An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach

Abstract

Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.

Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica

“…We also saw evidence of rich diversity across clusters; phages from sewage were assigned to different clusters (e.g., Clusters 1, 7, 8, 11, and 12) or could not be assigned a specific cluster (Figure 2). As wastewater is abundant in nutrients, bacterial hosts, and high rates of horizontal gene transfer, phages isolated from these sites represent a reservoir of novel and diverse genetic materials [45].…”

Bacteriophages in Natural and Artificial Environments

“…However, at the genome level they can be diverse and share no DNA sequence similarity. The most abundant of these is the Siphoviridae phage, which is not limited to the marine environments but also to many other habitats [71,72].…”

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria

“…In hot spring communities, the role of secondary metabolites as weapons of inter-microbial warfare (O'Brien and Wright, 2011) could be diminished and susceptible to loss. Furthermore, viral and exogenous nucleic acids are less diverse in hot springs (Parmar et al, 2018), and cyanobacteria are subjected to strong viral predation and potential coevolution (Guajardo-Leiva et al, 2018), as also seen for other thermophilic organisms (Breitbart et al, 2004). Therefore, the prevalence of the CRISPR-Cas system in their genomes could be more important than in non-thermal genomes as seen in other phyla (Weinberger et al, 2012).…”