Comparative 16s metagenomic analysis of prokaryotic diversity in freshwater and permanent snow-line glacial lakes in Türkiye

Authors

DOI:

https://doi.org/10.2298/ABS240324016P

Keywords:

freshwater lakes, glacial lakes, 16s metagenomics, prokaryotic diversity, high altitude ecosystems

Abstract

Paper description:

  • Freshwater lakes support diverse bacterial communities vital for healthy ecosystems. Pollution and climate change can disrupt these communities.
  • This study employed metagenomics to compare the bacterial diversity in three Turkish lakes: Beyşehir, Eber, and Uludağ Buzlu.
  • Distinct bacterial compositions were observed. Beyşehir had the highest diversity with Planktophila and Limnohabitans Eber Lake was characterized by Limnohabitans, Flavobacterium, and Sphingomonas. Uludağ Buzlu Lake had low diversity with Parabacteroides and Akkermansia being the most common.
  • This study provides foundational data on bacterial communities in Turkish lakes, highlighting pollution and altitude effects. This facilitates freshwater ecosystem monitoring and broader environmental change research.

Abstract: Freshwater lakes are critical to healthy ecosystems, providing vital services like drinking water and recreation for surrounding communities. Microorganisms within these ecosystems play essential roles, driving biogeochemical cycles for elements like carbon, nitrogen, and sulfur. This study utilized a metagenomic approach to examine the prokaryotic communities of three freshwater lakes in Türkiye: the Eber and Beyşehir lakes, located at close altitudes (967 m and 1,115 m, respectively), which serve as primary water sources for nearby communities, and Lake Uludag Buzlu (2,390 m) that lies at the permanent snow border within the Uludag glacial lake system. Metagenomics allowed us to identify species, genetic structures, and the functional roles of microorganisms. Employing high-throughput next-generation sequencing (NGS) technology, we analyzed 16S ribosomal DNA (rDNA) sequences (V3-V4 regions) from the lake samples. EzBioCloud software facilitated the analysis of prokaryotic diversity obtained using Illumina NovaSeq technology. While Eber and Beyşehir lakes had similar diversity, Bacillota dominated in the higher-altitude Lake Uludag Buzlu. Genus-level analysis revealed Parabacteroides as the most prevalent in Lake Uludag Buzlu, contrasting with Limnohabitans dominance in Lake Eber; Lake Beyşehir exhibited co-dominance of Limnohabitans and Planktophila.

Downloads

Download data is not yet available.

References

Ding C, Wu C, Guo C, Gui J, Wei Y, Sun J. The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean. Biology. 2021; 10(3):248. https://doi.org/10.3390/biology10030248

Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nature Reviews Microbiology. 2018;16(5):263-76. https://doi.org/10.1038/nrmicro.2018.9

Pat F, Fidan Pedük S, Akçay N, Kızıl Pat HK, Arıcan E. Characterisation of Lake Eber Prokaryotic Diversity by Metagenomics Study. Journal of the Institute of Science and Technology. 2024;14(1):437-46. https://doi.org/10.21597/jist.1265800

Pat F, Fidan Pedük S, Akçay N, Kızıl Pat HK, Arıcan E. The Characterization of Prokaryotic Diversity in Lake Beyşehir Using a 16s Metagenomics Study. Journal of Advanced Research in Natural and Applied Sciences. 2023;9(3):719-29. https://doi.org/10.28979/jarnas.1217912

Mutlu MB, Martinez-Garcia M, Santos F, Pena A, Guven K, Anton J. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS Microbiol Ecol. 2008;65(3):474-83. https://doi.org/10.1111/j.1574-6941.2008.00510.x

Cseke LJ, Kirakosyan A, Kaufman PB, Westfall MV, editors. Handbook of Molecular and Cellular Methods in Biology and Medicine. Boca Raton: CRC Press; 2016. 735 p. https://doi.org/10.1201/b11351

Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1. https://doi.org/10.1093/nar/gks808

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-20. https://doi.org/10.1093/bioinformatics/btu170

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. https://doi.org/10.7717/peerj.2584

Myers EW, Miller W. Optimal alignments in linear space. Bioinformatics. 1988;4(1):11-7. https://doi.org/10.1093/bioinformatics/4.1.11

Wheeler TJ, Eddy SR. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013;29(19):2487-9. https://doi.org/10.1093/bioinformatics/btt403

Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67(5):1613-7. https://doi.org/10.1099/ijsem.0.001755

Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194-200. https://doi.org/10.1093/bioinformatics/btr381

Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011;12(1):385. https://doi.org/10.1186/1471-2105-12-385

Soares LA, Santos ACA Dos, Duarte ICS, Romagnoli EM, Calijuri M do C. Distribution of Archaeal and Bacterial communities in a subtropical reservoir. Acta Limnol. Bras. 2015;27(4):411-20. https://doi.org/10.1590/S2179-975X3615

Lehours A-C, Evans P, Bardot C, Joblin K, Gérard F. Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France). Appl Environ Microbiol. 2007;73(6):2016-9. https://doi.org/10.1128/aem.01490-06

Liu J, Su J, Zhang M, Luo Z, Li X, Chai B. Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China. Front Microbiol. 2021;12:669131. https://doi.org/10.3389/fmicb.2021.669131

Saleem F, Azim MK, Mustafa A, Kori JA, Hussain MS. Metagenomic profiling of freshwater lakes at different altitudes in Pakistan. Ecol Inform. 2019;51:73-81. https://doi.org/10.1016/j.ecoinf.2019.02.013

Zhang K, Yang X, Kattel G, Lin Q, Shen J. Freshwater Lake ecosystem shift caused by social-economic transitions in Yangtze River Basin over the past century. Sci Rep. 2018;8(1):17146. https://doi.org/10.1038/s41598-018-35482-5

Parveen B, Mary I, Vellet A, Ravet V, Debroas D. Temporal dynamics and phylogenetic diversity of free-living and particle-associated Verrucomicrobia communities in relation to environmental variables in a mesotrophic lake. FEMS Microbiol Ecol. 2013;83(1):189-201. https://doi.org/10.1111/j.1574-6941.2012.01469.x

Freitas S, Hatosy S, Fuhrman JA, Huse SM, Mark Welch DB, Sogin ML, Martiny AC. Global distribution and diversity of marine Verrucomicrobia. ISME J. 2012;6(8):1499-505. https://doi.org/10.1038/ismej.2012.3

Arnds J, Knittel K, Buck U, Winkel M, Amann R. Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake. Syst Appl Microbiol. 2010;33(3):139-48. https://doi.org/10.1016/j.syapm.2009.12.005

Lindstrom ES. Response of a member of the Verrucomicrobia, among the dominating bacteria in a hypolimnion, to increased phosphorus availability. J Plankton Res. 2004;26(2):241-6.http://doi.org/10.1093/plankt/fbh010

Kolmonen E, Haukka K, Rantala-Ylinen A, Rajaniemi-Wacklin P, Lepistö L, Sivonen K. Bacterioplankton community composition in 67 Finnish lakes differs according to trophic status. Aquat Microb Ecol. 2011;62(3):241-50. https://doi.org/10.3354/ame01461

De Figueiredo DR, Pereira MJ, Moura A, Silva L, Barrios S, Fonseca F, Henriques I, Correia A. Bacterial community composition over a dry winter in meso- and eutrophic Portuguese water bodies. FEMS Microbiol Ecol. 2007;59(3):638-50. https://doi.org/10.1111/j.1574-6941.2006.00241.x

Dorador C, Vila I, Witzel K-P, Imhoff JF. Bacterial and archaeal diversity in high altitude wetlands of the Chilean Altiplano. Fundam Appl Limnol. 2013;182(2):135-59. http://doi.org/10.1127/1863-9135/2013/0393

Cheng W, Zhang J, Wang Z, Wang M, Xie S. Bacterial communities in sediments of a drinking water reservoir. Ann Microbiol. 2014;64(2):875-8. https://doi.org/10.1007/s13213-013-0712-z

Kwon S, Moon E, Kim T-S, Hong S, Park H-D. Pyrosequencing Demonstrated Complex Microbial Communities in a Membrane Filtration System for a Drinking Water Treatment Plant. Microbes Environ. 2011;26(2):149-55. https://doi.org/10.1264/jsme2.me10205

Sommaruga R, Casamayor EO. Bacterial ‘cosmopolitanism’ and importance of local environmental factors for community composition in remote high‐altitude lakes. Freshw Biol. 2009;54(5):994-1005. https://doi.org/10.1111/j.1365-2427.2008.02146.x

Simon C, Wiezer A, Strittmatter AW, Daniel R. Phylogenetic Diversity and Metabolic Potential Revealed in a Glacier Ice Metagenome. Applied and Environmental Microbiology. 2009;75(23):7519-26. https://doi.org/10.1128/aem.00946-09

Møller AK, Søborg DA, Abu Al-Soud W, Sørensen SJ, Kroer N. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation. Polar Research. 2013 25;32(1):17390. https://doi.org/10.3402/polar.v32i0.17390

Choudhari S, Lohia R, Grigoriev A. Comparative metagenome analysis of an Alaskan glacier.J Bioinform Comput Biol. 2014;12(2):1441003. https://doi.org/10.1142/S0219720014410030

Kirchman DL. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol. 2002;39(2):91-100. https://doi.org/10.1111/j.1574-6941.2002.tb00910.x

Jiang H, Dong H, Zhang G, Yu B, Chapman LR, Fields MW. Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China. Appl Environ Microbiol. 2006;72(6):3832-45. https://doi.org/10.1128/AEM.02869-05

Dong H, Zhang G, Jiang H, Yu B, Chapman LR, Lucas CR, Fields MW. Microbial Diversity in Sediments of Saline Qinghai Lake, China: Linking Geochemical Controls to Microbial Ecology. Microb Ecol. 2006;51(1):65-82. https://doi.org/10.1007/s00248-005-0228-6

Humayoun SB, Bano N, Hollibaugh JT. Depth Distribution of Microbial Diversity in Mono Lake, a Meromictic Soda Lake in California. Appl Environ Microbiol. 2003;69(2):1030-42. https://doi.org/10.1128/AEM.69.2.1030-1042.2003

Bowman JP, McCammon SA, Rea SM, McMeekin TA. The microbial composition of three limnologically disparate hypersaline Antarctic lakes. FEMS Microbiol Lett. 2000;183(1):81-8. https://doi.org/10.1111/j.1574-6968.2000.tb08937.x

Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez‐Valera F. Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing. Mol Ecol. 2014;23(24):6073-90. https://doi.org/10.1111/mec.12985

Parfenova V V., Gladkikh AS, Belykh OI. Comparative analysis of biodiversity in the planktonic and biofilm bacterial communities in Lake Baikal. Microbiology (N Y). 2013;82(1):91-101.https://doi.org/10.1134/S0026261713010128

Downloads

Published

2024-07-10

How to Cite

1.
Pat F, Fidan Pedük S, Akçay N, Kızıl Pat HK, Arıcan E. Comparative 16s metagenomic analysis of prokaryotic diversity in freshwater and permanent snow-line glacial lakes in Türkiye . Arch Biol Sci [Internet]. 2024Jul.10 [cited 2024Nov.22];76(2):233-4. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/9682

Issue

Vol. 76 No. 2 (2024)

Section

Articles

License

Copyright (c) 2024 Fahri Pat, Sultan Fidan Pedük, Neşe Akçay, Hatice Kübra Kızıl Pat, Ercan Arıcan

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Authors grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution 4.0 International License that allows others to share the work with an acknowledgment of the work’s authorship and initial publication in this journal.