Bacteriophages are the most dominant predators of prokaryotic communities in thermal springs yet understanding of the phage ecology remains limited in these hydrothermal environments. Here we examine the metagenomic phage profile from hot spring sediments (n = 4, 78°C-98°C) and microbial mats (n = 2, 57°C). Caudovirales comprised 91% of the 65 reconstructed phage genotypes, including members of the Myoviridae, Siphoviridae, Podoviridae, and Inoviridae. Siphoviridae were predominant in the sediment and Myoviridae in the microbial mats. Phage genomes were often more well-conserved across sediments compared with microbial mats, which could suggest that there are fewer hosts in the sediments, which represent an extreme environment (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, which are part of survival strategy of bacterial communities at thermophillic environments. We reconstructed bacterial genomes, including Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp), which were predicted to be hosts based on integrated phage DNA and unique CRISPR arrays, suggesting prior phage infections. This study provides detailed insight into the genetic give-and-take between hosts and phages in the ecological niches of thermal springs.
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