National Committee on Marine Sciences (NCMS)
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- In Silico supported nontarget analysis of contaminants of emerging concern: Increasing confidence in unknown identification in wastewater and surface watersAngeles, Luisa F.; Halwatura, Lahiruni M.; Antle, Jonathan P.; Simpson, Scott; Jaraula, Caroline M.B.; Aga, Diana S. (American Chemical Society, 2021-08-01)Nontarget analysis using liquid chromatography–high resolution mass spectrometry (LC–HRMS) is a valuable approach in characterizing for contaminants of emerging concern (CECs) in the environment. In this study, wastewater and surface water samples from three locations in Manila, Philippines were analyzed for CECs using a nontarget analysis approach with an LC-Orbitrap. A previously optimized semiautomated workflow was used for data processing with Compound Discoverer. A total of 157 compounds were identified, with 21 confirmed with reference standards, 83 confirmed with evidence from a mass spectral library (mzCloud), and 53 tentatively identified using in silico fragmentation (MetFrag). These compounds include pharmaceuticals such as antibiotics, antifungal, and antihypertensive compounds, human metabolites, natural products, pesticides, and industrial chemicals. Compounds confirmed with reference standards include antibiotics ciprofloxacin, clarithromycin, acetyl-sulfamethoxazole, and trimethoprim (2 to 19 ng/L), and antifungal compounds carbendazim and climbazole (3–47 ng/L). The pesticides diethyltoluamide (DEET) and diuron were also detected (37 ng/L). The utility of a preliminary multivariable linear regression quality structure-retention relationship (QSRR) model based on quantum chemical molecular descriptors is demonstrated. This study demonstrates the importance of using tools and software that are helpful for annotating HRMS data and reporting detections according to a standardized classification system. The detection of several CECs in wastewater and surface water samples show the importance of performing nontarget analysis in determining occurrence of CECs in the environment.We acknowledge support from the National Science Foundation PIRE-HEARD award number 1545756 and USAID PEER subaward number 2000009924. S.S. thanks the National Science Foundation (Award #1904825) for support of this research, and the Donors of the American Chemical Society Petroleum Research Fund (PRF-58954-UNI5). We also thank Shyrill Mae Mariano from the Marine Science Institute in the University of the Philippines − Diliman who helped with the sample collection and Rebecca Dickman from University at Buffalo for her help on technical work.
- Multifaceted assessment of wastewater-based epidemiology for SARS-CoV-2 in selected urban communities in Davao City, Philippines: A pilot studyOtero, Maria Catherine B.; Murao, Lyre Anni E.; Limen, Mary Antoinette G.; Caalim, Daniel Rev A.; Gaite, Paul Lorenzo A.; Bacus, Michael G.; Acaso, Joan T.; Miguel, Refeim M.; Corazo, Kahlil; Knot, Ineke E.; Sajonia, Homer; de los Reyes, Francis L.; Jaraula, Caroline Marie B.; Baja, Emmanuel S.; Del Mundo, Dann Marie N. (MDPI, 2022-07-19)Over 60 countries have integrated wastewater-based epidemiology (WBE) in their COVID-19 surveillance programs, focusing on wastewater treatment plants (WWTP). In this paper, we piloted the assessment of SARS-CoV-2 WBE as a complementary public health surveillance method in susceptible communities in a highly urbanized city without WWTP in the Philippines by exploring the extraction and detection methods, evaluating the contribution of physico-chemical–anthropogenic factors, and attempting whole-genome sequencing (WGS). Weekly wastewater samples were collected from sewer pipes or creeks in six communities with moderate-to-high risk of COVID-19 transmission, as categorized by the City Government of Davao from November to December 2020. Physico-chemical properties of the wastewater and anthropogenic conditions of the sites were noted. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. A subset of nine samples were subjected to WGS using the Minion sequencing platform. SARS-CoV-2 RNA was detected in twenty-two samples (91.7%) regardless of the presence of new cases. Cycle threshold values correlated with RNA concentration and attack rate. The lack of a sewershed map in the sampled areas highlights the need to integrate this in the WBE planning. A combined analysis of wastewater physico-chemical parameters such as flow rate, surface water temperature, salinity, dissolved oxygen, and total dissolved solids provided insights on the ideal sampling location, time, and method for WBE, and their impact on RNA recovery. The contribution of fecal matter in the wastewater may also be assessed through the coliform count and in the context of anthropogenic conditions in the area. Finally, our attempt on WGS detected single-nucleotide polymorphisms (SNPs) in wastewater which included clinically reported and newly identified mutations in the Philippines. This exploratory report provides a contextualized framework for applying WBE surveillance in low-sanitation areas.The authors thank the Davao City Health Office, the local government units under the City Government of Davao, the partner hospitals for their support and assistance, and Diana Aga for discussions on sample collection and analyses. The authors would also like to thank the members of the Bortz Virology Laboratory at the University of Alaska Anchorage- Ralf Dagdag and Matthew Redlinger, Amanda Warr from the Roslin Institute, Nicole Wheeler from the University of Birmingham, Lara Urban, co-founder of PuntSeq, and Joe Russell from MRI Global for their expert advice in nanopore and wastewater sequencing.
- Heavy metal fluxes in Bang Pakong River Estuary, Thailand: Sedimentary vs diffusive fluxesCheevaporn, V.; Jacinto, G. S.; San Diego-McGlone, M. L. (Elsevier BV, 1995-04)Estimates of the flux of heavy metals into the sediments (sedimentary flux) of Bang Pakong River Estuary and the diffusive flux of these metals across the sediment-water interface provide quantitative approximations on the movement of heavy metals from the water column into the sediments, and vice versa. Results showed higher sedimentary flux of Cu, Pb, Zn, Cd, Cr and Ni (0.1–16.8 μg cm−2 yr−1) relative to the diffusive flux of these metals (0.01–4.8 μg cm−2 yr−1). The percentage diagenetic contribution (ratio of diffusive flux to sedimentary flux) of these metals ranged from 10–91%. This suggests that diagenetic remobilization and release of these metals from the sediments into the overlying water may contribute to the subsequent redeposition of these metals into the sediments. Metal enrichment at the surface sediments when compared with deeper sections of the sediment may not necessarily be interpreted as evidence of recent natural, anthropogenic inputs alone, but may also be a consequence of the deposition of metals previously released from the sediments through diagenesis.
- Potential of sediment bacterial communities from Manila Bay (Philippines) to degrade low-density polyethylene (LDPE)Gomez, Norchel Corcia F.; Onda, Deo Florence L. (Springer, 2022-12-24)The persistence of plastics and its effects in different environments where they accumulate, particularly in coastal areas, is of serious concern. These plastics exhibit signs of degradation, possibly mediated by microorganisms. In this study, we investigated the potential of sediment microbial communities from Manila Bay, Philippines, which has a severe plastics problem, to degrade low-density polyethylene (LDPE). Plastics in selected sites were quantified and sediment samples from sites with the lowest and highest plastic accumulation were collected. These sediments were then introduced and incubated with LDPE in vitro for a period of 91 days. Fourier transform infrared spectroscopy detected the appearance of carbonyl and vinyl products on the plastic surface, indicating structural surface modifications attributed to polymer degradation. Communities attached to the plastics were profiled using high-throughput sequencing of the V4-V5 region of the 16S rRNA gene. Members of the phylum Proteobacteria dominated the plastic surface throughout the experiment. Several bacterial taxa associated with hydrocarbon degradation were also enriched, with some taxa positively correlating with the biodegradation indices, suggesting potential active roles in the partial biodegradation of plastics. Other taxa were also present, which might be consuming by-products or providing nourishment for other groups, indicating synergy in utilizing the plastic as the main carbon source and creation of a microenvironment within the plastics biofilm. This study showed that sediment microbes from Manila Bay may have naturally occurring microbial groups potentially capable of partially degrading plastics, supporting previous studies that the biodegradation potential for plastics is ubiquitously present in marine microbial assemblages.We would like to acknowledge the Protected Area Management and Biodiversity Section of the Conservation and Development Division of the Department of Environment and Natural Resources—National Capital region for allowing us to conduct field work in LPPCHEA. As well as local government units of Brgy. Bucana in Ternate, Brgy. Bucana Malaki in Naic, Brgy. San Rafael III in Noveleta, and Brgy. Baseco in Manila for allowing us to conduct field work and sample collection. We would also like to acknowledge the Marine Research Center under the Marine Environmental Protection Command of the Philippine Coast Guard for providing assistance during one of our fieldworks. Members of the Microbial Oceanography Laboratory for helping during field works. And to Daniel John E. Purganan and Justine Marey S. Bitalac for helping us obtain CLS micrographs.
- Feeding and reproductive phenotypic traits of the sea urchin Tripneustes gratilla in seagrass beds impacted by eutrophicationBangi, Helen Grace P.; Juinio-Meñez, Marie Antonette (MDPI AG, 2023-07-11)The sea urchin Tripneustes gratilla is a major grazer and is, hence, an excellent key model organism to study to gain a better understanding of responses to changes in its habitat. We investigated whether there are significant variations in the feeding and reproductive phenotypic traits of populations from three seagrass bed sites, with respect to their proximity to fish farms in Bolinao, northwestern Philippines. We established three stations in each of the three sites: the far, the intermediate, and those near the fish farms, and compared the sea urchins’ phenotypic traits and determined whether these were related to seagrass productivity and water parameters. Regardless of the sampling period, adult sea urchins (66.92 ± 0.27 mm test diameter, TD, n = 157) from the areas intermediate and near to the fish farms had significantly lower indices of Aristotle’s lantern, gut contents, gut and gonads, and lower gonad quality (high percentage of unusual black gonads), compared to those from the far stations. Multivariate analysis showed that the smaller feeding structures and gut, lower consumption rates and lower gonad indices and quality of sea urchins in the intermediate and near fish farms were positively related to lower shoot density, leaf production and species diversity, as well as lower water movement in those stations. The larger size of the Aristotle’s lantern in the far stations was not related to food limitations. More importantly, the phenotypic variability in the feeding structures and gonads of sea urchins in the same seagrass bed provides new evidence regarding the sensitivity of this species to environmental factors that may affect variability in food quality.The authors are very grateful to the anonymous reviewers for providing significant comments and suggestions to improve the manuscript. They are also indebted to the following: Rene R. Rollon, for providing advice on seagrass sampling techniques; Symon Dworjanyn, for providing valuable inputs in the earlier version of this manuscript; Marilou San Diego-McGlone, for providing some water quality data in Bolinao; Charissa M. Ferrerra, for the assistance provided on the Ocean Data View mapping software; Ma Josefa R. Pante, for some statistical advice. The authors would like to thank Jay R Gorospe for reviewing and providing valuable suggestions on the revised version of the manuscript, likewise to Lambert Meñez, for critically editing the manuscript, and to Jerwin Baure for additional assistance in copy editing the manuscript. The authors are thankful to Larry Milan, Jack Rengel, Lawrence Ramoran, for assisting the authors in field sampling and laboratory processing of samples. L. Milan, Jan Noelle Rimando and Aphrodite Entoma assisted in laboratory analysis of samples, particularly in gut content analysis.
- Accumulation and exposure classifications of plastics in the different coastal habitats in the western Philippine archipelagoGomez, Norchel Corcia F.; Cragg, Simon M.; Ghiglione, Jean-François; Onda, Deo Florence L. (Elsevier, 2023-11)Studies consistently ranked the Philippines as one of the top contributors of plastic wastes leaking into the ocean. However, most of these were based on probabilities and estimates due to lack of comprehensive ground-truth data, resulting also in the limited understanding of the contributing factors and drivers of local pollution. This makes it challenging to develop science-driven and locally-contextualized policies and interventions to mitigate the problem. Here, 56 sites from different coastal habitats in the western Philippine archipelago were surveyed for macroplastics standing stock, representing geographic regions with varying demography and economic activities. Clustering of sites revealed three potential influencing factors to plastic accumulation: population density, wind and oceanic transport, and habitat type. Notably, the amount and types of dominant plastics per geographic region varied significantly. Single-use plastics (food packaging and sachets) were the most abundant in sites adjacent to densely populated and highly urbanized areas (Manila Bay and eastern Palawan), while fishing-related materials dominated in less populated and fishing-dominated communities (western Palawan and Bolinao), suggesting the local industries significantly contributing to the mismanaged plastics in the surveyed sites. Meanwhile, isolated areas such as islands were characterized by the abundance of buoyant materials (drinking bottles and hygiene product containers), emphasizing the role of oceanic transport and strong connectivity in the oceans. Exposure assessment also identified single-use and fishing-related plastics to be of “high exposure (Type 4)” due to their high abundance and high occurrence. These increase their chances of encountering and interacting with organisms and habitats, thus, resulting into more potential harm. This study is the first comprehensive work done in western Philippines, and results will help contextualize local pollution, facilitating more effective management and policymaking.