Journal Articles - UP - MSI
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- Utility of low-cost recreational-grade echosounders in imaging and characterizing bubbly coastal submarine groundwater dischargeGabuyo, Mary Rose P.; Siringan, Fernando P. (Elsevier, 2022-01)Despite the growing knowledge on the significance of submarine groundwater discharge (SGD), mapping its occurrence is a continuing challenge. This study explores the capability and applicability of low-cost, off-the-shelf, recreational-grade echosounders (RGESs) to image different types and locate point sources of bubbly coastal SGD. Standard and systematic methodologies for efficient imaging and processing were established. The use of RGES was validated using a research-grade side scan sonar (RGSSS), continuous resistivity profiling, conductivity-temperature-depth casting, and MantaCam and SCUBA diving surveys. Lower frequencies (77/83 kHz) of RGESs showed more distinct acoustic signatures of bubbly SGD, as these were nearly the same as the effective resonance frequency of the bubbles. The clusters of bubbly discharges have higher backscatter strength than the water column noise, resulting in the definitive and convenient manual detection of SGD features. Hence, showing more accurate point sources of SGD. Three types of known SGD occurrence were identified and characterized based on acoustic behavior and spatial distribution: 1) sparse, discrete and sporadic discharge over wide area, 2) curtain, high and continuous bubble concentrations from widespread discharge, and 3) spring, direct bubble discharge from intense seafloor degassing at a single point source. These results showed that RGES provides a good alternative for more efficient and cost-effective preliminary coastal SGD works. Additional research on areas with water-dominated discharge but no bubbling is recommended.
- Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosettaMatriano, 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.
- Genomics and metabolomics-based assessment of the biosynthetic potential of the sponge-associated microorganism Streptomyces cacaoi strain R2A-843A from the PhilippinesMalto, 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.
- Physicochemical and biochemical characterization of collagen from Stichopus cf. horrens tissues for use as stimuli-responsive thin filmsSisican, 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 controlsBonita, 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, PhilippinesFlores, 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.
- Survival and growth of coral recruits in varying group sizesLigson, 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.