Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Area of Science:

• Microbiology
• Genomics
• Marine Biology

Background:

• Environmental virus metagenomes ('viromes') traditionally isolate virus-like particles (VLPs).
• Current VLP purification methods co-enrich extracellular vesicles (EVs) and gene transfer agents (GTAs), contaminating viromes with host-associated DNA.
• This host DNA originates from EVs and GTAs, complicating the study of viral communities.

Purpose of the Study:

• To propose a new term, protected environmental DNA (peDNA), for genetic material isolated from purified environmental samples.
• To develop and validate a bioinformatic pipeline for identifying the origin of peDNA.
• To investigate the role of EVs and GTAs in horizontal gene transfer (HGT) in marine environments.

Main Methods:

• Size-fractionation (0.22 µm) and DNase treatment of environmental samples to isolate peDNA.
• Development of a bioinformatic pipeline to analyze peDNA sequence origins.
• Application of the pipeline to North Sea marine samples and existing global marine virome datasets.

Main Results:

• The pipeline successfully identified known producers of GTAs and EVs, and organisms with actively transducing proviruses as sources of peDNA.
• Novel and widespread EV producers were identified in marine environments.
• Quantitative evidence indicates that EV-mediated gene transfer is a significant driver of HGT in oceans.

Conclusions:

• The term peDNA accurately describes the complex sequence space obtained from purified environmental samples.
• The developed bioinformatic pipeline reliably determines the origin of peDNA.
• EVs play a crucial role in HGT in marine ecosystems, impacting microbial evolution and adaptation.