There is a lively ex­change of ge­netic in­form­a­tion between the nu­mer­ous mi­croor­gan­isms in the oceans. This so-called ho­ri­zontal gene trans­fer (HGT) is cru­cial for the evol­u­tion of many or­gan­isms and is, for ex­ample, also the most im­port­ant mech­an­ism for the spread of an­ti­bi­otic res­ist­ance in bac­teria.

Un­til now, it was as­sumed that dir­ect con­tacts between cells, free DNA or vir­uses were primar­ily re­spons­ible for the ex­change of genes. A study led by Susanne Erd­mann from the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy in Bre­men now shows that so-called ex­tra­cel­lu­lar ves­icles are also very im­port­ant for the trans­fer of ge­netic in­form­a­tion in the sea and thus for the life of its smal­lest in­hab­it­ants.

Vir­uses, GTAs, EVs: tiny and nu­mer­ous

Most vir­uses are tiny. Up to 10 mil­lion of them can be found in every drop of sea­wa­ter. They can not only pack up their own ge­netic ma­ter­ial (their gen­ome), but also parts of their host's DNA—i.e., the DNA of the or­gan­ism they have in­fec­ted—and trans­port it into other cells. Study­ing vir­uses is chal­len­ging. Sea­wa­ter samples have to be filtered through fil­ters with a pore size of only 0.2 µm (which is about 300 times less than the thick­ness of a hu­man hair) to sep­ar­ate the vir­uses from the cells. In ad­di­tion to vir­uses, these filtered samples also con­tain so-called gene trans­fer agents (GTAs) and ex­tra­cel­lu­lar ves­icles (EVs). GTAs are virus-like particles that ex­clus­ively pack­age host DNA, and EVs are small ves­icles en­vel­oped by a mem­brane that de­tach from the cell sur­face of the host. These EVs can con­tain a vari­ety of mo­lecules. In ad­di­tion to en­zymes, nu­tri­ents and RNA, they of­ten trans­port frag­ments of DNA.

EVs are pro­lific trans­port­ers of ge­netic ma­ter­ial

Erd­mann and her team have now shown that, other than pre­vi­ously as­sumed, there is a lot of host DNA in the filtered sea­wa­ter samples that is not trans­por­ted by vir­uses. Prov­ing this was ex­tremely com­plic­ated. “After se­quen­cing, i.e., read­ing out the host DNA, we can no longer re­cog­nize how it got into our sample,” ex­plains Erd­mann, head of the Max Planck Re­search Group Ar­chaea Vir­o­logy at the Max Planck In­sti­tute in Bre­men. “There is no fea­ture to as­sign a se­quence to a spe­cific trans­port mech­an­ism.” To solve this prob­lem, the re­search­ers used a trick. In a first step, they as­signed each DNA se­quence to a host from which it ori­gin­ally stems. Then they de­term­ined a main trans­port mech­an­ism for each host as far as pos­sible—i.e. by vir­uses, GTAs or EVs. This en­abled them to as­sign a po­ten­tial trans­port mech­an­ism to a spe­cific DNA se­quence. “The res­ult was sur­pris­ing: Ap­par­ently, a large pro­por­tion of the DNA was not trans­por­ted via clas­sical routes, but via ex­tra­cel­lu­lar ves­icles,” says Erd­mann.

So much more than waste—in the ocean and bey­ond

“Ex­tra­cel­lu­lar ves­icles were long re­garded as cel­lu­lar waste. Only in the last fif­teen years sci­ent­ists were able to show their vari­ous func­tions for the cell. Our study clearly high­lights the fun­da­mental role that EVs play for the ex­change of ge­netic ma­ter­ial between cells,“ ex­plains Dominik Lück­ing, Ph.D. stu­dent in Erd­manns group and first au­thor of the study, which has now been pub­lished in the journal ISME Communications. Thus, the au­thors sug­gest to change ter­min­o­logy: “Tra­di­tion­ally, we are talk­ing of a vir­ome, a meta­gen­ome en­riched with vir­uses, when ex­tract­ing and se­quen­cing the DNA from the 0.2 µm frac­tion,” says Lück­ing. “However, that way we are miss­ing out on the vari­ety of the other, non-virus-like particles in this frac­tion, such as EVs. Thus, we sug­gest to call this frac­tion ‘pro­tec­ted ex­tra­cel­lu­lar DNA’, or peDNA.”

The study presen­ted here lays the found­a­tion for fu­ture re­search on peDNA across all eco­sys­tems, in the ocean and bey­ond. “The new no­men­clature will en­able us to talk more clearly about the mech­an­isms and pro­cesses not covered by the term vir­ome,” says Erd­mann. Fu­ture re­search can use this study as a guideline to as­sess the role of ex­tra­cel­lu­lar ves­icles in other en­vir­on­ments, such as soil and fresh­wa­ter sys­tems or the hu­man gut. “In view of the sig­ni­fic­ance of ho­ri­zontal gene trans­fer in many eco­sys­tems, we are very sure that there are quite a few more sur­prises on the way ahead of us,“ Erd­mann con­cludes.

Journal Reference:

1. Dominik Lück­ing, Cor­aline Mer­cier, To­mas Alarcón-Schu­macher und Susanne Erd­mann (2023): Ex­tra­cel­lu­lar ves­icles are the main con­trib­utor to the non-viral pro­tec­ted ex­tra­cel­lu­lar se­quence space. ISME Com­mu­nic­a­tions 3, 112 (2023). DOI: https://doi.org/10.1038/s43705-023-00317-6