Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

Abstract

Background: In aquatic ecosystems, bacteriophages play key roles in species diversity, host population dynamics and functional gene transfer. Due to a lack of high-throughput experimental tools to obtain robust associations between bacteriophages and hosts, the current metagenome-based phage community research generally predicts interactions based on various computational pipelines. In this study, by introducing an in vivo proximity-ligation chromosomal confirmation capture (Hi-C) technique combined with existing sequencing data from a freshwater metagenome study, we investigated double-stranded DNA (dsDNA) bacteriophages distribution, bacteriophage-host associations and abundance profiles at various depths in a deep alpine lake.Results: A total of 985 nonredundant viral genomes (containing 1,464 viral contigs measuring at least 10 kb) were identified using rigorous bioinformatic pipelines, and 67.3% of bacteriophages had never been reported previously. The bacteriophages had a significant depth-dependent distribution, and 56.9% of phage populations were only present in the epilimnion. Overall, 567 auxiliary metabolic genes (AMGs) were identified in 239 phages (24.26% of the total population). Hi-C reconstructed 58 bacteriophage-host association events encompassing eight bacterial phyla, among which 14 AMG-coding bacteriophages were clearly linked to their hosts. Three bacteriophages contained the mec gene, which was exactly complementary to their hosts in the sulfur-related pathway, and three other bacteriophages contained AMGs that likely participated in host fructose and mannose metabolism.Conclusions: The present study identifies bacteriophages in Lake Fuxian and describes the bacteriophages and their host dynamics along the depth profile. Our results indicate that metagenomics combined with the Hi-C technique has promise for future applications in high-throughput bacteriophage identification and bacteriophage-host association detection, which could further extend our knowledge of the functional roles played by bacteriophages in aquatic ecosystems.

Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species

“…It enables the identification of DNA molecules that are physically co-located near one another within a cell through next-generation sequencing. Hi-C sequencing has also been recently applied to artificial metagenomes [115] and recently to natural metagenomes [116] to assemble genomes of different species and identify the structure of chromosomes, the presence of plasmids within cells and potentially host and viral interactions [117]. Other molecular biology techniques, such as proximity ligation, have recently been applied to marine water samples to identify novel virus-host associations [118].…”

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

“…An alternative approach for phage-host identification, which has been shown to be quite accurate, is metagenomics proximity-ligation sequencing 55,56,[56][57][58][59][60][61] . This technique captures phage-bacterial chromosome interactions in three-dimensional space, enabling the identification of phage genomes and bacterial genomes that are in very close physical proximity to one another (i.e., in the same cell; Fig.…”