Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

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