National Committee on Marine Sciences (NCMS)
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- A conserved biosynthetic gene cluster is regulated by quorum sensing in a shipworm symbiontRobes, Jose Miguel D.; Altamia, Marvin A.; Murdock, Ethan G.; Concepcion, Gisela; Haygood, Margo G.; Puri, Aaron W. (American Society for Microbiology, 2022-06-14)Bacterial symbionts often provide critical functions for their hosts. For example, wood-boring bivalves called shipworms rely on cellulolytic endosymbionts for wood digestion. However, how the relationship between shipworms and their bacterial symbionts is formed and maintained remains unknown. Quorum sensing (QS) often plays an important role in regulating symbiotic relationships. We identified and characterized a QS system found in Teredinibacter sp. strain 2052S, a gill isolate of the wood-boring shipworm Bactronophorus cf. thoracites. We determined that 2052S produces the signal N-decanoyl-l-homoserine lactone (C10-HSL) and that this signal controls the activation of a biosynthetic gene cluster colocated in the symbiont genome that is conserved among all symbiotic Teredinibacter isolates. We subsequently identified extracellular metabolites associated with the QS regulon, including ones linked to the conserved biosynthetic gene cluster, using mass spectrometry-based molecular networking. Our results demonstrate that QS plays an important role in regulating secondary metabolism in this shipworm symbiont. This information provides a step toward deciphering the molecular details of the relationship between these symbionts and their hosts. Furthermore, because shipworm symbionts harbor vast yet underexplored biosynthetic potential, understanding how their secondary metabolism is regulated may aid future drug discovery efforts using these organisms.
- Somatostatin venom analogs evolved by fish-hunting cone snails: From prey capture behavior to identifying drug leadsRamiro, Iris Bea L.; Bjørn-Yoshimoto, Walden E.; Imperial, Julita S.; Gajewiak, Joanna; Salcedo, Paula Flórez; Watkins, Maren; Taylor, Dylan; Resager, William; Ueberheide, Beatrix; Bräuner-Osborne, Hans; Whitby, Frank G.; Hill, Christopher P.; Martin, Laurent F.; Patwardhan, Amol; Concepcion, Gisela; Olivera, Baldomero M.; Safavi-Hemami, Helena (American Association for the Advancement of Science, 2022-03-25)Somatostatin (SS) is a peptide hormone with diverse physiological roles. By investigating a deep-water clade of fish-hunting cone snails, we show that predator-prey evolution has generated a diverse set of SS analogs, each optimized to elicit specific systemic physiological effects in prey. The increased metabolic stability, distinct SS receptor activation profiles, and chemical diversity of the venom analogs make them suitable leads for therapeutic application, including pain, cancer, and endocrine disorders. Our findings not only establish the existence of SS-like peptides in animal venoms but also serve as a model for the synergy gained from combining molecular phylogenetics and behavioral observations to optimize the discovery of natural products with biomedical potential.
- Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabraOrdoñez, June Feliciano F.; Galindez, Gihanna Gaye S.T.; Gulay, Karina Therese; Ravago-Gotanco, Rachel (Elsevier, 2021-12)The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.The authors are grateful to the following individuals and institutions for providing samples and facilitating their collection: D. Ticao of (Finfish Hatcheries, Inc.); Dr. M.A. Juinio-Menez, ˜ J.R. Gorospe, C. Edullantes, B. Rodriguez, A. Rioja, T. Catbagan, and G. Peralta of Bolinao Marine Laboratory, University of the Philippines Marine Science Institute; and E. Tech (Palawan Aquaculture Corp.).
- The harmful raphidophyte Chattonella (Raphidophyceae) in Western Pacific: Its red tides and associated fisheries damage over the past 50 years (1969–2019)Lum, Wai Mun; Benico, Garry; Doan-Nhu, Hai; Furio, Elsa; Leaw, Chui Pin; Leong, Sandric Chee Yew; Lim, Po Teen; Lim, Weol Ae; Lirdwitayaprasit, Thaithaworn; Lu, Songhui; Nguyen, Nguyen Van; Orlova, Tatiana Yu.; Rachman, Arief; Sakamoto, Setsuko; Takahashi, Kazuya; Teng, Sing Tung; Thoha, Hikmah; Wang, Pengbin; Yñiguez, Aletta T.; Wakita, Kazumi; Iwataki, Mitsunori (Elsevier, 2021-07)Red tides and associated fisheries damage caused by the harmful raphidophyte Chattonella were reassessed based on the documented local records for 50 years to understand the distribution and economic impacts of the harmful species in the Western Pacific. Blooms of Chattonella with fisheries damage have been recorded in East Asia since 1969, whereas they have been only recorded in Southeast Asia since the 1980s. Occurrences of Chattonella have been documented from six Southeast Asian countries, Indonesia, Malaysia, Philippines, Singapore, Thailand and Viet Nam, with mass mortalities mainly of farmed shrimp in 1980–1990s, and farmed fish in 2000–2010s. These occurrences have been reported with the names of C. antiqua, C. marina, C. ovata, C. subsalsa and Chattonella sp., owing to the difficulty of microscopic species identification, and many were not supported with molecular data. To determine the distribution of C. marina complex and C. subsalsa in Southeast Asia, molecular phylogeny and microscopic observation were also carried out for cultures obtained from Indonesia, Malaysia, Japan, Philippines, Russia, Singapore and Thailand. The results revealed that only the genotype of C. marina complex has been detected from East Asia (China, Japan, Korea and Russia), whereas both C. marina complex (Indonesia and Malaysia) and C. subsalsa (Philippines, Singapore and Thailand) were found in Southeast Asia. Ejection of mucocysts has been recognized as a diagnostic character of C. subsalsa, but it was also observed in our cultures of C. marina isolated from Indonesia, Malaysia, Japan, and Russia. Meanwhile, the co-occurrences of the two harmful Chattonella species in Southeast Asia, which are difficult to distinguish solely based on their morphology, suggest the importance of molecular identification of Chattonella genotypes for further understanding of their distribution and negative impacts.We thank Drs Yuuki Kosaka, Winnie Lik Sing Lau, Ing Kuo Law and Toh Hii Tan for their sampling assistances. We thank Dr. Sadaaki Yoshimatsu for providing a culture strain TAI-93, and Drs Mineo Yamaguchi and Haruo Yamaguchi for support on maintenance and rDNA analysis of the culture. This work was carried out under international collaboration of the IOC/WESTPAC-HAB project and Core-to-Core Program (B. Asia-Africa Science Platforms) of the Japan Society for the Promotion of Science (JSPS). This work was partially supported by Japanese JSPS Kakenhi 19H03027 and 19KK0160 (MI), Malaysian MOHE HICOE IOES and FRGS (PTL), Vietnamese VAST NVCC17.02/21-21 (HD-N), and the Japanese Fund-in-Trust (MEXT).
- Genomic and targeted approaches unveil the cell membrane as a major target of the antifungal cytotoxin amantelide AElsadek, Lobna A.; Matthews, James H.; Nishimura, Shinichi; Nakatani, Takahiro; Ito, Airi; Gu, Tongjun; Luo, Danmeng; Salvador-Reyes, Lilibeth A.; Paul, Valerie J.; Kakeya, Hideaki; Luesch, Hendrik (Wiley, 2021-03-23)Amantelide A, a polyhydroxylated macrolide isolated from a marine cyanobacterium, displays broad-spectrum activity against mammalian cells, bacterial pathogens, and marine fungi. We conducted comprehensive mechanistic studies to identify the molecular targets and pathways affected by amantelide A. Our investigations relied on chemical structure similarities with compounds of known mechanisms, yeast knockout mutants, yeast chemogenomic profiling, and direct biochemical and biophysical methods. We established that amantelide A exerts its antifungal action by binding to ergosterol-containing membranes followed by pore formation and cell death, a mechanism partially shared with polyene antifungals. Binding assays demonstrated that amantelide A also binds to membranes containing epicholesterol or mammalian cholesterol, thus suggesting that the cytotoxicity to mammalian cells might be due to its affinity to cholesterol-containing membranes. However, membrane interactions were not completely dependent on sterols. Yeast chemogenomic profiling suggested additional direct or indirect effects on actin. Accordingly, we performed actin polymerization assays, which suggested that amantelide A also promotes actin polymerization in cell-free systems. However, the C-33 acetoxy derivative amantelide B showed a similar effect on actin dynamics in vitro but no significant activity against yeast. Overall, these studies suggest that the membrane effects are the most functionally relevant for amantelide A mechanism of action.This research was supported by the National Institutes of Health (grant R01CA172310 to H.L.), the Debbie and Sylvia DeSantis Chair Professorship (H.L), and a Grant-in Aid for Scientific Research (no. 17H06401 to S.N. and H.K.) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. L.E. was supported by the NIH/NIGMS T32GM136583 “Chemistry-Biology Interface Training Program at the University of Florida”. We thank Dr. Yanping Zhang (University of Florida) from the UF ICBR NextGen DNA Sequencing core facility for carrying out the nextgeneration sequencing, Dr. Maya Schuldiner (Weizmann Institute of Science, Israel) for providing the triple yeast deletion library, Dr. Kaoru Takegawa (Kyushu University, Japan) for providing the ergosterol mutants, Dr. Charles Boone laboratory (University of Toronto, Canada) for providing the wild-type S. cerevisiae Y7092 and Dr. Kalina Atanasova (CNPD3, University of Florida) for assistance with the imaging.
- Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, PhilippinesLabrador, Kevin; Palermo, Joseph Dominic; Agmata, Altair; Ravago-Gotanco, Rachel; Pante, Ma. Josefa (Frontiers Media SA, 2022-02-24)Stock identification and delineation are important in the management and conservation of marine resources. These were highlighted as priority research areas for Bali sardinella (Sardinella lemuru) which is among the most commercially important fishery resources in the Philippines. Previous studies have already assessed the stocks of S. lemuru between Northern Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding conflicting results. Phenotypic variation suggests distinct stocks between the two regions, while mitochondrial DNA did not detect evidence of genetic differentiation for this high gene flow species. This paper tested the hypothesis of regional structuring using genome-wide single nucleotide polymorphisms (SNPs) acquired through restriction site-associated DNA sequencing (RADseq). We examined patterns of population genomic structure using a full panel of 3,573 loci, which was then partitioned into a neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar inferences were obtained from the full and neutral panels, which were contrary to the inferences from the outlier panel. While the full and neutral panels suggested a panmictic population (global FST ∼ 0, p > 0.05), the outlier panel revealed genetic differentiation between the two regions (global FST = 0.161, p = 0.001; FCT = 0.263, p < 0.05). This indicated that while gene flow is apparent, selective forces due to environmental heterogeneity between the two regions play a role in maintaining adaptive variation. Annotation of the outlier loci returned five genes that were mostly involved in organismal development. Meanwhile, three unannotated loci had allele frequencies that correlated with sea surface temperature. Overall, our results provided support for local adaptation despite high levels of gene flow in S. lemuru. Management therefore should not only focus on demographic parameters (e.g., stock size and catch volume), but also consider the preservation of adaptive variation.We would like to acknowledge the assistance provided by Ma. Rio Naguit, Asuncion De Guzman, Jerry Garcia, Jhunrey Follante, Joshep Mercene, and John Christopher Azcarraga in sample collection and initial processing. We also acknowledge the research staff of the Marine Molecular Ecology and Evolution Laboratory (MMEEL), as well as the Marine Genomics and Molecular Genetics Laboratory (MGMGL) and its head, Arturo Lluisma, for providing valuable input in the conduct of the experiment and analysis of the data. Finally, we extend our gratitude to Demian Willette, Laura David, and Jonas Quilang for their valuable feedback on the manuscript.
- Age, growth, and population structure of Conomurex luhunuasSanchez-Escalona, Katherine; Aliño, Porfirio (National Fisheries Research and Development Institute, 2022-12)Age and growth dynamics of Conomurex luhuanus were investigated to determine the population structure. Age-specific change in shell shape determined with geometric morphometrics revealed discrimination of shape between 0-3 years old at 99–100% while 3–4 years old can be separated with 81% certainty. Using the age discrimination data, K and L∞ were estimated at 1.00 year and 7.28 cm, respectively. Recruitment is bimodal with natural mortality (M) of 0.71 and fishing mortality (F) approximated at 3.92 year. The exploitation rate (E) is 0.85 year, indicating probable overharvesting of the population under study. The presence of a deep-water population, age-specific burying behavior, and bimodal recruitment pattern are possible resilience factors.The study was supported by a grant from PCAARRD-DOST.
- Spatial planning insights for Philippine coral reef conservation using larval connectivity networksPata, Patrick R.; Yñiguez, Aletta T. (Frontiers Media SA, 2021-10-06)The marine habitats of the Philippines are recognized to be some of the most biodiverse systems globally yet only 1.7% of its seas are designated as marine protected areas (MPAs) with varying levels of implementation. Many of these MPAs were established based on local-scale conservation and fisheries objectives without considering larger-scale ecological connections. The connectivity of reefs through larval dispersal is important in the regional-scale resilience against anthropogenic disturbances and is considered a significant criterion in planning for MPAs. In this study, we provide insights into the delineation of ecologically connected MPA networks using larval dispersal modeling and network analysis. We characterized the network properties of the Philippine coral reefs, organized as 252 reef nodes, based on the larval connectivity networks of a branching coral, sea urchin, and grouper. We then evaluated the distribution of the existing 1,060 MPAs relative to the connectivity patterns. All reef nodes were found to be highly interconnected with a mean shortest path ranging from 1.96 to 4.06. Reef nodes were then ranked according to their relative importance in regional connectivity based on five connectivity indices. Despite the between-organism and between-index variability in rankings, there were reefs nodes, mostly located offshore and at major straits, which consistently ranked high. We found that the distribution of existing MPAs partially capture some of the regional connectivity functions but there is a spatial mismatch between the primarily coastal MPAs and the high-ranking reef nodes. Furthermore, network partitioning identified subnetworks and dispersal barriers. The existing MPAs were found to be disproportionately distributed to a few subnetworks and that the largest subnetworks do not contain the greatest number of MPAs. Considering these gaps, we suggest expanding the coverage of protected areas especially in underrepresented reef networks to meaningfully capture national-scale connectivity and meet global conservation objectives.We would like to thank Dr. Vera Horigue and Andrew Torres for constructive comments and suggestions during the early versions of this paper. We also thank the members of the Biological Oceanography and Modeling of Ecosystems (BiOME) Laboratory who assisted in running model simulations.
- Growth, nitrate uptake kinetics, and biofiltration potential of eucheumatoids with different thallus morphologiesNarvarte, Bienson Ceasar V.; Genovia, Tom Gerald T.; Hinaloc, Lourie Ann R.; Roleda, Michael Y. (Wiley, 2021-12-30)The declining production of commercially important eucheumatoids related to serious problems like increasing susceptibility to ice‐ice disease and epiphytism may be ameliorated by nutrition. This ushered to an increasing interest in incorporating seaweeds into an integrated multi‐trophic aquaculture (IMTA) setup to take up excess inorganic nutrients produced by fish farms for their nourishment. In this regard, it is important to understand the nutrient uptake capacity of candidate seaweeds for incorporation in an IMTA system. Here, we examined the growth, nitrate (NO3‐) uptake kinetics and biofiltration potential of Eucheuma denticulatum and three strains of Kappaphycus alvarezii (G‐O2, TR‐C16 and SW‐13) with distinct thallus morphologies. The NO3‐ uptake rates of the samples were determined under a range of NO3‐ concentration (1‐ 48 µM) and uptake rates were fitted to the Michaelis‐Menten saturation equation. Among the examined eucheumatoids, only SW‐13 had a linear response to NO3‐ concentration while other strains had uptake rates that followed the Michaelis‐Menten saturation equation. Eucheuma denticulatum had the lowest Km (9.78 ± 1.48 µM) while G‐O2 had the highest Vmax (307 ± 79.3 µmol · g‐1 · min‐1). The efficiency in NO3‐ uptake (highest Vmax/Km and α) was translated into the highest growth rate (3.41± 0.58 % · d‐1) measured in E. denticulatum. Our study provided evidence that eucheumatoids could potentially take up large amount of NO3‐ and fix CO2 when cultivated proximate to a fish farm as one component of an IMTA system. During a 45‐d cultivation period of eucheumatoids, as much as 370 g NO3‐ can be sequestered by every 1 kg initial biomass E. denticulatum growing at 3% · d‐1. Furthermore, based on our unpublished photosynthetic measurements, the congeneric K. striatus can fix 27.5 g C · kg‐1 DW during a 12‐h daylight period.
- Two hidden mtDNA-clades of crown-of-thorns starfish in the Pacific OceanYasuda, Nina; Inoue, Jun; Hall, Michael R.; Nair, Manoj R.; Adjeroud, Mehdi; Fortes, Miguel D.; Nishida, Mutsumi; Tuivavalagi, Nat; Ravago-Gotanco, Rachel; Forsman, Zac H.; Soliman, Taha; Koyanagi, Ryo; Hisata, Kanako; Motti, Cherie A.; Satoh, Noriyuki (Frontiers Media SA, 2022-04-27)Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals, especially in the Western Pacific Ocean. To obtain a better understanding of population genetics of COTS and historical colonization across the Pacific Ocean, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS (Acanthaster cf. solaris) comprise two major clades, an East-Central Pacific (ECP) clade and a Pan-Pacific (PP) clade, separation of which was supported by high bootstrap value. The ECP clade consists of COTS from French Polynesia, Fiji, Vanuatu and the Great Barrier Reef (GBR). The Hawaii population is unique within this clade, while California COTS are included in EPC clade. On the other hand, the PP clade comprises multiple lineages that contain COTS from Vietnam, the Philippines, Japan, Papua New Guinea, Micronesia, the Marshall Islands, GBR, Vanuatu, Fiji and French Polynesia. For example, a lineage of the PP clade, which has the largest geographic distribution, includes COTS from all of these locations. These results suggest two alternative histories of current geographic distributions of COTS in the Pacific Ocean, an ECP clade ancestry or Western Pacific clade ancestry. Although further questions remain to be explored, this discovery provides an evolutionary context for the interpretation of COTS population structure which will aid future coral reef research in the Pacific Ocean, and ultimately improve reef management of COTS.We thank the following people for their help with sample collection: Dr. Hugh Sweatman and the AIMS Bioresources Library for GBR samples, Dr. Molly Timmers for Hawaiian samples, Geoff Jones and Jeff Kinch for Papua New Guinean samples, Monal Lal for Fijian samples, Christina Shaw for Vanuatu samples, Hoang Dinh Chieu for Vietnamese samples, and Hiromitsu Ueno for Japanese samples. The DNA Sequencing Section and IT section of OIST are acknowledged for its expert help with genome sequencing and bioinfomatic analysis. Last, but not least, we acknowledge the traditional owners of the lands and sea country on which this research took place.