REP-PCR Analysis to Study Prokaryotic Biodiversity from Lake Meyghan Ali Naghoni 1,a , Giti Emtiazi 1,*b , Mohammad Ali Amoozegar 2,3,c , Zahra Etemadifar 1,d , Seyed Abolhassan Shahzadeh Fazeli 2,4,e 1 Department of Biology, Faculty of Science, University of Isfahan, Isfahan, Iran 2 Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran-Iran 3 Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran 4 Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in biology, University of Science and Culture, Tehran, Iran a alinaghoni@gmail.com, b emtiazi@yahoo.com, c alamoze@yahoo.com, d z.etemadifar@sci.ui.ac.ir, e fazeli@ibrc.ir Keywords: rep-PCR, 16S rRNA, microbial community, qPCR, prokaryotes Abstract. Repetitive extragenic palindromic elements-polymerase chain reaction (rep-PCR) with 16S ribosomal ribonucleic acid (16S rRNA) genes sequences successfully used for the analysis of microbial community. In this study, the prokaryotic community in Lake Meyghan described by using rep-PCR analysis along with 16S rRNA gene sequencing. The water samples were collected from Lake Meyghan in November 2013. All samples were diluted and cultured on three different media. To estimate the number of prokaryotes per milliliter of the lake we used quantitative realtime PCR (qPCR). Rep-PCR combination with 16S rRNA gene sequencing was performed to investigate prokaryotes biodiversity in the lake. 305 strains were isolated in this work; 113 isolates for green region, 102 isolates for red region, and 90 isolates for white region. The dendrograms generated 10, 7, and 9 clusters for a 70 % similarity cut-off for green, red, and white regions, respectively. Based on rep-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by (77.5 %) Halobacteriacae and many isolates were related to the genera Halorubrum, Haloarcula, Haloterrigena, Natrinema, and Halovivax in the white region. In the red region more isolated strains (57.5 %) belonged to Bacillaceae and the remaining 42.5 % of isolates belonged to archaea domain, Halorubrum, and Haloarcula. In the green region members of Gammaproteobacteria were recovered, this region was dominant with Pseudoalteromonas, Salinivibrio, and Aliidiomarina. Introduction Microorganisms despite their small size have a vast impact on our lives. In the 1960s, microbiologists began exploring the impact of biodiversity on the structure and function of microbial communities [1, 2]. Understanding patterns of prokaryotes (bacteria and archaea) biodiversity is of particular importance for the reason that prokaryotes may well comprise the majority of the earth's species diversity, many processes responsible for sustaining life on earth are mediated by them therefore their diversity is practically very important in bioprospecting (the search for novel biochemicals for use in medicine, agriculture, and industry) and bioremediation (the biological degradation of pollutants) [3-5]. Saline and hypersaline environments are very useful in studies on prokaryotes diversity. On the one hand, prokaryotes diversity decreases with increasing salinity [5-8]. On the other hand, aquatic hypersaline systems have proved to be an excellent source of new culturable microorganisms [9-12]. Hypersaline environments can be separated into two types, thalassohaline and athalassohaline [13]. Thalassohaline aquatic environments have an ionic compositions similar International Letters of Natural Sciences Submitted: 2016-09-15 ISSN: 2300-9675, Vol. 61, pp 69-84 Revised: 2016-12-08 doi:10.18052/www.scipress.com/ILNS.61.69 Accepted: 2016-12-08 © 2017 SciPress Ltd., Switzerland Online: 2017-01-10 SciPress applies the CC-BY 4.0 license to works we publish: https://creativecommons.org/licenses/by/4.0/