Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany.
Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan.
Viruses. 2021 Jan 13;13(1):102. doi: 10.3390/v13010102.
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 (R = 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.
病毒是海洋环境中高度丰富、多样和活跃的组成部分。流式细胞术有助于增加对它们在塑造浮游带微生物群落和生物地球化学循环方面的影响的理解。然而，迄今为止，流式细胞术定量检测沉积物病毒仍然受到沉积物基质干扰的阻碍。在这里，我们开发了一种基于使用 Nycodenz 密度梯度从沉积物颗粒中分离病毒来流式细胞术定量海洋沉积物病毒的方案。结果表明，有足够的去除背景干扰，以允许流式细胞术定量。将该新方案应用于深海和潮滩样品，流式细胞术计数的病毒丰度与通过荧光显微镜计数的病毒丰度在几个数量级上具有很好的相关性（R = 0.899），这些病毒丰度来自于各种组成的海洋沉积物。对于生物量低或有机含量高的沉积物，可能需要进一步优化。总体而言，该新方案可快速准确地定量海洋沉积物病毒，并为病毒分选、靶向病毒组学和单病毒测序提供了选择。
