In Silico Comparative Metagenomic Analysis of Microbial Communities of Chromium Contaminated Sites

Rabia Sadiq, Nazia Kanwal, Yasir Rehman

Abstract

Chromium is one of the highly toxic and carcinogenic heavy metals. Due to increased anthropogenic activities, high concentration of chromium is found in many areas. Many microorganisms have the ability to detoxify chromium. Metagenomics allow us to comprehensively study microbial communities present at different sites without culturing them. The objective of this study was to analyze the abundance of microbial groups in different environments contaminated with chromium. For this purpose, chromium contaminated soil, anaerobic sludge and reactor samples were chosen. 16S rRNA data of these samples was retrieved from NCBI SRA database. The sequences were analyzed by Mothur software accessed via Galaxy server, and were classified using SILVA database. Venn diagram, phylogenetic tree, heatmap, relative abundance graphs and Krona pie charts were generated. Statistical analysis was also performed in the form of AMOVA and HOMOVA tests. According to results of our study, Proteobacteria, Leucobacter, Actinomycetales, Actinobacteria, Arthrobacter, Rhizobiales, Sphingomonas, Bradyrizobium and Nucardioidaceae were present in all the samples. Firmicutes, Planctomycetes, Verrucomicrobia and Bacteroidetes were more abundant in chromium contaminated samples as compared to control samples. The results were also found to be statistically significant. The above-mentioned bacteria can be targeted and studied to discover their roles in bioremediation of chromium contaminated sites.