Challenge 09: Skills, knowledge, and technology for all

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Ocean Decade

Challenge 09:
Skills, knowledge, and technology for all

Ensure comprehensive capacity development and equitable access to data, information, knowledge and technology across all aspects of ocean science and for all stakeholders.

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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.
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.
Genetic connectivity and diversity between tropical and subtropical populations of the tropical horned sea star Protoreaster nodosus in the northwest Pacific
Nakajima, Yuichi; Yasuda, Nina; Matsuki, Yu; Arriesgado, Dan M.; Fortes, Miguel D.; Uy, Wilfredo H.; Campos, Wilfredo L.; Nadaoka, Kazuo; Lian, Chunlan (Springer, 2024-06-01)
Seagrass beds are ecologically and economically important coastal ecosystems, and seagrass-associated organisms are a key part of their biodiversity. Marine organisms that reproduce through broadcast spawning are likely to have less genetic differentiation among populations than those that use other modes of reproduction, but this has not been well studied. Here, we investigated the genetic diversity, genetic differentiation, and migration patterns of the seagrass-associated sea star Protoreaster nodosus across 12 sites spanning approximately 2500 km from the Ryukyu Archipelago, Japan, to the Philippines. We genotyped 405 individuals by using seven microsatellite loci and analyzed allelic richness and expected heterozygosity as indices of genetic diversity. Of these two indices, only expected heterozygosity decreased slightly with increasing latitude. These results suggest that genetic diversity has not clearly decreased, even in the isolated Ryukyu Archipelago populations. Geographic distance was significantly correlated with genetic differentiation (pairwise FST: − 0.005 to 0.049). However, populations in the Ryukyu Archipelago and the Philippines showed relatively low genetic structuring and the pairwise genetic differentiation between these regions was often non-significant. Analysis of historical migration rates showed bidirectional north–south migration, which appears to be influenced by the Kuroshio Current and its countercurrents.
We thank members of the project ‘Coastal Ecosystem Conservation and Adaptive Management under Local and Global Environmental Impacts in the Philippines’ (CECAM project: https://sites.google.com/view/cecam-project).
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.
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.
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.
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).
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.
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.