Determination Of Prokaryotic Diversity Of Salda Lake By Next Generation Sequencing Method

Year 2017, Volume: 7 Issue: 3, 99 - 106, 30.09.2017

Nilgün Poyraz , Mehmet Burçin Mutlu

Abstract

In our study, water sample was taken from Salda Lake and the pH and salinity data for the sample
were determined. After that, samples were fltered and DNA extraction was performed. The obtained DNA was
sequenced by the Illumina MiSeq sequencing system and data was analyzed by the QIIME program. When the
data obtained after the analysis were evaluated, it was determined that the most dominant bacterial phyla are
Proteobacteria and Actinobacteria. At class level, Gammaproteobacteria, Acidimicrobia and Actinobacteria were
dominant. In order level Enterobacteriales, Acidimicrobiales, Actinobacteriales were abundant. When the Archaea
domain was evaluated it was determined that the Euryarchaeota phylum was dominant. Halobacteria members
were abundant at the class level. In addition Halobacteria class, Halobacteriales order, Halobacteriaceae family
includes Haloarcula, Halobacterium, Halonotius, Halorhabdus, Halorubrum and Haloplanus genus members

Keywords

Alkaliphilic, prokaryotic diversity, Salda Lake, next generation sequencing

Salda Gölü Prokaryotik Çeşitliliğinin Yeni Nesil Dizileme Yöntemiyle Belirlenmesi

Abstract

Çalışmada Salda Gölü’nden örnekleme yapılmış ve örnek için pH ve tuzluluk değerleri belirlenmiştir.
Sonrasında örnekler fltreden geçirilerek, bu fltrelerden DNA ekstraksiyonu işlemi yapılmıştır. Elde edilen DNA
Illumina MiSeq dizileme sistemiyle dizilenmiş ve veriler QIIME Programı ile analiz edilmiştir. Analiz sonrası elde
edilen veriler değerlendirildiğinde en baskın bulunan Bacteria flumlarının Proteobacteria ve Actinobacteria olduğu
belirlenmiştir. Sınıf düzeyinde ise Gammaproteobacteria, Acidimicrobia ve Actinobacteria baskındır. Ordo düzeyinde
ise Enterobacteriales, Acidimicrobiales, Actinobacteriales baskındır. Archaea domaini değerlendirildiğinde ise
Euryarchaeota flumunun baskın olduğu belirlenmiştir. Sınıf düzeyinde Halobacteria üyeleri baskındır. Halobacteria
sınıfının Halobacterialaes ordosu Halobacteriaceae familyasının Haloarcula, Halobacterium, Halonotius,
Halorhabdus, Halorubrum ve Haloplanus cinsi üyeleri de baskın olarak bulunmaktadır

Keywords

Alkaliflik, prokaryotik çeşitlilik, Salda Gölü, yeni nesil dizileme

References

• Antony CP, Murrell JC, Shouche YS, 2012. Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS microbiology ecology, 81(1): 43-51.
• Asao M, Pinkart HC, Madigan MT, 2011. Diversity of extremophilic purple phototrophic bacteria in Soap Lake, a Central Washington (USA) Soda Lake. Environmental microbiology, 13(8): 2146-2157.
• Belkova N and Matyugina E, 2014. Vertical distribution of bacteria in Doroninskoe lake (Zabaikalie, Russia): Paradigm of Dominance. Acta Geologica Sinica (English Edition), 88(1): 53-55.
• Bent SJ, and Forney LJ, 2008. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. The ISME journal, 2(7): 689-695.
• Bowman JP, 2014. The Family Cryomorphaceae. The Prokaryotes. Springer, Berlin Heidelberg. 1028p.
• Braithwaite CJR and Zedef V, 1996. Hydromagnesite stromatolites and sediments in an alkaline lake, Salda Golu, Turkey. Journal of Sedimentary Research, 66(5): 991-1002.
• Burns DG, Janssen PH, Itoh T, Kamekura M, Echigo A, and Dyall-Smith ML, 2010. Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer. International journal of systematic and evolutionary microbiology, 60(5): 1196-1199.
• Cabral JP, 2010. Water microbiology. Bacterial pathogens and water. International journal of environmental research and public health, 7(10): 3657-3703.
• Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL and Knight R, 2010a. PyNAST: a flexibletool for aligning sequences to a template alignment. Bioinformatics, 26: 266–267.
• Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010b. QIIME allows analysis of high-throughput community sequencing data, Nature methods, 7(5): 335-336.
• Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108 : 4516-4522.
• Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R, 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal, 6(8): 1621-1624.
• Cifuentes A, Antón J, Benlloch S, Donnelly A, Herbert R A, and Rodríguez-Valera F, 2000. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Applied and environmental microbiology, 66(4): 1715-1719.
• DeLong EF, 2009. The microbial ocean from genomes to biomes. Nature, 459(7244): 200-206.
• Demirel C, Gül Karagüler N, Menekse-Kiliç M, Akçer-Ön S, Haydar Gültekin A, Balci N, 2016. Prokaryotic diversity in the extreme lakes of Turkey, SW Anatolia, Turkey. EGU General Assembly Conference Abstracts, 17-22 April 2016, Vienna, Austria.
• Duckworth AW, Grant WD, Jones BE and Van Steenbergen R, 1996. Phylogenetic diversity of soda lake alkaliphiles. FEMS Microbiology Ecology, 19 (3): 181-191.
• Dudhagara P, Ghelani A, Patel R, Chaudhari R and Bhatt S, 2015. Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India. Genomics data, 4: 8-11.
• Edgar RC, 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26: 2460–2461.
• Gonzalez A, King A, Robeson II MS, Song S, Shade A, Metcalf JL and Knight R, 2012. Characterizing microbial communities through space and time. Current opinion in biotechnology, 23(3): 431-436.
• Grant WD, Kamekura M, Ventosa A, McGenity TJ, 2001. Order Halobacteriales. Bergey’s manual of systematic bacteriology, Springer, New York, 722p.
• Grant S, Grant WD, Jones BE, Kato C, Li L, 1999. Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles, 3(2): 139-145.
• Grant WD and Heaphy S, 2010. Metagenomics and recovery of enzyme genes from alkaline saline environments. Environmental technology, 31(10): 1135-1143.
• Grant WD, 2006. Alkaline environments and biodiversity, in extremophiles. Encyclopaedia of life support systems (EOLSS), Developed under the Auspices of the UNESCO: Oxford: Eolss Publishers.
• Grant WD and Sorokin DY, 2011. Distribution and diversity of soda lake alkaliphiles. Extremophiles Handbook, Springer, Tokyo. 1247p.
• Green JL, Bohannan BJ and Whitaker RJ, 2008. Microbial biogeography: from taxonomy to traits. Science, 320(5879): 1039-1043.
• Horikoshi K, 2006. Alkaliphiles: genetic properties and applications of enzymes. Springer, New York. 256p.
• Humayoun SB, Bano N and Hollibaugh JT, 2003. Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Applied and environmental microbiology, 69(2): 1030-1042.
• Jiang H, Dong H, Zhang G, Yu B, Chapman LR and Fields MW, 2006. Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China. Applied and environmental microbiology, 72(6): 3832-3845.
• Kavak N, 2013. Van gölü prokaryotik çeşitliliğinin araştırılması. Anadolu Üniversitesi Fen Bilimleri Enstitüsü, Yüksek lisans tezi, 140s.
• Kazanci N, Girgin S, Dügel M, 2004. On the limnology of Salda Lake, a large and deep soda lake in southwestern Turkey: future management proposals. Aquatic Conservation: Marine and Freshwater Ecosystems, 14(2): 151-162.
• Kellogg CA, Ross SW, and Brooke SD, 2016. Bacterial community diversity of the deep-sea octocoral Paramuricea placomus. PeerJ, 4: e2529.
• Kersters K, Lisdiyanti P, Komagata K and Swings J, 2006. The family Acetobacteraceae: the genera Acetobacter, Acidomonas, Asaia, Gluconacetobacter, Gluconobacter, and Kozakia. The prokaryotes, Springer New York. 1115p.
• Kumar Sanjeevi A, Palanisamy K and Prabhu Balasubramani G, 2014. Productıon Of Protease From Rıce Mıll Waste By Serratia Species. International Journal of Advances in Interdisciplinary Research, 1(2): 49-54
• Lanzen A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L, 2013. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One, 8(8): e72577.
• Lin JL, Joye SB, Scholten JC, Schäfer H, McDonald IR and Murrell JC, 2005. Analysis of methane monooxygenase genes in Mono Lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure. Applied and environmental microbiology, 71(10): 6458-6462.
• López-García P, Kazmierczak J, Benzerara K, Kempe S, Guyot F, Moreira D, 2005. Bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline Lake Van, Turkey. Extremophiles, 9(4): 263-274.
• Mutlu MB, Martínez-García M, Santos F, Peña A, Guven K and Antón J, 2008. Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey. FEMS microbiology ecology, 65(3): 474-483.
• Nogales B, Moore ER, Abraham WR and Timmis KN, 1999. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl‐polluted moorland soil. Environmental microbiology, 1(3): 199-212.
• Özcan B, Cokmus C, Coleri A, Caliskan M, 2006. Characterization of extremely halophilic archaea isolated from saline environment in different parts of Turkey. Microbiology, 75(6): 739-746.
• Özcan B, Özcengiz G, Colleri A, Çökmüş C, 2007. Diversity of halophilic Archaea from six hypersaline environments in Turkey. Journal of Microbiology and Biotechnology, 17: 985-992.
• Reimer A, Landmann G, Kempe S, 2009. Lake Van, eastern Anatolia, hydrochemistry and history. Aquatic Geochemistry, 15(1-2): 195-222.
• Simachew A, Lanzén A, Gessesse A, Øvreås L, 2016. Prokaryotic community diversity along an increasing salt gradient in a soda ash concentration pond. Microbial ecology, 71(2): 326-338.
• Sorokin DY and Kuenen JG, 2005. Haloalkaliphilic sulfur-oxidizing bacteria in soda lakes. FEMS microbiology reviews, 29(4): 685-702.
• Thorpe CL, Morris K, Boothman C and Lloyd JR, 2012. Alkaline Fe (III) reduction by a novel alkali-tolerant Serratia sp. isolated from surface sediments close to Sellafield nuclear facility, UK. FEMS microbiology letters, 327(2): 87-92.
• Tourova TP, Grechnikova MA, Kuznetsov BB and Sorokin DY, 2014. Phylogenetic diversity of bacteria in soda lake stratified sediments. Microbiology, 83(6): 869-879.
• Urbach E, Vergin KL, Young L, Morse A, Larson GL, and Giovannoni SJ, 2001. Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake. Limnology and Oceanography, 46(3): 557-572.
• Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P and Muyzer G, 2016. Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in microbiology, 7:211.
• Yang J, Ma LA, Jiang H, Wu G and Dong H, 2016. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes. Scientific reports, 6:25078.
• Zwart G, Crump BC, Kamst-van Agterveld MP, Hagen F and Han SK, 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquatic Microbial Ecology, 28(2): 141-155.