A new study reveals the important role of extracellular vesicles in lateral gene transfer between marine microorganisms. This discovery challenges existing views on gene exchange mechanisms and proposes a new term "protected extracellular DNA" (peDNA) to cover a variety of gene vectors other than viruses, pointing out new directions for future research in various ecosystems.

Extracellular vesicles contribute much more to lateral gene transfer in the ocean than previously thought.

The ocean is teeming with microorganisms that engage in a dynamic exchange of genetic material. This process, known as horizontal gene transfer (HGT), plays a key role in the evolution of numerous species and is a key factor in the spread of bacterial resistance. Traditionally, this genetic exchange was thought to occur primarily through direct cell contact, free-floating DNA, or viruses.

A study led by Suzanne Erdmann from the Max Planck Institute for Marine Microbiology in Bremen now shows that so-called extracellular vesicles are also important for the transfer of genetic information in the ocean and therefore for the life of its smallest inhabitants.

Viruses, GTA, EV: tiny yet numerous

Most viruses are tiny. Up to 10 million viruses can be found in every drop of seawater. Not only do they package their own genetic material (genome), they also deliver parts of the host's DNA (that is, the DNA of the organism they infect) into other cells.

Studying viruses is extremely challenging. Seawater samples must be filtered through a filter with a pore size of only 0.2 microns (about 300 times smaller than the thickness of a human hair) to separate viruses and cells. In addition to viruses, these filtered samples also contain so-called gene transfer agents (GTAs) and extracellular vesicles (EVs).

For the study, researchers at the Max Planck Institute in Bremen also collected water samples near the North Sea island of Helgoland. Image source: SilviaVidal/Max Planck Institute for Marine Microbiology

GTAs are virus-like particles that specifically encapsulate host DNA, and EVs are small vesicles wrapped by membranes that detach from the host cell surface. These EVs can contain a variety of molecules. In addition to enzymes, nutrients and RNA, they often transport DNA fragments.

Erdmann and her team have now shown that, contrary to previous assumptions, there is a significant amount of host DNA in filtered seawater samples that is not transported by the virus. Proving this is extremely complex. "After sequencing (i.e. reading out the host DNA), we can no longer discern how it got into our samples. But there are no signatures that would attribute the sequence to a specific transport mechanism," explains Edmann, head of the Max Planck Research Group for Archaeal Virology at the Max Planck Institute in Bremen.

To solve this problem, the researchers used a trick. In the first step, they assigned each DNA sequence to the host from which it originally came. They then determined where possible the primary transport mechanism for each host—that is, via viruses, GTAs, or EVs. In this way, they were able to assign a potential transport mechanism to a specific DNA sequence.

"The results were surprising: Apparently, a large portion of the DNA was transported not via conventional pathways but via extracellular vesicles," Edelman said.

Not just waste

"Extracellular vesicles have long been regarded as cellular waste. Only in the last 15 years have scientists been able to demonstrate their various functions for cells. Our study clearly highlights the fundamental role that extracellular vesicles play in the exchange of genetic material between cells," explains Dominik Lücking, a doctoral student in Edman's research group and first author of the study, which has now been published in the journal ISME Communications.

Therefore, the authors recommend a change in terminology. "Traditionally, when DNA is extracted and sequenced from the 0.2-micron fraction, we talk about the virome, the virus-rich metagenome," said Lücking. "However, this way we ignore the diversity of other non-virus-like particles in this fraction, such as EVs. Therefore, we propose to call this fraction 'protected extracellular DNA,' or peDNA."

The research presented here lays the foundation for future peDNA research in the ocean and all other ecosystems. "The new nomenclature will allow us to talk more clearly about mechanisms and processes that are not covered by the term virion," says Erdmann.

Future studies could use this study as a guide to evaluate the role of extracellular vesicles in other environments such as soil, freshwater systems, or the human gut. "Given the important role of lateral gene transfer in many ecosystems, we are sure there are many more surprises to come along the way."