Environmental Research 192 (2021) 110332 Available online 15 October 2020 0013-9351/© 2020 Elsevier Inc. All rights reserved. Functional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants Rakeshkumar Yadav a, b , Vinay Rajput a , Mahesh Dharne a, b, * a National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India b Academy of Scientifc and Innovative Research (AcSIR), Ghaziabad, India A R T I C L E INFO Keywords: MinION Xenobiotics Benzoate Riverine system Bioremediation ABSTRACT Rapid industrialization contributes substantially to xenobiotic pollutants in rivers. As a result, most of the rivers traversing urban settlements are in signifcantly deteriorated conditions. These pollutants are recalcitrant, requiring robust catabolic machinery for their complete transformation into bioavailable and non-toxic by- products. Microbes are versatile dwellers that could adapt to such contaminants by using them as a source of nutrients during growth. However, effcient bioremediation requires an in-depth knowledge of microbial di- versity and their metabolism related genes in the polluted niches. We employed MinION shotgun sequencing, to comprehend the biodegradation related genes and their function potential operating in the polluted urban riverine system of Western India. A vast number of catabolic genes were detected for the xenobiotic pollutants such as Benzoate, Nitrotoluene, Aminobenzoate, Drug metabolism, and Polycyclic Aromatic Hydrocarbons. Aerobic, and anaerobic catabolism genes, were mapped for their ability of degradation of xenobiotics. Inter- estingly, catabolism profles of multiple aromatic compounds culminated into the Benzoate degradation pathway, suggesting it as a plausible central pathway for the autochthonous bacterial communities. Further mapping with RemeDB database, predicted plastic and dye degrading enzymes. Moreover, the diversity indices for the pollutant degrading enzymes suggested little variations (R 2 value of 18%) between the city and non-city (outskirts of city limits) riverine stretch indicating the impact of industrialization in the outskirts of the city stretch as well. Altogether, this study would serve as a preliminary baseline for future explorations concerning river cleaning programs and also exploiting such microbes for bioremediation applications. 1. Introduction Conservation and safeguarding of water is an absolute necessity to save all the life forms on planet Earth. Rapid population explosion, ur- banization and industrialization along the river basins have severely impacted river health and resulted in its deterioration (Suthar et al., 2009). Undoubtedly, industrialization has provided an immense op- portunity and have transformed human life with economic and social developments; however, it has also brought unpleasant environmental pollution with it. This has resulted in generation and dumping of various toxic contaminants and xenobiotics to the water bodies, especially in the rivers traversing the urban settlements (Malla et al., 2018; Mittal et al., 2019). India has a vast network of rivers. However, most of the rivers are in extremely dismal conditions (Water Quality data, CPCB). Urban rivers have a multitude of benefts for the city dwellers; however, the pollution of the urban river is becoming more critical (Wang et al., 2012; Suthar et al., 2009). The untreated sewage or wastewater is one of the main reasons for their contamination and pollution (Marathe et al., 2017). Pune is among the fastest-growing cities in the western part of India. Mula, Mutha, Pawana, Ramnadi, Indrayani, and Bhima Rivers that fow in Pune district. The Mula-Mutha, Ramnadi, and Pawana rivers mostly traverse urban stretches and are affected by wastewaters from in- dustries, domestic sources and hospitals. The Mula and Mutha join Bhima River in the downstream outside the city stretches. Presently, these rivers are in dismal conditions, and it is progressively worsening (Water Quality data CPCB, Yewale et al., 2019; Nawani et al., 2016). Xenobiotic pollutants such as Polycyclic aromatic hydrocarbons, azodyes, halogenated compounds, nitroaromatic compounds triazines and many more are recalcitrant and persistent chemicals having adverse and toxic effects (Godheja et al., 2016). Untreated sewage and industrial effuents result in the pollution of the surface water bodies, especially * Corresponding author. NCIM Resource Centre, CSIR-NCL, Dr. Homi Bhabha Road, Pune, 411008, India. E-mail addresses: rj.yadav@ncl.res.in (R. Yadav), v.rajput@ncl.res.in (V. Rajput), ms.dharne@ncl.res.in (M. Dharne). Contents lists available at ScienceDirect Environmental Research journal homepage: www.elsevier.com/locate/envres https://doi.org/10.1016/j.envres.2020.110332 Received 3 June 2020; Received in revised form 3 September 2020; Accepted 7 October 2020