Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana

Integrating 'cry for help' strategies for sustainable agriculture

Plants recruit specific soil microbes through a sophisticated 'cry for help' strategy to mitigate environmental stresses. Recent advances highlight the potential of leveraging this mechanism to develop microbe-based approaches for enhancing crop health, but challenges remain in refining the criteria and conceptual frameworks to effectively investigate and harness these plant-microbe interactions.

Temporal dynamics of walnut phyllosphere microbiota under synergistic pathogen exposure and environmental perturbation

Introduction

Phyllosphere-associated microbes directly influence plant-pathogen interactions, and the external environment and the plant shape the phyllosphere microbiome.

Methods

In this study, we integrated 16S rRNA and ITS high-throughput sequencing to systematically investigate changes in the phyllosphere microbiome between symptomatic and asymptomatic walnut leaves affected by spot disease, with consideration of phenological stage progression. Additionally, we explored how abiotic (AT, DT, SCTCC & LPDD) and biotic factors (Pn & Gs) impact microbial communities.

Results

Our findings revealed significant differences in the diversity of the phyllosphere microbiome between symptomatic and asymptomatic leaves at the same phenological stage. Furthermore, the structure and function of phyllosphere-associated microbiome changed as the phenological stage progressed. Fungal taxa that related to the function Plant_Pathogen and bacterial taxa that related to the KEGG pathway functions Fatty acid biosynthesis and Biotin metabolism were increased in the symptomatic group. The keystone species driving the walnut phyllosphere microbiome was Pseudomonas spp., which substantially influenced the microbiome of symptomatic vs. asymptomatic leaves. Notably, Pseudomonas spp. interacted with Xanthomonas spp. and Pantoea spp. Correlation analysis revealed that the dew point temperature constituted the primary abiotic factor of phyllosphere bacterial community composition, whereas liquid precipitation depth dimension was identified as the dominant factor shaping fungal taxa. Additionally, leaf net photosynthetic rate and stomatal conductance were closely linked to the phyllosphere microbiome.

Discussion

These results advance our understanding of community-level microbial responses to pathogen invasion and highlight the multifactorial drivers of phyllosphere microbiome assembly. Ultimately, they contribute to predicting and managing walnut leaf-related diseases.

Seed tuber microbiome can predict growth potential of potato varieties

Potato vigour, the growth potential of seed potatoes, is a key agronomic trait that varies significantly across production fields due to factors such as genetic background and environmental conditions. Seed tuber microbiomes are thought to influence plant health and crop performance, yet the precise relationships between microbiome composition and potato vigour remain unclear. Here we conducted microbiome sequencing on seed tuber eyes and heel ends from 6 potato varieties grown in 240 fields. By using time-resolved drone imaging of three trial fields in the next season to track crop development, we were able to link microbiome composition with potato vigour. We used microbiome data at varying taxonomic resolutions to build random forest predictive models and found that amplicon sequence variants provided the highest predictive accuracy for potato vigour. The model revealed variety-specific relationships between the seed tuber microbiome and next season's crop vigour in independent trial fields. With a coefficient of determination value of 0.69 for the best-performing variety, the model accurately predicted vigour in seed tubers from fields not previously included in the analysis. Moreover, the model identified key microbial indicators of vigour from which a Streptomyces, an Acinetobacter and a Cellvibrio amplicon sequence variant stood out as the most important contributors to the model's accuracy. This study shows that seed potato vigour can be reliably predicted based on the microbiota associated with seed tuber eyes, potentially guiding future microbiome-informed breeding strategies.

Plant growth-promoting microorganisms drive K strategists through deterministic processes to alleviate biological stress caused by Fusarium oxysporum

Soybean root rot, caused by soil-borne pathogens such as Fusarium oxysporum, frequently occurs in Northeast China and leads to a decline in soil health and becoming a bottleneck for soybean yield in the region. To address this issue, applying beneficial microorganisms and altering soil microbial community structure have become effective strategies. In this study, the 90-day soybean pot experiment was conducted to explore the assembly process and life strategy selection of bacterial communities in the rhizosphere of healthy (inoculated with Funneliformis mosseae, F group and treated with Pseudomonas putida, P group) and diseased (inoculated with F. oxysporum, O group) soybean plants, as well as the recovery effect of beneficial microorganisms on soil-borne diseases (combined treatments OP and OF). Results indicated that in healthy soils (P and F), microbial community assembly process in the soybean rhizosphere was entirely governed by heterogeneous selection (HeS, 100 %). However, inoculated with P. putida (OP) was primarily driven by stochastic processes (HeS 40 %, dispersal limitation (DL) 60 %), and the F. mosseae treatment (OF) predominantly followed a deterministic process (HeS 89 %, DL 11 %) in diseased soils. Inoculation of plant growth-promoting microorganisms (PGPMs) in diseased soil drove the life strategy of the rhizosphere bacterial community from r- to K-strategy, evident from the lower rRNA operon (rrn) copy numbers (O 3.7, OP 2.1, OF 2.3), higher G+ to G- ratios (O 0.47, OP 0.58, OF 0.57), and a higher abundance of oligotrophs (O 50 %, OP 53 %, OF 54 %). In healthy (P and F) and diseased (O, OP, OF) rhizosphere soils, OTU820, OTU6142, and OTU8841 under the K-strategy, and OTU6032 and OTU6917 under the r-strategy, which served as keystone species, had a significant promoting relationship with plant biomass and defense capabilities ( p ＜0.05). Additionally, inoculation of PGPMs improved autotoxin degradation and positively correlated with bacterial life strategies in both healthy and diseased soils (P, F, OP and OF) ( p ＜0.05). These findings enhance our understanding of soil-microbe interactions and offer new insights and precise control measures for soybean disease management and soil environment remediation.

Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere

Resident microbiota produces small molecules that influence the chemical microenvironments on leaves, but its signalling roles in pathogen defence are not yet well understood. Here we show that Aspergillus cvjetkovicii, enriched in rice leaf microbiota, subverts Rhizoctonia solani infections via small-molecule-mediated interspecies signalling. 2,4-Di-tert-butylphenol (2,4-DTBP), identified as a key signalling molecule within the Aspergillus-enriched microbiota, effectively neutralizes reactive oxygen species-dependent pathogenicity by switching off bZIP-activated AMT1 transcription in R. solani. Exogenous application of A. cvjetkovicii and 2,4-DTBP demonstrated varying degrees of protective effects against R. solani infection in diverse crops, including cucumber, maize, soybean and tomato. In rice field experiments, they reduced the R. solani-caused disease index to 19.7-32.2%, compared with 67.2-82.6% in the control group. Moreover, 2,4-DTBP showed activity against other rice phytopathogens, such as Fusarium fujikuroi. These findings reveal a defensive strategy against phytopathogens in the phyllosphere, highlighting the potential of symbiotic microbiota-driven neutralization of pathogenicity.

Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations

BACKGROUND

The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing.

RESULTS

We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections.

CONCLUSIONS

Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. Video Abstract.

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates

The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.

Microbiome-conferred herbicides resistance

This article is a Commentary on Hu et al. (2023), 242: 333–343.

Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis

The soil microbial community plays a critical role in promoting robust plant growth and serves as an effective defence mechanism against root pathogens. Current research has focused on unravelling the compositions and functions of diverse microbial taxa in plant rhizospheres invaded by Ralstonia solanacearum, however, the specific mechanisms by which key microbial groups with distinct functions exert their effects remain unclear. In this study, we employed a combination of amplicon sequencing and metabolomics analysis to investigate the principal metabolic mechanisms of key microbial taxa in plant rhizosphere soil. Compared to the healthy tobacco rhizosphere samples, the bacterial diversity and co-occurrence network of the diseased tobacco rhizosphere soil were significantly reduced. Notably, certain genera, including Gaiella, Rhodoplanes, and MND1 (Nitrosomonadaceae), were found to be significantly more abundant in the rhizosphere of healthy plants than in that of diseased plants. Eight environmental factors, including exchangeable magnesium, available phosphorus, and pH, were found to be crucial factors influencing the composition of the microbial community. Ralstonia displayed negative correlations with pH, exchangeable magnesium, and cation exchange flux, but showed a positive correlation with available iron. Furthermore, metabolomic analysis revealed that the metabolic pathways related to the synthesis of various antibacterial compounds were significantly enriched in the healthy group. The correlation analysis results indicate that the bacterial genera Polycyclovorans, Lysobacter, Pseudomonas, and Nitrosospira may participate in the synthesis of antibacterial compounds. Collectively, our findings contribute to a more in-depth understanding of disease resistance mechanisms within healthy microbial communities and provide a theoretical foundation for the development of targeted strategies using beneficial microorganisms to suppress disease occurrence.

Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens

In healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.