Molecular genetic monitoring of bacterial communities in manzala lake, egypt, based on 16S rRNA gene analysis

Abstract

A first molecular genetic study on the diversity of bacterial communities at Manzala Lake, Egypt, was determined by culture-independent 16S rRNA gene analysis. Bulk DNAs were extracted from water and sediment at two different sampling sites namely; Bashtir and Genka, in the lake. The 16S rRNA gene was positively amplified by polymerase chain reaction (PCR) from bulk DNA of each sample, cloned and sequenced. The sequence analysis of one hundred clones from each clone library obtained number of phylotypes ranged from 8 phylotypes, in Genka water, to 20 phylotypes in each of the sediment samples. The 16S rRNA gene showed diversity in sediment samples higher than in water samples. Based on Libshuff pairwise clone library comparisons, the 16S rRNA gene phylotypes from Bashtir water encompassed the phylotypes of Genka water, while the phylotypes of Genka water account only a portion of those of Bashtir water. Both water and sediment samples were dominated by phylotypes closely related to different classes of the phylum Proteobacteria. Most of the recovered water phylotypes from the two sites were localized in the branches of Cyanobacteria, Proteobacteria and Bacteroidetes. Genka water was differentiated from Bashtir by harbouring a phylotype related to the phylum Firmicutes. Several phylotypes from Bashtir and Genka sediments were affiliated to species from the phyla Proteobacteria, Chloroflexi, Bacteroidetes, and Planctomycetes. Genka sediment sample had two phylotypes affiliated to Fusobacteria, a character differentiated this sample from that of Bashtir, which characterized by a phylotype belonging to Actinobacteria. Other sediment phylotypes constituted unique phylogenetic lineages, suggesting new bacterial phyla. The obtained results clearly demonstrated that each studied site has unique bacterial phylotypes that can be used as site-characterizing biomarkers. The successes of this study were the determination of the actual composition of bacterial populations in the studied samples and the discovery of novel bacterial phylotypes, never recorded by traditional techniques.