Quantification of diverse virus populations in the environment using the polony method

Nature Microbiology
Nava BaranDebbie Lindell

Abstract

Viruses are globally abundant and extremely diverse in their genetic make-up and in the hosts they infect. Although they influence the abundance, diversity and evolution of their hosts, current methods are inadequate for gaining a quantitative understanding of their impact on these processes. Here we report the adaptation of the solid-phase single-molecule PCR polony method for the quantification of taxonomically relevant groups of diverse viruses. Using T7-like cyanophages as our model, we found the polony method to be far superior to regular quantitative PCR methods and droplet digital PCR when degenerate primers were used to encompass the group's diversity. This method revealed that T7-like cyanophages were highly abundant in the Red Sea in spring 2013, reaching 770,000 phages ml-1, and displaying a similar depth distribution pattern to cyanobacteria. Furthermore, the abundances of two major clades within the T7-like cyanophages differed dramatically throughout the water column: clade B phages that carry the psbA photosynthesis gene and infect either Synechococcus or Prochlorococcus were at least 20-fold more abundant than clade A phages that lack psbA and infect Synechococcus hosts. Such measurements are of paramount import...Continue Reading

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Citations

Feb 28, 2019·Environmental Microbiology Reports·Branko RihtmanDavid J Scanlan
Oct 30, 2019·Environmental Microbiology Reports·Africa McMullenManuel Martinez-Garcia
May 5, 2020·Environmental Microbiology·David R OlivenzaMireille Ansaldi
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Aug 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Sophia Zborowsky, Debbie Lindell
Mar 17, 2018·Frontiers in Microbiology·B B CaelMichael J Follows
Jun 28, 2019·Frontiers in Microbiology·Francisco Martinez-HernandezManuel Martinez-Garcia
Feb 27, 2021·Nature Microbiology·Eric G SakowskiSarah P Preheim
Mar 13, 2021·Proceedings of the National Academy of Sciences of the United States of America·Flora VincentAssaf Vardi
Mar 26, 2021·Nature Reviews. Microbiology·Adrienne M S CorreaJoshua S Weitz
May 22, 2021·Trends in Microbiology·Mohammadali Khan Mirzaei, Li Deng
May 26, 2021·Annual Review of Virology·Pacifica SommersGareth Trubl

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Datasets Mentioned

BETA
KY788381

Methods Mentioned

BETA
PCR
electron
flow cytometry
Fluorescence
PCRs

Software Mentioned

QuantaSoft
MUSCLE
MEGA7
GenePix Pro
ImageJ
Lmodel2
R
stats
LightCycler 480

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