Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

Abstract

Background Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. ‘primary phages’) and (2) that ‘secondary phages’ that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly ‘helping’ the pathogen. Results Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, ‘secondary phages’ that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and ‘secondary phages’ were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen. Conclusions Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields.

Phages indirectly maintain plant pathogen defense through regulation of the commensal microbiome

“…Phages may suppress disease by (a) directly reducing pathogen population sizes (11–13,49–51), (b) reducing the population sizes of microbiome members that facilitate pathogen infection, or (c) restricting dominant bacteria and in turn facilitating other protective bacterial species that would have otherwise gone extinct. Phages may facilitate disease by d) reducing the population sizes of protective microbiome members (16), or e) reprogramming host immunity to trigger an antiviral response and suppress the antibacterial response (currently documented only in mammalian hosts, (23)).…”

“…For example, variation in the severity of bacterial wilt disease in the tomato rhizosphere was attributed to the presence of pathogen-inhibiting bacteria and their associated phages. Tomato plants inoculated with inhibitory bacteria were more resistant to bacterial wilt, but this protective effect vanished in the presence of inhibitor-associated phages (16).…”

Trophic interactions in microbiomes influence plant host population size and ecosystem function

“…For instance, these two types of consumers may show considerable variation in diet breath. Bacteriophages are highly specialized and can specifically target certain groups of microbes [23, 29], such as plant growth-promoting or growth-suppressing bacteria. As such, they may strongly affect the richness and composition of microbiomes and the directionality (positive or negative) of microbiome effects on plant populations.…”

“…Despite the prevalence and significance of microbial bacterivorous consumers in plant microbiomes, little is known about how they impact microbiomes and how the impacts translate into changes in plant populations and ecosystem functions. Specifically, while bacteriophages and protozoa have been studied separately [23, 26, 28, 29], their influences on plant hosts and ecosystem functions have not been directly compared.…”

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere

“…These can include complex networks involving competition, cooperation [23] or interaction with other microbes. Also grazing by phagotrophic protists [31] and infection by bacteriophages [32,33], can prevent an effective colonisation of the rhizosphere microbiome by inoculants. An important factor governing inoculant proliferation is the availability of nutrients in the rhizosphere environment to support the community growth and development [34][35][36], which will be different from the bulk soil nutrients, often scarce, limiting bacterial growth and soil microbial processes [37].…”