Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India.

Bijay Kumar Behera,Hirak Jyoti Chakraborty,Pranaya Kumar Parida,Basanta Kumar Das,Trilochan Mohapatra,Dhruba Jyoti Sarkar,Biswanath Patra,Rohan Kumar Raman,Atmakuri Ramakrishna Rao,Ajaya Kumar Rout,Budheswar Dehury,Anil Rai

doi:10.3389/fmicb.2020.556136

Abstract

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus–Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

Highlights

Aquatic environmental pollution is a global threat to natural biodiversity and human health (Nicolopoulou-Stamati et al, 2016)
The present results suggested that the relative abundance of bioremediation microbial communities was significantly correlated with polluted sites at river Ganga and Yamuna
The present analysis showed that the relative abundance of bacterial and fungal species of bioremediation potential is better correlated with the polluted sites of the river as compared to less polluted sites i.e., Farakka stretch

Summary

Introduction

Aquatic environmental pollution is a global threat to natural biodiversity and human health (Nicolopoulou-Stamati et al, 2016). The indiscriminate use of pesticides in agriculture and household results in a significant amount of their residues in an environment which eventually washes out to natural streams like rivers, wetlands, and to sea, causing a huge disruption in the natural aquatic biodiversity. Several aquatic ecosystems including rivers, wetlands, and sea were being continuously monitored regularly for assessing the level of OC and their risk assessment on aquatic life (DiScenza et al, 2017; Fair et al, 2018; Unyimadu et al, 2018) Due to their high lipophilicity properties, they are being adsorbed on the river sediments and by the aquatic fauna. Lambda-cigalothrine, a pyrithroid insecticide has been reported to cause the alleviation of free amino acid content in the muscle, liver, and brain of fishes in the Alazani River (Dzhikiia et al, 2011)

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Conclusion