A metagenomic snapshot of metabolic potentials in wintertime eutrophic sediments of Lake Taihu inferred from metagenome-assembled genomes

Abstract

Understanding the metabolic potential of microbial communities in eutrophic lake sediments at the genome-resolved level is essential for predicting nutrient cycling and stress responses in contaminated freshwater ecosystems. In this study, we reconstructed 206 dereplicated metagenome-assembled genomes (MAGs) from sediment cores collected across four regions of Lake Taihu. These dereplicated MAGs spanned 34 classified phyla and 72 classified genera, with 97.6% unclassified at the species level, indicating substantial genomic novelty. The cyanobacterial MAGs harbored diverse secondary metabolite biosynthetic gene clusters, suggesting a genomic basis for potential adaptive traits. Across all dereplicated MAGs, the highest biosynthetic potential for secondary metabolites was observed in Chloroflexota and Pseudomonadota. Putative antibiotic resistance genes were predominantly represented by glycopeptide resistance determinants (vanT/vanW) and resistance-nodulation-division (RND) efflux pumps, which together accounted for 86.1% of the detected resistome. Additionally, 490 predicted horizontal gene transfer (HGT) events were identified, with transferred genes being most prevalent in energy metabolism (12.4%), translation (10.8%), and transcriptional regulation (7.2%). This genome-resolved survey provides a foundation for understanding the metabolic and genomic potential of sediment microbiomes in eutrophic freshwater systems.