Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations

Area of Science:

• Marine microbiology
• Virology
• Deep-sea ecology

Background:

• Viruses are abundant in oceans, but deep-sea virome diversity remains poorly understood due to technical limitations.
• Benthic abyssal ecosystems present unique challenges for studying viral communities.

Purpose of the Study:

• To compare the advantages and limitations of amplified versus unamplified viral DNA for shotgun sequencing.
• To assess the utility of single-molecule long-read sequencing for deep-sea virome analysis.

Main Methods:

• Shotgun sequencing-by-synthesis was applied to amplified and unamplified DNA from benthic abyssal samples.
• Comparative analysis included single-molecule long-read sequencing of one amplified sample.
• Viral Operational Taxonomic Units (vOTUs) were identified and classified into viral families.

Main Results:

• Direct sequencing of unamplified DNA revealed greater viral diversity and detected viruses missed in amplified samples.
• Amplified DNA samples showed higher viral read abundance but lower diversity.
• 11-16% of double-stranded DNA (dsDNA) viruses were nearly undetectable in amplified samples.

Conclusions:

• Direct sequencing provides a more comprehensive view of viral diversity, including single-stranded (ss) and dsDNA viruses.
• Random amplification and long-read technology, when used contextually, can improve deep-sea virome assessment by minimizing off-target reads.
• Methodological choices significantly impact the understanding of deep-sea viral assemblages.