Abstract
Hot spring-associated viruses, particularly the archaeal viruses, remain under-examined compared to bacteriophages. Previous metagenomic studies of the Manikaran hot springs in India suggested an abundance of viral DNA, which prompted us to examine the virus–host (bacterial and archaeal) interactions in sediment and microbial mat samples collected from the thermal discharges. Here, we characterize the viruses (both bacterial and archaeal) from this Himalayan hot spring using both metagenomics assembly and electron microscopy. We utilized four shotgun samples from sediment (78–98°C) and two from microbial mats (50°C) to reconstruct 65 bacteriophage genomes (24–200 kb). We also identified 59 archaeal viruses that were notably abundant across the sediment samples. Whole-genome analyses of the reconstructed bacteriophage genomes revealed greater genomic conservation in sediments (65%) compared to microbial mats (49%). However, a minimal phage genome was still maintained across both sediment and microbial mats suggesting a common origin. To complement the metagenomic data, scanning-electron and helium-ion microscopy were used to reveal diverse morphotypes of Caudovirales and archaeal viruses. The genome level annotations provide further evidence for gene-level exchange between virus and host in these hot springs, and augments our knowledgebase for bacteriophages, archaeal viruses and Clustered Regularly Interspaced Short Palindromic Repeat cassettes, which provide a critical resource for studying viromes in extreme natural environments.
Highlights
Viruses are the most prominent predators and mediators of genetic transmission in prokaryotic communities in extreme thermal environments, which are characterized by lack of eukaryotes (Breitbart et al, 2004)
The Himalayan hot springs located at Manikaran were analyzed for prokaryotic viral genomic signatures
We demonstrated that the microbial mats at Manikaran are enriched in bacterial genera such as Enterobacter, Bdellovibrio, Clostridium, and Achromobacter (Sangwan et al, 2015)
Summary
Viruses are the most prominent predators and mediators of genetic transmission in prokaryotic communities in extreme thermal environments, which are characterized by lack of eukaryotes (Breitbart et al, 2004). A series of Himalayan hot springs (surface temperature > 95◦C) located at an altitude of 1,760 m at Manikaran (32◦02 N, 72◦21 E) have previously been investigated using sequencing approaches to characterize the bacterial communities (Dwivedi et al, 2012; Mahato et al, 2014; Sharma et al, 2014, 2016b; Tripathi et al, 2016). Cultureindependent analysis of the sediment and microbial mat samples demonstrated unexpectedly high microbial diversity in these hot springs (Sangwan et al, 2015; Sharma et al, 2016a). Sediment samples with temperatures ranging from 78 to 98◦C were dominated by archaeal genotypes, while microbial mats maintained high abundance of resident bacterial populations with integrated phage DNA (Sangwan et al, 2015). The role of these viruses in microbial community dynamics remains undetermined
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