Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India

Abstract

Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.