An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported

In this study, we infer SYBR-stained fluorescent particles that pass through some size cutoff, generally 0.2 μm, to be viruses. This operational definition will exclude prophage, giant viruses, and may exclude viruses that do not stain efficiently such as ssDNA and RNA viruses. It will also encompass membrane vesicles, gene transfer agents and very small cells. However, recent studies have suggested that membrane vesicles are only a minor portion of SYBR-stained particles compared to viruses (Biller et al., 2017). The majority of studies employing fluorescent staining techniques use this general criterion when determining values for “viral abundance” and “virus counts.” The term “virus-like particle” (VLP) has also been used to describe these particles, however, this can cause confusion because the term is also used in immunology to refer to virus-derived particles that lack nucleic acids. Even within the same study, the terms “VLP” and “virus” are often used interchangeably. Therefore, for the sake of consistency, we use only the term “virus,” inferred by SYBR-stained particles that pass through 0.2 μm filtration, throughout this paper. Some studies of sedimentary viruses include a nuclease treatment step in order to reduce background fluorescence or to degrade extracellular DNA which may appear as fluorescing particles (Fischer et al., 2005; Helton et al., 2006; Danovaro and M...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research