Applications of environmental DNA for marine biodiversity monitoring in Sumberkima Village, Bali, Indonesia
Article Sidebar
Abstract Views: 483
File Views: 52
Main Article Content
Abstract
Abstract. Prasetia IND, Amelia JM, Sitepu GSB, Maharani MDK, Wulandari D, Ampou EE, Malik MDA, Nursalim N, Kholilah N, Cahyani NKD. 2025. Applications of environmental DNA for marine biodiversity monitoring in Sumberkima Village, Bali, Indonesia. Biodiversitas 26: 3939-3951. Sumberkima Village in North Bali, Indonesia, is known for its high marine diversity, yet it increasingly faces ecological stress from fishing and tourism activities. This study aims to assess the biodiversity of coral reef ecosystems in Sumberkima using a combination of visual census and environmental DNA (eDNA) metabarcoding. A Line Transect Method was conducted through SCUBA for a visual census to detect coral diversity and coral cover. Then, eDNA samples were collected from three stations (i) coral reef ecosystems, (ii) the transitional zone between seagrass and coral reef ecosystems, and (iii) coral reef ecosystems near the bay close to the mainland and analyzed using the COI locus to detect invertebrates and vertebrates. Seawater was taken for 1 L per station. A total of 200,709 reads and 662 Amplicon Sequence Variants (ASVs) of Eukaryotes, enabling the detection of cryptic and hard-to-observe species. Meanwhile, visual census using the Line Transect Method assessed coral diversity and cover, identifying 39 genera with conditions ranging from poor to medium. The integration of eDNA with traditional visual census techniques provides a more comprehensive biodiversity assessment, particularly in ecologically rich yet threatened marine environments such as Sumberkima, North Bali, Indonesia.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Aglieri G, Baillie C, Mariani S, Cattano C, Cal`o A, Turco G, Spatofora G, Di Franco A, Di Lorenzo M, Guidetti P, Milazzo M. 2021. Environmental DNA effectively captures functional diversity of coastal fish communities. Mol Ecol 30: 3127-3139. DOI: 10.1111/mec.15661.
Allan EA, Zhang WG, Lavery AC, Govindarajan AF. 2021. Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes. Environ DNA 3: 492-514. DOI: 10.1002/edn3.141.
Andriyono S, Alam MJ, Kim HW. 2021. Marine fish detection by environmental DNA (eDNA) metabarcoding approach in the Pelabuhan Ratu Bay, Indonesia. Intl J Adv Sci Eng Inf Technol 11 (2): 729-737. DOI: 10.18517/ijaseit.11.2.9528.
Anugrah AP, Putra BA, Burhanuddin. 2020. Implementation of coral triangle initiative on coral reefs, fisheries, and food security (CTI- CFF) in Indonesia and Philippines. IOP Conf Ser Earth Environ Sci 575: 012154. DOI: 10.1088/1755-1315/575/1/012154.
Bakker J, Wangensteen OS, Baillie C, Buddo D, Chapman DD, Gallagher AJ, Guttridge TL, Hertler H, Mariani S. 2019. Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding. Ecol Evol 9: 14341-14355. DOI: 10.1002/ece3.5871.
Bessey C, Jarman SN, Simpson T, Miller H, Stewart T, Keesing JK, Berry O. 2021. Passive eDNA collection enhances aquatic biodiversity analysis. Commun Biol 4: 236. DOI: 10.1038/s42003-021-01760-8.
Boakes Z. Hall AE, Ampou EE, Jones GC, Suryaputra IGNA, Mahyuni LP, Prasetijo R, Stafford R. 2022. Coral reef conservation in Bali in light of international best practice, a literature review. J Nat Conserv 67: 126190. DOI: 10.1016/j.jnc.2022.126190.
Bolyen E, Rideout JR, Dillon MR et al. 2019. Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nat Biotecnol 37: 852-857. DOI: 10.1038/s41587-019-0209-9.
Branchini S, Pensa F, Neri P, Tonucci BM, Mattielli L, Collavo A, Sillingardi ME, Piccinetti C, Zaccanti F, Goffredo S. 2015. Using a citizen science program to monitor coral reef biodiversity through space and time. Biodivers Conserv 24 (2): 319-336. DOI: 10.1007/s10531-014-0810-7.
Burke L, Reytar K, Spalding K, Perry A. 2012. Reefs At Risk Revisited in The Coral Triangle: World Resources Institute. World Resource Institute, Wahington DC.
Buxton A, Matechou E, Griffin J, Diana A, Griffiths RA. 2021. Optimising sampling and analysis protocols in environmental DNA studies. Sci Rep 11 (1): 11637. DOI: 10.1038/s41598-021-91166-7.
Cahyani NKD, Anggoro AW, Malik MDA, Subhan B, Sani LMI, Madduppa H. 2024. Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: Comparative high throughput analysis using different bioinformatic pipelines. Mar Biodivers 54 (3): 39. DOI: 10.1007/s12526-024-01432-w.
Cai W, MacDonald B, Korabik M, Gradin I, Neave EF, Harper LR, Kenchington E, Riesgo A, Whoriskey FG, Mariani S. 2024. Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring. Sci Tot Environ 946: 174148. DOI: 10.1016/j.scitotenv.2024.174148.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13: 581-583. DOI: 10.1038/nmeth.3869.
Casey JM, Ransome E, Collins AG, Mahardini A, Kurniasih EM, Sembiring A, Schiettekatte MD, Cahyani, NKD, Anggoro AW, Moore M, Uehling A, Belcaid M, Barber PH, Geller JB, Meyer CP. 2021. DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity. Environ DNA 3 (6): 1229-1246. DOI: 10.1002/edn3.245.
Chen X, Li S, Zhao J, Yao M. 2024. Passive eDNA sampling facilitates biodiversity monitoring and rare species detection. Environ Intl 187: 108706. DOI: 10.1016/j.envint.2024.108706.
Clarke LJ, Beard JM, Swadling KM, Deagle BE. 2017. Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecol Evol 7: 873-883. DOI: 10.1002/ece3.2667.
Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner M, Mariani S. 2019. Non?specific amplification compromises environmental DNA metabarcoding with COI. Method Ecol Evol 10 (11): 1985-2001. DOI: 10.1111/2041-210x.13276.
Cowman PF, Bellwood DR. 2013. The historical biogeography of coral reef fishes: Global patterns of origination and dispersal. J Biogeogr 40 (2): 209-224. DOI: 10.1111/jbi.12003.
Curd EE, Gold Z, Kandlikar GS, Gomer J, Ogden M, O’Connell T, Pipes L, Schweizer TM, Rabichow L, Lin M, Shi B. 2019. Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets. Method Ecol Evol 10 (9): 1469-1475. DOI: 10.1111/2041-210X.13214.
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière?Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfender ME, Bernatchez L. 2017. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Mol. Ecol 26 (21): 5872-5895. DOI: 10.1111/mec.14350
Desvianti D, Choesin DN. 2015. Comparison between coral reef ecosystem in the marine tourism zone and core zone in Toyapakeh, Nusa Penida, Bali, Indonesia. International Conference on Food, Ecological and Life Sciences (FELS-2015) June 15-16, 2015 Bangkok.
Doherty O, Milner C, Dustan P, Campbell S, Pardede S, Kartawijaya T, Alling A. 2013. Report on Menjangan Island’s coral reef: A Bali Barat National Park marine protected area. Atoll Res Bull 19 (599): 1-18. DOI: 10.5479/si.00775630.599.
Edinger EN, Jompa J, Limmon GV, Widjatmoko W, Risk MJ. 1998. Reef degradation and coral biodiversity in Indonesia: effects of land-based pollution, destructive fishing practices and changes over time. Mar Pollut Bull 36 (8): 617-630. DOI: 10.1016/S0025-326X(98)00047-2.
English S, Wilkinson C, Baker V. 1994. Line intercept transect. In: English S, Wilkinson C, Baker V (eds). Survey Manual for Tropical Marine Resources, Australian Institute of Marine Science, Townsville.
Formel N, Enochs IC, Sinigalliano C, Anderson SR, Thompson LR. 2021. Subsurface automated samplers for eDNA (SASe) for biological monitoring and research. HardwareX 10: e00239. DOI: 10.1016/j.ohx.2021.e00239.
Gold Z, Sprague J, Kushner DJ, Zerecero Marin E, Barber PH. 2021. eDNA metabarcoding as a biomonitoring tool for marine protected areas. PLoS One 16: e0238557. DOI: 10.1371/journal.pone.0238557.
Habibi A, Setiasih N, Sartin J. 2007. A decade of reef check monitoring: Indonesian coral reefs, condition and trends. The Indonesian Reef Check Network, Denpasar.
Hughes TP, Anderson KD, Connolly SR. 2018. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359 (6371): 80-83. DOI: 10.1126/science.aan8048.
Jia H, Ji D, Zhang L, Zhang T, Xian W, Zhang H. 2023. Application of environmental DNA technology in marine ranching-case study of Bailong Pearl Bay Demonstration area in Beibu Gulfm. Ecol Indic 154: 110906. DOI: 10.1016/j.ecolind.2023.110906.
Juhel JB, Utama RS, Marques V, Vimono IB, Sugeha HY, Kadarusman, Pouyaud L, Dejean T, Mouillot D, Hocdé R. 2020. Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle. Proceed R Soc B 287 (1930): 20200248. DOI: 10.1098/rspb.2020.0248.
Kandlikar GS, Gold ZJ, Cowen MC, Meyer RS, Freise AC, Kraft NJB, Moberg-Parker J, Sprague J, Kushner DJ, Curd EE. 2018. Ranacapa: An R package and shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000 Res 7: 1734. DOI: 10.12688/f1000research.16680.1.
Karim W. 2019. Status of coral diseases and compromised health syndromes on Pemuteran shallow reefs, North Bali Island. IOP Conf Ser Earth Environ Sci 236 (1): 012048. DOI: 10.1088/1755-1315/236/1/012048.
Komai T, Gotoh RO, Sado T, Miya M. 2019. Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans. Metabarcoding Metagenomic 3: e33835. DOI: 10.3897/mbmg/3.33835.
Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents. Front Zool 10 (1): 34. DOI: 10.1186/1742-9994-10-34.
Li C, Long H, Yang S, Zhang Y, Tang F, Jin W, Wang G, Chang W, Pi Y, Gao L, Ma M, Zhao M, Zheng H, Gong Y, Liu Y, Jiang K. 2022. eDNA assessment of pelagic fish diversity, distribution, and abundance in the Central Pacific Ocean. Reg Stud Mar Sci 56: 102661. DOI: 10.1016/j.rsma.2022.102661.
Linggi PP, Burhanuddin A. 2019. The role of coral triangle initiative on coral reefs, fisheries, and food securities in Indonesia’s environmental conservation. IOP Conf Ser Earth Environ Sci 343 (1): 012092. DOI: 10.1088/1755-1315/343/1/012092.
Madduppa H, Cahyani NKD, Anggoro AW, Subhan B, Jefri E, Sani LMI, Arafat D, Nebuchadnezzar A, Bengen DG. 2021. eDNA metabarcoding illuminates species diversity and composition of three phyla (chordata, mollusca and echinodermata) across Indonesian coral reefs. J Biodivers Conserv 30 (11): 3087-3114. DOI: 10.1007/s10531-021-02237-0.
Malik MDA, Ambariyanto A, Hartati R, Nursalim N, Kholilah N, Kurniasih EM, Anggoro AW, Prasetia R, Syamsyuni Y, Muh F, Cahyani NKD. 2025. EDNA uncovers hidden fish diversity in the coral reef ecosystems of Karimunjawa National Park, Indonesia. Reg Stud Mar Sci 81: 103945. DOI: 10.1016/j.rsma.2024.103945.
Marwayana ON, Gold Z, Meyer CP, Barber PH. 2022. Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago. Environ DNA 4 (1): 222-238. DOI: 10.1002/edn3.257.
McMurdie PJ, Holmes S. 2013. Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8 (4): e61217. DOI: 10.1371/journal.pone.0061217.
Melinda T, Nurhidayah N. 2023. Analysis of seawater quality in Gili Air North Lombok District. Jurnal Pijar MIPA 18 (1): 112-117. DOI: 10.29303/jpm.v18i1.4488.
Meyer CP. 2003. Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol J Linn Soc 79 (3): 401-459. DOI: 10.1046/j.1095-8312.2003.00197.x.
Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W. 2015. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. Roy Soc Open Sci 2 (7): 150088. DOI: 10.1098/rsos.150088.
Moberg F, Folke C. 1999. Ecological goods and services of coral reef ecosystems. Ecol Econ 29 (2): 215-233. DOI: 10.1016/S0921-8009(99)00009-9.
Muenzel D, Bani A, De Brauwer M, Stewart E, Djakiman C, Halwi, Purnama R, Yusif S, Santoso P, Hukom FD, Struebig M, Jompa J, Limmon G, Dumbrell A, Beger M. 2024. Combining environmental DNA and visual surveys can inform conservation planning for coral reefs. Proceed Natl Acad Sci 121 (17): e2307214121. DOI: 10.1073/pnas.2307214121.
Muir PR, Obura DO, Hoeksema BW, Sheppard C, Pichon M, Richards ZT. 2022. Conclusions of low extinc-tion risk for most species of reef-building corals are premature. Nat Ecol Evol 6 (4): 357-358. DOI: 10.1038/s41559-022-01659-5.
Munian K, Ramli FF, Othman N, Mahyudin NAA, Sariyati NH, Abdullah?Fauzi NAF, Haris H, Ilham-Norhakim ML, Abdul?Latiff MAB. 2024. Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short?read nanopore sequencing as a potential biomonitoring tool. Mol Ecol Resour 24 (4): e13936. DOI: 10.1111/1755-0998.13936.
Naputo CFP, Isowa Y, Gerona-Daga ME, Artigas MD, Kajita T, Salmo SG. 2024. Application of eDNA metabarcoding in the assessment of fish biodiversity in Philippine mangroves: Challenges and opportunities. Reg Stud Mar Sci 77: 1036. DOI: 10.1016/j.rsma.2024.103642.
O’Hara CC, Frazier M, Halpern BS. 2021. At-riskmarine biodiversity faces extensive, expanding and inten-sify human impacts. Science 372 (6537): 84-87. DOI: 10.1126/science. abe6731.
Oka SI, Doi H, Miyamoto K, Hanahara N, Sado T, Miya M. 2021. Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation. Environ DNA 3 (1): 55-69. DOI: 10.1002/edn3.132.
Parikh A, Pansu J, Stow A, Warne MSJ, Chivas C, Greenfield P, Boyer F, Simpson S, Smith R, Gruythuysen J, Carlin G, Caulfield N, Viard F, Chariton AA. 2024. Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region. Environ Pollut 349: 123954. DOI: 10.1016/j.envpol.2024.123954.
Parravicini V, Kulbicki M, Bellwood DR, Friedlander AM, Arias-Gonzalez JE, Chabanet P, Floeter SR, Myers R, Vigliola L, D’Agata S, Mouillot D. 2013. Global patterns and predictors of tropical reef fish species richness. Ecography 36 (12): 001-009. DOI: 10.1111/j.1600- 0587.2013. 00291.x.
Pilliod DS, Goldberg CS, Laramie MB, Waits LP. 2013. Application of Environmental DNA for Inventory and Monitoring of Aquatic Species. U.S. Geological Survey, Reston. DOI: 10.3133/fs20123146.
Polanco Fernández A, Marques V, Fopp F, Juhel JB, Borrero?Pérez GH, Cheutin MC, Dejean T, Corredor JDG, Acosta-Chaparro A, Hocde R, Eme D, Maire E, Spescha M, Valentini A, Manel S, Mouillot D, Albouy C, Pellissier L. 2021. Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes. Environ DNA 3 (1): 142-156. DOI: 10.1002/edn3.140
Rourke ML, Fowler AM, Hughes JM, Broadhurst MK, DiBattista JD, Fielder S, Walburn JW, Furlan EM. 2021. Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys. Environ DNA 4 (1): 9-33. DOI: 10.1002/edn3.185.
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.
Sahu A, Kumar N, Singh CP, Singh M. 2022. Environmental DNA (eDNA): Powerful technique for biodiversity conservation. J Nat Conserv 71: 126325. DOI: 10.1016/j.jnc.2022.126325
Sanchez L, Boulanger E, Arnal V, Boissery P, Dalongeville A, Dejean T, Deter J, Guellati N, Holon F, Juhel JB, Lenfant P, Leprieur F, Valentini A, Manel S, Mouillot D. 2022 Ecological indicators based on quantitative eDNA metabarcoding: The case of marine reserves. Ecol Indic 140: 108966. DOI: 10.1016/j.ecolind.2022.108966.
Sara M. 1986. Sessile macrofauna and marine ecosystem. Italy J Zool 53 (4): 329-337. DOI: 10.1080/11250008609355518.
Sembiring A, Al Malik MD, Wahyudi A, Cahyani NKD, Pertiwi NPD, Yusmalinda NLA, Anggoro AW. 2023. Utilizing the Autonomous Reef Monitoring Structure (ARMS) to study the temporal variation of benthic community on coral reef ecosystems in Pemuteran, Bali, Indonesia. Reg Stud Mar Sci 62: 102925. DOI: 10.1016/j.rsma.2023.102925.
Thalinger B, Deiner K, Harper LR, Rees HC, Blackman RC, Sint D, Traugott M, Goldberg CS, Bruce K. 2021. A validation scale to determine the readiness of environmental DNA assays for routine species monitoring. Environ DNA 3: 823-836. DOI: 10.1002/edn3.189.
Veron JE, Devantier LM, Turak E, Green AL, Kininmonth S, Stafford-Smith M, Peterson N. 2009. Delineating the coral triangle. Galaxea 11 (2): 91-100. DOI: 10.3755/galaxea.11.91.
Veron JEN, Devantier LM, Turak E, Green AL, Kininmonth S, Stafford-Smith M, Peterson N. 2011. The Coral Triangle. In: Dubinsky Z, Stambler N (eds). Coral Reefs: An Ecosystem in Transition. Springer, Dordrecht. DOI: 10.1007/978-94-007-0114-4_5.
Whittaker RJ, Araújo MB, Jepson P, Ladle RJ, Watson JE, Willis KJ. 2005. Conservation biogeography: assessment and prospect. Divers Distrib 11 (1): 3-23. DOI: 10.1111/j.1366-9516.2005.00143.x.
Wickham H. 2009. Ggplot2: Elegant Graphics for Data Analysis. Springer, New York. DOI: 10.1007/978-0-387-98141-3.
Widiastuti W, Faiqoh E. 2020. Abundance assessment of indicator bacteria for coral health in the Pemuteran Waters, North Bali, Indonesia. Aquacult Aquarium Conserv Legis 13 (3): 1300-1307.
Wu Y, Colborne SF, Charron MR, Heath DD. 2023. Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates. Environ DNA 5 (1): 73-84. DOI: 10.1002/edn3.359.
Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. 2017. GGTREE: An R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 8 (1): 28-36. DOI: 10.1111/2041-210X.12628.