Abstract
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.
Highlights
Viruses are key agents of prokaryotic mortality in the global oceans and by killing their hosts they play an important role in the functioning of marine food webs and carbon and nutrient cycling[1, 2]
Available information suggests that thousands to more than a million viral genotypes can be present in marine ecosystems[5, 6] recent studies carried out in open ocean systems suggest that viral diversity could be lower than expected[7, 8]
The advent of metagenomic approaches has represented a novel opportunity for characterizing viral diversity as it allows us to capture, to a large extent, the genetic richness of viral assemblages in marine ecosystems[5,6,7,8,9, 11]
Summary
Viruses are key agents of prokaryotic mortality in the global oceans and by killing their hosts they play an important role in the functioning of marine food webs and carbon and nutrient cycling[1, 2]. While a number of studies have investigated viral diversity in the water column[8, 12, 13], only two investigations, one in shallow sediments and the other in deep-sea floor, have been carried out so far in benthic ecosystems[14, 15]. Different protocols have been used to recover viruses from water samples including ultracentrifugation, chemical flocculation, size fractionation and tangential flow filtration[12, 13, 18, 19]. Such protocols cannot be applied directly to sediment samples since viral particles need to be www.nature.com/scientificreports/. Dislodged and recovered from the sedimentary matrix before purification from non-viral particles (i.e. prokaryotes and micro-eukaryotes)[19]
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