Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Characterizing Mechanistic Roles of Viruses in Driving Biogeochemical Cycles in the Rhizosphere


Jonelle T. R. Basso* (, Axel Visel, Nigel Mouncey


DOE Joint Genome Institute


The information and tools generated from this project will address the need for the exploration of interkingdom interactions, specifically viruses, which has been highlighted as a priority by the Biological Systems Science Division strategic plan. The project seeks to develop a dynamic visualization tool that will rapidly allow for the identification of plant-microbe linkages. Through inter- and intracellular interrogation of viral-mediated signaling, regulation, and communication within plant-microbe interactions, the team aims to determine and predict how the soil virome affects ecological functions in soil and modulates global nutrient cycling.


Plant phenotypes are influenced by their microbiome, which consists of a dynamic consortium of bacteria that can provide benefits to the plant such as increased nutrient availability and stress resilience. There are well-studied examples of bacteria that have positive and negative effects on plants. There is also circumstantial evidence that viruses infecting these bacteria (bacteriophages) can alter their metabolism, as observed where phages are integrated into bacterial genomes (prophages). However, while viruses are ubiquitous, diverse, and the most abundant biological entities on the planet, their role in modulating plant-associated microbiomes remains poorly understood. The potential of viruses to impact global elemental cycles at massive scale is exemplified by the discovery of a “viral shunt” mechanism in marine ecosystems, where viral activity redirects nutrients and causes the release of up to three gigatons of carbon annually (Breitbart et al. 2018). A similar phenomenon has been described in soil systems, where viruses can influence nutrient availability and plant productivity (Wang et al. 2022).

Despite the clear importance of viruses in soil microbiomes, their role in regulating microbe-microbe and plant-microbe interactions in the rhizosphere (the microenvironment at the interface of roots and soil) is unknown. To understand these processes, it is necessary to study the properties of plants, bacteria, and viruses within the context of a multipartite functional system, establishing links between viruses and the ability of infected bacteria to colonize plant roots and influence plant phenotypes.

A recent Laboratory Directed Research and Development (LDRD) Lawrence Berkeley National Laboratory award has enabled the team to identify a viral-bacterial-plant tripartite system where prophages of the root-colonizing bacterium Pseudomonas simiae WCS417 were detected and experimentally determined to be active. The project also leveraged high-throughput mutagenesis (randomly barcoded transposon insertion sequencing; RB-TnSeq) to evaluate the potential for viral genes to modulate the colonization efficiency of their bacterial host. Two of these genes that cause reduced fitness in the rhizosphere when mutated are components of a latent bacteriophage and are present among two phage loci ranging in size from 15 to 65 kilobase pairs.

Using a loss of function approach, researchers generated green fluorescent protein–labeled phage gene deletion mutants to conduct experimental characterization studies such as competition tests, root colonization assays, and phenotypic comparative assessments. The team identified clear changes in metabolic profile between no bacteria controls and bacteria treatments from pilot in vivo targeted metabolomics experiments conducted in liquid growth media. These findings suggest the possibility that bacteriophages are involved in modulating the ability of bacteria to colonize plants. This approach therefore supports understanding and predicting how viruses may impact a given microbiome. However, extending understanding of these relationships more broadly across the rhizosphere is limited by the ability to connect the diversity of bacteria and prophages, as it relates to plants.

The project proposes to further understand the role of soil viruses in modulating plant-associated bacteria and to shed light on interkingdom signaling, resource sharing, and global nutrient cycling. By using an integrated computational and experimental design, the team seeks to understand how viruses modulate plant-microbe interactions, contribute to nutrient cycling, and work in response to dramatically altered water availability wrought by a changing climate.


Breitbart, M., et al. 2018. “Phage Puppet Masters of the Marine Microbial Realm,” Nature Microbiology 3, 754–66.

Wang, S., et al. 2022. “Experimental Evidence for the Impact of Phages on Mineralization of Soil-Derived Dissolved Organic Matter Under Different Temperature Regimes,” Science of the Total Environment 846, 157517.

Funding Information

This work was supported by the Lawrence Berkeley National Laboratory, Laboratory Directed Research and Development Program (LBNL LDRD #23-105).