• Open Access

Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses

Authors

  • Elke Allers,

    1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Search for more papers by this author
    • Authors contributed equally to the manuscript.
  • Cristina Moraru,

    1. Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    Current affiliation:
    1. Centro de Astrobiología (CSIC/INTA), Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
    Search for more papers by this author
    • Authors contributed equally to the manuscript.
  • Melissa B. Duhaime,

    1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Current affiliation:
    1. University of Michigan, Department of Ecology and Evolutionary Biology, C.C. Little, North University, Ann Arbor, MI, USA
    Search for more papers by this author
  • Erica Beneze,

    1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Search for more papers by this author
  • Natalie Solonenko,

    1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Search for more papers by this author
  • Jimena Barrero-Canosa,

    1. Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    Search for more papers by this author
  • Rudolf Amann,

    Corresponding author
    • Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
    Search for more papers by this author
  • Matthew B. Sullivan

    Corresponding author
    • Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    Search for more papers by this author

For correspondence. E-mail mbsulli@email.arizona.edu; Tel. (+1) (520) 626 9100; Fax (+1) (520) 621 9903; E-mail ramann@mpi-bremen.de; Tel. (+49) (421) 2028930; Fax (+49) (421) 2028 790.

Summary

Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, and metabolic capacity. However, our ability to understand and quantify phage–host interactions is technique-limited. Here, we introduce phageFISH – a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to > 92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus–gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g. early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage–host system, and debut phageFISH as a much-needed tool for studying phage–host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages.

Ancillary