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Implementation of 16S rRNA Gene for Fish and Shrimp Barcoding in Mangrove Ecosystems in North Sumatra and Aceh, Indonesia
Corresponding Author(s) : Mohammad Basyuni
Jurnal Ilmiah Perikanan dan Kelautan,
Vol. 15 No. 1 (2023): JURNAL ILMIAH PERIKANAN DAN KELAUTAN
Abstract
Highlight Research
- The genetic diversity of fish and shrimp from mangrove habitats was relatively substantial, with a heterozygosity of 0.926 and the exception of Langsa samples.
- AMOVA revealed that the diversity among individuals in the populations were higher compared to those within individuals.
- DNA barcode in mangroves is useful in developing mangrove conservation and restoration initiatives
Abstract
Fish and shrimp are among the species that are vulnerable to high level of disturbance in mangrove ecosystem. This study aimed to investigate the implementation of 16S rRNA gene for fish and shrimp barcoding in mangrove ecosystems in North Sumatra and Aceh, Indonesia. 50 samples fresh fish and shrimp were collected from five mangrove ecosystems in North Sumatra, namely Belawan, Lubuk Kertang, Percut Sei Tuan, and Pulau Sembilan and Langsa of Aceh for DNA extraction process. The research was divided into four activities: sample collection, DNA isolation, PCR amplification, and data analysis. DNA was extracted using kit extraction (kit Reliaprep gDNA Tissue Miniprep System) and with PCR amplification. Genetic parameters were analyzed using Gen Alex 6.51 software and the relationship between sites was examined using the MVSP 3.22. The genetic diversity of fish and shrimp from mangrove habitats was relatively substantial, according to the findings, with a heterozygosity of 0.926, with the exception of Langsa samples, which were only identified in subclass A1. Genetic relationship between sites revealed that all samples clustered into two branches and were randomly dispersed within each site. This work confirmed the 16S rRNA gene worked for fish and shrimp barcoding in mangrove ecosystems, North Sumatra and Aceh, Indonesia and our findings are expected to be useful in developing mangrove conservation and restoration initiatives.
Keywords
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- Almasi, M., Milow, P., & Zakaria, R. M. (2019). The study of participatory mangrove forest ecosystem management in Malaysia, the case of the Matang mangrove forest. World Journal of Environmental Biosciences, 8(4):23-34.
- Balke, T., Swales, A., Levelock, C. E., Herman, P. M. J., & Bouma, T. J. (2015). Limits to seaward expansion of mangroves: Translating physical disturbance mechanisms into seedling survival gradients. Journal of Experimental Marine Biology and Ecology, 467:16-25.
- Basyuni, M., & Sulistiyono, N. (2018). Deforestation and reforestation analysis from land-use changes in North Sumatran Mangroves, 1990-2015. IOP Conference Series: Materials Science and Engineering, 309(1):012018.
- Basyuni, M., Baba, S., & Oku, H. (2017). Microsatellite analysis on genetic variation in two populations of red mangrove Rhizophora mangle L. (Rhizophoraceae) and its implication to conservation. In IOP Conference Series: Materials Science and Engineering, 180(1):012243.
- Basyuni, M., Slamet, B., Sulistiyono, N., Munir, E., Vovides, A., & Bunting, P. (2021). Physicochemical characteristics, nutrients, and fish production in different types of mangrove forests in North Sumatra and the Aceh Provinces of Indonesia. Kuwait Journal of Science, 48(3):1-14.
- Basyuni, M., Sasmito, S. D., Analuddin, K., Ulqodry, T. Z., Saragi-Sasmito, M. F., Eddy, S. & Milantara, N. (2022). Mangrove biodiversity, conservation and roles for livelihoods in Indonesia. In S. C. Das, Pullaiah, & E. C. Ashton (Ed.), Mangroves: Biodiversity, livelihoods and conservation. (pp. 397-445). Singapore: Springer.
- Biba, A., Hoda, A., Bozgo, V., & Mali, S. (2017). Genetic diversity of Cyprinus carpio of natural lakes in Albania estimated by microsatellite loci. Endocytobiosis and Cell Research, 28(1):1-8.
- Becker, S., Hanner, R., & Steinke, D. (2011). Five years of FISH-BOL: brief status report. Mitochondrial DNA, 22(1):3-9.
- Chen, W., Hou, L., Zhang, Z., Pang, X., & Li, Y. (2017). Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. Frontiers in Plant Science, 8(575):1-14.
- Consuegra, S., O'Rorke, R., Rodriguez-Barreto, D., Fernandez, S., Jones, J., & de Leaniz, C. G. (2021). Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding. Science of the Total Environment, 790:148054.
- Crandall, K. A., & Fitzpatrick, Jr. J. F. (1996). Crayfish molecular systematics: using a combination of procedures to estimate phylogeny. Systematic Biology, 45(1):1-26.
- Fitri, A., Basyuni, M., Wati, R., Sulistiyono, N., Slamet, B., Harahap, Z. A., Thorste, B., & Bunting, P. (2018). Management of mangrove ecosystems for increasing fisheries production in Lubuk Kertang village, North Sumatra, Indonesia. Aquaculture, Aquarium, Conservation & Legislation Bioflux, 11(4):1252-1264.
- Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M., Dudash, M. R., Fenster, C. B., Lacy, R. C., & Sunnucks, P. (2017). Genetic management of fragmented animal and plant populations. Oxford: Oxford University Press.
- Fu, H., Wang, W., Ma, W., & Wang, M. (2018). Differential in surface elevation change across mangrove forests in the intertidal zone. Estuarine, Coastal and Shelf Science, 207:203-208.
- Galví£o, M. S. N., Pereira, O. M., & Hilsdorf, A. W. S. (2013). Molecular identification and distribution of mangrove oysters (Crassostrea) in an estuarine ecosystem in Southeast Brazil: implications for aquaculture and fisheries management. Aquaculture Research, 44(10):1589-1601.
- Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H, Groeneveld, E, Weigend, F, & The GLOBALDIV Consortium. (2010). Genetic diversity in farm animals–a review. Animal Genetics, 41:6-31.
- Habib, K. A., Neogi, A. K., Rahman, M., Oh, J., Lee, Y. H., & Kim, C. G. (2021). DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem. Plos one, 16(8):e0255110.
- Hariyono, D. N. H., Maharani, D., Cho, S., Manjula, P., Seo, D., Choi, N., Sidadolog, J. H. P., & Lee, J. H. (2019). Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations. Asian-Australasian Journal of Animal Sciences, 32(1):31-37.
- Hayati, R., Basyuni, M., & Chalil, D. (2020). Genetic diversity, sequence and bioinformatic analysis of Ganoderma boninense isolates. International Journal of Agriculture & Biology, 23(4):763-770.
- Hogarth, P. J. (2015). The biology of mangroves and seagrasses. Oxford: Oxford University Press.
- Holsinger, K. E., & Weir, B. S. (2009). Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics, 10(9):639-650.
- Ilman, M., Dargusch, P., Dart, P., & Onrizal. (2016). A historical analysis of the drivers of loss and degradation of Indonesia's mangroves. Land Use Policy, 54:448-459.
- Istiqomah, M. A., Basyuni, M., & Hasibuan, P. A. Z. (2020). Development of DNA extraction on mangrove leaves. International Journal of Scientific & Technology Research, 9(4):139-141.
- Joseph, A. V., Sasidharan, R. S., Nair, H. P., & Bhat, S. G. (2013). Occurrence of potential pathogenic Aeromonas species in tropical seafood, aquafarms and mangroves off Cochin coast in South India. Veterinary World, 6(6):300-306.
- Karabağ, K., Balcıoğlu, M. S., Karlı, T., & Alkan, S. (2016). Determination of genetic diversity using 15 simple sequence repeats markers in long term selected Japanese quail lines. Asian-Australasian Journal of Animal Sciences, 29(12):1696-1701.
- Kwak, Y. H., Kim, K. R., Kim, M. S., & Bang, I. C. (2020). Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker. Genes & Genomics, 42(11):1291-1298.
- Maharani, D., Hariyono, D. N. H., Cho, S., Manjula, P., Seo, D., Choi, N, Sidadolog, J. H. P, & Lee, J. H. (2017). Genetic diversity among Indonesian local duck populations in Java Island assessed by microsatellite markers. Journal of Animal Breeding and Genomics, 1(2):136-142.
- Parreira, B., Quéméré, E., Vanpé, C., Carvalho, I., & Chikhi, L. (2020). Genetic consequences of social structure in the golden-crowned sifaka. Heredity, 125(5):328-339.
- Peakall, R., & Smouse, P. E. (2006). GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1):288-295.
- Richards, D. R., & Friess, D. A. (2016). Rates and drivers of mangrove deforestation in Southeast Asia, 2000–2012. Proceedings of the National Academy of Sciences, 113(2):344-349.
- Rizal, A., Sahidin, A., & Herawati, H. (2018). Economic value estimation of mangrove ecosystems in Indonesia. Biodiversity International Journal, 2(1):98-100.
- Shokoohmand, M., Zolgharnein, H., Mashjoor, S., Laloi, F., Foroughmand, A. M., & Savari, A. (2018). Analysis of genetic diversity of white shrimp (Metapenaeus affinis) from the Northwest of the Persian Gulf using microsatellite markers. Turkish Journal of Fisheries and Aquatic Sciences, 18(3):385-394.
- Sitorus, H., Lesmana, I., & Tarigan, R. (2017). Relationship of mangrove density with fish diversity in the waters of mangrove area in Lubuk Kertang Village, Langkat District of North Sumatera. International Journal of Fisheries and Aquatic Studies, 5(5):266-271.
- Srikanth, S., Lum, S. K. Y., & Chen, Z. (2016). Mangrove root: adaptations and ecological importance. Trees, 30(2):451-465.
- Szczecińska, M., Sramko, G., Wołosz, K., & Sawicki, J. (2016). Genetic diversity and population structure of the rare and endangered plant species Pulsatilla patens (L.) Mill in East Central Europe. PloS one, 11(3):e0151730.
- Wang, J. (2018). Effects of sampling close relatives on some elementary population genetics analyses. Mol Ecol Resour, 18(1):41-54.
- Wilwet, L., Jeyasekaran, G., Shakila, R. J., Sivaraman, B., & Padmavathy, P. (2018). A single enzyme PCR-RFLP protocol targeting 16S rRNA/tRNAval region to authenticate four commercially important shrimp species in India. Food chemistry, 239:369-376.
- Winata, A., Yuliana, E., & Rusdiyanto, E. (2017). Diversity and natural regeneration of mangrove vegetation in the tracking area on Kemujan Island Karimunjawa National Park, Indonesia. Advances in Environmental Sciences, 9(2):109-119.
- Woodroffe, C. D., Rogers, K., McKee, K. L., Lovelock, C. E., Mendelssohn, I. A., & Saintilan, N. (2016). Mangrove sedimentation and response to relative sea-level rise. Annual Review of Marine Science, 8:243-266.
- Zhu, K., Yu, W., Huang, J., Zhou, F., Guo, H., Zhang, N., Jiang, S., & Zhang, D. (2017). Parentage determination in black tiger shrimp (Penaeus monodon) based on microsatellite DNA markers. Aquaculture international, 25(2):827-836.
References
Almasi, M., Milow, P., & Zakaria, R. M. (2019). The study of participatory mangrove forest ecosystem management in Malaysia, the case of the Matang mangrove forest. World Journal of Environmental Biosciences, 8(4):23-34.
Balke, T., Swales, A., Levelock, C. E., Herman, P. M. J., & Bouma, T. J. (2015). Limits to seaward expansion of mangroves: Translating physical disturbance mechanisms into seedling survival gradients. Journal of Experimental Marine Biology and Ecology, 467:16-25.
Basyuni, M., & Sulistiyono, N. (2018). Deforestation and reforestation analysis from land-use changes in North Sumatran Mangroves, 1990-2015. IOP Conference Series: Materials Science and Engineering, 309(1):012018.
Basyuni, M., Baba, S., & Oku, H. (2017). Microsatellite analysis on genetic variation in two populations of red mangrove Rhizophora mangle L. (Rhizophoraceae) and its implication to conservation. In IOP Conference Series: Materials Science and Engineering, 180(1):012243.
Basyuni, M., Slamet, B., Sulistiyono, N., Munir, E., Vovides, A., & Bunting, P. (2021). Physicochemical characteristics, nutrients, and fish production in different types of mangrove forests in North Sumatra and the Aceh Provinces of Indonesia. Kuwait Journal of Science, 48(3):1-14.
Basyuni, M., Sasmito, S. D., Analuddin, K., Ulqodry, T. Z., Saragi-Sasmito, M. F., Eddy, S. & Milantara, N. (2022). Mangrove biodiversity, conservation and roles for livelihoods in Indonesia. In S. C. Das, Pullaiah, & E. C. Ashton (Ed.), Mangroves: Biodiversity, livelihoods and conservation. (pp. 397-445). Singapore: Springer.
Biba, A., Hoda, A., Bozgo, V., & Mali, S. (2017). Genetic diversity of Cyprinus carpio of natural lakes in Albania estimated by microsatellite loci. Endocytobiosis and Cell Research, 28(1):1-8.
Becker, S., Hanner, R., & Steinke, D. (2011). Five years of FISH-BOL: brief status report. Mitochondrial DNA, 22(1):3-9.
Chen, W., Hou, L., Zhang, Z., Pang, X., & Li, Y. (2017). Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. Frontiers in Plant Science, 8(575):1-14.
Consuegra, S., O'Rorke, R., Rodriguez-Barreto, D., Fernandez, S., Jones, J., & de Leaniz, C. G. (2021). Impacts of large and small barriers on fish assemblage composition assessed using environmental DNA metabarcoding. Science of the Total Environment, 790:148054.
Crandall, K. A., & Fitzpatrick, Jr. J. F. (1996). Crayfish molecular systematics: using a combination of procedures to estimate phylogeny. Systematic Biology, 45(1):1-26.
Fitri, A., Basyuni, M., Wati, R., Sulistiyono, N., Slamet, B., Harahap, Z. A., Thorste, B., & Bunting, P. (2018). Management of mangrove ecosystems for increasing fisheries production in Lubuk Kertang village, North Sumatra, Indonesia. Aquaculture, Aquarium, Conservation & Legislation Bioflux, 11(4):1252-1264.
Frankham, R., Ballou, J. D., Ralls, K., Eldridge, M., Dudash, M. R., Fenster, C. B., Lacy, R. C., & Sunnucks, P. (2017). Genetic management of fragmented animal and plant populations. Oxford: Oxford University Press.
Fu, H., Wang, W., Ma, W., & Wang, M. (2018). Differential in surface elevation change across mangrove forests in the intertidal zone. Estuarine, Coastal and Shelf Science, 207:203-208.
Galví£o, M. S. N., Pereira, O. M., & Hilsdorf, A. W. S. (2013). Molecular identification and distribution of mangrove oysters (Crassostrea) in an estuarine ecosystem in Southeast Brazil: implications for aquaculture and fisheries management. Aquaculture Research, 44(10):1589-1601.
Groeneveld, L. F., Lenstra, J. A., Eding, H., Toro, M. A., Scherf, B., Pilling, D., Negrini, R., Finlay, E. K., Jianlin, H, Groeneveld, E, Weigend, F, & The GLOBALDIV Consortium. (2010). Genetic diversity in farm animals–a review. Animal Genetics, 41:6-31.
Habib, K. A., Neogi, A. K., Rahman, M., Oh, J., Lee, Y. H., & Kim, C. G. (2021). DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem. Plos one, 16(8):e0255110.
Hariyono, D. N. H., Maharani, D., Cho, S., Manjula, P., Seo, D., Choi, N., Sidadolog, J. H. P., & Lee, J. H. (2019). Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations. Asian-Australasian Journal of Animal Sciences, 32(1):31-37.
Hayati, R., Basyuni, M., & Chalil, D. (2020). Genetic diversity, sequence and bioinformatic analysis of Ganoderma boninense isolates. International Journal of Agriculture & Biology, 23(4):763-770.
Hogarth, P. J. (2015). The biology of mangroves and seagrasses. Oxford: Oxford University Press.
Holsinger, K. E., & Weir, B. S. (2009). Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics, 10(9):639-650.
Ilman, M., Dargusch, P., Dart, P., & Onrizal. (2016). A historical analysis of the drivers of loss and degradation of Indonesia's mangroves. Land Use Policy, 54:448-459.
Istiqomah, M. A., Basyuni, M., & Hasibuan, P. A. Z. (2020). Development of DNA extraction on mangrove leaves. International Journal of Scientific & Technology Research, 9(4):139-141.
Joseph, A. V., Sasidharan, R. S., Nair, H. P., & Bhat, S. G. (2013). Occurrence of potential pathogenic Aeromonas species in tropical seafood, aquafarms and mangroves off Cochin coast in South India. Veterinary World, 6(6):300-306.
Karabağ, K., Balcıoğlu, M. S., Karlı, T., & Alkan, S. (2016). Determination of genetic diversity using 15 simple sequence repeats markers in long term selected Japanese quail lines. Asian-Australasian Journal of Animal Sciences, 29(12):1696-1701.
Kwak, Y. H., Kim, K. R., Kim, M. S., & Bang, I. C. (2020). Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker. Genes & Genomics, 42(11):1291-1298.
Maharani, D., Hariyono, D. N. H., Cho, S., Manjula, P., Seo, D., Choi, N, Sidadolog, J. H. P, & Lee, J. H. (2017). Genetic diversity among Indonesian local duck populations in Java Island assessed by microsatellite markers. Journal of Animal Breeding and Genomics, 1(2):136-142.
Parreira, B., Quéméré, E., Vanpé, C., Carvalho, I., & Chikhi, L. (2020). Genetic consequences of social structure in the golden-crowned sifaka. Heredity, 125(5):328-339.
Peakall, R., & Smouse, P. E. (2006). GENALEX 6: genetic analysis in excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1):288-295.
Richards, D. R., & Friess, D. A. (2016). Rates and drivers of mangrove deforestation in Southeast Asia, 2000–2012. Proceedings of the National Academy of Sciences, 113(2):344-349.
Rizal, A., Sahidin, A., & Herawati, H. (2018). Economic value estimation of mangrove ecosystems in Indonesia. Biodiversity International Journal, 2(1):98-100.
Shokoohmand, M., Zolgharnein, H., Mashjoor, S., Laloi, F., Foroughmand, A. M., & Savari, A. (2018). Analysis of genetic diversity of white shrimp (Metapenaeus affinis) from the Northwest of the Persian Gulf using microsatellite markers. Turkish Journal of Fisheries and Aquatic Sciences, 18(3):385-394.
Sitorus, H., Lesmana, I., & Tarigan, R. (2017). Relationship of mangrove density with fish diversity in the waters of mangrove area in Lubuk Kertang Village, Langkat District of North Sumatera. International Journal of Fisheries and Aquatic Studies, 5(5):266-271.
Srikanth, S., Lum, S. K. Y., & Chen, Z. (2016). Mangrove root: adaptations and ecological importance. Trees, 30(2):451-465.
Szczecińska, M., Sramko, G., Wołosz, K., & Sawicki, J. (2016). Genetic diversity and population structure of the rare and endangered plant species Pulsatilla patens (L.) Mill in East Central Europe. PloS one, 11(3):e0151730.
Wang, J. (2018). Effects of sampling close relatives on some elementary population genetics analyses. Mol Ecol Resour, 18(1):41-54.
Wilwet, L., Jeyasekaran, G., Shakila, R. J., Sivaraman, B., & Padmavathy, P. (2018). A single enzyme PCR-RFLP protocol targeting 16S rRNA/tRNAval region to authenticate four commercially important shrimp species in India. Food chemistry, 239:369-376.
Winata, A., Yuliana, E., & Rusdiyanto, E. (2017). Diversity and natural regeneration of mangrove vegetation in the tracking area on Kemujan Island Karimunjawa National Park, Indonesia. Advances in Environmental Sciences, 9(2):109-119.
Woodroffe, C. D., Rogers, K., McKee, K. L., Lovelock, C. E., Mendelssohn, I. A., & Saintilan, N. (2016). Mangrove sedimentation and response to relative sea-level rise. Annual Review of Marine Science, 8:243-266.
Zhu, K., Yu, W., Huang, J., Zhou, F., Guo, H., Zhang, N., Jiang, S., & Zhang, D. (2017). Parentage determination in black tiger shrimp (Penaeus monodon) based on microsatellite DNA markers. Aquaculture international, 25(2):827-836.