A 16s rRNA amplicon-based study on the microbial taxonomic and functional diversity of eutrophic urban lakes in Dhaka, Bangladesh

Abstract

Natural bioremediation mechanisms and strategies of lakes largely depend on its bacterial community. Abundance of core bacterial taxa collectively determines the dominant bioremediation and metabolic adaptation strategies. Understanding the microbial diversity in urban lakes could contribute significantly in lake health management. 16s rRNA amplicon sequencing can capture the taxonomic and functional abundance which can generalize the functional trends in the given system and implement in bioremediation. This study implemented metagenomic approach to unveil the taxonomic diversity and functional potential of two eutrophic urban lakes (Ramna and Gulshan Lake) of Dhaka, Bangladesh. Our findings suggest that, sediment of Ramna lake (OTUs = 4864; Shannon Index = 7.369) was more diverse and enriched with taxa than water of Ramna (OTUs = 1520; Shannon Index = 4.572) and Gulshan Lake (OTUs = 1671; Shannon Index = 4.987). Proteobacteria and actinobacteria dominated the water of both Ramna (Proteobacteria = 31.01% and Actinobacteria = 50.94%) and Gulshan Lake (47.73% and 11.8%), while Acidobacteria was the key phylum in sediment of Ramna Lake (23.25%). Interestingly, water and sediment of the lakes shared extensive similarity in terms of functions, where transporters, amino acid, carbohydrate and xenobiotic metabolism were prominent. However, the comparatively less eutrophic lake was more abundant with transporters and metabolism and less abundant with bacterial motility and secretory function. Overall, we report a significant functional homogeneity and taxonomic heterogeneity in the trophic levels of the studied lakes. Given the predicted abundance of mercury-resistance function in KEGG annotation, we isolated and identified a Bacillus or Cytobacillus species bacteria that can withstand approximately 150 ppm mercury, which can have implication in metal bioremediation.