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CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY

Year 2020, , 80 - 88, 31.01.2020
https://doi.org/10.18036/estubtdc.680795

Abstract

Van Lake, located in Eastern Anatolia Region, is the largest lake in Turkey. This lake features alkaline and saline soda lake. Since there are few studies focused on microbial diversity of alkaline environments, it is very important to reveal the diversity of microorganisms of Van Lake because of the wide range of biotechnological uses of these microorganisms and their ecological roles in lake ecosystem.
Next generation sequencing (NGS) allow us to sequence DNA and RNA much more quickly and cheaply than the previously used Sanger sequencing for the rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of Van Lake, by assessing its PCR amplicon of 16S rDNA sequences (V3–V4 regions). The analyses revealed Proteobacteria, Actinobacteria and Verrucomicrobia phyla were most abundant. Archaea members were represented by Euryarchaeota phylum. Results concluded that Bacteria domain were dominant in Van Lake.

References

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  • [2] Reimer A, Landmann G, & Kempe S. Lake Van, eastern Anatolia, hydrochemistry and history. Aquat Geochem 2009;15(1-2):195-222.
  • [3] Kempe S, Khoo F, and Gürleyik Y. Hydrography of Lake Van and its drainage area. In: The Geology of Lake Van, E.T. Degens and F. Kurtman (eds.), The Mineral Research and Exploration Institute of Turkey (MTA) Publication 1978;169:30-44.
  • [4] Kempe S, Kazmlerczak J, Landmann G, Konuk T, Reimer A, Lipp A. Largest known Microbialites discovered in Lake Van, Turkey. Nature 1991;349: 605-608.
  • [5] Grant WD, Jones BE, Mwatha WE. Alkaliphiles: ecology, diversity and applications. FEMS Microbiol Rev 1999a; 75: 255-270.
  • [6] Dimitriu PA, Pinkart HC, Peyton BM, Mormile MR. Spatial and temporal patterns in the microbial diversity of a meromictic soda lake in Washington State. Appl Environ Microbiol 2008;74:4877– 4888.
  • [7] Grant S, Grant WD, Jones BE, Kato C, Li L. Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 1999b; 3:139–145
  • [8] Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified gene coding for 16S rRNA. Appl Environ Microbiol 1993;59:695–700
  • [9] Medova H, Boldareva EN, Hrouzek P, Borzenko SV, Namsaraev ZB, Gorlenko VM, Namsaraev BB, and Koblízek M. High abundances of aerobic anoxygenic phototrophs in saline steppe lakes. FEMS Microbiol Ecol 2011;76:393–400.
  • [10] Asao M, Pinkart HC, Madigan MT. Diversity of extremophilic purple phototrophic bacteria in Soap Lake, a central Washington (USA) soda lake. Environ Microbiol 2011;13:2146–2157
  • [11] Lanzen A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Ovreas L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS ONE 2013; 8:e72577
  • [12] López-García P, Kazmierczak J, Benzerara K, Kempe S, Guyot F, Moreira D. Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey. Extremophiles 2005;9(4):263-274.
  • [13] Berber İ, Yenidünya E. Identification of alkaliphilic Bacillus species isolated from Lake Van and its surroundings by computerized analysis of extracellular protein profiles. Turk J Biol 2005; 29(3): 181-188.
  • [14] Poyraz N. Alkaliphilic bacterial diversity of Lake Van/Turkey. Biological Diversity and Conservation 2017;10(1):92-103.
  • [15] Fenchel, T, & Jørgensen BB. Detritus food chains of aquatic ecosystems: the role of bacteria. Adv Microb Ecol 1977;(1-58).
  • [16] Nogales B., Moore ER, Abraham WR and Timmis KN. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl‐polluted moorland soil. Environ Microbiol 1999;1(3), 199-212.
  • [17] Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert RA and Rodríguez-Valera F. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 2000; 66(4):1715-1719.
  • [18] Mutlu MB, Martínez-García M, Santos F, Peña A., Guven K and Antón, J. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS Microbiol Ecol 2008; 65(3), 474-483.
  • [19] Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, and Knight R. PyNAST: a flexibletool for aligning sequences to a template alignment. Bioinformatics, 2010a; 26: 266–267.
  • [20] Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods, 2010b; 7(5):335-336.
  • [21] Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(Supplement 1), 2011;4516-4522. doi:10.1073/pnas.1000080107.
  • [22] Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer, N et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME J 2012; 6(8):1621-1624.
  • [23] Duckworth AW, Grant WD, Jones BE and Van Steenbergen R. Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 1996;19(3):181-191.
  • [24] Jones BE, Grant WD, Duckworth AW and Owenson GG. Microbial diversity of soda lakes, Extremophiles 1998; 2(3), 191-200.
  • [25] Duckworth AW, Grant S, Grant WD, Jones BE and Meijer D 1998. Dietzia natronolimnaios sp. nov., a new member of the genus Dietzia isolated from an East African soda lake. Extremophiles 1998; 2(3), 359-366.
  • [26] Sorokin DY, van Pelt S, Tourova TP and Evtushenko LI. Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. Int J Syst Evol Microbiol 2009; 59(2), 248-253.
  • [27] Zavarzin, GA, Zhilina TN and Kevbrin VV. 1999. The alkaliphilic microbial community and its functional diversity. Microbiology-Aibs-C/C Of Mikrobiologiia 1999;68:503-521.
  • [28] Wani, AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D and Shouche YS. Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 2006; 157(10): 928-937.
  • [29] Hawley ER and Hess M. Metagenome sequencing of the prokaryotic microbiota of the hypersaline and meromictic Soap Lake, Washington. Genome announc 2014; 2(1):e01212-13.
  • [30] Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P and Muyzer G. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Front Microbiol 2016;7.
  • [31] Burgin AJ and Hamilton SK. Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 2007;5(2): 89-96.
Year 2020, , 80 - 88, 31.01.2020
https://doi.org/10.18036/estubtdc.680795

Abstract

References

  • [1] Üner S, Yeşilova Ç, Yakupoğlu T, & Üner T. Pekişmemiş sedimanlarda depremlerle oluşan deformasyon yapıları (sismitler): Van Gölü Havzası, Doğu Anadolu. Bulletin for Earth Sciences 2010; 31:53-66.
  • [2] Reimer A, Landmann G, & Kempe S. Lake Van, eastern Anatolia, hydrochemistry and history. Aquat Geochem 2009;15(1-2):195-222.
  • [3] Kempe S, Khoo F, and Gürleyik Y. Hydrography of Lake Van and its drainage area. In: The Geology of Lake Van, E.T. Degens and F. Kurtman (eds.), The Mineral Research and Exploration Institute of Turkey (MTA) Publication 1978;169:30-44.
  • [4] Kempe S, Kazmlerczak J, Landmann G, Konuk T, Reimer A, Lipp A. Largest known Microbialites discovered in Lake Van, Turkey. Nature 1991;349: 605-608.
  • [5] Grant WD, Jones BE, Mwatha WE. Alkaliphiles: ecology, diversity and applications. FEMS Microbiol Rev 1999a; 75: 255-270.
  • [6] Dimitriu PA, Pinkart HC, Peyton BM, Mormile MR. Spatial and temporal patterns in the microbial diversity of a meromictic soda lake in Washington State. Appl Environ Microbiol 2008;74:4877– 4888.
  • [7] Grant S, Grant WD, Jones BE, Kato C, Li L. Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 1999b; 3:139–145
  • [8] Muyzer G, de Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified gene coding for 16S rRNA. Appl Environ Microbiol 1993;59:695–700
  • [9] Medova H, Boldareva EN, Hrouzek P, Borzenko SV, Namsaraev ZB, Gorlenko VM, Namsaraev BB, and Koblízek M. High abundances of aerobic anoxygenic phototrophs in saline steppe lakes. FEMS Microbiol Ecol 2011;76:393–400.
  • [10] Asao M, Pinkart HC, Madigan MT. Diversity of extremophilic purple phototrophic bacteria in Soap Lake, a central Washington (USA) soda lake. Environ Microbiol 2011;13:2146–2157
  • [11] Lanzen A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Ovreas L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS ONE 2013; 8:e72577
  • [12] López-García P, Kazmierczak J, Benzerara K, Kempe S, Guyot F, Moreira D. Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey. Extremophiles 2005;9(4):263-274.
  • [13] Berber İ, Yenidünya E. Identification of alkaliphilic Bacillus species isolated from Lake Van and its surroundings by computerized analysis of extracellular protein profiles. Turk J Biol 2005; 29(3): 181-188.
  • [14] Poyraz N. Alkaliphilic bacterial diversity of Lake Van/Turkey. Biological Diversity and Conservation 2017;10(1):92-103.
  • [15] Fenchel, T, & Jørgensen BB. Detritus food chains of aquatic ecosystems: the role of bacteria. Adv Microb Ecol 1977;(1-58).
  • [16] Nogales B., Moore ER, Abraham WR and Timmis KN. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl‐polluted moorland soil. Environ Microbiol 1999;1(3), 199-212.
  • [17] Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert RA and Rodríguez-Valera F. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl Environ Microbiol 2000; 66(4):1715-1719.
  • [18] Mutlu MB, Martínez-García M, Santos F, Peña A., Guven K and Antón, J. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS Microbiol Ecol 2008; 65(3), 474-483.
  • [19] Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, and Knight R. PyNAST: a flexibletool for aligning sequences to a template alignment. Bioinformatics, 2010a; 26: 266–267.
  • [20] Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. QIIME allows analysis of high-throughput community sequencing data. Nature methods, 2010b; 7(5):335-336.
  • [21] Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(Supplement 1), 2011;4516-4522. doi:10.1073/pnas.1000080107.
  • [22] Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer, N et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME J 2012; 6(8):1621-1624.
  • [23] Duckworth AW, Grant WD, Jones BE and Van Steenbergen R. Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiol Ecol 1996;19(3):181-191.
  • [24] Jones BE, Grant WD, Duckworth AW and Owenson GG. Microbial diversity of soda lakes, Extremophiles 1998; 2(3), 191-200.
  • [25] Duckworth AW, Grant S, Grant WD, Jones BE and Meijer D 1998. Dietzia natronolimnaios sp. nov., a new member of the genus Dietzia isolated from an East African soda lake. Extremophiles 1998; 2(3), 359-366.
  • [26] Sorokin DY, van Pelt S, Tourova TP and Evtushenko LI. Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. Int J Syst Evol Microbiol 2009; 59(2), 248-253.
  • [27] Zavarzin, GA, Zhilina TN and Kevbrin VV. 1999. The alkaliphilic microbial community and its functional diversity. Microbiology-Aibs-C/C Of Mikrobiologiia 1999;68:503-521.
  • [28] Wani, AA, Surakasi VP, Siddharth J, Raghavan RG, Patole MS, Ranade D and Shouche YS. Molecular analyses of microbial diversity associated with the Lonar soda lake in India: an impact crater in a basalt area. Res Microbiol 2006; 157(10): 928-937.
  • [29] Hawley ER and Hess M. Metagenome sequencing of the prokaryotic microbiota of the hypersaline and meromictic Soap Lake, Washington. Genome announc 2014; 2(1):e01212-13.
  • [30] Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P and Muyzer G. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Front Microbiol 2016;7.
  • [31] Burgin AJ and Hamilton SK. Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 2007;5(2): 89-96.
There are 31 citations in total.

Details

Primary Language English
Subjects Structural Biology
Journal Section Articles
Authors

Nilgün Poyraz 0000-0002-5861-7922

Mehmet Mutlu 0000-0002-9404-6389

Publication Date January 31, 2020
Published in Issue Year 2020

Cite

APA Poyraz, N., & Mutlu, M. (2020). CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY. Eskişehir Teknik Üniversitesi Bilim Ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji, 9(1), 80-88. https://doi.org/10.18036/estubtdc.680795
AMA Poyraz N, Mutlu M. CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji. January 2020;9(1):80-88. doi:10.18036/estubtdc.680795
Chicago Poyraz, Nilgün, and Mehmet Mutlu. “CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY”. Eskişehir Teknik Üniversitesi Bilim Ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji 9, no. 1 (January 2020): 80-88. https://doi.org/10.18036/estubtdc.680795.
EndNote Poyraz N, Mutlu M (January 1, 2020) CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji 9 1 80–88.
IEEE N. Poyraz and M. Mutlu, “CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY”, Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji, vol. 9, no. 1, pp. 80–88, 2020, doi: 10.18036/estubtdc.680795.
ISNAD Poyraz, Nilgün - Mutlu, Mehmet. “CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY”. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji 9/1 (January 2020), 80-88. https://doi.org/10.18036/estubtdc.680795.
JAMA Poyraz N, Mutlu M. CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji. 2020;9:80–88.
MLA Poyraz, Nilgün and Mehmet Mutlu. “CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY”. Eskişehir Teknik Üniversitesi Bilim Ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji, vol. 9, no. 1, 2020, pp. 80-88, doi:10.18036/estubtdc.680795.
Vancouver Poyraz N, Mutlu M. CHARACTERIZATION OF MICROBIAL POPULATIONS OF LAKE VAN BY 16S METAGENOMICS STUDY. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi - C Yaşam Bilimleri Ve Biyoteknoloji. 2020;9(1):80-8.