38River confluences are a hub of biodiversity with limited information with respect to the structure and the 39 functions of the microbial communities. The 'River Ganges' is the national river of India, having manifold 40 significance such as social, mythological, historic, geographic and agro-economic. It forms a sacred confluence 41 (known as Triveni Sangam) with River Yamuna at Prayagraj, India. Recent reports indicated the presence of fecal 42 coliform bacteria, an indicator recognized for water contamination in Ganges River leading to pollution. However,
43Fungi are also gaining attention as potential biological indicators of the trophic status of some rivers globally, but 44 remain under-explored in terms of diversity, ecology and functional aspects. We performed whole long read, 45 metagenome sequencing (MinION) of the sediment samples collected in December 2017 from confluence zone of 46 Ganges and Yamuna Rivers spanning the pre-confluence, confluence and post-confluence zones. Mycobiome reads 47 revealed a plethora of fungal communities, extending from saprophytes, endoparasites and edible fungi, to human 48 pathogens, plant pathogens and toxin producers. The fungal genera recognized as bio-indicators of river pollution 49 (Aspergillus, Penicillium) and eutrophication (Kluveromyces, Lodderomyces, and Nakaseomyces), were present in 50 all samples. Functional gene analyses of myco-communities uncovered hits for neurodegenerative diseases and 51 xenobiotic degradation potential, supporting bio-indicators of pollution. This study forms a foundational basis for 52 understanding the impact of various anthropogenic activities on the mycobiome, as a bio-indicator of pollution 53 across the confluence of Ganges and Yamuna Rivers and post-confluence of River Ganges, and could be useful in 54 mitigating strategies for cleaning strategies of the Ganges River.55