Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

Abstract

SummaryRoots of healthy plants are inhabited by soil-derived bacteria, fungi, and oomycetes that have evolved independently in distinct kingdoms of life. How these microorganisms interact and to what extent those interactions affect plant health are poorly understood. We examined root-associated microbial communities from three Arabidopsis thaliana populations and detected mostly negative correlations between bacteria and filamentous microbial eukaryotes. We established microbial culture collections for reconstitution experiments using germ-free A. thaliana. In plants inoculated with mono- or multi-kingdom synthetic microbial consortia, we observed a profound impact of the bacterial root microbiota on fungal and oomycetal community structure and diversity. We demonstrate that the bacterial microbiota is essential for plant survival and protection against root-derived filamentous eukaryotes. Deconvolution of 2,862 binary bacterial-fungal interactions ex situ, combined with community perturbation experiments in planta, indicate that biocontrol activity of bacterial root commensals is a redundant trait that maintains microbial interkingdom balance for plant health.

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

“…Five Oomycetes were also categorized as core taxa with three of them affiliated to the Pythium genus and one to Phytophthora that are both described as potential plant pathogens. These observations are consistent with previous plant microbiome studies considering oomycetes diversity, that always described Pythium as the most dominant taxa among oomycetes [38,40,41]. These results confirm that protists are an integral part of the plant holobiont and their roles in controlling microbial populations through predation, disease incidence or contribution to nutrient cycles through the microbial loop deserve more attention [13].…”

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

“…Daidzein possesses antimicrobial activity (Gorniak, Bartoszewski, & Kroliczewski, ) and serves as a carbon source for a particular group of bacteria that metabolize daidzein. The reduction of α‐diversity is a typical change observed in the bacterial communities in the rhizosphere (Duran et al, ).…”

“…Recent progress in sequencing technologies and the establishment of synthetic communities of culturable bacteria has provided insights into the molecular mechanisms underlying the assemblage and function of rhizosphere microbes (Bulgarelli et al, 2012;Duran et al, 2018;Lundberg et al, 2012); for example, Arabidopsis secretes coumarins that encourage assembly of a microbiome adapted to iron deficiency (Stringlis et al, 2018;Voges, Bai, Schulze-Lefert, & Sattely, 2019). Although these advancements have deepened our understanding of the rhizosphere, a large gap remains between these achievements in microbial ecology and a comprehensive understanding of the rhizosphere in field-grown plants, which are essential for the application of these insights to sustainable agriculture.…”

Pathogen‐inducedpHchanges regulate the growth‐defense balance in plants

“…To determine whether the observed reduced Fo5176 vascular colonization in cc1cc2 was a consequence of a reduced total colonization of the root, we quantified fungal biomass inside the roots following two complementary methods. We measured the amount of N‐acetylglucosamine within infected roots that is proportional to the amount of fungal cell wall (i.e., chitin; Fig EV4B and C) and quantified the amount of live fungus by counting fungal colonies that developed after grinding and plating surface‐sterilized roots (Durán et al , ) (Fig EV4D). Both analyses showed no differences between total fungal biomass in WT and cc1cc2 roots, indicating that the cc1cc2 mutation hinders Fo5176 from colonizing the vasculature but not previous root cell layers.…”

“…Subsequently, roots of infected plants were harvested and weighed. The roots were surface-sterilized for 1 min in 80% EtOH, followed by a second sterilization step for 1 min in 0.25% NaClO as recently described (Durán et al, 2018) to remove and kill the fungus growing at the root surface. Roots were washed three times with sterile H 2 O and finally taken up in 1 ml H 2 O/g fresh weight.…”