Rhizosphere protists are key determinants of plant health

Abstract

Background: Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators-protists-are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results: We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions: We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance.

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures

“…Plant tissues were fully ground into powder in a mortar with liquid nitrogen. Then DNA was extracted from rice samples and bulk soil using the PowerSoil DNA isolation kit (Mo Bio Laboratories) as per the manufacturer’s instructions [ 31 , 32 ]. DNA was quantified with a Qubit Fluorometer by using the Qubit dsDNA BR Assay kit (Life technologies, USA) and the quality was assessed by running an aliquot on a 1% agarose gel.…”

Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

“…Recent studies have shown that protists play important roles in the soil microbiome and in plant health (Thakur and Geisen, 2019). For example, Xiong et al (2020) found that the pathogen dynamics is best predicted by protists, which were found to be negatively correlated with pathogen abundance during the growth of tomato plants. By directly feeding on the pathogen or indirectly by inducing shifts in the taxonomic and functional composition of bacteria via predation, protists might provide plant protection.…”

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

“…This is, for example, the case of Sphagnum and peatland-mosses-associated protists for which both V4 (TAReuk) and V9 (1380F/1510R) primers have been used [ 137 , 138 ]. Both V4 (V4_1f/TAReukREV3) and V9 (1380F/1510R) primers have also been employed to study rhizospheric protists [ 139 , 140 ]. Although plant sequences could represent the majority of reads in such plant-associated protist metabarcoding datasets, strategies to reduce the co-amplification of the associated plant(s), for example, the utilization of blocking oligos, have not yet been implemented.…”