Skip to main content

Advertisement

SpringerLink
Log in

Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle

  • Published:
Environmental Biology of Fishes Aims and scope Submit manuscript

Abstract

Coral reef fishes perform a range of vital ecosystem functions, and can serve as indicators of ecological stress and resilience. However, many species are not observed when using Underwater Visual Census (UVC) during biomonitoring, and therefore overall biodiversity is often underestimated. Environmental DNA (eDNA) is proposed as an advanced and non-invasive next-generation biomonitoring method for determining the presence of aquatic organisms such as fish. Therefore, this study aimed to assess the community structure of coral fish from three different marine protected area reef zones (utility zone, open access zone, core zone) around Lombok Island using eDNA metabarcoding. Biological community composition, richness, and diversity were evaluated based on reads from mid-column water and sediment samples. A total of 58 species were identified from the eDNA samples using the Multiplex Barcode Research And Visualization Environment (mBRAVE) pipeline. The Shannon–Wiener index (H') showed significantly higher species diversity in the core zone than the utility and open access zones. There was no significant between-zone difference in community structure (ANOSIM, R = 0.11 < 0.25). NMDS analysis using the Bray–Curtis test showed significant between-zone differences in species diversity and abundance (PERMANOVA Adonis Pr (> F) = 0.001, p < 0.05). Based on the high number of fish species detected in this study, eDNA can be recommended as an alternative tool or as a complement to visual survey methods for biological monitoring and diversity assessment of remote reefs, with less stringent requirements in terms of field conditions (e.g. visibility) and taxonomic expertise.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Ahyadi H, Jufri A (2008) Analisis perubahan ekosistem terumbu karang untuk menunjang pengelolaan kawasan TWAL Gili Indah yang berkelanjutan. Laporan kegiatan riset dan pengembangan daerah. Badan Perencanaan Pembangunan Daerah, Nusa Tenggara Barat, Mataram

  • Allen GR, Adrim M (2003) Coral reef fishes of Indonesia. Zoological Studies-Taipei 42(1):1–72

  • Anderson AB, Batista MB, Gibran FZ, Félix-Hackradt FC, Hackradt CW, García-Charton JA, Floeter SR (2019) Habitat use of five key species of reef fish in rocky reef systems of southern Brazil: evidences of MPA effectiveness. Mar Biodivers 49(2):1027–1036

    Article  Google Scholar 

  • Andruszkiewicz EA, Koseff JR, Fringer OB, Ouellette NT, Lowe AB, Edwards CA, Boehm AB (2019) Modeling environmental DNA transport in the coastal ocean using Lagrangian particle tracking. Front Mar Sci 6:1–14. https://doi.org/10.3389/fmars.2019.00477

    Article  Google Scholar 

  • Agardy T, Di Sciara GN, Christie P (2011) Mind the gap: addressing the shortcomings of marine protected areas through large scale marine spatial planning. Mar Pol 2:226–232

    Article  Google Scholar 

  • Arifin MA, Yulianda F (2003) Coral reef diversity in East Lombok, Nusa Tenggara Barat. Jurnal Ikhtiologi 3:1–8. https://doi.org/10.32491/jii.v3i1.268

  • Bakker J, Wangensteen OS, Chapman DD, Boussarie G, Buddo D, Guttridge TL, Hertler H, Mouillot D, Vigliola L, Mariani S (2017) Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact. Sci Rep 1:1–11. https://doi.org/10.1038/s41598-017-17150-2

    Article  CAS  Google Scholar 

  • Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Technol 48:819–1827

    Article  Google Scholar 

  • Barnes MA, Turner CR (2016) The ecology of environmental DNA and implications for conservation genetics. Conserv Gen 17(1):1–17. https://doi.org/10.1007/s10592-015-0775-4

    Article  CAS  Google Scholar 

  • Bell J, Galzin R (1984) Influence of live coral cover on coral-reef fish communities. Mar Ecol Prog Ser 15:265–274. https://doi.org/10.3354/meps015265

    Article  Google Scholar 

  • Blowes SA, Chase JM, Di Franco A, Frid O, Gotelli NJ, Guidetti P, Knight TM, May F, McGlinn DJ, Micheli F, Sala E (2020) Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance. J Appl Ecol 57(3):578–589

    Article  Google Scholar 

  • Bonaldo RM, Pires MM, Guimarães PR, Hoey AS, Hay ME (2017) Small marine protected areas in Fiji provide refuge for reef fish assemblages, feeding groups, and corals. PloS one 12(1): e0170638

  • Cilleros K, Valentini A, Allard L, Dejean T, Etienne R, Grenouillet G, Iribar A, Taberlet P, Vigouroux R, Brosse S (2018) Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes. Mol Ecol Resour 19(1):27–46. https://doi.org/10.1111/1755-0998.12900

    Article  CAS  PubMed  Google Scholar 

  • Chabanet P, Ralambondrainy H, Amanieu M, Faure G, Galzin R (1997) Relationships between coral reef substrata and fish. Coral Reefs 16(2):93–102. https://doi.org/10.1007/s003380050063

    Article  Google Scholar 

  • Cleary DF (2017) Linking fish species traits to environmental conditions in the Jakarta Bay-Pulau Seribu coral reef system. Mar Pollut Bull 122(1-2):259–62

  • Collette BB, Carpenter KE, Polidoro BA, Boustany A, Die DJ, Elfes C, Fox W, Graves J, Nelson R et al (2011) High value and long life-double jeopardy for tunas and billfishes. Sci J 333:291–292. https://doi.org/10.1126/science.1208730

    Article  CAS  Google Scholar 

  • Collins RA, Wangensteen OS, O’Gorman EJ et al (2018) Persistence of environmental DNA in marine systems. Comm Biol 1:1–11. https://doi.org/10.1038/s42003-018-0192-6

    Article  CAS  Google Scholar 

  • Colwell RK, Chao A, Gotelli NJ, Lin S, Mao CX, Chazdon RL, Longino JT (2012) Models and estimators linking rarefaction, extrapolation and comparison of assemblages. J Plant Ecol 5(1):3–21. https://doi.org/10.1093/jpe/rtr044

    Article  Google Scholar 

  • Deiner K, Altermatt F (2014) Transport distance of invertebrate environmental DNA in a natural river. PLoS One 9(2):e88786. https://doi.org/10.1371/journal.pone.0088786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deiner K, Bik HM, Elvira M, Seymour M, Creer S, Bista I, Pfrender ME, Bernatchez L, Altermatt F, Lodge DM et al (2017) Environmental DNA metabarcoding : transforming how we survey animal and plant communities. Mol Ecol 26:5872–5895. https://doi.org/10.1111/mec.14350

    Article  PubMed  Google Scholar 

  • Deiner K, Lopez J, Bourne S et al (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding : the effects of filter material, pore size and extraction method. Metabarcod Metagen 2:1–15. https://doi.org/10.3897/mbmg.2.28963

    Article  Google Scholar 

  • Dell’Anno AD, Corinaldesi C (2004) Degradation and turnover of extracellular DNA in marine sediments : ecological and methodological considerations. Appl Environ Microbiol 70(7):4384–4386. https://doi.org/10.1128/AEM.70.7.4384

    Article  PubMed  PubMed Central  Google Scholar 

  • Dell’Anno A, Danovaro R (2005) Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 309(5744):2179

    Article  CAS  Google Scholar 

  • Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C (2011) Persistence of environmental DNA in freshwater ecosystems. PloS One 6:8–11. https://doi.org/10.1371/journal.pone.0023398

    Article  CAS  Google Scholar 

  • Dewi CSU, Sukandar HCJ (2018) Karang dan Ikan Terumbu Pulau Bawean. UB Press, Malang (ID)

    Google Scholar 

  • DiBattista JD, Coker DJ, Sinclair-Taylor TH, Stat M, Berumen ML, Bunce M (2017) Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea. Coral Reefs 36(4):1245–1252. https://doi.org/10.1007/s00338-017-1618-1

    Article  Google Scholar 

  • English S, Wilkinson C, Baker V (1997) Survey Manual for Tropical Marine Resources. Australia Institute of Marine Science, Townsville (AU)

  • Eschmeyer WN, Fricke R, Fong JD, Polack DA (2010) Marine fish diversity: history of knowledge and discovery (Pisces). Zootaxa 2525:19–50. https://doi.org/10.11646/zootaxa.2525.1.2

  • Friedlander AM, Brown E, Monaco ME (2007) Defining reef fish habitat utilization patterns in Hawaii: comparisons between marine protected areas and areas open to fishing. Mar Ecol Prog Ser 6(351):221–233

    Article  Google Scholar 

  • Galzin R, Planes S, Dufour V, Salvat B (1994) Variation in diversity of coral reef fish between French Polynesian atolls. Coral Reefs 13(3):175–180. https://doi.org/10.1007/BF00301196

    Article  Google Scholar 

  • Giakoumi S, McGowan J, Mills M, Beger M, Bustamante RH, Charles A, Christie P, Fox M, Garcia-Borboroglu P, Gelcich S, Guidetti P (2018) Revisiting “success” and “failure” of marine protected areas: a conservation scientist perspective. Front Mar Sci 5:p223

  • Gimmler A, Korn R, Vargas C De, Audic S, Stoeck T (2016) The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Nature 6:33555. https://doi.org/10.1038/srep33555

  • Gilbey J, Carvalho G, Castilho R, Coscia I, Coulson MW, Dahle G, Derycke S, Francisco SM, Helyar SJ, Johansen T, Junge C (2021) Life in a drop: sampling environmental DNA for marine fishery management and ecosystem monitoring. Mar Pol 124:104331. https://doi.org/10.1016/j.marpol.2020.104331

  • Goldberg CS, Pilliod DS, Arkle RS, Waits LP (2011) Molecular detection of vertebrates in stream water: a demonstration using rocky mountain tailed frogs and Idaho giant salamanders. PLoS one 6(7): https://doi.org/10.1371/journal.pone.0022746

  • Goldberg C, Strickler K (2017) eDNA Protocol Sample Collection. Adapted from Protocol Version 04/12/2012 (D.S. Pilliod, R.S. Arkle, and M.B. Laramie) USGS Snake River Field Station. Washington State University. https://s3.wp.wsu.edu/uploads/sites/686/2017/01/WSU-eDNA-sampling-protocol-Jan2017.pdf. Accessed 30 May 2017

  • Green AL (1996) Spatial, temporal and ontogenetic patterns of habitat use by coral reef fishes (Family Labridae). Mar Ecol Prog Ser 133:1–1

  • Green HC, Shanks OC, Sivaganesan M, Haugland RA, Field KG (2011) Differential decay of human faecal Bacteroides in marine and freshwater. Environ Microbiol 13:3235–3249

    Article  Google Scholar 

  • Hadi S, Andayani N, Muttaqin E, Simeon BM, Ichsan M, Subhan B, Madduppa H (2020) Genetic connectivity of the scalloped hammerhead shark Sphyrna lewini across Indonesia and the Western Indian Ocean. PLoS One 0230763:1–14. https://doi.org/10.1371/journal.pone.0230763

    Article  CAS  Google Scholar 

  • Hansen BK, Bekkevold D, Clausen LW, Nielsen EE (2018) The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries. Fish Fish 19(5):1–18. https://doi.org/10.1111/faf.12286

    Article  Google Scholar 

  • Huhn M, Madduppa HH, Khair M, Sabrian A, Irawati Y, Anggraini NP, Wilkinson SP, Simpson T, Iwasaki K, Setiamarga DH, Dias PJ (2019) Keeping up with introduced marine species at a remote biodiversity hotspot: awareness, training and collaboration across different sectors is key. Biol Inv. https://doi.org/10.1007/s10530-019-02126-2

  • Hutchings JA (2000) Collapse and recovery of marine fish. Nature 406:882–885. https://doi.org/10.1038/35022565

    Article  CAS  PubMed  Google Scholar 

  • Jackson JBC, Kirby MX, Berger WH, Bjorndal KA, Botsford LW, Bourque BJ, Bradbury RH, Cooke R, Erlandson J, Warner RR et al (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 293(5530):629–637. https://doi.org/10.1126/science.1059199

    Article  CAS  PubMed  Google Scholar 

  • Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4(2):150–157. https://doi.org/10.1111/j.1755-263X.2010.00158.x

    Article  Google Scholar 

  • Jerde CL, Wilson EA, Dressler TL (2019) Measuring global fish species richness with eDNA metabarcoding. Mol Ecol 19:19–22. https://doi.org/10.1111/1755-0998.12929

    Article  Google Scholar 

  • Kelly RP, Port JA, Yamahara KM, Martone RG, Lowell N, Thomsen PF, Mach ME, Bennett M, Prahler E, Caldwell MR et al (2014) Harnessing DNA to improve environmental management. Science 344:1455–1456. https://doi.org/10.1126/science.1251156

    Article  CAS  PubMed  Google Scholar 

  • Kruschel C, Schultz ST, Bakran-Petricioli T, Petricioli D (2012) Comparing predator abundance and fish diversity in MPA sites (Kornati NP, Croatia) and adjacent sites exploited by fisheries. Croatian J Fish: 65–78

  • Lacoursière-Roussel A, Howland K, Normandeau E, Grey EK, Archambault P, Deiner K, Lodge DM, Hernandez C, Leduc N, Bernatchez L (2018) eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol 8:7763–7777. https://doi.org/10.1002/ece3.4213

    Article  PubMed  PubMed Central  Google Scholar 

  • Laramie MB, Pilliod DS, Goldberg CS (2015) Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol Conserv 183:29–37. https://doi.org/10.1016/j.biocon.2014.11.025

    Article  Google Scholar 

  • Leduc N, Lacoursière-Roussel A, Howland KL, Archambault P, Sevellec M, Normandeau E, Dispas A, Winkler G, McKindsey CW, Simard N, Bernatchez L (2019) Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity. Environ DNA 1:1–17. https://doi.org/10.1002/edn3.35

    Article  Google Scholar 

  • 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. https://doi.org/10.1186/1742-9994-10-34

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leray M, Haenel Q, Bourlat SJ (2016) Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina Miseq: the adapter ligation method. Mar Genom 1452(14):1–10. https://doi.org/10.1007/978-1-4939-3774-5

    Article  Google Scholar 

  • Levy-Booth DJ, Campbell RG, Gulden RH, Hart MM, Powell JR, Klironomos JN, Pauls KP, Swanton CJ, Trevors JT, Dunfield KE (2007) Cycling of extracellular DNA in the soil environment. Soil Biol Biochem 39:2977–2991. https://doi.org/10.1016/j.soilbio.2007.06.020

    Article  CAS  Google Scholar 

  • Li J, Handley LJL, Harper LR, Brys R, Watson HV, Di C, Xiang M, Bernd Z (2019) Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding. Environ DNA 1:238–250. https://doi.org/10.1002/edn3.24

    Article  Google Scholar 

  • Li Y, Evans NT, Renshaw MA, Jerde CL, Olds BP, Shogren AJ, Pfrender ME (2018) Estimating fish alpha and beta diversity along a small stream with environmental DNA metabarcoding. Metabarcod Metagen 2:e24262. https://doi.org/10.3897/mbmg.2.24262

  • Lodge DM, Turner CR, Jerde CL, Barnes MA, Chadderton L, Egan SP, Feder JL, Mahon AR, Pfrender ME (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol 21:2555–2558. https://doi.org/10.1111/j.1365-294X.2012.05600.x

    Article  PubMed  PubMed Central  Google Scholar 

  • Madduppa H, Ayuningtyas RU, Subhan B, Arafat DP (2016) Exploited but unevaluated: DNA barcoding reveals skates and stingrays (Chordata, Chondrichthyes) species landed in the Indonesian fish market. IJMS 21:77–84. https://doi.org/10.14710/ik.ijms.0.0

    Article  Google Scholar 

  • Madduppa HH, Ferse SCA, Aktani U, Palm HW (2012) Seasonal trends and fish-habitat associations around Pari Island, Indonesia: setting a baseline for environmental monitoring. Environ Biol Fish 95(3):383–398

    Article  Google Scholar 

  • Madduppa HH, Subhan B, Suparyani E, Siregar AM, Arafat D, Tarigan SA, Alimuddin KD, Rahmawati F, Bramandito A (2013) Â Dynamics of fish diversity across an environmental gradient in the Seribu Islands reefs off Jakarta. Biodiversitas 14:17–24

    Google Scholar 

  • Madduppa HH, von Juterzenka K, Syakir M, Kochzius M (2014) Socio-economy of marine ornamental fishery and its impact on the population structure of the clown anemonefish Amphiprion ocellaris and its host anemones in Spermonde Archipelago, Indonesia. Ocean Coast Manag 100:41–50

    Article  Google Scholar 

  • McCoy CM, Dromard CR, Turner JR (2010) An evaluation of Grand Cayman MPA performance: a comparative study of coral reef fish communities. Proc 62nd Gulf Caribb Fish Ins 337–345

  • McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS one. 8:e61217. https://doi.org/10.1371/journal.pone.0061217

  • Meekan MG, Steven AD, Fortin MJ (1995) Spatial patterns in the distribution of damselfishes on a fringing coral reef. Coral Reefs 14(3):151–61

  • Meyer CP (2003) Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biol J Linn Soc 79:401–459

    Article  Google Scholar 

  • Mirimin L, Hickey A, Barrett D, et al (2020) Environmental DNA detection of Arctic char (Salvelinus alpinus) in Irish lakes : development and application of a species-specific molecular assay. Environ DNA 221–233. https://doi.org/10.1002/edn3.60

  • Moore AM, Jompa J, Tassaka ACMAR, Yasir I, Ndobe S, Umar W, Gold Z, Barber PH (2021) Sharks and rays (Chondrichthyes) around Banggai Island, Banggai MPA, Indonesia: biodiversity data from an environmental DNA pilot study. AACL Bioflux 14:725–745

    Google Scholar 

  • Muniaha H, Andi IN, Ramadhani (2016) Studi kelimpahan ikan karang berdasarkan kondisi terumbu karang di Desa Tanjung Tiram Kabupaten Konawe Selatan. Jurnal Manajemen Sumber Daya Perairan 2(1): 9-19

  • Murakami H, Yoon S, Kasai A, et al (2019) Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fish Sci https://doi.org/10.1007/s12562-018-1282-6

  • Mustaruddin LRTS, Pandu S (2013) Penurunan hasil tangkap ikan karang akibat kegiatan industri pariwisata di kawasan Gili Sulat dan Gili Lawang, Kabupaten Lombok Timur. Jurnal Ilmu Dan Teknologi Kelautan Tropis 2(2337):113–120

    Google Scholar 

  • Nguyen BN, Shen EW, Seemann J, Correa AM, O’Donnell JL, Altieri AH, Knowlton N, Crandall KA, Egan SP, McMillan WO, Leray M (2020) Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape. Sci Rep 10(1):1–4

    Article  Google Scholar 

  • Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MH, Wagner H, Oksanen MJ (2013) Package ‘vegan.’ Comm Ecol Pack 10:631–637

    Google Scholar 

  • Parks JE, Pomeroy RS, Philibotte J (2006) Experiences and lessons learned from evaluating the management effectiveness of marine protected areas in Southeast Asia and the Pacific Islands. Invited Paper Presentation from the CBD/IUCN International Workshop for Better Management of Protected Areas, Jeju Island, Korea

  • Pauly D, Christensen V, Guénette S, Pitcher TJ, Sumaila UR, Walters CJ, Zeller D (2002) Towards sustainability in world fisheries. Nature 418(6898):689–695. https://doi.org/10.1038/nature01017

    Article  CAS  PubMed  Google Scholar 

  • Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C (2015) Open science resources for the discovery and analysis of Tara Oceans data. Nature 2:150023. https://doi.org/10.1038/sdata.2015.23

  • Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G, Nannipieri P (2009) Extracellular DNA in soil and sediment : fate and ecological relevance. Biol Fertil Soils 219–235. https://doi.org/10.1007/s00374-008-0345-8

  • Prato G, Thiriet P, Di Franco A, Francour P (2017) Enhancing fish Underwater Visual Census to move forward assessment of fish assemblages: An application in three mediterranean marine protected areas. PLoS One 12(6):e0178511

  • R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/. Accessed 28 Sept 2017

  • Ramírez-Ortiz G, Reyes-Bonilla H, Balart EF, Olivier D, Huato-Soberanis L, Micheli F, Edgar GJ (2020) Reduced fish diversity despite increased fish biomass in a Gulf of California Marine Protected Area. Peer J 8: p.e8885

  • Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life datasystem. Mol Ecol 7:355–364

    Article  CAS  Google Scholar 

  • Sard NM, Herbst SJ, Nathan L, Uhrig G, Kanefsky J, Robinson JD, Scribner KT (2019) Comparison of fish detections, community diversity , and relative abundance using environmental DNA metabarcoding and traditional gears. Environ DNA 368–384. https://doi.org/10.1002/edn3.38

  • Scianna C, Niccolini F, Gaines SD, Guidetti P (2015) ‘Organization Science’: a new prospective to assess marine protected areas effectiveness. Ocean Coast Manag 116:443–448

    Article  Google Scholar 

  • Searle D, Sible E, Cooper A, Putonti C (2016) 18s rDNA dataset profiling microeukaryotic populations within Chicago area nearshore waters. Data in Brief 6:526–529

    Article  Google Scholar 

  • Setiawan F, Muttaqin A, Tarigan SA, Sabil A, Pinkan J (2017) Pemutihan karang akibat pemanasan global tahun 2016 terhadap ekosistem terumbu karang: studi kasus di TWP Gili Matra (Gili Air, Gili Meno dan Gili Trawangan) Provinsi NTB. J Fish Mar Sci 1:39–54. https://doi.org/10.21776/ub.jfmr.2017.001.02.1

  • Shaw JLA, Clarke LJ, Wedderburn SD, Barnes TC, Weyrich LS, Cooper A (2016) Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol Conserv 197:131–138. https://doi.org/10.1016/j.biocon.2016.03.010

    Article  Google Scholar 

  • Shelton AO, O’Donnell JL, Samhouri JF, Lowell N, Williams GD, Kelly RP (2016) A framework for inferring biological communities from environmental DNA. Ecol Appl 26:1645–1659

    Article  Google Scholar 

  • Sigsgaard EE, Broman I, Henrik N, Anders M, Steen K, Knudsen W, Xing Y, Hejl T, Hansen H, Rask P, et al (2017) Seawater environmental DNA reflects seasonality of a coastal fish community. Mar Biol. https://doi.org/10.1007/s00227-017-3147-4

  • Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Mol Ecol 21(8):1789–1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x

    Article  CAS  PubMed  Google Scholar 

  • Taberlet P, Bonin A, Lucie Z, Coissac E (2018) Environmental DNA: For Biodiversity Research and Monitoring. Oxford Press, UK

    Book  Google Scholar 

  • Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS one 8(2):e56584. https://doi.org/10.1371/journal.pone.0056584

  • Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012) Detection of a diverse marine fish fauna using environmental dna from seawater samples. PLoS One 7(8):1–9. https://doi.org/10.1371/journal.pone.0041732

    Article  CAS  Google Scholar 

  • Thomsen PF, Willerslev E (2015) Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18. https://doi.org/10.1016/j.biocon.2014.11.019

    Article  Google Scholar 

  • Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA, Willerslev E (2016) Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS One 11:e0165252. 10.1371/ journal.pone.0165252

  • Turner CR, Uy KL, Everhart RC (2014) Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biol Conserv 183:93–102. https://doi.org/10.1016/j.biocon.2014.11.017

    Article  Google Scholar 

  • Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nature 6(11):805–814. https://doi.org/10.1038/nrg1709

    Article  CAS  Google Scholar 

  • Varkey D, Ainsworth CH, Pitcher TJ (2012) Modelling reef fish population responses to fisheries restrictions in marine protected areas in the coral triangle. J Mar Biol https://doi.org/10.1155/2012/721483

  • Verma D, Satyanarayana T (2011) An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries. Appl Biochem Biotechnol 165:454–464. https://doi.org/10.1007/s12010-011-9264-5

    Article  CAS  PubMed  Google Scholar 

  • Wahyu TAP, Mubarak H, Rolian DL, Pardede HG, Safitri DR, Putri KZ, Kenedi MI, Shanti AG, Afrizal SN, Santoso NL, Maharani K (2018) Associated of Coral Reef with reef fish in Northern and Southern Gili Air Island and Gili Trawangan Island Lombok. SCiFiMaS 47: p04003 EDP Sciences

  • Wahyudewantoro G (2018) The fish diversity of mangrove waters in Lombok Island, West Nusa Tenggara Indonesia. Biodivers J Biol Divers 19(1):71–76

    Article  Google Scholar 

  • Wickham H (2009) ggplot2: Elegant graphics for data analysis. Springer, New York

    Book  Google Scholar 

  • Zhang S, Zhao J, Yao M (2020) A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods Ecol Evol 11(12):1609–1625

    Article  Google Scholar 

  • Zubcoff J (2012) ANOSIM ANalysis Of SIMilarities. J Nat Lang Process 18(4):367–381

Download references

Acknowledgements

This research was supported by USAID through the Sustainable Higher Education Research Alliances (SHERA) Program – Centre for Collaborative Research on Animal Biotechnology and Coral Reef Fisheries (CCR ANBIOCORE).

Author information

Authors and Affiliations

  1. Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, IPB University, Bogor, 16680, Indonesia

    Ester Restiana Endang Gelis, Beginer Subhan & Hawis Madduppa

  2. Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, IPB University, Bogor, 16680, Indonesia

    M. Mukhlis Kamal

  3. Department of Biology Education, Faculty of Education, Universitas Mataram, Jl. Majapahit 62, Mataram, 83125, Indonesia

    Imam Bachtiar

  4. Oceanogen Environmental Biotechnology Laboklinikum, Bogor, 16112, Indonesia

    Lalu M. Iqbal Sani & Hawis Madduppa

Authors
  1. Ester Restiana Endang Gelis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Mukhlis Kamal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Beginer Subhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Imam Bachtiar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lalu M. Iqbal Sani
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hawis Madduppa
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Ester Restiana and Hawis Madduppa conceived the research idea; Ester Restiana, Hawis Madduppa, Beginer Subhan, and Imam Bachtiar collected and processed eDNA samples; Ester Restiana performed laboratory work and data analysis; Ester Restiana and Lalu M Iqbal Sani produced the graphics; Hawis Madduppa and M Mukhlis Kamal led the writing of the manuscript then edited and improved the manuscript together with Lalu M Iqbal Sani and Ester Restina.

Corresponding author

Correspondence to Hawis Madduppa.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 20 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gelis, E.R.E., Kamal, M.M., Subhan, B. et al. Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle. Environ Biol Fish 104, 887–903 (2021). https://doi.org/10.1007/s10641-021-01118-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10641-021-01118-3

Keywords

Search

Navigation