The Characterization of Prokaryotic Diversity in Lake Beyşehir Using a 16s Metagenomics Study

Year 2023, Volume: 9 Issue: 3, 719 - 729, 20.09.2023

Fahri Pat , Sultan Fidan Pedük , Neşe Akçay , Hatice Kübra Kızıl Pat , Ercan Arıcan

https://doi.org/10.28979/jarnas.1217912

Cited By: 1

Abstract

Lake Beysehir, located in the Central Anatolia Region, is the biggest lake in Central Anatolia, providing drinking water and irrigation. It is Turkey's third-largest lake and the largest freshwater lake. Its waters are fresh water and its depth is around 8-9 m at most. The deepest point is mentioned as 12, 14, and 15 m in different sources. Although there is a lake used by such a large population in our country, there are not enough studies on microbial diversity, so revealing the diversity is important for the lake and the population around the lake.
Next-generation sequencing (NGS) research has made it possible to sequence RNA and DNA considerably quicker and cheaply than in by assessing the PCR amplicon, we utilized NGS high-throughput methods for the metagenomic research of Lake Beyşehir sequences of 16S rDNA (regions V3–V4). The analyzes revealed the phylum Proteobacteria, Verrucomicrobia, Bacteroidetes and Actinobacteria.

Keywords

Metagenomic, NGS, 16S rRNA, Ecology, Microbial diversity

Supporting Institution

İstanbul Üniversitesi Bilimsel Araştırma Projeleri Birimi

Project Number

FDK-2019-34349

Thanks

The laboratory studies of this study were carried out in the molecular biology and genetics laboratories of Istanbul University, Faculty of Science. Endless thanks to KOSKİ for providing biochemical measurements of Beyşehir lake, which is our study area. The Scientific Research Projects Coordination Unit of Istanbul University financed this study.

References

• Bosshard, P. P., Santini, Y., Grüter, D., Stettler, R., & Bachofen, R. (2000). Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS microbiology ecology, 31(2), 173–182. doi:https://doi.org/10.1111/j.1574-6941.2000.tb00682.x
• Carvalho, L., McDonald, C., De Hoyos, C., Mischke, U., Phillips, G., Borics, G., Cardoso, A. C. (2013). Sustaining recreational quality of European lakes: Minimizing the health risks from algal blooms through phosphorus control. Journal of Applied Ecology, 50(2), 315-323. doi:10.1111/1365-2664.12059
• Cseke, L.J., Kaufman, P.B., Podila, G.K., & Tsai, C.-J. (2003). Handbook of Molecular and Cellular Methods in Biology and Medicine (2nd ed.). Boca Raton: CRC Press. doi:https://doi.org/10.1201/9781420041712
• Dinç, A. & Öztürk, R. (2013). Investigation of Beyşehir Lake National Park in terms of Ecology and Tourism. Turkish Journal of Scientific Reviews, 118-123. erişim adresi: https://dergipark.org.tr/tr/pub/derleme/issue/35088/389202
• Fenchel, T.M., Jorgensen, B.B. (1977). Detritus food chains of aquatic ecosystems: the role of bacteria. Advances in Microbial Ecology, 1-58. doi:https://doi.org/10.1007/978-1-4615-8219-9
• Fisher, M. M., & Triplett, E. W. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Applied and environmental microbiology, 65(10), 4630–4636. doi:https://doi.org/10.1128/AEM.65.10.4630-4636.1999
• Gilbert et al. (2011). The earth microbiome project: The meeting report for the 1st international Earth Microbiome project conference, Shenzhen, China, June 13th–15th 2011. Standards in Genomic Sciences, 5(2), 243–247. doi:https://doi.org/10.4056/sigs.2134923
• Glöckner, F. O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A., & Amann, R. (2000). Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Applied and environmental microbiology, 66(11), 5053–5065. doi:https://doi.org/10.1128/AEM.66.11.5053-5065.2000
• Google Maps. (2023, February 16). erişim adresi: https://www.google.com/maps/place/Bey%C5%9Fehir+G%C3%B6l%C3%BC/@37.7792921,31.2339629,10z/data=!3m1!4b1!4m6!3m5!1s0x14c54f3a7d53feb7:0x4a3d6596ad8ea733!8m2!3d37.7723989!4d31.5212113!16zL20vMGZuZjZw
• Hobbie, John & Bahr, Michele & Bettez, Neil & Rublee, Parke. (1999). Microbial food webs in oligotrophic Arctic Lakes. Archiv für Hydrobiologie Special Issues Advances in Limnology, 54. erişim adresi: http://plato.acadiau.ca/isme/Symposium10/hobbie.PDF
• Iliev, I., Yahubyan, G., Marhova, M., Apostolova, E., Gozmanova, M., Gecheva, G., Kostadinova, S., Ivanova, A., & Baev, V. (2017). Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs. Journal of basic microbiology, 57(8), 669–679. doi: https://doi.org/10.1002/jobm.201700137
• Kayani, M., Doyle, S.M., Sangwan, N., et al. (2018). Metagenomic analysis of basal ice from an Alaskan glacier. Microbiome, 6, 123. doi:https://doi.org/10.1186/s40168-018-0505-5
• Keegan, K. P., Glass, E. M., & Meyer, F. (2016). MG-Rast, a metagenomics service for analysis of Microbial Community Structure and function. Microbial Environmental Genomics (MEG), 207-233. doi:10.1007/978-1-4939-3369-3_13
• Klindworth, et al. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and nextgeneration sequencing-based diversity studies. Nucleic acids Research, 41(1), e1. doi: https://doi.org/10.1093/nar/gks808
• Kolbert, C. and Persing, D. (1999). Ribosomal DNA Sequencing as a Tool for Identification of Bacterial Pathogens. Current Opinion in Microbiology, 2, 299-305. doi:http://dx.doi.org/10.1016/S1369-5274(99)80052-6 Kuczynski et.al. (2011). Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current Protocols in Bioinformatics, 36(1), 1-20. doi: https://doi.org/10.1002/0471250953.bi1007s36
• López-García A, Pineda-Quiroga C, Atxaerandio R, Pérez A, Hernández I, García-Rodríguez A and González-Recio O. (2018). Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences. Front. Microbiol, 9:3010. doi:http://dx.doi.org/10.3389/fmicb.2018.03010 Miller, S. and Chiu, C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis, Clinical Chemistry, Volume 68, Issue 1, January 2022, Pages 115–124, https://doi.org/10.1093/clinchem/hvab173
• Mutlu, M. B., Martínez-García, M., Santos, F., Peña, A., Guven, K., & Antón, J. (2008). Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. Federation of European Microbiological Societies (FEMS) Microbiology Ecology, 65, 474-483. doi: https://doi.org/10.1111/j.1574- 6941.2008.00510.x
• Oh, S., Caro-Quintero, A., Tsementzi, D., DeLeon-Rodriguez, N., Luo, C., Poretsky, R., & Konstantinidis, K. T. (2011). Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem. Applied and Environmental Microbiology, 77(17), 6000-6011. doi: https://doi.org/10.1128/AEM.00107-11
• Ondov BD, Bergman NH, Phillippy AM. (2011). Interactive metagenomic. BMC Bioinf, 12:385. doi:https://doi.org/10.1186/1471-2105-12-385
• Oulas, A., Pavloudi, C., Polymenakou, P., Pavlopoulos, G. A., Papanikolaou, N., Kotoulas, G., Arvanitidis, C., & Iliopoulos, I. (2015). Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinformatics and biology insights, 9, 75–88. doi:https://doi.org/10.4137/BBI.S12462
• Özparlak, H. , Arslan, G. & Arslan, E. (2012). Determination of Some Metal Levels in Muscle Tissue of Nine Fish Species from the Beyşehir Lake, Turkey. Turkish Journal of Fisheries and Aquatic Sciences, 12 (4). erişim adresi: https://dergipark.org.tr/tr/pub/trjfas-ayrildi/issue/13267/160203
• Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing. Nucleic Acids Res., 41, D590–D596. doi:https://doi.org/10.1093/nar/gks1219
• Rognes, T., Flouri, T., Nichols, B., Quince, C., and Mahé, F. (2016). VSEARCH: a versatile open-source tool for metagenomics. PeerJ, 1–22. doi:https://doi.org/10.7717/peerj.2584
• Saleem, F., Azim, M. K., Mustafa, A., Kori, J. A., & Hussain, M. S. (2019). Metagenomic profiling of freshwater lakes at different altitudes in Pakistan. Ecological Informatics, 51, 73-81. doi: https://doi.org/10.1016/j.ecoinf.2019.02.013
• Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister,. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol, 75, 7537–7541. doi:https://doi.org/10.1128/AEM.01541-1549
• Şener, Ş. & Taştekin, N. (2019). HYDROGEOLOGICAL AND HYDROGEOCHEMICAL INVESTIGATION OF BEYŞEHİR (KONYA) PLAIN. Mühendislik Bilimleri ve Tasarım Dergisi, (3) , 647-661. doi: https://doi.org/10.21923/jesd.541781
• Tang, X., Xie, G., Shao, K., Dai, J., Chen, Y., Xu, Q., Gao, G. (2015). Bacterial community composition in oligosaline lake Bosten: Low overlap of betaproteobacteria and bacteroidetes with freshwater ecosystems. Microbes and Environments, 30(2), 180-188. doi:https://doi.org/10.1264/jsme2.ME14177
• Tank, S. E., F. W. Lesack, L., & McQueen, D. J. (2009). Elevated pH regulates bacterial carbon cycling in lakes with high photosynthetic activity. Ecology, 90(7):1910-22. doi:10.1890/08-1010.1.
• Toyama, D., et. al. (2016). Metagenomics Analysis of Microorganisms in Freshwater Lakes of the Amazon Basin. Genome announcements, 4(6), e01440-16. doi:https://doi.org/10.1128/genomeA.01440-16
• W D Hiorns., B A Methé., S A Nierzwicki-Bauer., J P Zehr. (1997). Bacterial diversity in Adirondack mountain lakes as revealed by 16S rRNA gene sequences. Applied and Environmental Microbiology, 2957-2960. doi:https://doi.org/10.1128/aem.63.7.2957-2960.1997
• Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261–5267. doi:https://doi.org/10.1128/AEM.00062-67
• Wang, Y., Sheng, H. F., He, Y., Wu, J. Y., Jiang, Y. X., Tam, N. F. Y., & Zhou, H. W. (2012). Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of Illumina tags. Applied and environmental microbiology, 78(23), 8264-8271. doi:https://doi.org/10.1128/AEM.01821-12
• Westcott, S. L., and Schloss, P. D. (2017). OptiClust, an improved method for assigning amplicon-based sequence data to Operational Taxonomic Units. mSphere, 2:e00073-17. doi:https://doi.org/10.1128/mSphereDirect.00073-17
• Zhang, K., Yang, X., Kattel, G. et al.(2018) Freshwater lake ecosystem shift caused by social-economic transitions in Yangtze River Basin over the past century. Sci Rep 8, 17146. https://doi.org/10.1038/s41598-018-35482-5
• Zwart, G., Hiorns, W. D., Methé, B. A., van Agterveld, M. P., Huismans, R., Nold, S. C., Zehr, J. P., & Laanbroek, H. J. (1998). Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Systematic and applied microbiology, 21(4), 546–556. doi:https://doi.org/10.1016/S0723-2020(98)80067-2