Bacterial diversity in sediments of river Mahananda (Siliguri) as determined by 16S rRNA gene analysis

Abstract

Analyses of 16S ribosomal (r) DNA clone library have enabled to assess the bacterial diversity in the sediment of an anthropogenically stressed river Mahananda at Siliguri, India. A total of 178 clones were examined by amplified rDNA restriction analysis (ARDRA) using <i>Hae</i>III (four base specific restriction enzyme). According to the restriction patterns generated from ARDRA, 71 clones were selected as operational taxonomic units (OTUs) and sequenced. No clones were identical to any of the known 16S rRNA sequences or to each other. Sequencing analysis revealed eight distinct major lineages of bacteria [α-, β-, γ-, ε-<i>Proteobacteria</i>, <i>Bacteroidetes</i>, <i>Firmicutes</i>, <i> Chloroflexi</i> & <i>Planctomycetes</i>]. About 69.66% of the sequenced clones were grouped into <i>Proteobacteria</i> [comprising α (12.90%), β (45.96%), γ (2.41%) & ε (38.70%)] and 29.21% were included amongst the divisions other than <i>Proteobacteria</i> represented by <i>Bacteroidetes</i> (34.61%), <i>Firmicutes</i>(57.69%),<i>Chloroflexi</i> (3.84%) and <i>Planctomycetes</i> (3.84%). 16S rRNA gene phylotypes only distantly related to any of the previously identified sequences (non-affiliated rRNA genes) represent a significant fraction of the total cloned sequences. This is the first report describing microbial diversity of Mahananda river sediment by using metagenomic approach. The results suggest that the sediment of river Mahananda is the reservoir of unexplored microbial resources.