Metagenomics of India's largest River Ganges confluence at Prayagraj, India using MinION sequencing

Mahesh Dharne of the CSIR – National Chemical Laboratory in India, closed this Environmental metagenomics breakout session with a fascinating presentation on the metagenomics of the River Ganges. The Ganges, which winds 1,560 miles across northern India, is the most sacred river in Hindu religion. It drains a quarter of the Indian subcontinent and acts as a lifeline for millions of people. Mahesh described how, over 100 years ago, scientists demonstrated that the river contains antibacterial properties which were later assigned to the presence of bacteriophages. More recent research has demonstrated the presence of bacteriophages in the water even at its origin in Devprayag. Although pollution of the river is increasing, many religious events are held at the Ganges, and Mahesh played a short video showing tens of thousands of people lining the riverbank and bathing in the water. In 2017, a comprehensive multi-centre project to assess the water quality and special properties of the river was initiated, covering many scientific disciplines, including biological analysis. The CSIR, is central to this work, and under Mahesh’s guidance conducted a metagenomic analysis of the river. They carried out their research on water and sediment samples collected from the Ganga-Yamuna confluence. The Yamuna is the longest tributary to the Ganges, contributing 16% of its water volume. It is also the most polluted river in India. This project aimed to understand the influence of the Yamuna on the microbial community at the confluence and further downstream.

The team at CSIR utilised a metagenomic sequencing approach on the MinION to characterise samples taken from seven different locations along the river. Using the WIMP workflow available within Oxford Nanopore’s EPI2ME real-time data analysis platform, they were able to accurately assess the diversity of microbial samples. Mahesh reported how, using this approach, they identified the relative abundance different genera of bacteria, archaea, fungi, and viruses.

While most sampling locations displayed similar microbial composition, there were clear differences in the relative abundance of specific genera for sampling sites near the confluence of the two rivers. Expanding on the metavirome analysis, Mahesh stated that the Ganges displayed a unique viral diversity, encompassing a plethora of bacteriophages against several pathogenic and putrefying bacteria such as Vibrio, Campylobacter, Salmonella, Shigella, Klebsiella, Enterobacter, Clostridium, and Bacillus. He postulated that this may correlate with previous scientific discovery of the river’s non-putrefying properties.

In summarising this work, Mahesh commented that while the similar microbial composition and abundance of samples taken further up and downstream of the confluence showed the effect of the Yamuna river to be transitory.

The team are now performing additional analyses to, amongst other things, assess the impact of mass bathing events on the microbiome, and understanding the impact of the Ganja rejuvenation plan. Mahesh revealed that his lab is also currently utilising the MinION to characterise the microbiome of the Lonar Lake (India) and Unkeshwar hot spring.