Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome.

Bijay Kumar Behera,Pranaya Kumar Parida,Biswanath Patra,Rohan Kumar Raman,Dhruba Jyoti Sarkar,Basanta Kumar Das,Anil Rai,Atmakuri Ramakrishna Rao,Ajaya Kumar Rout,Trilochan Mohapatra,Joykrushna Jena,Hirak Jyoti Chakraborty,Parameswar Sahu,Manas Ranjan Dikhit

doi:10.1371/journal.pone.0239594

Abstract

Beneficial microbes are all around us and it remains to be seen, whether all diseases and disorders can be prevented or treated with beneficial microbes. In this study, the presence of various beneficial bacteria were identified from the sediments of Indian major Rivers Ganga and Yamuna from nine different sites using a metagenomic approach. The metagenome sequence analysis using the Kaiju Web server revealed the presence of 69 beneficial bacteria. Phylogenetic analysis among these bacterial species revealed that they were highly diverse. Relative abundance analysis of these bacterial species is highly correlated with different pollution levels among the sampling sites. The PCA analysis revealed that Lactobacillus spp. group of beneficial bacteria are more associated with sediment sampling sites, KAN-2 and ND-3; whereas Bacillus spp. are more associated with sites, FAR-2 and ND-2. This is the first report revealing the richness of beneficial bacteria in the Indian rivers, Ganga and Yamuna. The study might be useful in isolating different important beneficial microorganisms from these river sediments, for possible industrial applications.

Highlights

Rivers are known to be important for the development of human civilization, culture, and welfare
Higher diversity in the microbial species associated with the different land uses in the water and sediments of the Apies River was revealed in this study [21]
Our research indicates that the sediment metagenome of the river Ganga and Yamuna manifests the enriched microbial distribution of beneficial bacteria

Summary

Introduction

Rivers are known to be important for the development of human civilization, culture, and welfare. Since rivers are significant reservoirs of the microbiome, they are relentlessly being explored for the search of de novo microbiota These bacteria are of greater importance due to their different benefits to humans as well as all other strata of organisms present in the trophic pyramid [1]. It provides its rewarding effects generally through four main mechanisms i.e. enhancement of barrier function, intervention with host pathogens, immunomodulation, and assembly of neurotransmitters [2].

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