eDNA metabarcoding in mangrove ecosystems for fish conservation and stock assessment of Sardinops sagax melanostictus in the Philippines
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
TRICKSIE P. BALATERO
ZILJIH MOLINA
RODELYN M. DALAYAP
RANDE DECHAVEZ
JANECE JEAN MANUBAG
NANETTE HOPE SUMAYA
JUSUA DELA PEÑA
SHARON ROSE TABUGO
♥
https://orcid.org/0000-0001-6813-840X
Abstract
Abstract. Balatero TP, Molina Z, Dalayap RM, Dechavez R, Manubag JJ, Sumaya NH, Peña JD, Tabugo SRM. 2025. eDNA metabarcoding in mangrove ecosystems for fish conservation and stock assessment of Sardinops sagax melanostictus in the Philippines. Biodiversitas 26: 347-357. Mangrove forests are essential ecosystems that provide many benefits, including nursery grounds for various marine species; however, identifying juveniles is often challenging, as visual fish surveys primarily rely on the characteristics of adult specimens for accurate classification. These vital ecosystems are threatened by overfishing, habitat destruction, pollution, and climate change. Therefore, this study employs environmental DNA (eDNA) metabarcoding as a non-invasive tool to identify fish species in the mangrove ecosystems of Mindanao, Philippines. eDNA metabarcoding facilitates species detection by analyzing genetic material found in environmental samples, offering a cost-effective and sensitive method for identifying fish species. Seawater samples were collected from selected mangrove areas, and the extracted eDNA was analyzed using high-throughput next-generation sequencing (NGS). The sampling sites were South Cotabato, Surigao del Norte, Misamis Oriental, and Tawi-Tawi, which recorded 29 species across 20 families. Notable species included Zenarchopterus dunckeri (Zenarchopteridae), a rare fish in the aquarium hobby; Hippocampus comes (Syngnathidae), the tiger-tail seahorse, which is classified as Vulnerable by the IUCN; Sardinops melanostictus (Clupeidae), known for its high commercial value; Siganus corallinus (Siganidae), valued for both food and the aquarium trade; and Gymnothorax flavimarginatus (Muraenidae), an invasive species, that plays a vital role in the food chain as a natural predator of lionfish. Tawi-Tawi Island emerged as the most diverse site, recording species from 11 families. The results highlight the critical role of mangroves as nurseries in supporting diverse fish populations and underscore the effectiveness of eDNA metabarcoding as complementary to traditional species inventory techniques.
##plugins.themes.bootstrap3.article.details##
References
Anneboina LR, Kumar KK. 2017. Economic analysis of mangrove and marine fishery linkages in India. Ecosyst Serv 24: 114-123. DOI: 10.1016/j.ecoser.2017.02.004.
Babcock RC, Bustamante RH, Fulton EA, Fulton DJ, Haywood MD, Hobday AJ, Vanderklift MA. 2019. Severe continental-scale impacts of climate change are happening now: Extreme climate events impact marine habitats, forming communities along 45% of Australia's coast. Front Mar Sci 6: 466674. DOI: 10.3389/fmars.2019.00411.
Barnes MA, Turner CR. 2016. The ecology of environmental DNA and implications for conservation genetics. Conserv Genet 17 (1): 1-17. DOI: 10.1007/s10592-015-0775-4.
Bautista JA, Manubag JJ, Sumaya NH, Martinez JG, Tabugo SR. 2023. Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines. Biodiversitas 24: 3063-3072. DOI: 10.13057/biodiv/d240562.
Bellwood DR, Goatley CH, Khan JA, Tebbett SB. 2016. Site fidelity and homing in juvenile rabbitfishes (Siganidae). Coral Reefs 35: 1151-1155. DOI: 10.1007/s00338-016-1466-4.
Beng KC, Corlett RT. 2020. Environmental DNA (eDNA) applications in ecology and conservation: Opportunities, challenges, and prospects. Biodivers Conserv 29 (7): 2089-2121. DOI: 10.1007/s10531-020-01980-0.
Berry TE, Osterrieder SK, Murray DC, Coghlan ML, Richardson AJ, Grealy AK, Stat M, Bejder L, Bunce M. 2017. DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea). Ecol Evol 7 (14): 5435-5453. DOI: 10.1002/ece3.3123.
Brown J, Pirrung M, McCue LA. 2017. FQC Dashboard: Integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinform 33 (19): 3137-3139. DOI: 10.1093/bioinformatics/btx373.
Carrasquilla-Henao M, Ban N, Rueda M, Juanes F. 2019. The mangrove-fishery relationship: A local ecological knowledge perspective. Mar Pol 108: 103656. DOI: 10.1016/j.marpol.2019.103656.
Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, Chen Q. 2018. SOAPnuke: A map reduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7 (1): gix120. DOI: 10.1093/gigascience/gix120.
Conlu PV. 1986. Guide to Philippine flora and fauna. IX. Manila, Philippines: National Resources Management Center, Ministry of Natural Resources, and University of the Philippines.
Costanza R, De Groot R, Braat L, Kubiszewski I, Fioramonti L, Sutton P, Grasso M. 2017. Twenty years of ecosystem services: How far have we come, and how far do we still need to go?. Ecosyst Serv 28: 1-16. DOI: 10.1016/j.ecoser.2017.09.008.
Cruz-Torres J, Reyes-Bonilla H. 2020. Herbivory by reef fishes and its importance in maintaining coral reef ecosystems: A review. Mar Ecol Prog Ser 644: 151-164. DOI: 10.3354/meps13277.
Dao HV, Pham KX, Hoang BX, Tanioka M, Watanabe R, Suzuki T. 2020. Occurrence of tetrodotoxin in three Nassarius gastropod species in Khanh Hoa Province, Vietnam. Fish Sci 86: 181-186. DOI: 10.1007/s12562-019-01375-3.
De Carvalho BM, Ferreira Junior AL, Fávaro LF, Artoni RF, Vitule J. 2020. Human?facilitated dispersal of the Gulf toadfish Opsanus beta (Goode & Bean, 1880) in Guaratuba Bay, south?eastern Brazil. J Fish Biol 97 (3): 686-690. DOI: 10.1111/jfb.14421.
Duarte CM, Agusti S, Barbier E, Britten GL, Castilla JC, Gattuso JP, Worm B. 2020. We are rebuilding marine life. Nature 580 (7801): 39-51. DOI: 10.1038/s41586-020-2146-7.
Enochs IC, Glynn PW. 2017. Trophodynamics of eastern Pacific coral reefs. In: Glynn P, Manzello D, Enochs I (eds). Coral Reefs of The Eastern Tropical Pacific: Persistence And Loss in A Dynamic Environment. Springer, Dordrecht. DOI: 10.1007/978-94-017-7499-4_9.
Eschmeyer WN, Fricke R, Van der Laan R. 2017. Catalogue of Fishes: Genera, Species, References. Zootaxa, New Zealand. DOI: 10.11646/zootaxa.3882.1.1.
Foster SJ, Kuo TC, Wan AKY, Vincent AC. 2019. Global seahorse trade defies export bans under CITES action and national legislation. Mar Pol 103: 33-41. DOI: 10.1016/j.marpol.2019.01.014.
Friedlander AM, Parrish JD. 2020. The role of predation in reef fish assemblages: Implications for fisheries management. Ecol Appl 30 (5): e02138. DOI: 10.1002/eap.2138.
Froese R, Pauly D. 2024. FishBase. Sardinops sagax (Jenyns, 1842). World Register of Marine Species. https://www.marinespecies.org/ aphia.php?p=taxdetails&id=217452 on 2024-10-03
Froese R, Zeller D, Kleisner K, Pauly D. 2012. What catch data can tell us about the status of global fisheries. Mar Biol 159: 1283-1292. DOI: 10.1007/s00227-012-1909-6.
Fujii K, Doi H, Matsuoka S, Nagano M, Sato H, Yamanaka H. 2019. Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods. PLoS One 14 (1): e0210357. DOI: 10.1371/journal.pone.0210357.
Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Taberlet P. 2016. Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol Evol 7 (11): 1299-1307. DOI: 10.1111/2041-210X.12595.
He Q, Silliman BR. 2019. Climate change, human impacts, and coastal ecosystems in the Anthropocene. Curr Biol 29 (19): R1021-R1035. DOI: 10.1016/j.cub.2019.08.042.
Herre AW. 1953. Check list of Philippine fishes. 20. US Government Printing Office.
Hirota K, Asaoka R, Nakae M, Sasaki K. 2015. The lateral line system and its innervation in Zenarchopterus dunckeri (Beloniformes: Exocoetoidei: Zenarchopteridae). Ichtiol Res 62: 286-292. DOI: 10.1007/s10228-014-0442-7.
Hou F, Wen L, Peng C, Guo J. 2018. Identification of marine traditional Chinese medicine dried seahorses in the traditional Chinese medicine market using DNA barcoding. Mitochondrial DNA A: DNA Mapping Seq Anal 29 (1): 107-112. DOI: 10.1080/24701394.2016.1248430.
Kano Y, Ohnishi K, Tomida Y, Ikeda N, Iwawaki N, Miyagawa M, Watanabe K. 2011. Fluctuation and variation in stream-fish assemblages after a catastrophic flood in the Miyagawa River, Japan. Environ Biol Fish 92: 447-460. DOI: 10.1007/s10641-011-9861-8.
Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: Multiple sequence alignment, interactive sequence choice, and visualization. Brief Bioinform 20 (4): 1160-1166. DOI: 10.1093/bib/bbx108.
Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 30 (4): 772-780. DOI: 10.1093/molbev/mst010.
Lourie SA, Pollom RA, Foster SJ. 2016. A global revision of the seahorse's Hippocampus Rafinesque 1810 (Actinopterygii: Syngnathiformes): Taxonomy and biogeography with recommendations for further research. Zootaxa 4146 (1): 1-66. DOI: 10.11646/zootaxa.4146.1.1.
McDevitt AD, Sales NG, Browett SS, Sparnenn AO, Mariani S, Wangensteen OS, Benvenuto C. 2019. Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals. J Fish Biol 9 5(2): 679-682. DOI: 10.1111/jfb.14053.
Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Iwasaki W. 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. R Soc Open Sci 2 (7): 150088. DOI: 10.1098/rsos.150088.
Munday PL, Jones GP. 2020. Parrotfish: The key to coral reef health. Trends Ecol Evol 35 (7): 610-622. DOI: 10.1016/j.tree.2020.02.013.
Mutalipassi M, D’Anza E, Pugliano M, Firmamento R, Murano C, Ruocco N. 2024. Casting light on the European anchovy: From biology to conservation and industry. Front Ecol Evol 12: 1352055. DOI: 10.3389/fevo.2024.1352055.
Nagelkerken I, Huebert KB, Serafy JE, Grol MGG, Dorenbosch M, Bradshaw CJA. 2017. Highly localized replenishment of coral reef fish populations near nursery habitats. Mar Ecol Prog Ser 568: 137-150. DOI: 10.3354/meps12062.
Nester GM, De Brauwer M, Koziol A, West KM, DiBattista JD, White NE, Power M, Heydenrych MJ, Harvey E, Bunce M. 2020. Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (Family: Syngnathidae). Environ DNA 2 (4): 614-626. DOI: 10.1002/edn3.93.
Neumann B, Vafeidis AT, Zimmermann J, Nicholls RJ. 2015. Future coastal population growth and exposure to sea-level rise and coastal flooding: A global assessment. PLoS One 10 (3): e0118571. DOI: 10.1371/journal.pone.0118571.
Park BK, Jang WJ, Park KH, Lee HS, Lee WO, Choi KS, Lee J. 2021. Tetrodotoxin and its analogues: A review of analysis methods and levels in pufferfish. J Food Hyg Saf 36 (2): 105-117. DOI: 10.13103/JFHS.2021.36.2.105.
Podda C, Palmas F, Pusceddu A, Sabatini A. 2021. Hard times for catadromous fish: The case of the European eel (Anguilla anguilla, L. 1758). Adv Oceanogr Limnol 12: 47-64. DOI: 10.4081/aiol.2021.9997.
Pollom RA, Ralph GM, Pollock CM, Vincent AC. 2021. Global extinction risk for seahorses, pipefishes, and their near relatives (Syngnathiformes). Oryx 55 (4): 497-506. DOI: 10.1017/S0030605320000782.
Reis V, Hermoso V, Hamilton SK, Bunn SE, Fluet?Chouinard E, Venables B, Linke S. 2019. Characterizing seasonal dynamics of Amazonian wetlands for conservation and decision making. Aquat Conserv Mar Freshw Ecosyst 29: 1073-1082. DOI: 10.1002/aqc.3051.
Romañach SS, DeAngelis DL, Koh HL, Li Y, Barizan RSR, Zhai L. 2018. Conservation and restoration of mangroves: Global status, perspectives, and prognosis. Ocean Coast Manag 154: 72-82. DOI: 10.1016/j.ocecoaman.2018.01.009.
Ruppert KM, Kline RJ, Rahman MS. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 17: e00547. DOI: 10.1016/j.gecco.2019.e00547.
Sato H, Sogo Y, Doi H, Yamanaka H. 2017. Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Sci Rep 7: 14860. DOI: 10.1038/s41598-017-14978-6.
Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. 2018. MitoFish and MiFish pipeline: A mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Mol Biol Evol 35 (6): 1553-1555. DOI: 10.1093/molbev/msy074.
Sarr O, Kindong R, Tian, S. 2021. Knowledge on the biological and fisheries aspects of the Japanese sardine, Sardinops melanostictus (Schlegel, 1846). J Mar Sci Eng 9: 1403. DOI: 10.3390/jmse9121403.
Serafy JE, Shideler GS, Araújo RJ, Nagelkerken I. 2015. Mangroves enhance reef fish abundance at the Caribbean regional scale. PLoS One 10 (11): e0142022. DOI: 10.1371/journal.pone.0142022.
Serag KJ, Elloran C, Serag K. 2024. Tawi Tawi, Reef Fishes, Philippines. Version 1.21. ASEAN Centre for Biodiversity (ACB). Occurrence dataset. https://www.gbif.org/dataset/7f30b6c4-bdd7-4dc0-b32e-699a8d96dc47/project. DOI: 10.15468/nvy0u9.
Šlechtová V, Musilova Z, Tan HH, Kottelat M, Bohlen J. 2021. One northward, one southward: Contrasting biogeographical history in two benthic freshwater fish genera across Southeast Asia (Teleostei: Cobitoidea: Nemacheilus, Pangio). Mol Phylogenet Evol 161: 107139. DOI: 10.1016/j.ympev.2021.107139.
Smale DA, Wernberg T, Oliver EC, Thomsen M, Harvey BP, Straub SC, Moore PJ. 2019. Marine heatwaves threaten global biodiversity and the provision of ecosystem services. Nat Clim Chang 9 (4): 306-312. DOI: 10.1038/s41558-019-0412-1.
Southwick R, Holdsworth JC, Rea T, Bragg L, Allen T. 2018. Estimating marine recreational fishing’s economic contributions in New Zealand. Fish Res 208: 116-123. DOI: 10.1016/j.fishres.2018.06.016.
Sun D, Cheney KL, Werminghausen J, McClure EC, Meekan MG, McCormick MI, Grutter AS. 2016. Cleaner wrasse influences habitat selection of young damselfish. Coral Reefs 35: 427-436. DOI: 10.1007/s00338-015-1391-y.
Thomas N, Lucas R, Bunting P, Hardy A, Rosenqvist A, Simard M. 2017. Distribution and drivers of global mangrove forest change, 1996-2010. PLoS One 12: e0179302. DOI: 10.1371/journal.pone.0179302.
Vanderklift MA, Pillans RD, Hutton M, De Wever L, Kendrick GA, Zavala-Perez A, Howard A. 2021. High herbivory rates in remote northwest Australian seagrass meadows by rabbitfish and green turtles. Mar Ecol Prog Ser 665: 63-73. DOI: 10.3354/meps13657.
Whitehead PJ. 1985. FAO species catalogue. 7. Clupeoid fishes of the world (Suborder Clupeoidei). An annotated and illustrated catalogue of the herrings, sardines, pilchards, sprats, shads, anchovies, and wolf-herrings. Part 1. Chirocentridae, Clupeidae & Pristigasteridae.
Willette DA, Bognot ED, Mutia M, Santos MD. 2011. Biology and ecology of sardines in the Philippines: A review. BFAR Tech Pap Ser 13: 1-20.
Wolfe K, Kenyon TM, Mumby PJ. 2021. The biology and ecology of coral rubble and implications for the future of coral reefs. Coral Reefs 40 (6): 1769-1806. DOI: 10.1007/s00338-021-02185-9.
Zapata?Hernández G, Sellanes J, Letourneur Y, Harrod C, Morales NA, Plaza P, Gaymer CF. 2021. Tracing trophic pathways through the marine ecosystem of Rapa Nui (Easter Island). Aquat Conserv Mar Freshw Ecosyst 31 (2): 304-323. DOI: 10.1002/aqc.3500.
Zhang Y, Pavlovska M, Stoica E, Prekrasna I, Yang J, Slobodnik J, Dykyi E. 2020. Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals. Environ Intl 135: 105307. DOI: 10.1016/j.envint.2019.105307.
Zou K, Chen J, Ruan H, Li Z, Guo W, Li M, Liu L. 2020. eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci Total Environ 702: 134704. DOI: 10.1016/j.scitotenv.2019.134704.
Zu EPS, Mukherjee N, Worthington TA et al. 2020. Fishers who rely on mangroves: Modelling and mapping the global intensity of mangrove-associated fisheries. Estuar Coast Shelf Sci 248: 107159. DOI: 10.1016/j.ecss.2020.106975.
Most read articles by the same author(s)
- NITCEL AYMIE ALBARIDO, SHARON ROSE TABUGO, High-throughput analysis using 16S rRNA gene of bacterial communities present in selected bivalves and gastropods species from Bayug Island, Iligan City, Philippines , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 1 (2024)
- CHENCY GRACE O. LIGUEZ, SHARON ROSE TABUGO, Antibacterial activity of sea hare (Dolabella auricularia) egg string extracts against potentially pathogenic bacteria , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 12 (2023)
- RANDE DECHAVEZ, MA. LYN CALUB, DONA ROSE GENOBATA, RAUL BALACUIT, REIZL JOSE, SHARON ROSE TABUGO, Identification of culture-dependent microbes from mangroves reveals dominance of Bacillus including medically important species based on DNA signature , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 10 (2022)
- JOHN ARLU BAUTISTA, JANECE JEAN MANUBAG, NANETTE HOPE SUMAYA, JOEY GENEVIEVE MARTINEZ, SHARON ROSE TABUGO, Environmental DNA (eDNA) metabarcoding and fish visual census reveals the first record of Doboatherina magnidentata in the Philippines , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 5 (2023)
- MARY GRACE EREGUERO, MARY ANNE CORDERO, RODELYN DALAYAP, SHARON ROSE TABUGO, Antifungal activity of selected sea cucumber species from Tukuran, Zamboanga del Sur, Mindanao, Philippines using modified SPOTi assay , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 11 (2022)
- DARSHEL ESTER P. ESTOR, SHARON ROSE TABUGO, High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 11 (2023)
- LOEL DALAN, VERONICA TAÑAN, MICHELLE ANNE DIANO, CESAR DEMAYO, MYLAH TABELIN, NANETTE HOPE SUMAYA, Life history traits of the gastropod-associated bacterivorous nematode Caenorhabditis brenneri (Nematoda: Rhabditida) , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 7 (2024)