Awaking the Dormant Virome in the Rhizosphere
Viruses are the most abundant and diverse biological entities on Earth, expected to be essential players in any ecosystem functioning. They can establish lytic or lysogenic interactions with their bacterial hosts. In the latter, they assume a dormant state integrated in the host genome and can be awaken by different perturbations that impact host cell physiology, triggering a viral bloom, which could be potentially a fundamental ecological mechanism driving soil viral diversity, as 22-68% of soil bacteria are predicted to harbor dormant viruses. Rhizosphere is a vital soil compartment providing key plant-beneficial functions. However, little is known about the mechanisms driving viral diversity in rhizosphere. Here we assessed the viral bloom response in rhizospheric viromes by exposing them to three contrasting soil perturbation agents: earthworms, herbicide and antibiotic pollutant. The viromes were next screened for rhizosphere-relevant genes and also used as inoculant on microcosms incubations to test their impacts on pristine microbiomes. Our results show that viral blooms in rhizosphere can be triggered by these perturbations. While post-perturbation viromes diverged from control condition, viral communities exposed to both herbicide and antibiotic pollutant were more similar between each other but divergent from those influenced by earthworms. The latter also favored an increase in viral populations harboring genes involved in plant-beneficial functions associated with N2 fixation (Mo storage) and protection against osmotic stress. Finally, post-perturbation viromes inoculated in soil microcosms were able to change microbial community diversity and propagate perturbation impacts across pristine microbiomes, suggesting that viromes are important components of the soil ecological memory driving eco-evolutionary processes that shape micro-heterogeneity, highlighting their capacity to determine future soil microbiome trajectories according to past events. Overall, these findings show that viromes are active players in the rhizosphere and need to be considered in efforts to understand and control the vital microbial processes towards sustainable crop production.