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.

Disease-resistant varieties of Chinese cabbage (Brassica rapa L. ssp. pekinensis) inhibit Plasmodiophora brassicae infestation by stabilising root flora structure

The application of disease-resistant varieties is the most cost-effective method for solving the problem of clubroot. "Shangpin," a disease-resistant variety of Chinese cabbage with broad-spectrum immunity to Plasmodiophora brassicae (P. brassicae), was screened in a previous study. Based on 16S rRNA sequencing technology, we annotated the compositional differences between the rhizosphere, rhizoplane, and endosphere bacterial communities of "Shangpin" and "83-1" under P. brassicae stress. Alpha diversity analysis showed that the abundance of microorganisms in the root system of "83-1" changed more than that of "Shangpin" after P. brassicae infestation, and Beta diversity analysis indicated that Flavobacterium and Sphingomonas may mediate clubroot resistance, while Nitrospira, Nitrosospira, and Pseudomonas may mediate P. brassicae infestation among the bacteria in the Top 10 abundances. Microbial functional analyses showed that the root microorganisms of "83-1" were metabolically weakened after P. brassicae inoculation and were inhibited in competition with pathogenic bacteria. Conversely, the root microorganisms of "Shangpin" maintained the strength of their metabolic capacity, which took a favorable position in competition with the pathogen and inhibited the growth and development of the pathogen, thus showing resistance. Root secretions of "Shangpin" significantly inhibited the incidence and disease index of clubroot, which indicated that under clubroot stress, resistant varieties maintain root microbial diversity and microbial community functions through specific root exudates, enriching the genera Flavobacterium and Sphingomonas, thus showing resistance. The results of this study reveal the resistance mechanism of resistant varieties to clubroot and provide new insights into the prevention and control of clubroot in Chinese cabbage.

Heterosis in root microbiota inhibits growth of soil-borne fungal pathogens in hybrid rice

In nature, plants are colonized by various microbes that play essential roles in their growth and health. Heterosis is a natural genetic phenomenon whereby first-generation hybrids exhibit superior phenotypic performance relative to their parents. It remains unclear whether this concept can be extended to the "hybridization" of microbiota from two parents in their descendants and what benefits the hybrid microbiota might convey. Here, we investigated the structure and function of the root microbiota from three hybrid rice varieties and their parents through amplicon sequencing analysis of bacterial 16S ribosomal DNA (rDNA) and fungal internal transcribed spacer (ITS) regions. We show that the bacterial and fungal root microbiota of the varieties are distinct from those of their parental lines and exhibit potential heterosis features in diversity and composition. Moreover, the root bacterial microbiota of hybrid variety LYP9 protects rice against soil-borne fungal pathogens. Systematic analysis of the protective capabilities of individual strains from a 30-member bacterial synthetic community derived from LYP9 roots indicated that community members have additive protective roles. Global transcription profiling analyses suggested that LYP9 root bacterial microbiota activate rice reactive oxygen species production and cell wall biogenesis, contributing to heterosis for protection. In addition, we demonstrate that the protection conferred by the LYP9 root microbiota is transferable to neighboring plants, potentially explaining the observed hybrid-mediated superior effects of mixed planting. Our findings suggest that some hybrids exhibit heterosis in their microbiota composition that promotes plant health, highlighting the potential for microbiota heterosis in breeding hybrid crops.

The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease

The root microbiota contributes to the plant's defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08-61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.

Crafting the plant root metabolome for improved microbe-assisted stress resilience

Plants and microbes coinhabit the earth and have coevolved during environmental changes over time. Root metabolites are the key to mediating the dynamic association between plants and microbes, yet the underlying functions and mechanisms behind this remain largely illusive. Knowledge of metabolite-mediated alteration of the root microbiota in response to environmental stress will open avenues for engineering root microbiotas for improved plant stress resistance and health. Here, we synthesize recent advances connecting environmental stresses, the root metabolome and microbiota, and propose integrated synthetic biology-based strategies for tuning the plant root metabolome in situ for microbe-assisted stress resistance, offering potential solutions to combat climate change. The current limitations, challenges and perspectives for engineering the plant root metabolome for modulating microbiota are collectively discussed.

Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates

Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2-3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora.

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain

Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.

Maize Field Study Reveals Covaried Microbiota and Metabolic Changes in Roots over Plant Growth

Plant roots are colonized by microorganisms from the surrounding soil that belong to different kingdoms and form a multikingdom microbial community called the root microbiota. Despite their importance for plant growth, the relationship between soil management, the root microbiota, and plant performance remains unknown. Here, we characterize the maize root-associated bacterial, fungal, and oomycetal communities during the vegetative and reproductive growth stages of four maize inbred lines and the pht1;6 phosphate transporter mutant. These plants were grown in two long-term experimental fields under four contrasting soil managements, including phosphate-deficient and -sufficient conditions. We showed that the maize root-associated microbiota is influenced by soil management and changes during host growth stages. We identified stable bacterial and fungal root-associated taxa that persist throughout the host life cycle. These taxa were accompanied by dynamic members that covary with changes in root metabolites. We observed an inverse stable-to-dynamic ratio between root-associated bacterial and fungal communities. We also found a host footprint on the soil biota, characterized by a convergence between soil, rhizosphere, and root bacterial communities during reproductive maize growth. Our study reveals the spatiotemporal dynamics of the maize root-associated microbiota and suggests that the fungal assemblage is less responsive to changes in root metabolites than the bacterial community.

Gnotobiotic Plant Systems for Reconstitution and Functional Studies of the Root Microbiota

Healthy plants host a multi-kingdom community of microbes, which is known as the plant microbiota. Amplicon sequencing technologies for microbial genomic markers were a milestone in revealing the taxonomic composition of the microbiota and its variation associated with a plant host in natural environments. However, this method alone does not allow conclusions to be drawn about functions of these microbial assemblages for the plant. The development of culture collections, which recapitulate natural microbial communities in their diversity, and multiple gnotobiotic plant systems therefore represent a breakthrough in plant-microbiota research such that plants can be inoculated with defined communities to study proposed microbiota functions. These systems provided, for the root microbiota, first insights into mechanisms underlying microbial community establishment and contributions of its microbial members to indirect pathogen protection and mineral nutrition of the host. We argue that the choice of a gnotobiotic system for microbiota reconstitution and subsequent functional analysis depends on the particular plant trait that is influenced by the microbiota. We start by discussing the advantages and limitations of using individual gnotobiotic systems and then describe the general procedures for preparing bacterial cultures from the Arabidopsis thaliana At-R-SPHERE culture collection for inoculation and cocultivation in two gnotobiotic plant growth systems using agar and perlite matrix. Additionally, a protocol for inoculation of plants with opportunistic Pseudomonas pathogens is provided. Lastly, we describe a high-throughput system for visual assessment of roots after inoculation with individual mutants of a transposon library generated from a root-derived bacterial commensal. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of bacterial cultures from At-R-SPHERE Support Protocol 1: Validation of strains by sequencing hypervariable regions of the 16S rRNA gene Basic Protocol 2: Coinoculation of plants grown on an agar matrix with microbial elicitor and a defined microbial community Alternate Protocol: Inoculation of plants cultivated in a perlite-based growth system Support Protocol 2: Surface sterilization of Arabidopsis thaliana seeds Basic Protocol 3: Inoculation using a Pseudomonas opportunistic pathogen Basic Protocol 4: Assessment of commensal-mediated root phenotypes using phytostrips.

Nitrogen Deficiency-induced Bacterial Community Shifts in Soybean Roots

Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root microbiota remain unclear. A bacterial community analysis by 16S rRNA gene amplicon sequencing showed nitrogen deficiency-induced bacterial community shifts in soybean roots with the marked enrichment of Methylobacteriaceae. The abundance of Methylobacteriaceae was low in the roots of field-grown soybean without symptoms of nitrogen deficiency. Although Methylobacteriaceae isolated from soybean roots under nitrogen deficiency did not promote growth or nodulation when inoculated into soybean roots, these results indicate that the enrichment of Methylobacteriaceae in soybean roots is triggered by nitrogen-deficiency stress.

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis

Plants benefit from associations with a diverse community of root-colonizing microbes. Deciphering the mechanisms underpinning these beneficial services are of interest for improving plant productivity. We report a plant-beneficial interaction between Arabidopsis thaliana and the root microbiota under iron deprivation that is dependent on the secretion of plant-derived coumarins. Disrupting this pathway alters the microbiota and impairs plant growth in iron-limiting soil. Furthermore, the microbiota improves iron-limiting plant performance via a mechanism dependent on plant iron import and secretion of the coumarin fraxetin. This beneficial trait is strain specific yet functionally redundant across phylogenetic lineages of the microbiota. Transcriptomic and elemental analyses revealed that this interaction between commensals and coumarins promotes growth by relieving iron starvation. These results show that coumarins improve plant performance by eliciting microbe-assisted iron nutrition. We propose that the bacterial root microbiota, stimulated by secreted coumarins, is an integral mediator of plant adaptation to iron-limiting soils.

Cannabis Microbiome and the Role of Endophytes in Modulating the Production of Secondary Metabolites: An Overview

Plants, including cannabis (Cannabis sativa subsp. sativa), host distinct beneficial microbial communities on and inside their tissues and organs, including seeds. They contribute to plant growth, facilitating mineral nutrient uptake, inducing defence resistance against pathogens, and modulating the production of plant secondary metabolites. Understanding the microbial partnerships with cannabis has the potential to affect the agricultural practices by improving plant fitness and the yield of cannabinoids. Little is known about this beneficial cannabis-microbe partnership, and the complex relationship between the endogenous microbes associated with various tissues of the plant, and the role that cannabis may play in supporting or enhancing them. This review will consider cannabis microbiota studies and the effects of endophytes on the elicitation of secondary metabolite production in cannabis plants. The review aims to shed light on the importance of the cannabis microbiome and how cannabinoid compound concentrations can be stimulated through symbiotic and/or mutualistic relationships with endophytes.

Plant terpenes that mediate below-ground interactions: prospects for bioengineering terpenoids for plant protection

Plants are sessile organisms that have evolved various mechanisms to adapt to complex and changing environments. One important feature of plant adaption is the production of specialised metabolites. Terpenes are the largest class of specialised metabolites, with over 80 000 structures reported so far, and they have important ecological functions in plant adaptation. Here, we review the current knowledge on plant terpenes that mediate below-ground interactions between plants and other organisms, including microbes, herbivores and other plants. The discovery, functions and biosynthesis of these terpenes are discussed, and prospects for bioengineering terpenoids for plant protection are considered. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.