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

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.

Ganga river water quality assessment using combined approaches: physico-chemical parameters and cyanobacterial toxicity detection with special reference to microcystins and molecular characterization of microcystin synthetase (mcy) genes carrying cyanobacteria

“…Molecular technique such as polymerase chain reaction (PCR) based detection of mcy genes (mcyA, mcyB, mcyD, mcyE and mcyG) is rapid, cost-effective as well as facilitated the culture independent identi cation of toxic cyanobacteria in environmental samples (Genuario et al 2010; Ribeiro et al 2020). Numbers of studies were available on the assessment of river Ganga water quality based on physico-chemical parameters, bacterial and fungal diversity and metal toxicity (Behera et al 2020;Matta et al 2020;Prasad et al 2020;Dimri et al 2020). But so far, only one report has published that monitored the pollution in river Ganga in relation to the appearance of MCs producers (two strains isolated were named Oscillatoria sp.…”

Biofloc Microbiome With Bioremediation and Health Benefits

“…Bioremediation is a process of contaminated water or waste treatment into less toxic form using beneficial microorganisms ( Das et al, 2019 , 2020 ; Behera et al, 2020a , b ). It is achieved by inducing the biological process that leads to reduction, removal, and conversion of the contaminated compounds ( Table 2 ) ( Divya et al, 2015 ; Jasmin et al, 2020 ).…”

New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain

“…On the contrary, positive impacts of these fungi include their use in food fermentations, the production of many bioactive compounds of medical interest (antimicrobial agents, immunosuppressants), and the production of enzymes with a variety of industrial applications (Houbraken et al 2014;Visagie et al 2014a;Abdelwahab et al 2018;Park et al 2019;Ogaki et al 2020a, b). Other recent applications are the potential use of some species as biocontrol agents against plant pathogens or for bioremediation in polluted environments (Guijarro et al 2017;Cecchi et al 2019;Behera et al 2020;Thambugala et al 2020;Liang et al 2021). The discovery of novel lineages in the genus Penicillium, therefore, represents an opportunity to find and characterize new fungi or molecules with a wide range of applications.…”