Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
https://orcid.org/0000-0002-2566-1636
Abstract
Abstract. Andriyono S, Jobaidul Alam Md, Kim HW. 2019. Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia. Biodiversitas 20: 3772-3781. Molecular identification of species is now fast growing and currently widely applied method in the diversity estimation of aquatic biota; even though morphological identification is still carried out. The molecular approach is beneficial complementing on regular surveys, e.g. use of nets, traps, fishing rods, and even with poisons. In this study, the eDNA metabarcoding was applied to water samples around the Pondok Dadap fish landing station, Indonesia to determine the diversity of fish around the waters and also to identify marine fish landed in this area. Molecular identification was carried out on fish samples obtained from the fish market improved GenBank database on COI and ITS. While, seawater samples were carried out by using the next-generation sequencing (NGS) platform to obtain the eDNA metabarcoding data for the first time. Molecular identification obtained 34 species (68 sequences of COI and ITS regions) belonging to 28 genera, 18 families, 4 orders, while the eDNA metabarcoding approach identified 53 marine fish species by using the MiFish pipeline representing 38 genera, 27 families, and 7 orders. From the present study, we can able to estimated fish diversity by eDNA metabarcoding, and this finding will be helpful for baseline data preparation for future effective management of resources in this area.
##plugins.themes.bootstrap3.article.details##
References
Anderson-Carpenter LL, McLachlan JS, Jackson ST, Kuch M, Lumibao CY, Poinar HN. 2011. Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics. BMC evolutionary biology. 11(1):30-45.
Aziz NMA, Esa Y, Arshad A. 2016. DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene. Journal of environmental biology. 37(4 Spec No):725-733.
Badotti F, de Oliveira FS, Garcia CF, Vaz ABM, Fonseca PLC, Nahum LA, Oliveira G, Góes-Neto A. 2017. Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC microbiology. 17(1):42.
Baldwin CC, Mounts JH, Smith DG, Weigt LA. 2009. Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa. 2008:1-22.
Das S, Deb B. 2015. DNA barcoding of fungi using Ribosomal ITS Marker for genetic diversity analysis: a review. Int J Pure Appl Biosci. 3:160-167.
de Vargas C, Bonzon M, Rees NW, Pawlowski J, Zaninetti L. 2002. A molecular approach to biodiversity and biogeography in the planktonic foraminifer Globigerinella siphonifera (d’Orbigny). Marine Micropaleontology. 45(2):101-116.
Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C. 2012. Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of applied ecology. 49(4):953-959.
Douglas WY, Ji Y, Emerson BC, Wang X, Ye C, Yang C, Ding Z. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution. 3(4):613-623.
Faizah R, Aisayah A. 2017. Komposisi Jenis dan Distribusi Ukuran Ikan Pelagis Besar Hasil Tangkapan Pancing Ulur di Sendang Biru, Jawa Timur. Bawal Widya Riset Perikanan Tangkap. 3(6):377-385.
Ferrol-Schulte D, Gorris P, Baitoningsih W, Adhuri DS, Ferse SC. 2015. Coastal livelihood vulnerability to marine resource degradation: A review of the Indonesian national coastal and marine policy framework. Marine Policy. 52:163-171.
Firdaus M, Witomo CM. 2014. Analisis Tingkat Kesejahteraan dan Ketimpangan Pendapatan Rumah Tangga Nelayan Pelagis Besar di Sendang Biru, Kabupaten Malang, Jawa Timur. Jurnal Sosial Ekonomi Kelautan dan Perikanan. 9(2):155-168.
Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MTP. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PloS one. 7(8):e41781.
Giusti A, Armani A, Sotelo CG. 2017. Advances in the analysis of complex food matrices: Species identification in surimi-based products using Next Generation Sequencing technologies. PloS one. 12(10):1-18.
Handy SM, Deeds JR, Ivanova NV, Hebert PD, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF. 2011. A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. Journal of AOAC International. 94(1):201-210.
Hermawan D. 2006. Prospektif Pengembangan Kawasan Pesisir Sendang Biru untuk Industri Perikanan Terpadu. Prospektif Pengembangan Kawasan Pesisir Sendang Biru. 13(2).
Ikeda K, Doi H, Tanaka K, Kawai T, Negishi JN. 2016. Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams. Conservation Genetics Resources. 8(3):231-234.
Jaafar TNAM, Taylor MI, Nor SAM, de Bruyn M, Carvalho GR. 2012. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One. 7(11):e49623.
Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011. “Sight?unseen” detection of rare aquatic species using environmental DNA. Conservation Letters. 4(2):150-157.
Karp A, Edwards KJ, Bruford M, Funk S, Vosman B, Morgante M, Seberg O, Kremer A, Boursot P, Arctander P. 1997. Molecular technologies for biodiversity evaluation: opportunities and challenges. Nature biotechnology. 15(7):625.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution. 33(7):1870-1874.
Lakra W, Verma M, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh K, Ward RD, Hebert P. 2011. DNA barcoding Indian marine fishes. Molecular Ecology Resources. 11(1):60-71.
Laramie MB, Pilliod DS, Goldberg CS. 2015. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biological Conservation. 183:29-37.
Luthfi OM, Pujarahayu P, Wahyudiarto A, Fakri SR, Sofyan M, Ramadhan F, Murian S, Tovani I, Mahmud M, Adi D. 2016. Biodiversitas dan Populasi Ikan Karang Di Perairan Selat Sempu Sendang Biru Kabupaten Malang Jawa Timur. Jurnal Kelautan: Indonesian Journal of Marine Science and Technology. 9(1):43-49.
Matzen da Silva J, Creer S, dos Santos A, Costa A, Cunha M. 2011. Systematic and Evolutionary Insights Derived from mtDNA COI Barcode.
Meyer CP, Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS biology. 3(12):e422.
Pepe T, Trotta M, Di Marco I, Anastasio A, Bautista JM, Cortesi ML. 2007. Fish species identification in surimi-based products. Journal of agricultural and food chemistry. 55(9):3681-3685.
Piggott MP. 2016. Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish. Ecology and evolution. 6(9):2739-2750.
Pilliod DS, Goldberg CS, Laramie MB, Waits LP. 2013. Application of environmental DNA for inventory and monitoring of aquatic species. US Department of the Interior, US Geological Survey.
Rees HC, Maddison BC, Middleditch DJ, Patmore JR, Gough KC. 2014. The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology. 51(5):1450-1459.
Roussel JM, Paillisson JM, Treguier A, Petit E. 2015. The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology. 52(4):823-826.
Smart AS, Weeks AR, Rooyen AR, Moore A, McCarthy MA, Tingley R. 2016. Assessing the cost?efficiency of environmental DNA sampling. Methods in Ecology and Evolution. 7(11):1291-1298.
Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH. 2012. Environmental DNA. Molecular ecology. 21(8):1789-1793.
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.
Teletchea F. 2009. Molecular identification methods of fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries. 19(3):265.
Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E. 2012. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular ecology. 21(11):2565-2573.
Udayasuriyan R, Kalpana R. 2018. DNA Barcoding of Freshwater Prawn Species of Two Genera Macrobrachium and Caridina Using mt-COI Gene. Journal of Genes and Proteins. 2017.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B: Biological Sciences. 360(1462):1847-1857.
Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK. 2013. Robust detection of rare species using environmental DNA: the importance of primer specificity. PloS one. 8(3):e59520.
Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science. 300(5620):791-795.
Willerslev E, Hansen AJ, Poinar HN. 2004. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology & Evolution. 19(3):141-147.
Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific reports. 7:40368.
Aziz NMA, Esa Y, Arshad A. 2016. DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene. Journal of environmental biology. 37(4 Spec No):725-733.
Badotti F, de Oliveira FS, Garcia CF, Vaz ABM, Fonseca PLC, Nahum LA, Oliveira G, Góes-Neto A. 2017. Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC microbiology. 17(1):42.
Baldwin CC, Mounts JH, Smith DG, Weigt LA. 2009. Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa. 2008:1-22.
Das S, Deb B. 2015. DNA barcoding of fungi using Ribosomal ITS Marker for genetic diversity analysis: a review. Int J Pure Appl Biosci. 3:160-167.
de Vargas C, Bonzon M, Rees NW, Pawlowski J, Zaninetti L. 2002. A molecular approach to biodiversity and biogeography in the planktonic foraminifer Globigerinella siphonifera (d’Orbigny). Marine Micropaleontology. 45(2):101-116.
Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C. 2012. Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of applied ecology. 49(4):953-959.
Douglas WY, Ji Y, Emerson BC, Wang X, Ye C, Yang C, Ding Z. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution. 3(4):613-623.
Faizah R, Aisayah A. 2017. Komposisi Jenis dan Distribusi Ukuran Ikan Pelagis Besar Hasil Tangkapan Pancing Ulur di Sendang Biru, Jawa Timur. Bawal Widya Riset Perikanan Tangkap. 3(6):377-385.
Ferrol-Schulte D, Gorris P, Baitoningsih W, Adhuri DS, Ferse SC. 2015. Coastal livelihood vulnerability to marine resource degradation: A review of the Indonesian national coastal and marine policy framework. Marine Policy. 52:163-171.
Firdaus M, Witomo CM. 2014. Analisis Tingkat Kesejahteraan dan Ketimpangan Pendapatan Rumah Tangga Nelayan Pelagis Besar di Sendang Biru, Kabupaten Malang, Jawa Timur. Jurnal Sosial Ekonomi Kelautan dan Perikanan. 9(2):155-168.
Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MTP. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PloS one. 7(8):e41781.
Giusti A, Armani A, Sotelo CG. 2017. Advances in the analysis of complex food matrices: Species identification in surimi-based products using Next Generation Sequencing technologies. PloS one. 12(10):1-18.
Handy SM, Deeds JR, Ivanova NV, Hebert PD, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF. 2011. A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. Journal of AOAC International. 94(1):201-210.
Hermawan D. 2006. Prospektif Pengembangan Kawasan Pesisir Sendang Biru untuk Industri Perikanan Terpadu. Prospektif Pengembangan Kawasan Pesisir Sendang Biru. 13(2).
Ikeda K, Doi H, Tanaka K, Kawai T, Negishi JN. 2016. Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams. Conservation Genetics Resources. 8(3):231-234.
Jaafar TNAM, Taylor MI, Nor SAM, de Bruyn M, Carvalho GR. 2012. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One. 7(11):e49623.
Jerde CL, Mahon AR, Chadderton WL, Lodge DM. 2011. “Sight?unseen” detection of rare aquatic species using environmental DNA. Conservation Letters. 4(2):150-157.
Karp A, Edwards KJ, Bruford M, Funk S, Vosman B, Morgante M, Seberg O, Kremer A, Boursot P, Arctander P. 1997. Molecular technologies for biodiversity evaluation: opportunities and challenges. Nature biotechnology. 15(7):625.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution. 33(7):1870-1874.
Lakra W, Verma M, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh K, Ward RD, Hebert P. 2011. DNA barcoding Indian marine fishes. Molecular Ecology Resources. 11(1):60-71.
Laramie MB, Pilliod DS, Goldberg CS. 2015. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biological Conservation. 183:29-37.
Luthfi OM, Pujarahayu P, Wahyudiarto A, Fakri SR, Sofyan M, Ramadhan F, Murian S, Tovani I, Mahmud M, Adi D. 2016. Biodiversitas dan Populasi Ikan Karang Di Perairan Selat Sempu Sendang Biru Kabupaten Malang Jawa Timur. Jurnal Kelautan: Indonesian Journal of Marine Science and Technology. 9(1):43-49.
Matzen da Silva J, Creer S, dos Santos A, Costa A, Cunha M. 2011. Systematic and Evolutionary Insights Derived from mtDNA COI Barcode.
Meyer CP, Paulay G. 2005. DNA barcoding: error rates based on comprehensive sampling. PLoS biology. 3(12):e422.
Pepe T, Trotta M, Di Marco I, Anastasio A, Bautista JM, Cortesi ML. 2007. Fish species identification in surimi-based products. Journal of agricultural and food chemistry. 55(9):3681-3685.
Piggott MP. 2016. Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish. Ecology and evolution. 6(9):2739-2750.
Pilliod DS, Goldberg CS, Laramie MB, Waits LP. 2013. Application of environmental DNA for inventory and monitoring of aquatic species. US Department of the Interior, US Geological Survey.
Rees HC, Maddison BC, Middleditch DJ, Patmore JR, Gough KC. 2014. The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology. 51(5):1450-1459.
Roussel JM, Paillisson JM, Treguier A, Petit E. 2015. The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology. 52(4):823-826.
Smart AS, Weeks AR, Rooyen AR, Moore A, McCarthy MA, Tingley R. 2016. Assessing the cost?efficiency of environmental DNA sampling. Methods in Ecology and Evolution. 7(11):1291-1298.
Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH. 2012. Environmental DNA. Molecular ecology. 21(8):1789-1793.
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.
Teletchea F. 2009. Molecular identification methods of fish species: reassessment and possible applications. Reviews in Fish Biology and Fisheries. 19(3):265.
Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E. 2012. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular ecology. 21(11):2565-2573.
Udayasuriyan R, Kalpana R. 2018. DNA Barcoding of Freshwater Prawn Species of Two Genera Macrobrachium and Caridina Using mt-COI Gene. Journal of Genes and Proteins. 2017.
Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B: Biological Sciences. 360(1462):1847-1857.
Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK. 2013. Robust detection of rare species using environmental DNA: the importance of primer specificity. PloS one. 8(3):e59520.
Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science. 300(5620):791-795.
Willerslev E, Hansen AJ, Poinar HN. 2004. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology & Evolution. 19(3):141-147.
Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Scientific reports. 7:40368.
Most read articles by the same author(s)
- JURNIATI, DIANA ARFIATI, SAPTO ANDRIYONO, ASUS MAIZAR SURYANTO HERTIKA, ANDI KURNIAWAN, WENDY ALEXANDER TANOD, The morphological characters and DNA barcoding identification of sweet river prawn Macrobrachium esculentum (Thallwitz, 1891) from Rongkong watershed of South Sulawesi, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 1 (2021)
- SAPTO ANDRIYONO, MD. JOBAIDUL ALAM, LAKSMI SULMARTIWI, A. SHOFY MUBARAK, HERU PRAMONO, SUCIYONO, GDE RAKA ANGGA KARTIKA, ALFI HERMAWATI WASKITA SARI, SINAR PAGI SEKTIANA, The diversity of Carangidae (Carangiformes) was revealed by DNA barcoding collected from the traditional fish markets in Java and Bali, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 6 (2022)
- SINAR PAGI SEKTIANA, ANNUR AHADI ABDILLAH, MD. JOBAIDUL ALAM, WAHYU ISRONI, NINA NURMALIA DEWI, HYUN WOO KIM, SAPTO ANDRIYONO, Diversity of the Tabuhan Island coral reef fish revealed by DNA barcoding and implication on conservation strategy in Banyuwangi, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 9 (2022)
- BAYU PRANATA, ARADEA BUJANA KUSUMA, VERA SABARIAH, HYUN WOO KIM, SAPTO ANDRIYONO, Environmental DNA metabarcoding reveals biodiversity marine fish diversity of a small island at Manokwari District, West Papua, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 11 (2022)
- SAPTO ANDRIYONO, NITA RUKMINASARI, ANDI ALIAH HIDAYANI, INDRA JUNAIDI ZAKARIA, MD. JOBAIDUL ALAM, HYUN-WOO KIM, Diversity of dinoflagellate cysts isolated from estuarine sediments of the Bengawan Solo and Brantas rivers, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 24 No. 2 (2023)