Metagenomic Characterization of Fungal Diversity in Lotic and Lentic Freshwater Ecosystems of Palghar District, India

Abstract

Freshwater fungal communities remain poorly characterized in many tropical regions, particularly through culture-independent approaches. The present study employed shotgun metagenomic sequencing to characterize fungal diversity in selected lotic and lentic freshwater habitats of Palghar District, Maharashtra, India. Four environmental samples representing two lotic and two lentic habitats were sequenced on an Illumina NovaSeq X Plus platform, generating approximately 25 Gb of paired-end data per sample. Fungal taxa were identified using Kaiju, and community diversity was evaluated using species richness, Shannon diversity, Simpson diversity, Pielou evenness and Bray–Curtis dissimilarity. Estimated fungal relative abundance ranged from 0.98% to 2.82%, with the highest abundance observed in Lentic 1. Basidiomycota and Chytridiomycota were prominent among the resolved fungal groups. Chytridiomycota occurred in all four samples and showed comparatively greater representation in the lotic habitats, while Lentic 1 was characterized by a strong contribution of Agaricales, particularly Coprinopsis cinerea. Lentic 1 showed the highest resolved species richness but the lowest diversity and evenness, whereas the lotic samples exhibited higher Shannon and Simpson diversity and greater evenness. Bray–Curtis analysis showed the greatest similarity between Lotic 1 and Lotic 2, while Lentic 1 was compositionally distinct. The findings demonstrate that Palghar freshwater habitats support heterogeneous fungal assemblages comprising both aquatic-associated and terrestrially derived fungal signatures and highlight the value of shotgun metagenomics for assessing understudied freshwater mycobiomes.