Abstract
Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities involved in efficiently extracting viruses from a sediment matrix. Here, we developed a new method for the extraction of viruses from sediment based on density separation using a Nycodenz density step gradient. The density separation method resulted in up to 2 orders of magnitude greater recovery of viruses from diverse subseafloor sediments compared to conventional methods. The density separation method also showed more consistent performance between samples of different sediment lithology, whereas conventional virus extraction methods were highly inconsistent. Using this new method, we show that previously published virus counts have underestimated viral abundances by up to 2 orders of magnitude. These improvements suggest that the carbon contained within viral biomass in the subseafloor environment may potentially be revised upward to 0.8–3.7 Gt from current estimates of 0.2 Gt. The vastly improved recovery of viruses indicate that viruses represent a far larger pool of organic carbon in subseafloor environments than previously estimated.
Highlights
Marine sediments are a major biome on Earth, covering 3/4 of the Earth’s surface and containing approximately 1029 cells (Kallmeyer et al, 2012)
The extraction was performed using conventional protocols used for virus counts of subseafloor sediment cores (Engelhardt et al, 2014; Yanagawa et al, 2014)
The density separation method resulted in dramatically greater numbers of extractable viruses
Summary
Marine sediments are a major biome on Earth, covering 3/4 of the Earth’s surface and containing approximately 1029 cells (Kallmeyer et al, 2012). Improving the efficiency of separation from subsurface sediment may make it possible to extract more viral DNA from less sediment, opening the doors to a wide spectrum of viral metagenomic studies in subseafloor sediments. To this end, we developed a buoyant density based separation method modified from similar cell separation methods used for deep subseafloor sediments (Morono et al, 2013). Using a variety of diverse subseafloor sediments, we compared the density separation method to conventional methods used for deep subseafloor virus enumeration (Engelhardt et al, 2014; Yanagawa et al, 2014)
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