The root bacterial microbiome is important for the general health of the plant. Additionally, it can enhance tolerance to abiotic stresses, exemplified by plant species found in extreme ecological niches like deserts. These complex microbe-plant interactions can be simplified by constructing synthetic bacterial communities or SynComs from the root microbiome. Furthermore, SynComs can be applied as biocontrol agents to protect crops against abiotic stresses such as high salinity. However, there is little knowledge on the design of a SynCom that offers a consistent protection against salt stress for plants growing in a natural and, therefore, non-sterile soil which is more realistic to an agricultural setting. Here we show that a SynCom of five bacterial strains, originating from the root of the desert plant Indigofera argentea, protected tomato plants growing in a non-sterile substrate against a high salt stress. This phenotype correlated with the differential expression of salt stress related genes and ion accumulation in tomato. Quantification of the SynCom strains indicated a low penetrance into the natural soil used as the non-sterile substrate. Our results demonstrate how a desert microbiome could be engineered into a simplified SynCom that protected tomato plants growing in a natural soil against an abiotic stress.

As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species' average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

BackgroundDiazotrophic Bradyrhizobium spp. are well known for their ability to trigger nodule formation on a variety of legume species. In nodules, Bradyrhizobium utilizes plant-derived carbohydrates in exchange for fixed nitrogen. The genes essential for the nodulation and nitrogen-fixation trait are clustered in a genomic region, which is known as the ‘symbiotic island’. Recently, novel non-diazotrophic Bradyrhizobium spp. have been found to be highly abundant in soils, suggesting that these species can also have a ‘free-living’ life history. However, whether non-diazotrophic Bradyrhizobium spp. can live in association with plants remains elusive.ResultsIn this study, we show that Bradyrhizobium spp. are common root endophytes of non-legume plant species – including Arabidopsis thaliana (Arabidopsis) – grown in an ecological setting. From a single Arabidopsis root, four Bradyrhizobium sp. strains (designated MOS001 to MOS004) were isolated. Comparative genome analysis revealed that these strains were genetically and functionally highly diverse, but did not harbour the nodulation and the nitrogen fixation gene clusters. Comparative colonization experiments, with MOS strains and nitrogen-fixing symbiotic strains, revealed that all tested Bradyrhizobium spp. can colonize the root endophytic compartment of Arabidopsis.ConclusionThis study provides evidence that both diazotrophic and non-diazotrophic Bradyrhizobium spp. colonize the root endophytic compartment of a wide variety of plant species, including the model species Arabidopsis. This demonstrates that plant roots form a major ecological niche for Bradyrhizobium spp., which might be ancestral to the evolution of the nodulation and nitrogen-fixation trait in this genus.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1272-y) contains supplementary material, which is available to authorized users.

BackgroundSome tree species can become hundreds and even thousands years old. However, other species only grow for a few decades. This lifespan is genome dependent and longevity of trees appears positively correlated with increased numbers of defence related genes and negative plant soil feedback causes a short life span. In addition to defence related genes, microbiomes of the plant are important for its growth and health. However, the role of microbiomes in tree longevity has never been studied. To test whether the microbiomes of centuries-old trees reflect absence of such negative plant soil feedback and whether they harbour microbes with antagonistic activities against their major pathogens, we used a chrono-series of Chinese chestnut (Castanea mollissima) from a Ming orchard at the Great Wall. It has trees of various ages ranging from centuries to tens of years and the oldest tree in this orchard is more than 800 years old. This orchard provides unique opportunities to test the hypothesis that the root microbiome composition of trees with the potential to become old, does not depend on the age of the tree and is not affected by negative plant soil feedback.ResultsMicrobiomes of soil, rhizosphere and endophytic compartment from young (~10 years) and old trees (up to ~800 years) were analysed by meta-amplicon sequencing, Mantel test and linear regression analysis. Using the Bray-Curtis dissimilarity measure on rarefied OTUs, PCoA plots showed that in each compartment, microbiomes of the young tree clustered well with that of the old trees. Mantel test and linear regression analyses of the relation between Bray-Curtis dissimilarity values and age difference, showed that these values remain rather similar with increasing age difference. Moreover, bioactivity tests showed that the most abundant OTU has strong antagonistic activities against 2 major pathogens of chestnut.ConclusionsWe showed that the root and soil microbiomes of a chrono-series of chestnut trees, ranging from 8 to about 800 years are similar. This strongly indicates that Chinese chestnut is able to avoid a negative feedback with its soil, establish root microbiomes that are age independent and this can contribute to its longevity.