Genome-resolved metagenomics of Naini Lake reveals a diverse microbial community and uncharacterized biosynthetic gene clusters

Background Freshwater lakes are an important source of water for drinking and irrigation, and a habitat for aquatic plants and animals. These crucial ecosystems harbor diverse microbial communities and drive biogeochemical cycles. Here, we present the metagenomic characterization of the microbial community and the functional potential of surface water from the mid-altitude Naini Lake in India. Results Shotgun metagenomic sequencing of the lake water revealed a diverse and potentially novel microbial community comprising 212 species, of which 74% remain taxonomically uncharacterized. We reconstructed 56 metagenome assembled genomes (MAGs), including 29 high-quality draft genomes spanning diverse phyla such as Pseudomonadota, Actinomycetota, and Bacteroidota. The MAG (NTL.71) corresponding to the dominant taxon in Naini Lake (GGB26613_SGB38793; 17% relative abundance) encoded pmoABC genes, indicating potential for methane oxidation. The MAGs exhibited functional potential in nutrient cycling, metalloid metabolism, and xenobiotic transformation, reflecting the adaptive microbial architecture of an anthropogenically impacted freshwater ecosystem. The MAG collection contained 184 biosynthetic gene clusters (BGCs), with most predicted BGC families lacking overlap with MIBiG 4.0, indicates novelty relative to experimentally characterized reference data. We detected 37 unique antimicrobial resistance genes across 11 drug classes, including 21 clinically relevant markers like aadA-ANT(3''-IIa , tet(M) , erm(O), APH(3'')-Ib, erm(E), APH(6)-Id , pmrF , and sul2 as well as 66 virulence factors predominantly associated with immune modulation and motility. Conclusions Together, these findings establish a baseline genomic resource for Naini Lake, documenting its microbial diversity, functional potential, determinants of antimicrobial resistance, and biosynthetic capacity, and providing a reference point for future genome-resolved studies of mid-altitude freshwater ecosystems.