Abstract
Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron-based flocculation and large-pore-size filtration, followed by resuspension of virus-containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.
Highlights
Twenty years since the discovery that viruses are abundant in aquatic systems (Bergh et al, 1989; Proctor and Fuhrman, 1990), it is clear that they are significant ecosystem drivers through their impact on their globally important microbial hosts (Fuhrman, 1999; 2000; Weinbauer and Rassoulzadegan, 2004; Suttle, 2005; 2007; Breitbart et al, 2007)
For example, the cyanobacterial viruses encode and express core photosynthesis genes obtained from their hosts (Lindell et al, 2004; 2005; 2007; Millard et al, 2004; Clokie et al, 2006; Sullivan et al, 2006; Bragg and Chisholm, 2008; Hellweger, 2009)
Cyanobacterial viruses often contain other genes likely critical in ocean systems, including those involved in scavenging phosphate (Sullivan et al, 2005; 2010; Weigele et al, 2007; Millard et al, 2009) and even nitrogen (Sullivan et al, 2010) from seawater
Summary
Twenty years since the discovery that viruses are abundant in aquatic systems (Bergh et al, 1989; Proctor and Fuhrman, 1990), it is clear that they are significant ecosystem drivers through their impact on their globally important microbial hosts (Fuhrman, 1999; 2000; Weinbauer and Rassoulzadegan, 2004; Suttle, 2005; 2007; Breitbart et al, 2007). For example, the cyanobacterial viruses encode and express core photosynthesis genes obtained from their hosts (Lindell et al, 2004; 2005; 2007; Millard et al, 2004; Clokie et al, 2006; Sullivan et al, 2006; Bragg and Chisholm, 2008; Hellweger, 2009). Cyanobacterial viruses often contain other genes likely critical in ocean systems, including those involved in scavenging phosphate (Sullivan et al, 2005; 2010; Weigele et al, 2007; Millard et al, 2009) and even nitrogen (Sullivan et al, 2010) from seawater. Investigations of wild viral populations often depend on the concentration of large volumes of water for various assays. The expanding field of viral metagenomics requires large-scale concentrations of seawater (10s to 100s of litres) to obtain enough genetic material for sequencing In spite of the importance of research on wild viral populations and their dependence on concentration methods, existing largescale concentration methods are inefficient, costly and variably reliable
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