Bacterial and archaeal communities in near-surface marine sediments from İzmir Bay (Eastern Aegean Sea), using Quantitative PCR

Abstract

Marine sediments are good sources of both subsistent and anthropogenic ingredients. Recently, an assessment of phylogenetic analysis at the genotypic and molecular levels has revealed the phylogenetic relationships of the prokaryotes. In our study, samples were collected from the surface of sediments in the İ zmir Bay, located in the eastern Aegean Sea and surrounded by the coastal city of İ zmir. Total genomic DNA was extracted from 0.25 g sediment of each sample and used in real-time qPCR to detect 16S rDNA genes of archaea, bacteria, sulfate-reducing bacteria, Desulfobulbus , and Desulfosarcina - Desulfococcus . Our results showed that the maximum number of all samples was found in bacterial primers (1.24×10 9 DNA copy numbers/g), while the minimum number was observed in Desulfosarcina-Desulfococcus primers (1.17×10 2 DNA copy numbers/g). Consequently, genetic studies should focus on investigating the abundance levels of seasonal and annual microbial groups in future studies. analyzed by real-time PCR were identified as a comparative This study was conducted in shallow and deeply buried sediments, and real-time qPCR was used to quantify various groups of microbial primers. Copy number of 16S rRNA gene for prokaryotes, bacteria, Geobacteraceae and sulfate-reducing prokaryotes (dissimilatory (bi)sulfite reductase gene - dsrA) was also investigated. This study shows that the number of all genes in the sediment decreased with increasing depth. The gene numbers of prokaryotes and bacteria showed similar results with a maximum of 10 8 – 10 10 cm -3 gene copies in shallow sediments. The number of copies of the genes of Geobacteraceae and the sulfate-reducing prokaryotes was 10 6 – 10 8 cm -3 gene copies in the sediments. Unlike the present study, Schippers and Neretin 19 examined sulfate-reducing bacteria and common bacteria according to different genes, besides the abundance of Geobacteraceae and prokaryotes. The results of our study were similar in the number of DNA copies of sulfate-reducing bacteria and common bacteria 19 . q-PCR analysis was performed by Einen et al. 40 to quantify and detect archaea and bacteria existing in the glass shell of seabed basalts of different ages and water depths. Results of this study showed that the total number of cells present in the basalt ranged from 6×10 5 to 4×10 6 cells per gram of basalt glass. The samples were taken from different ages and water depths, however, no significant differences were found in the concentrations or relative abundance of archaea and bacteria. In contrast to our study, Einen et al. 40 with common primers for archaea and bacteria, and the study was based on the number of microbes on the surface of basalts. The study in the of