Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots

In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host–microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.

Evolutionarily Conserved Core Rhizosphere Microbiota Promotes Host Performance and Fitness in Heavy Metal Accumulating Plants

Background: Persistent microbial symbioses offer the potential to confer greater fitness to the host under unfavorable conditions, but manipulation of such beneficial interactions requires a mechanistic understanding of the consistently important microbiome members for the plant. Here, use five phylogenetically divergent heavy metal (HM) accumulating plants as a model, we examined the composition, assembly and relationships of the core and active rhizosphere microbiota across diverse soils with varying concentrations of HMs and further explored their roles in host performance.Results: Our results showed that the rhizosphere bacterial communities were primarily determined by soil type, with plant species having a stronger influence on the microbial diversity and composition than rhizocompartment and soil pollution level. We found that different HM accumulating plants harbored a unique set of core taxa in the rhizosphere with Sphingomonas and Burkholderiaceae shared among them. Use of RNA-SIP further revealed that the core rhizosphere taxa phylogenetically overlapped with the active rhizobacteria feeding on carbon-rich rhizodeposits, suggesting that the specific root exudate components driving the core microbiomes may be common across different plant species. Several keystone taxa were part of the core microbiota and facilitated plant metal tolerance and accumulation when inoculated with SynCom comprising the core cohorts.Conclusions: Our results suggest that a conserved core root microbiota has evolved with HM accumulating plants via root metabolic cues and exhibited potential to increase plant fitness and phytoextraction of HM. This study has important implications for harnessing the persistent microbiome members to improve host performance and accelerate the plant-assisted restoration of contaminated soil ecosystems.

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are largely unknown and can rely on the ability to degrade plant-derived compounds such as cell-wall polysaccharides and on the production of specialised metabolites. To address whether Streptomyces strains recruited into root microbiota share genomic specificities related to these two functions, we engaged a comparative genomic analysis using a newly sequenced rhizospheric strain, Streptomyces sp. AgN23 and strains from the phylogenetically related S. violaceusniger clade. This analysis enlightens a shared prominent CAZyome potentially involved in plant polysaccharides degradation and a strong conservation of antimicrobials biosynthetic clusters (rustmicin, mediomycin, niphimycin, nigericin) as well as plant bioactive compounds (nigericin, echosides, elaiophylin). Taken together, our work supports the hypothesis that specific hydrolytic enzymes and specialised metabolites repertoires may play important roles in the development of Streptomyces strains in the rhizosphere.

The drivers of vine-plant root microbiota endosphere composition include both abiotic and plant-specific factors

Microorganisms associated with plants are determinant for their fitness, but also in the case of vine grapes, for the quality and quantity of the wine. Plant microbiota is, however highly variable in space despite deterministic recruitment from the soil reservoir. Therefore, understanding the drivers that shape this microbiota is a key issue. Most studies that have analysed microorganisms associated with vines have been conducted at large scales (e.g., over 100 km) and have analysed the bulk soil and the rhizosphere. In this study, we focused on the root-microbiota endosphere, the most intimate fraction of microorganisms associated with plants. We sampled vine roots in 37 fields distributed throughout a vineyard to investigate drivers shaping the grapevine microbiota at the α- (i.e., within-field) and γ- (i.e., between-field) diversity scales. We demonstrated that vine endospheric microbiota differed according to both the edaphic and plant-specific parameters including cultivar type and age. This work supports the idea of an existing microbial terroir occurring within a domain and offers a new perspective for winemakers to include the microbial terroir in their management practices.

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota

Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.

Bio-Fertilizer Amendment Alleviates The Replanting Disease By Reshaping Leaf And Root Microbiome

A growing problem in intensive agricultural systems is replanting disease. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields and characterized the associated microbiota by bacterial 16S rRNA gene sequencing and qRT-PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium, and enhancing positive connections of the bacterial community across the two compartments. Bio-fertilizer had a positive and indirect effect as indicated by a structural equation models on both yield and quality by shaping the leaf microbiota rather than the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving the plant-microbe interactions.