Prokaryotic Diversity of the Alkaline Lake Acıgöl, Turkey by Using Culture-dependent and Culture-Independent Methods

Abstract

Aims: The prokaryotic diversity of Acıgöl lake, Turkey, was studied in samples taken from soil, water and mud. Culture -dependent and -independent methods were used to analyse the results. Methodology: Bacterial cultures were isolated by using six different growth media. Isolates were identified according to their 16S rDNA sequence analysis. Liquid media were used to test antibacterial substance production of the isolates. Bacillus cereus, Serratia marcescens, Pectobacterium carotovorum, Enterococcus faecalis, Listeria monocytogenes, Staphylococcus aureus, Micrococcus luteus, Escherichia coli and Listeria innocua were used as indicator bacteria. The extracted DNA samples taken from soil, water and mud were used in PCR reactions to amplify 16S rDNA genes by using universal bacterial primers. Amplicons were cloned by TA cloning after which white colonies were selected and colony PCR were applied for the amplification of the fragments. Each amplicon obtained from clones was sequenced and similarities were compared to those of the other bacterial groups. The DNA extracted from water sample was also used to amplify archeal 16S rDNAs. For the amplification reaction, the primers used were specific to the archaeal domain and their amplicons were cloned by TA cloning. Randomly picked white colonies were used for M13 PCR. The sequences of amplicons were analyzed by BLAST to determine the highest similarities with the other archeal groups. Results: In this study, fourty-nine strains were identified as belonging to Bacillus, Halomonas Enterococcus, Exiquobacterium, Piscibacillus, Haloalkalibacillus, Aerococcus, Acinetobacter, Lysinibacillus, Oceanobacillus, Planococcus, Micrococcus genera according to 16S rDNA analysis. Among these isolates, the GBA17, GBA34 and GBA36 weakly inhibit the growth of M. luteus. The analysis of 16S rDNA from different environmental samples suggests that the bacterial clones belong to the class of Gemmatimonadetes (n=1), Alphaproteobacteria (n=4), Flavobacteria (n=1), Opitutae (n=2), Gammaproteobacteria (n=1), Saprospira (n=1), Verrucomicrobia (n=1). All of the identified archeal clones were affiliated to the Class Halobacteria with 12 members belonging to the Halobacteriales order and two members belonging to the Haloferaceles order. No match was found between the taxa determined by culture-dependent method and those determined by independent method. Growth media used in the isolation experiments might not support the growth of extreme halo-alkaliphilic bacteria found as a result of cloning. Haloalkaliphilic and alkaliphilic isolates obtained in our study may be ideal candidates as industrially important substance producers.