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

Area of Science:

• Environmental microbiology
• Virology
• Molecular biology

Background:

• Viruses are globally abundant and diverse, significantly impacting host populations, diversity, and evolution.
• Current quantitative methods are insufficient for assessing the full impact of diverse viruses on microbial communities.
• Understanding viral quantitative dynamics is crucial for microbial ecology and global ecosystem modeling.

Purpose of the Study:

• To adapt and validate the solid-phase single-molecule PCR polony method for quantifying diverse viral groups.
• To assess the abundance and distribution of T7-like cyanophages in the Red Sea.
• To compare the abundance of different T7-like cyanophage clades and their ecological implications.

Main Methods:

• Adaptation of the solid-phase single-molecule PCR polony method for viral quantification.
• Application of degenerate primers to capture the diversity within T7-like cyanophages.
• Comparison of the polony method with quantitative PCR and droplet digital PCR.

Main Results:

• The polony method demonstrated superior performance compared to quantitative PCR and droplet digital PCR for diverse viral quantification.
• T7-like cyanophages were highly abundant in the Red Sea (770,000 phages ml^-1) in spring 2013, with a depth distribution mirroring cyanobacteria.
• Clade B T7-like cyanophages (carrying psbA) were over 20-fold more abundant than Clade A phages (lacking psbA) throughout the water column.

Conclusions:

• The adapted polony method provides a robust tool for quantifying diverse viruses, overcoming limitations of existing techniques.
• T7-like cyanophages are significant components of Red Sea microbial ecosystems, with distinct clade abundances influencing host populations.
• Accurate viral quantification is essential for understanding virus-host dynamics and their role in global biogeochemical cycles.