Sains Malaysiana 51(5)(2022): 1339-1352

http://doi.org/10.17576/jsm-2022-5105-06

Water Quality and Microbial Community Assessment in Artisanal Mining- Affected Sediments of Cikidang River, Banten, Java, Indonesia 

(Penilaian Kualiti Air dan Komuniti Mikrob dalam Perlombongan Artisanal- Sedimen Terjejas Sungai Cikidang, Banten, Java, Indonesia)

NOVERITA DIAN TAKARINA^1*, AYU MAULIDA SUKMA² , ANDRIO ADIWIBOWO³ & SITARESMI¹

¹Department of Biology, Faculty of Mathematics and Natural Sciences University of Indonesia, 16424 Beji Depok, West Java, Indonesia

²Biology Post Graduate Program, Department of Biology, Faculty of Mathematics and Natural Sciences University of Indonesia, 16424 Beji Depok, West Java, Indonesia

³Faculty of Public Health University of Indonesia, 16424 Beji Depok, West Java Indonesia

Received: 5 December 2020/Accepted: 22 September 2021

Abstract

The total microbial diversity and community in submerged sediments near mining sites, transition and intact sites at Cikidang River, Banten were assessed using 16S rDNA sequence data and biodiversity indices. Assessed water quality parameters in the river were water current, dissolved oxygen (DO), pH, redox potential, salinity, temperature and turbidity. Microbial alpha diversity used were Shannon diversity index, ChaoI index and Operational Taxonomic Units (OTUs). These analyses indicated a total of 50 taxa of sediment microbes. Based on Shannon diversity index, the highest value was observed at mining site. High abundant microbes in sediments at mining sites for phylum, class, order, family and genera levels were represented by Proteobacteria, Gammaproteobacteria, Pseudomonadales, Moraxellaceae, and Acinetobacter, respectively. In contrast, high abundant microbes in the sediment of the intact site for each taxon consisted of Firmicutes, Alphaproteobacteria, Erysipelotrichales, Erysipelotrichaceae, and Erysipelothrix. The water quality of mining sites was characterised by alkaline pH (8.807, 95% CI: 8.624 - 8.990) and lower redox potential (59.000 mV, 95% CI: 36.233 - 81.767) that differed significantly from the intact sites (P<0.05). This study also confirmed that mining sites have a higher genus diversity. Research on potential microbes of related genus as bioremediators could be recommended for further study.

Keywords: Community; microorganism; mining; sediment; 16S rDNA sequence data

Abstrak

Seluruh kepelbagaian dan komuniti mikrob dalam sedimen terendam berdekatan dengan tapak perlombongan, peralihan dan lokasi utuh di Sungai Cikidang, Banten telah dinilai menggunakan data jujukan 16S rDNA dan indeks kepelbagaian biologi. Parameter kualiti air yang dinilai di sungai termasuk arus air, oksigen terlarut (DO), pH, potensi redoks, saliniti, suhu dan kekeruhan. Kepelbagaian alfa mikrob yang digunakan adalah indeks kepelbagaian Shannon, indeks ChaoI dan Unit Taksonomi Operasi (OTU). Analisis ini menunjukkan sejumlah 50 taksa mikrob sedimen. Berdasarkan indeks kepelbagaian Shannon, nilai tertinggi diperhatikan di tapak perlombongan. Kelimpahan mikrob yang tinggi dalam sedimen di tapak perlombongan bagi tahap filum, kelas, order, famili dan genus masing-masing diwakili oleh Proteobacteria, Gammaproteobacteria, Pseudomonadales, Moraxellaceae dan Acinetobacter. Sebaliknya, mikrob yang banyak terdapat dalam sedimen di tapak utuh bagi setiap takson terdiri daripada Firmicutes, Alphaproteobacteria, Erysipelotrichales, Erysipelotrichaceae dan Erysipelothrix. Kualiti air di tapak perlombongan dicirikan oleh pH alkali (8.807, 95% CI: 8.624-8.990) dan potensi redoks rendah (59.000 mV, 95% CI:36.233-81.767) yang sangat berbeza secara signifikan daripada tapak utuh (P<0.05). Kajian ini juga mengesahkan bahawa tapak perlombongan mempunyai kepelbagaian genus yang lebih tinggi. Penyelidikan mengenai mikrob yang berpotensi daripada genus yang berkaitan sebagai bioremediasi boleh disarankan untuk kajian lanjutan.

Kata kunci: Data jujukan 16S rDNA; komuniti; mikroorganisma; perlombongan; sedimen

REFERENCES

Abundo, M.E.C., Ngunjiri, J.M., Taylor, K.J.M., Ji, H., Ghorbani, A., Mahesh, K.C., Weber, B.P., Johnson, T.J. & Lee, C.W. 2021. Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types. PLoS ONE 16(1): e0241732.

Adibe, A., Onuoha, G. & Chibo, J. 2020. Microbiological examination of water and sediment samples collected from the Imo River at the Onuimo Market Section in Obowo, Imo State, Nigeria. East African Scholars Journal of Agriculture and Life Science 3(6): 181-188.

Amelia, T.S.M., Lau, N.S., Amirul, A.A. & Bhubalan, K. 2020. Metagenomic data on bacterial diversity profiling of high-microbial-abundance tropical marine sponges Aaptos aaptos and Xestospongia muta from waters off Terengganu, South China Sea. Data in Brief  31(10957): 1-11.

Anderson, C.R. & Cook, G.M. 2004. Isolation and characterization of arsenate-reducing bacteria from arsenic-contaminated sites in New Zealand. Current Microbiology 48(5): 341-347.

Atapaththu, K.S.S., Asaeda, T., Yamamuro, M. & Kamiya, H. 2017. Effects of water turbulence on plant, sediment and water quality in reed (Phragmites australis) community. Ekológia (Bratislava) 36(1): 1-9.

Bachmann, T.M., Friese, K. & Zachmann, D.W. 2001. Redox and pH conditions in the water column and in the sediments of an acidic mining lake. Journal of Geochemical Exploration 73(2): 75-86.

Basu, A., Panda, S.S. & Dhal, N.K. 2015. Potential microbial diversity in chromium mining areas: A review. Bulletin of Environment, Pharmacology and Life Sciences 4(8): 158-169.

Batt, C.A. 2014. Alcaligenes. In Encyclopedia of Food and Microbiology, 2nd ed., edited by Batt, C.A. & Tortorello, M.L., Amsterdam: Elsevier. pp. 38-41.

Bergogne-Bérézin, E. 2014. Bacteria: Acinetobacter. In Encyclopedia of Food Safety, Vol 1, edited by Motarjemi, Y. Elsevier Science & Technology. pp. 337-341.

Bowman, J.P. 2011. 14 - Protein-based analysis and other new and emerging non-nucleic acid-based methods for tracing and investigating foodborne pathogens. In Tracing Pathogens in the Food Chain, edited by Brul, S., Fratamico, P.M. & McMeekin, T.A., Elsevier. pp. 292-341.

Böer, S.I., Hedtkamp, S.I.C., Van Beusekom, J.E.E., Fuhrman, J.A., Boetius, A. & Ramette, A. 2009. Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. Multidisciplinary Journal of Microbial Ecology 3(7): 780-791.

Cai, Y., Zhang, H., Yuan, G. & Li, F. 2017. Sources, speciation and transformation of arsenic in the gold mining impacted Jiehe River, China. Appllied Geochemistry 84: 254-261.

Campaner, V.P., Luiz-Silva, W. & Machado, W. 2014. Geochemistry of acid mine drainage from a coal mining area and processes controlling metal attenuation in stream waters, southern Brazil. Anais da Academia Brasileira de Ciências 86(2): 539-554.

Chidambaram, D., Hennebel, T., Taghavi, S., Mast, J., Boon, N., Verstraete, W., van der Lelie, D. & Fitts, J.P. 2010. Concomitant microbial generation of palladium nanoparticles and hydrogen to immobilize chromate. Environmental Science & Technology 44 (19): 7635-7640.

Chodak, M., Gołębiewski, M., Morawska-Płoskonka, J., Kuduk, K. & Niklińska, M. 2015. Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress. Annals of Microbiology 65(3): 1627-1637.

Chorost, M.S., Smith, N.C., Hutter, J.N., Ong, A.C., Stam, J.A., McGann, P.T., Hinkle, M.K., Schaecher, K.E. & Kamau, E. 2018. Bacteraemia due to Microbacterium paraoxydans in a patient with chronic kidney disease, refractory hypertension and sarcoidosis. Journal of Medical Microbiology Case Report 5(11): e005169.

Deng, R., Tang, Z., Hou, B., Ren, B., Wang, Z., Zhu, C., Kelly, S. & Hursthouse, A. 2020. Microbial diversity in soils from antimony mining sites: Geochemical control promotes species enrichment. Environmental Chemistry Letters 18(3): 911-922.

de Jesus Pereira, A. 2009. Environmental impact of artisanal gold mining in the Pungwe River Basin. In Proceedings of Mining and Water. DAAD alumni expert seminar Freiberg Online Geology.

dos Santos Furtado, A.L. & Casper, P. 2000. Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples. Journal of Microbiological Methods 41(3): 249-257.

Du, Y., Yu, X. & Wang, G. 2012. Massilia tieshanensis sp. nov., isolated from mining soil. International Journal of Systematic and Evolutionary Microbiology 62(10): 2356-2362.

Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. & Knight, R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16): 2194-200.

Edgar, R.C. 2013. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10(10): 996-998.

Eisler, R. 2004. Arsenic hazards to humans, plants, and animals from gold mining. Reviews of Environmental Contamination and Toxicology 180: 133-165.

Fatimawali, Kepel, B.J., Gani, M.A. & Tallei, T.E. 2020. Comparison of bacterial community structure and diversity in traditional gold mining waste disposal site and rice field by using a metabarcoding approach. International Journal of Microbiology 2020: 1858732.

 Fernandes, C.C., Kishi, L.T., Lopes, E.M., Omori, W.P., Souza, J.A.M., de, Alves, L.M.C. & de M. Lemos, E.G. 2018. Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Brazilian Journal of Microbiology 49(3): 489-502.

Figueiredo, G.G.O., Lopes, V.R., Romano, T. & Camara, M.C. 2020. Chapter 22 - Clostridium. In Beneficial Microbes in Agro-Ecology, edited by Amaresan, N., Kumar, M.S., Annapurna, K., Kumar, K. & Sankaranarayanan, A. Elsevier.

Fukami, J., Nogueira, M.A., Araujo, R.S. & Hungria, M. 2016. Accessing inoculation methods of maize and wheat with Azospirillum brasilense. AMB Express 6(1): 1-13.

Funoh, K.N. 2014. The Impacts of Artisanal Gold Mining on Local Livelihoods and the Environment in the Forested Areas of Cameroon. Working Paper 150, Bogor: CIFOR.

Gafur, N.A., Sakakibara, M., Sano, S. & Sera, K. 2018. A case study of heavy metal pollution in water of bone river by artisanal small-scale gold mine activities in eastern part of Gorontalo, Indonesia. Water 10(11): 1507.

Gibbons, S.M., Jones, E., Bearquiver, A., Blackwolf, F., Roundstone, W., Scott, N., Hooker, J., Madsen, R., Coleman, M.L. & Gilbert, J.A. 2014. Human and environmental impacts on river sediment microbial communities. PLoS ONE 9(5): e97435.

Girmay, M. 2018. Assessment for artisanal gold mining impacts on vegetation ecology at Shire Districts. International Journal of Mining Science 4(4): 38-43. 

Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E. & Methé, B. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 21(3): 494-504.

Hatam, I., Petticrew, E.L., French, T.D., Owen, N., Laval, B. & Baldwin, S.A. 2019. The bacterial community of Quesnel Lake sediments impacted by a catastrophic mine tailings spill differ in composition from those at undisturbed locations-two years post-spill. Scientific Reports 9(1): 2705.

He, M.Z., Hu, T.G., Cheng, B.R., Chen, X.H., Nie, K.H., Zhang, L.Y. & Cheng, S.Y. 2014. Research progress on phytoremediation to polluted environments by mine tailings in arid regions. China Desert 34(5): 1329-1336.

Hewson, I. & Fuhrman, J.A. 2006. Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities. Marine Ecology Progress Series 306: 79-86.

Hewson, I., Jacobson-Meyers, M.E. & Fuhrman, J.A. 2007. Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environmental Microbiology 9(4): 923-933.

Hofacker, A.F., Behrens, S., Voegelin, A., Kaegi, R., Lösekann-Behrens, T., Kappler, A. & Kretzschmar, R. 2015. Clostridium species as metallic copper-forming bacteria in soil under reducing conditions. Geomicrobiology Journal 32(2): 130-139.

Ji, H., Zhang, Y., Bararunyeretse, P. & Li, H. 2018. Characterization of microbial communities of soils from gold mine tailings and identification of mercury-resistant strain. Ecotoxicology and Environmental Safety 165: 182-193.

Kurniawan, W., Kusmana, C., Basuni, S., Munandar, A. & Kholil, K. 2013. Landuse conflicts analysis at Mount Halimun Salak National Park. Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan 3(1): 23-30.

Ke, L.Q., Li, P.D., Xu, J.P., Wang, Q.S., Wang, L.L. & Wen, H.P. 2019. Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil. Scientific Reports 9(1): 15839.

Li, S., Wu, J., Huo, Y., Zhao, X. & Xue, L. 2021. Profiling multiple heavy metal contamination and bacterial communities surrounding an iron tailing pond in Northwest China. Science of The Total Environment 752: 141827.

Locey, K.J. & Lennon, J.T. 2016. Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences of the United States of America 113(21): 5970-5975.

Macdonald, K., Lund, M. & Blanchette, M. 2015. Impacts of artisanal small-scale gold mining on water quality of a tropical river (Surow River, Ghana). In Proceeding of the 10th International Conference on Acid Rock Drainage & IMWA Annual Conference.

Magoč, T. & Salzberg, S.L. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21): 2957-2963.

Maleke, M., Valverde, A., Gomez-Arias, A., Cason, E.D., Vermeulen, J.G., Coetsee-Hugo, L., Swart, H., van Heerden, E. & Castillo, J. 2019. Anaerobic reduction of europium by a Clostridium strain as a strategy for rare earth biorecovery. Scientific Reports 9(1): 14339.

Martín, A., Arias, J., López, J., Santos, L., Venegas, C., Duarte, M., Ortíz-Ardila, A., de Parra, N., Campos, C. & Zambrano, C.C. 2020. Evaluation of the effect of gold mining on the water quality in Monterrey, Bolívar (Colombia). Water 12(9): 2523.

Meaza, H., Ali, M., Tesfamariam, Z. & Abebe, N. 2017. Impacts of artisanal gold mining systems on soil and woody vegetation in the semi-arid environment of northern Ethiopia. Singapore Journal of Tropical Geography 38(3): 386-401.

Melchiorre, E.B., Orwin, P.M., Reith, F., Rea, M.A.D., Yahn, J. & Allison, R. 2018. Biological and geochemical development of placer gold deposits at Rich Hill, Arizona, USA. Minerals 8(2): 56.

Navitasari, L., Joko, T., Murti, R.H. & Ariwiyanto T. 2020. Rhizobacterial community structure in grafted tomato plants infected by Ralstonia solanacearum. Biodiversitas 21(10): 4888-4895.

Poduch, E. & Kotra, L.P. 2007. Acinetobacter Infections. In xPharm: The Comprehensive Pharmacology Reference, edited by Enna, S.J. & Bylund, D.B. Amsterdam, Boston: Elsevier.

Polymenakou, P.N., Bertilsson, S., Tselepides, A. & Stephanou, E.G. 2005. Links between geographic location, environmental factors, and microbial community composition in sediments of the Eastern Mediterranean Sea. Microbial Ecology 49(3): 367-378.

Pomaranski, E.K., Griffin, M.J., Camus, A.C., Armwood, A.R., Shelley, J., Waldbieser, G.C., LaFrentz, B.R., García, J.C., Yanong, R. & Soto, E. 2020. Description of Erysipelothrix piscisicarius sp. nov., an emergent fish pathogen, and assessment of virulence using a tiger barb (Puntigrus tetrazona) infection model. International Journal of Systematic and Evolutionary Microbiology 70(2): 857-867.

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. & Glöckner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41(1): D590-D596.

Samanta, I. & Bandyopadhyay, S. 2020. Antimicrobial Resistance in Agriculture: Perspective, Policy and Mitigation. Elsevier.

Sheaves, M., Johnston, R., Miller, K. & Nelson, P.N. 2018. Impact of oil palm development on the integrity of riparian vegetation of a tropical coastal. Agriculture, Ecosystems and Environment 262: 1-10.

Shukla, D., Vaghela, K. & Jain, N. 2017. Assessment of physico-chemical and bacteriologic water quality parameters: A review. International Journal of Pharmacy and Integrated Life Sciences 5(2): 1-17.

Steenhoudt, O. & Vanderleyden, J. 2000. Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: Genetic, biochemical and ecological aspects. FEMS Microbiology Reviews 24(4): 487-506.

Wang, J., Wang, C., Li, J., Bai, P., Li, Q., Shen, M., Li, R., Li, T. & Zhao, J. 2018. Comparative genomics of degradative Novosphingobium strains with special reference to microcystin-degrading Novosphingobium sp. THN1. Frontiers in Microbiology 9(2238): 1-17.

Zhang, W., Ki, J.S. & Qian, P.Y. 2008. Microbial diversity in polluted harbor sediments I: Bacterial community assessment based on four clone libraries of 16S rDNA. Estuarine, Coastal and Shelf Science 76(3): 668-681.

Zhang, L., Zhao, T., Wang, Q., Li, L., Shen, T. & Gao, G. 2019. Bacterial community composition in aquatic and sediment samples with spatiotemporal dynamics in large, shallow, eutrophic Lake Chaohu, China. Journal of Freshwater Ecology 34(1): 575-589.

Zhang, X., Wang, P., Ma, L., Guo, R., Zhang, Y., Wang, P., Zhao, J. & Liu, J. 2021. Differences in the oral and intestinal microbiotas in pregnant women varying in periodontitis and gestational diabetes mellitus conditions. Journal of Oral Microbiology 13(1): 1883382.

^*Corresponding author; email: noverita.dian@sci.ui.ac.id