Metagenomic recovery of phage assemblage from Manikaran hot springs. Metagenomic recovery of phage ensemble

Phages are the most dominant predators of prokaryotic community at thermal springs characterized by restricted eukaryotic grazing pressures yet understanding of the phage ecology remains limited at hydrothermal environments. This study examines the metagenomic profiles of phages across Himalayan hot springs (1760 m) at Manikaran by employing the environmental data from sediment (n = 4, 78°C-98°C) and microbial mat (n = 2, 57°C) deposited around thermal discharges that led to de novo reconstruction of 65 phages (24-200 Kbp). 91% (60/65) of the phages belonged to the order Caudovirales including members from Myoviridae, Siphoviridae, Podoviridae and Inoviridae with distinguishing enrichment of Siphoviridae and Myoviridae across sediment and microbial mats, respectively highlighting the temperature driven shaping of phage community. Whole genome based analysis of the phages demonstrated well-conserved phages across sediments in contrast to the microbial mat owing to moderately mesophilic microbial mats (57°C) compared to the thermophillic sediments (78°C-98°C). A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m. In an attempt to reconstruct potential hosts for phages from the metagenome data, genomes for Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp) were assembled with integrated phages and unique CRISPR arrays suggesting prior phage infections and rapidly acquired immunity against future phage attacks at these hot springs. This study provides detailed insights into the genetic give-and-take between hosts and their phages in specific ecological niches of Manikaran thermal springs.