Abstract
Viruses are highly abundant, diverse, and active components of marine environments. Flow cytometry has helped to increase the understanding of their impact on shaping microbial communities and biogeochemical cycles in the pelagic zone. However, to date, flow cytometric quantification of sediment viruses is still hindered by interference from the sediment matrix. Here, we developed a protocol for the enumeration of marine sediment viruses by flow cytometry based on separation of viruses from sediment particles using a Nycodenz density gradient. Results indicated that there was sufficient removal of background interference to allow for flow cytometric quantification. Applying this new protocol to deep-sea and tidal-flat samples, viral abundances enumerated by flow cytometry correlated well (R2 = 0.899) with counts assessed by epifluorescence microscopy over several orders of magnitude from marine sediments of various compositions. Further optimization may be needed for sediments with low biomass or high organic content. Overall, the new protocol enables fast and accurate quantification of marine sediment viruses, and opens up the options for virus sorting, targeted viromics, and single-virus sequencing.
Highlights
Accepted: 11 January 2021Viral particles are highly abundant in marine sediments and typically range between107 and 1010 per g of dry sediment [1], which exceeds bacterial cells
We measured a strong correlation (R2 = 0.899) between virus counts conducted via flow cytometry (FCM) and Epifluorescence microscopy (EfM), indicating that the method proposed here is suitable for the quantification of marine sediment viruses
While some authors have reported the usage of FCM for soil-associated viruses, the protocols have largely been optimized for limited applications such as microbial mats [36] (R2 = 0.74) or activated sludge flocs [37] (R2 = 0.77)
Summary
Accepted: 11 January 2021Viral particles are highly abundant in marine sediments and typically range between107 and 1010 per g of dry sediment [1], which exceeds bacterial cells. Viral particles are highly abundant in marine sediments and typically range between. While knowledge of planktonic viruses has grown considerably in recent decades, there are still many questions regarding the function of viruses in marine sediments due to the difficulty of sample recovery and the analytical challenges associated with the sediment matrix. Viral abundance is a basic parameter for understanding virus-host interactions and the dynamics of viruses in sediments. Has long been a standard technique for viral enumeration in aquatic environments [7,8]. Flow cytometry (FCM) has emerged as a common method for the quantification of aquatic viruses [9,10]. Compared to EfM, FCM analysis is fast and allows a high sample throughput. Flow cytometric enumeration of sediment viruses is still challenging
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