Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis.

Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem.

The core microbiota across the green lineage.

The study of plant-microbe interactions and the characterization of plant-associated microbiota has been the focus of plant researchers in the last decades due to its importance for plant health in natural conditions. Here, I explore the persistent core microbiota associated with different plant species and across different environments by performing a meta-analysis of publicly available datasets. Intra-specific analyses revealed that diverse plant genotypes growing in similar habitats interact with a common set of microbial groups but that some of these core groups are species- or environment-specific. Furthermore, interspecific meta-analysis demonstrates the conservation of seven bacterial orders across diverse photosynthetic organisms, including microalgae, suggesting a conserved capacity for interaction with these core microbes throughout evolutionary history. However, the specific functions of these core members and whether these functions are conserved across hosts remain largely unexplored. I therefore discuss the importance of understanding the roles of the core microbiota and propose future research directions, including the exploration of microbial interactions across different kingdoms. By investigating the core microbiota and its functions, it will be possible to leverage this knowledge for sustainable agricultural management and conservation goals.

Climate drives rhizosphere microbiome variation and divergent selection between geographically distant Arabidopsis populations.

Disentangling the contribution of climatic and edaphic factors to microbiome variation and local adaptation in plants requires an experimental approach to uncouple their effects and test for causality. We used microbial inocula, soil matrices and plant genotypes derived from two natural Arabidopsis thaliana populations in northern and southern Europe in an experiment conducted in climatic chambers mimicking seasonal changes in temperature, day length and light intensity of the home sites of the two genotypes. The southern A. thaliana genotype outperformed the northern genotype in the southern climate chamber, whereas the opposite was true in the northern climate chamber. Recipient soil matrix, but not microbial composition, affected plant fitness, and effects did not differ between genotypes. Differences between chambers significantly affected rhizosphere microbiome assembly, although these effects were small in comparison with the shifts induced by physicochemical differences between soil matrices. The results suggest that differences in seasonal changes in temperature, day length and light intensity between northern and southern Europe have strongly influenced adaptive differentiation between the two A. thaliana populations, whereas effects of differences in soil factors have been weak. By contrast, below-ground differences in soil characteristics were more important than differences in climate for rhizosphere microbiome differentiation.

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota.

Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms.

A fungal powdery mildew pathogen induces extensive local and marginal systemic changes in the Arabidopsis thaliana microbiota.

Powdery mildew is a foliar disease caused by epiphytically growing obligate biotrophic ascomycete fungi. How powdery mildew colonization affects host resident microbial communities locally and systemically remains poorly explored. We performed powdery mildew (Golovinomyces orontii) infection experiments with Arabidopsis thaliana grown in either natural soil or a gnotobiotic system and studied the influence of pathogen invasion into standing natural multi-kingdom or synthetic bacterial communities (SynComs). We found that after infection of soil-grown plants, G. orontii outcompeted numerous resident leaf-associated fungi while fungal community structure in roots remained unaltered. We further detected a significant shift in foliar but not root-associated bacterial communities in this setup. Pre-colonization of germ-free A. thaliana leaves with a bacterial leaf-derived SynCom, followed by G. orontii invasion, induced an overall similar shift in the foliar bacterial microbiota and minor changes in the root-associated bacterial assemblage. However, a standing root-derived SynCom in root samples remained robust against foliar infection with G. orontii. Although pathogen growth was unaffected by the leaf SynCom, fungal infection caused a twofold increase in leaf bacterial load. Our findings indicate that G. orontii infection affects mainly microbial communities in local plant tissue, possibly driven by pathogen-induced changes in source-sink relationships and host immune status.

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations.

Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-occurring grasses at 17 European sites across 3 years. We observed strong geographic structuring of the soil biome, but not of the root microbiota. A few phylogenetically diverse and geographically widespread bacteria consistently colonized plant roots. Among-site and across-year similarity in microbial community composition was stronger for the bacterial root microbiota than for filamentous eukaryotes. In a reciprocal transplant between two A. thaliana populations in Sweden and Italy, we uncoupled soil from location effects and tested their contributions to root microbiota variation and plant adaptation. Community differentiation in plant roots was explained primarily by location for filamentous eukaryotes and by soil origin for bacteria, whereas host genotype effects were marginal. Strong local adaptation between the two A. thaliana populations was observed, with differences in soil properties and microbes of little importance for the observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, climate is more important than soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities, whereas soil properties are primary drivers of bacterial community differentiation in roots.

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival.

Roots 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.

2-Tridecanone impacts surface-associated bacterial behaviours and hinders plant-bacteria interactions.

Surface motility and biofilm formation are behaviours which enable bacteria to infect their hosts and are controlled by different chemical signals. In the plant symbiotic alpha-proteobacterium Sinorhizobium meliloti, the lack of long-chain fatty acyl-coenzyme A synthetase activity (FadD) leads to increased surface motility, defects in biofilm development and impaired root colonization. In this study, analyses of lipid extracts and volatiles revealed that a fadD mutant accumulates 2-tridecanone (2-TDC), a methylketone (MK) known as a natural insecticide. Application of pure 2-TDC to the wild-type strain phenocopies the free-living and symbiotic behaviours of the fadD mutant. Structural features of the MK determine its ability to promote S. meliloti surface translocation, which is mainly mediated by a flagella-independent motility. Transcriptomic analyses showed that 2-TDC induces differential expression of iron uptake, redox and stress-related genes. Interestingly, this MK also influences surface motility and impairs biofilm formation in plant and animal pathogenic bacteria. Moreover, 2-TDC not only hampers alfalfa nodulation but also the development of tomato bacterial speck disease. This work assigns a new role to 2-TDC as an infochemical that affects important bacterial traits and hampers plant-bacteria interactions by interfering with microbial colonization of plant tissues.

Microbial interactions within the plant holobiont.

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.