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

•First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved...

Full description

Saved in:
Bibliographic Details
Published in:Virus research 2023-06, Vol.330, p.199110-199110, Article 199110
Main Authors: Mukhopadhyay, Adhip, Choudhury, Shubham, Kumar, Manoj
Format: Article
Language:English
Subjects:
Antibiotic resistance gene
Auxiliary metabolic gene
Bacteriophage
Bacteriophages - genetics
DNA Viruses - genetics
Ecosystem
Freshwater
Metagenomics
N-Choe
Rivers
ssDNA virus
Stream
Virome
Viruses - genetics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:•First insight into the viral community composition in a stream sediment ecosystem.•Classified virome fraction indicated the dominance of ssDNA viruses.•Recovered uncultivated viral genomes (UViGs) hint at novel community structure as per existing databases.•Auxiliary metabolic genes (AMGs) involved in pyrimidine, carbohydrate, and organosulfur metabolism were detected.•Identified antibiotic resistance genes indicate the potential roles of viruses as ARG reservoirs. 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.
ISSN:0168-1702
1872-7492
DOI:10.1016/j.virusres.2023.199110