabaitan, Patrick C.; Harrison, Peter L. (Elsevier, 2022-11)
Coral larvae usually settle as solitary individuals but sometimes also in aggregations, especially when settlement sites are limited. Fusion of coral individuals can consist of different group sizes with varying numbers of adjacent coral spat. However, little is known about the performance of coral individuals in different group sizes, especially during the early post-settlement phase, where high mortality usually occurs. Here, we investigated the performance of Acropora verweyi juveniles in varying group sizes of fused coral spat. Specifically, we examined the survival and growth rate of coral individuals, with four group size levels: solitary spat, 2, 3–5, 6–9, and 10–28-spat group size, over 21 weeks post-settlement. The highest survival was detected in the 6–9 spat group size followed by the 3–5 and 10–28 group sizes, with lower survival in the 2-spat group size and solitary spat. Overall, 7.4% of the 338 coral individuals reared in ex-situ hatchery conditions survived up to the last monitoring at 21 weeks. At 15 weeks post-settlement, the mean surface areas of solitary and 2-spat group sizes were five- to eight-fold smaller than in larger fused coral individuals. However, there were no significant differences between the percent growth changes among the coral group sizes. The present study suggests that fused coral spat of larger group sizes can immediately gain size, but not necessarily have higher growth rates within the first 15 weeks post-settlement. Results also revealed that fusions of at least six A. verweyi spat had higher survival than small fused individuals and solitary spat, at least in the first few months after settlement. The advantage of such fusions, especially in larger group sizes, may offer an enhanced survival for coral spat during the critical period of early post-settlement. This outcome provides potential advantages for coral restoration using sexual production of larvae.
We are grateful to all the staff and research assistants at the Bolinao Marine Laboratory, especially to D. dela Cruz, E. Gomez, R. Adolfo, K. Adolfo, and M. Ponce for logistical support. We also thank K. Cameron for comments on an earlier version of this manuscript. This study was funded by an Australian Centre for International Agricultural Research (ACIAR) grants FIS/2014/063 and FIS/2019/123 to PLH. We thank C. Barlow and A. Fleming from ACIAR for their project support.
Fisheries Administrative Order No. 270: Series of 2023. Rules and regulations on the operations of the Philippine flagged fishing vessels operating in distant waters (beyond national jurisdiction).
(Department of Agriculture, 2023-01-27)
This Administrative Order provides for the conditions on the registry of the fishing vessels further to Republic Act No. 8550 and the requirements for the implementation of flag state responsibilities to not engaging vessels in IUU fishing. The Order requires update of fishing vessel listing that are operating in the High Seas area by BFAR and compliance with the vessel marking and specification requirements of the RFMO. This Order applies to all Philippine- flagged fishing vessels engaged in distant water fishing regardless of type. The text consists of 27 Articles divided into 5 Chapters as follow: General Provisions (I); Measures for High Seas (II); Measures for Vessels Operating in Waters of Other Coastal States (III); Prohibited Acts and Penalties (IV); Miscellaneous Provisions (V). The text has one Appendix on list of acronyms.
Fisheries Administrative Order No. 269: Series of 2023. Rules and regulations on tuna purse seine/ring net operations in the pacific seaboard of the Philippines exclusive economic zone (EEZ).
(Department of Agriculture, 2023-01-27)
This Administrative Order covers Philippine registered purse seine and ringnet catcher fishing vessels of more than thirty (30) Gross Tons (GT) targeting tuna with valid Commercial Fishing Vessel License (CFVL) and their corresponding support vessels operating within the Pacific Seaboard of the Philippine EEZ and listed in the WCPFC Records of Fishing Vessels. The Order provides on fishing days limit, qualification to access fishing in Philippine Pacific EEZ, vessel monitoring measures, vessel listing, catch logsheet, use of fish aggregating device and access right. The text consists of 18 Articles.
Effects of monsoons and storms on the structuring and diversity of picoeukaryotic microbial communities in a tropical coastal environment
De La Cruz, Maria Anna Michaela; Hingpit, Brian William; Guillou, Laure; Onda, Deo Florence L. (Elsevier, 2023-06)
Picoeukaryotes are key components in marine ecosystems that play crucial roles in food webs and biogeochemical cycles. Despite their significance, many aspects of their community ecology and diversity remain understudied. Here, we investigated the taxonomic and functional diversity of picoeukaryotic communities in response to monsoonal patterns and weather disturbances brought about by storms, characterizing tropical coastal regions. To do this, water samples were collected almost weekly or bi-weekly at a single location in a tropical coastal environment covering the late northeast (NE) and southwest (SW) monsoons. We then performed high-throughput amplicon sequencing of the V4 region of the 18S rRNA gene to generate taxonomic profiles of the communities across time. Clustering based on environmental parameters grouped our samples into months associated with NE monsoon, SW monsoon, and stormy SW monsoon, demonstrating seasonality influenced by monsoons and storms, typically observed in tropical coastal waters. In comparison, clustering based on abundance only grouped the samples into NE and SW monsoon, with most communities during storm period joining the NE monsoon samples. These samples exhibited greater diversity, with smaller taxa such as Syndiniales, Prymnesiophyceae, Picozoa, Cercozoa, Stramenopiles, and Chlorophytes being the most abundant groups present. In contrast, SW monsoon samples have lower diversity but have become generally dominated by large-celled taxa, mostly diatoms. Multivariate and correlation analyses both revealed nitrate as the strongest environmental driver of the picoeukaryotic community structuring. Meanwhile, network analysis grouped the taxa into three modules, more consistent with the clustering based on environmental parameters, implying that although storms may not significantly change the community composition, they may however influence the dominating taxa. Each module was composed of a unique set of co-occurring taxa, highlighting high turnover of picoeukaryotic communities between each season. In addition, our results showed that SW monsoon-associated module had higher interconnectivity than other modules, suggesting that the interactions during this period may be less species-specific, thus, more adaptable than during NE monsoon. However, we observed that extreme fluctuations caused by storms could have possibly allowed for selection of dominant taxa. Shotgun metagenomic sequencing of representative samples from each monsoon period also revealed that differently abundant functional genes, particularly genes associated to nitrogen metabolism, might have also helped in adaptation to the changing nutrient conditions. Our observations provide new insights on the potential trajectory of microbial communities under environmental stresses, which are important in understanding the implications of emerging threats such as coastal eutrophication and climate change.
Shallow structures, interactions, and recurrent vertical motions of active faults in Lingayen Gulf, Philippines
Flores, Paul Caesar M.; Siringan, Fernando P.; Mateo, Zenon Richard P.; Marfito, Bryan J.; Sarmiento, Keanu Jershon S.; Abigania, Maria Isabel T.; Daag, Arturo S.; Maac-Aguilar, Yolanda (Elsevier, 2023-06-01)
The surface trace of the East Zambales Fault (EZF) and its associated faults in the Lingayen Gulf have been previously mapped but no other characteristics were reported. This study utilized seismic reflection, multi-beam bathymetry, and side scan sonar to characterize the offshore EZF in terms of magnitudes of vertical displacement. Sequence stratigraphy and radiocarbon dates provided age constraints on the recurrence interval within the Holocene. The EZF extends for ∼ 57 km into the gulf, follows a north-northwest trend, and bounds the karstic terrane (west) and fluvio-deltaic deposits (east). Sinistral motion is indicated by: 1) normal and reverse drag geometries, 2) reversal in the sense of throw with depth, 3) flower structure, and 4) right-stepping and the uplift of a pressure ridge named Pudoc Bathymetric High. The Central Lingayen Gulf Fault (CLGF), to the east of EZF, follows the same trend. The Lingayen Gulf Transverse Fault (LGTF), oriented east–west, forms a flower structure with the CLGF. The EZF, CLGF, and LGTF combined form the Lingayen Gulf Fault System, which divides the gulf into five fault blocks where uplift and subsidence locally occurred. A paleo-delta at −60 m yielded an age of 6.8 kyBP, indicating it was formed during the first Holocene highstand. With natural compaction considered, fault-associated subsidence of 46–53 m may have occurred. The average Holocene vertical displacement is 2.1–2.2 m, which translates to a recurrence interval of 320–270 years for the fault system. The faults can likely generate earthquakes with magnitudes 7.5 (EZF), 6.7 (CLGF), and 6.6 (LGTF).
This work was supported by grants to F. P. Siringan by the Department of Science and Technology – Philippine Council for Industry, Energy and Emerging Technology Research and Development through the Mapping of Active Offshore Faults for Resilient Coasts Project; and the Department of Environment and Natural Resources – Biodiversity Management Bureau through the Coral Reef Visualization and Assessment - Deep Coral Mapping Project. We are thankful to Deo Carlo Llamas for the meaningful discussions about the current knowledge of the East Zambales Fault. We also thank the anonymous reviewers who provided significant insights for the improvement of this manuscript.
Spatial variation in the benthic community structure of a coral reef system in the central Philippines: Highlighting hard coral, octocoral, and sponge assemblages
Lalas, Jue Alef A.; Manzano, Geminne G.; Desabelle, Lee Arraby B.; Baria-Rodriguez, Maria Vanessa (Elsevier, 2023-07)
Coral reefs are complex habitats that contain very high biodiversity and provide different ecosystem services. In the Coral Triangle, however, various major benthic components are still understudied. This can limit our understanding of coral reef community dynamics, especially in the presence of a changing climate coupled with local disturbances (e.g., decreased water quality). This study describes the benthic community structure of an ecologically and economically important coral reef system in the central Philippines through characterizing the assemblages of three major components (hard corals, octocorals, and sponges) among sites and stations with varying environmental conditions (i.e., exposure to monsoons, water quality levels). Results reveal significant variations in the mean percentage covers of hard corals, octocorals, and sponges at the site and station levels (ANOVA, p < 0.05), with hard corals dominating in Site 1, which is more exposed to the southwest monsoon, and Site 3, which is an embayed and unexposed site with low water quality, while soft corals dominated in Site 2, which is more exposed to the northeast monsoon. Multivariate analyses also revealed significant variations in the benthic community structure at different spatial scales (ANOSIM, p < 0.05). Interestingly, even stations within a site had significant variations in community structure, with different taxa being dominant. This study highlights the importance of conducting more detailed analyses of understudied taxa (i.e., octocorals and sponges) during coral reef surveys to improve our understanding of coral reef community dynamics that is very important for management.
Physicochemical and biochemical characterization of collagen from Stichopus cf. horrens tissues for use as stimuli-responsive thin films
Sisican, Kim Marie D.; Torreno, Vicenzo Paolo M.; Yu, Eizadora T.; Conato, Marlon T. (American Chemical Society, 2023-09-20)
The mutable collagenous tissue (MCT) of sea cucumber, with its ability to rapidly change its stiffness and extensibility in response to different environmental stress conditions, serves as inspiration for the design of new smart functional biomaterials. Collagen, extracted from the body wall of Stichopus cf. horrens, a species commonly found in the Philippines, was characterized for its suitability as stimuli-responsive films. Protein BLAST search showed the presence of sequences commonly found in type VII and IX collagen, suggesting that Stichopus horrens collagen is heterotypic. The maximum transition temperature recorded was 56.0 ± 2 °C, which is higher than those of other known sources of marine collagen. This suggests that S. horrens collagen has better thermal stability and durability. Collagen-based thin films were then prepared, and atomic force microscopy (AFM) imaging showed the visible collagen network comprising the films. The thin films were subjected to thermomechanical analysis with degradation starting at >175 °C. At 100–150 °C, the collagen-based films apparently lose their translucency due to the removal of moisture. Upon exposure to ambient temperature, instead of degrading, the films were able to revert to the original state due to the readsorption of moisture. This study is a demonstration of a smart biomaterial developed from S. cf. horrens collagen with potential applications in food, pharmaceutical, biomedical, and other collagen-based research.
This research was funded by the Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development of the Department of Science and Technology (DOST-PCAARRD).
Genomics and metabolomics-based assessment of the biosynthetic potential of the sponge-associated microorganism Streptomyces cacaoi strain R2A-843A from the Philippines
Malto, Zabrina Bernice L.; Reyes, Joeriggo M.; Lo, Bernard Isaiah; Davis, Kevin Bossie S.; Concepcion, Gisela; Salvador-Reyes, Lilibeth A. (Philippine-American Academy of Science and Engineering, 2023-10-20)
The biosynthetic machinery of the sponge-associated Streptomyces cacaoi strain R2A-843A was assessed using a combined genomics and metabolomics approach. Whole genome sequencing and molecular networking showed the high biosynthetic potential of this actinomycete. A significant proportion of the genome is dedicated to secondary metabolite production, with biosynthetic gene clusters for nonribosomal peptides, polyketides, and terpenes being the most represented. Seven cyclic pentapeptides, including a putative new analogue, and a glycosylated lanthipeptide were identified using HRMS and untargeted MS/MS analysis. To validate our genome and metabolome analysis, we undertook a mass spectrometry-guided purification and confirmed the production of the known peptides BE-18257A (1) and BE-18257B (2). The production of 1 and 2 and the growth of the microorganism were monitored for eight days. Compound 2 was produced at a higher concentration, starting at 48 h post-incubation. Both compounds were noncytotoxic against colorectal and breast cancer cell lines.
The authors acknowledge funding support from the Department of Science and Technology - Philippine Council for Health Research and Development through the Discovery and Development of Health Products - Marine Component Program. Genome sequencing was made possible through the CHEDPCARI IHITM63 Project. We thank Ms. Shalice R. SusanaGuevarra for conducting the bioactivity assay. This work was done under the supervision of the Bureau of Fisheries and Aquatic Resources under Gratuitous Permit No. FBP-0035-10. This is MSI Contribution No. 501.
Assessing the efficiency of microplastics extraction methods for tropical beach sediments and matrix preparation for experimental controls
Bonita, Jan Danielle P.; Gomez, Norchel Corcia F.; Onda, Deo Florence L. (Frontiers Media SA, 2023-11-03)
Introduction: Microplastic pollution has become a global issue, eliciting attention not just from the scientific community but also both from the public and governmental bodies. Drawing data-driven policies and interventions, however, remain difficult due to the severely lacking baseline information from different environments such as beaches. One of the challenges in doing baseline studies is the lack of harmonized methodologies that will allow for comparison of results, integration of data, and its effective translation to evidence-based policies. Emphasis on quality control measures among baselining efforts through the proper implementation of experimental controls is also lacking. Methodology: To address these gaps, we compared methodologies for preparing the sediment matrix for experimental controls, as well as evaluated protocols for extracting microplastics from tropical beach sediments. Beach sediments were collected, dried, sieved, and spiked with known amounts of microplastics of different polymer types. The removal and extraction efficiencies of the protocols being compared were evaluated. Results and discussion: Our results showed that subjecting beach sediments to a furnace at 550° C for 4 hours is the most efficient way to remove plastic contamination, implying its applicability for preparing experimental controls. Meanwhile, a modified version of Masura et al. (2015), one of the widely cited methodologies for microplastics extraction, exhibited the highest mean extraction efficiency (99.05 ± 0.82%) among the protocols being compared. Results of this work will be useful in identifying methods that can be adopted and utilized for research and baselining efforts not just in the Philippines but also in Southeast Asia. This will also be helpful in the harmonization of methods, data reporting, and even skills as implemented through the regional and national action plans to address marine plastic pollution.
The authors would like to thank the members of the Microbial Oceanography Laboratory of the University of the Philippines, The Marine Science Institute, especially Mark Prudente and Kim John Balboa who provided assistance during the conduct of the experiment, and the staff and administrative personnel of the Bolinao Marine Laboratory.
Natural and anthropogenic climate variability sgnals in a 237-year-long coral record from the Philippines
Inoue, Mayuri; Fukushima, A.; Chihara, M.; Genda, A.; Ikehara, Minoru; Okai, T.; Kawahata, Hodaka; Siringan, F. P.; Suzuki, Atsushi (American Geophysical Union, 2023-11-29)
Both proxy and model studies conducted to understand anthropogenic warming have revealed historical variations in sea-surface temperature (SST) since the industrial revolution. However, because of discrepancies between observations and models in the late nineteenth century, the timing and degree of anthropogenic warming remain unclear. In this study, we reconstructed a 237-year-long record of SST and salinity using a coral core collected from Bicol, southern Luzon, Philippines, which is located at the northern edge of the western Pacific warm pool. The SST record showed volcanic cooling after several volcanic eruptions, including the 1815 Tambora eruption, but the pattern of change differed. Decadal SST variations at Bicol are connected to Pacific Decadal Variability (PDV). Therefore, it is suggested that the PDV conditions at the time of the eruption may have influenced marine conditions, such as the degree and duration of cooling and/or salinity, after the eruptions. Although there were discrepancies in SST variations among the modeled, observed, and proxy SST data from the late nineteenth to early twentieth centuries, SST data from the late twentieth century showed globally coherent anthropogenic warming, especially after 1976. In particular, summer SST in the northwestern Pacific has become more sensitive to anthropogenic forcing since 1976.
Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers
Lizano, Apollo Marco D.; Kim, Kenneth M.; Juinio-Meñez, Marie Antonette; Ravago-Gotanco, Rachel (Nature Research, 2024)
Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35–2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex. © The Author(s) 2024.
Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra
Ordoñez, June F.; Ravago-Gotanco, Rachel (Elsevier, 2024-01-30)
The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.
Intact shallow and mesophotic assemblages of large carnivorous reef fishes underscore the importance of large and remote protected areas in the Coral Triangle
Salvador, Mikaela L.; Utzurrum, Jean Asuncion T.; Murray, Ryan; Delijero, Kymry; Conales, Segundo F.; Bird, Christopher E.; Gauthier, David T.; Abesamis, Rene A. (Wiley, 2024-02-23)
1. Overfishing remains a threat to coral reef fishes worldwide, with large carnivores often disproportionately vulnerable. Marine protected areas (MPAs) can restore fish populations and biodiversity, but their effect has been understudied in mesophotic coral ecosystems (MCEs), particularly in the Coral Triangle. 2. Videos were analysed from baited remote underwater video systems deployed in 2016 to investigate the assemblage structure of large carnivorous fishes at shallow (4–12 m) and mesophotic (45–96 m) depths in two of the largest and most isolated MPAs in the Philippines: an uninhabited, fully no-take MPA enacted in 1988 (Tubbataha Reefs Natural Park) and an archipelagic municipality surrounded by an extensive but not fully no-take MPA declared in 2016 (Cagayancillo). Taxa focused on were groupers (Serranidae), snappers (Lutjanidae), emperors (Lethrinidae), jacks (Carangidae) and the endangered Cheilinus undulatus (Labridae). 3. Mean abundance and species richness were not greater in TRNP than in Cagayancillo regardless of depth despite long-term protection in the former. Limited impacts of fishing in Cagayancillo may explain this result. Differentiation of fish assemblages was evident between TRNP and Cagayancillo but more obvious between depths at each location, probably due more to habitat than MPA effects. In Cagayancillo, overall carnivorous reef fish, grouper and jack mean abundance were 2, 2 and 10 times higher, respectively, at mesophotic depths, suggesting that MCEs can serve as deep refugia from fishing. 4. These findings of differentiation between depths and higher abundance of certain taxa in mesophotic depths emphasize that MCEs are distinct from shallow reefs, serve as important habitat for species susceptible to overfishing and, thus, must be explicitly included in the design of MPAs. This study also highlights the value of maintaining strict protection of MPAs like TRNP for the Coral Triangle and an opportunity to safeguard intact fish assemblages in Cagayancillo by expanding its no-take zones.