Recent research sheds new light on the fascinating dynamics of gene transfer among marine microorganisms, particularly focusing on the role of extracellular vesicles (EVs) and virus-like particles (VLPs) as vehicles for horizontal gene transfer (HGT). These two types of nanoparticles, prevalent within oceans, differ significantly not only in their structure but also in their capacity to transport genetic material, which is pivotal for microbial evolution. The study, involving long-read sequencing, explores the distinct genetic potential held within EVs and VLPs, highlighting their impact on microbial ecosystems.
Horizontal gene transfer is understood as the process through which organisms exchange genetic material, facilitating genome evolution and the acquisition of new functions. It is particularly significant within marine microbiomes, where bacteria and archaea constantly adapt to varying ecological conditions. Traditional mechanisms of HGT include conjugation, natural transformation, and viral transduction. This study adds complexity to the existing model of HGT by introducing EVs as another means of genetic exchange, alongside the established VLPs.
Conducted at Station ALOHA, located approximately at 22°45' N, 158° W, during the Hawaii Ocean Time-series cruise 319, samples were collected from 25 meters deep within the oligotrophic North Pacific Subtropical Gyre. The research employed density gradient ultracentrifugation to separate EVs and VLPs, yielding two distinct fractions for analysis. The research team uncovered notable differences between the genetic material contained within these two types of nanoparticles.
“Both marine EVs and VLPs can transport genetic material of sufficient length to mediate HGT of individual genes, complete operons, or more,” wrote the authors of the article. This finding is primarily attributed to the differing sizes of the DNA fragments carried by EVs and VLPs, which can range significantly depending on the type of nanoparticle. VLPs, for example, tend to harbor longer DNA sequences, reflective of their composition and roles as carriers for viral genomes.
Analyzing the composition of EVs and VLPs, the research revealed they differ not only structurally but also functionally, thereby influencing their interactions with microbial communities. It was found, for example, 81% of sequences from the VLP-enriched samples contained at least one mobile genetic element (MGE) hallmark gene, which are fundamental to mobile DNA’s capacity to recombine and integrate within different cellular environments. Conversely, the EVs' data showed they too encapsulated significant amounts of genetic diversity, with 50% of reads containing MGE signature genes.
This partitioning of genetic content within EVs and VLPs could have gradual yet significant effects on microbial HGT outcomes. The study indicates biases exist in the incorporation of genomic regions, substantially influencing how easily genetic material moves among closely related organisms versus more distantly related ones. The interplay of various HGT modalities can not only facilitate adaptation among organisms within the ocean's depths, but can also contribute to niche specialization.
An interesting insight from the research is the specific case of the marine bacterium Pelagibacter, one of the most abundant and ubiquitous species found within the ocean. Notably, the genetic diversity sourced from Pelagibacter plays a significant role within its ecological interactions mediated by nanoparticle-associated DNA. It accounts for varying gene functions necessary for its survival, indicating the depth of adaptability conferred through the HGT processes involving both EVs and VLPs.
“We show here for the first time how EVs and VLPs represent genetically distinct vehicles for HGT in planktonic marine ecosystems,” asserted the authors of the article. This assertion is pivotal to the scientific community, as it highlights not just the necessity of varied mechanisms of gene exchange but also their ecological ramifications within the broader marine environment.
Concisely, the currents of the ocean may carry much more than just the visible inhabitants; they are also replete with invisible gene exchange networks, operating at micro scales between organisms foundational to marine ecosystems. This research informs our broader comprehension of microbial dynamics and indicates potential future inquiries focusing on the mechanisms of HGT across ecological contexts.