Metagenome-derived virus-microbe ratios across ecosystems

Area of Science:

• Microbiology
• Virology
• Genomics
• Environmental Science

Background:

• Previous estimates suggest viruses outnumber cells tenfold globally, primarily based on fluorescently labeled virus-like particles.
• Existing methods may exclude intracellular viruses and include false positives, potentially skewing virus-to-microbe ratio (VMR) calculations.

Purpose of the Study:

• To develop a more accurate metagenome-based VMR (mVMR) estimation method.
• To account for DNA viruses across all replication stages, including intracellular forms.
• To reassess global virus abundance relative to cellular life.

Main Methods:

• Developed mVMR using normalized RPKM counts of major capsid protein (MCP) genes for viruses and universal single-copy genes (USCGs) for cells.
• Benchmarked the mVMR strategy with mock metagenomes.
• Generated metagenomes from aquatic (freshwater, seawater, solar salterns) and diverse non-aquatic biomes (soils, sediments, microbial mats, etc.).

Main Results:

• Aquatic ecosystems showed viruses outnumbering cells by ~13-fold in freshwater and ~2-4 fold in marine/saline waters.
• Non-aquatic environments exhibited a lower virus-to-cell ratio, with viruses outnumbering cells by approximately twofold on average.
• The mVMR method provides a more comprehensive assessment of viral abundance across various life stages and environments.

Conclusions:

• Global virus numbers may be closer to cellular counts than previously estimated, challenging the long-held tenfold ratio.
• Metagenomic approaches offer a robust method for quantifying viruses, including intracellular and diverse viral forms.
• Viruses, while highly diverse, might not be as numerically dominant over cells as previously thought across all Earth biomes.