Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics
Graphical abstract
Introduction
Microbes play a critical part in the functioning and balancing of an ecosystem. The sediments near riverbanks harbour unique microbial assemblages for performing the metabolic functions like biogeochemical and nutrient cycling, biophysical processes, and energy flow in the river ecosystems (Liu et al., 2011; Shade et al., 2012, Zhang et al., 2016). Microbial load in the sediments, and their sensitivity towards environmental cues and anthropogenic disturbances are often considered as indicators of river ecosystem health (Chen et al., 2018). Studies have shown that most anthropogenically disturbed river sites foster various pathogenic taxa and fecal indicators that impose serious health issues (Bojarczuk et al., 2018, Páll et al., 2013). Population explosion, industrialization, direct discharge of waste (agricultural, industrial, and fecal matter), and water scarcity are significant contributors to the present degradation of these ecosystems (Chakarvorty et al., 2015). Emergence of novel antibiotic resistant bacterial strains and its associated health risks urge us to explore the microbial community structure of the riverine ecosystems.
Waterborne diseases contribute to about 2.2 M annual deaths globally (Maramraj et al., 2020) and in India, 37.7 million people are affected by this (Ananth et al., 2018). Cholera, gastroenteritis, and diarrhoea break out annually during summer and rainy seasons due to low-quality drinking water and sanitation in the country (Jofre et al., 2009). Therefore, it is vital to monitor fecal contamination and pathogens in the river systems used for human consumption. Conventional monitoring studies rely heavily on the microbial culture-based enumeration of fecal/sewage (F/S) indicator bacteria and assessment of pathogenic bacteria (Srivastava et al., 2017; Vincy et al., 2017). However, since these methods target a few pathogens/fecal/sewage indicator bacteria, comprehensive range monitoring of water bodies is an essential prerequisite. High throughput amplicon sequencing (16S rRNA) through Next Generation Sequencing (NGS) approach could overcome these limitations in exploring the microbial communities and indicators. Few recent studies have utilized such platforms for monitoring various biomes like river (Vadde et al., 2019), shellfish growing areas (Leight et al., 2018) and dairy farm (Zhang et al., 2019a) validating its wide application.
Himalayan and Peninsular river systems of India differ in their origin, geographical aspects, and physicochemical characteristics. River Ganga-Yamuna of the Himalayan river system is amongst the heavily polluted rivers worldwide (Chaudhary and Walker, 2019, Malik et al., 2014). Likewise, Periyar river of the Peninsular river system is considered as exemplars of industrial pollution (Lakshmi and Madhu, 2020). Recently, metagenomics has been utilized to study the microbial diversity of some Indian rivers like Ganga- Yamuna (Reddy and Dubey, 2019; Samson et al., 2019), Godavari (Jani et al., 2018) and Cauvery (Suriya et al., 2017). Meanwhile, in the Periyar river, studies have primarily focused on determining the physicochemical parameters of water/sediments, isolation of heavy metals and antibiotic resistant microbes (Lakshmi and Madhu, 2020, Prasanth and Mahesh, 2016, Salas et al., 2017). Further, there lies a void in ascertaining the factors responsible for framing the distinct microbial communities and indicators in these ecosystems.
In this backdrop, the present study aims to utilize metagenomics to explore differences between the microbial communities in the Himalayan and Peninsular river systems. Association of microbiomes with diverse environmental factors in these rivers was also figured out. Additionally, abundance of microbial pollution indicators (fecal/sewage and pathogens) was also examined to reveal the health risks associated with these major river systems.
Section snippets
Sampling area description, design, and collection
Areas around the major metropolitan city landscapes with high domestic and industrial pollution, namely Delhi and Kochi for Himalayan and Peninsular rivers respectively, were chosen for the study. Capturing the patterns of microbial diversity and pathogenic taxa in this gradient of anthropogenically influenced areas were assured by sampling both upstream and downstream of the industrial belts. Since following the entire river course is not feasible due to the rivers’ extensive length, we tried
Environmental parameters
Physicochemical parameters like pH, temperature, salinity, and different major/minor elements in the sediments were estimated from the eleven samples and summarized in Table S2. The pH values (7.06 ± 0.5) indicated neutral to alkaline nature of the studied samples. Himalayan samples were significantly more alkaline than Peninsular samples (p < 0.01). Salinity values ranged within 1.65 ± 2.7, with Peninsular samples being slightly more saline in nature. The temperature in Peninsular samples was
Discussion
The recent explosion of metagenomics studies based on next-generation sequencing has immensely enabled exploring microbial communities of unique ecosystems ranging from gut microflora to deep seafloors (De et al., 2020; Grossart et al., 2020). The tool is slowly gaining momentum with increasing number of applications like surveillance of microbiome quality changes with ecological disturbances or pollution (Alves et al., 2018; Chen et al., 2019). One such monitoring application currently being
Conclusions
Overall, our study indicates that microbiomes are shaped through the significant influence of intrinsic and extrinsic factors existing in the Himalayan and Peninsular riverine ecosystems. Besides, detection of various potentially pathogenic and F/S associated indicators reveals the impending health risks owing to sewage and domestic pollution of these water bodies. The study recommends the urgency to devise effective strategies for proper management of domestic sewage and industrial effluents
Credit author statement
Aparna Chakkamadathil Rajeev: Conceptualization, Methodology, Investigation, Writing – original draft, Writing - Review & Editing, Validation, Formal analysis, Visualization, Software Nishi Sahu: Conceptualization, Methodology, Investigation, Writing – original draft, Writing - Review & Editing, Validation, Formal analysis, Visualization Kumar Arvind: Software, Formal analysis Maushumi Deori: Resources Tony Grace: Resources, Validation, Writing - Review & Editing Suma Arun Dev: Visualization,
Funding
Financial assistance for this study was provided by UGC, JNU DST-PURSE, and JNU UPE-II. The funders had no role in the study design, data collection, interpretation, or the decision to submit the work for publication.
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgments
We appreciate the late Vijay Pal Yadav contributions to the design and initial execution of (Peninsular river project) this research project. We also thank Krishna Kumar (IFS), former deputy director of Periyar Tiger Reserve, and P. S. Easa, former director, Kerala Forest Research Institute, for their help during the sample collection in Periyar Lake. We would like to appreciate the wholehearted support from Bishi E. Balan for sample collection (Peninsular samples). We would like to appreciate
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