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Aim Trichoderma guizhouense NJAU 4742 (Tgui) can serve as a promising strain for the development of novel biofertilizers and biofungicides. Plants primed with Tgui via inoculation were investigated to clarify the underlying mechanisms that promote root growth and development and activate the plant innate immune response. Methods The relative expression of defence-related genes and of genes involved in the auxin signalling pathway in Zea mays and Arabidopsis thaliana was quantified. Scanning electron microscopy (SEM) was performed to visualize the colonization of Tgui in maize roots, and a proteomic approach was used to identify Tgui-derived elicitors. Results The establishment of Tgui in the rhizosphere of maize leads to the stimulation of the auxin synthesis pathway in maize and subsequently leads to increased plant growth. And the extracellular proteins of Tgui induced systemic resistance (ISR) of maize plants to Fusarium verticillioides (Fv) (Hypocreales, Ascomycota); the ISR of maize plants may be linked to the accumulation of reactive oxygen species (ROS) and increased deposition of callose in maize tissue. Conclusions Activation of the maize immune response was triggered by the mixture of extracellular proteins secreted by Tgui into the rhizosphere. Our study thereby contributes to a better understanding of the interaction between T. guizhouense and plant roots.

Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant ( Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus , a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions. Interference competition exemplified by antagonism remains controversial. Using comparative genomic analysis and antagonistic assessments, this study shows that the distribution profile of biosynthetic gene clusters within Bacillus genomes is consistent with their phylogenetic relationship and that congeneric antagonism among Bacillus strains is positively correlated with phylogenetic distance.

Silicon (Si), the second most abundant element in Earth’s crust, exerts beneficial effects on the growth and productivity of a variety of plant species under various environmental conditions. However, the benefits of Si and its importance to plants are controversial due to differences among the species, genotypes, and the environmental conditions. Although Si has been widely reported to alleviate plant drought stress in both the Si-accumulating and nonaccumulating plants, the underlying mechanisms through which Si improves plant water status and maintains water balance remain unclear. The aim of this review is to summarize the morphoanatomical, physiological, biochemical, and molecular processes that are involved in plant water status that are regulated by Si in response to drought stress, especially the integrated modulation of Si-triggered drought stress responses in Si accumulators and intermediate- and excluder-type plants. The key mechanisms influencing the ability of Si to mitigate the effects of drought stress include enhancing water uptake and transport, regulating stomatal behavior and transpirational water loss, accumulating solutes and osmoregulatory substances, and inducing plant defense- associated with signaling events, consequently maintaining whole-plant water balance. This study evaluates the ability of Si to maintain water balance under drought stress conditions and suggests future research that is needed to implement the use of Si in agriculture. Considering the complex relationships between Si and different plant species, genotypes, and the environment, detailed studies are needed to understand the interactions between Si and plant responses under stress conditions.

Nitrogen (N) and carbon (C) are essential elements for plant growth and crop yield. Thus, improved N and C utilisation contributes to agricultural productivity and reduces the need for fertilisation. In the present study, we find that overexpression of a single rice gene, Oryza sativa plasma membrane (PM) H + -ATPase 1 ( OSA1 ), facilitates ammonium absorption and assimilation in roots and enhanced light-induced stomatal opening with higher photosynthesis rate in leaves. As a result, OSA1 overexpression in rice plants causes a 33% increase in grain yield and a 46% increase in N use efficiency overall. As PM H + -ATPase is highly conserved in plants, these findings indicate that the manipulation of PM H + -ATPase could cooperatively improve N and C utilisation, potentially providing a vital tool for food security and sustainable agriculture. Improved utilisation of nitrogen and carbon could boost agricultural productivity. Here Zhang et al. show that overexpression of a single gene, encoding the plasma membrane H +  -ATPase 1 OSA1, is able to increase both carbon fixation via photosynthesis and nitrogen assimilation via ammonium uptake in rice.

Bacteriophages have been proposed as an alternative to pesticides to kill bacterial pathogens of crops. However, the efficacy of phage biocontrol is variable and poorly understood in natural rhizosphere microbiomes. We studied biocontrol efficacy of different phage combinations on Ralstonia solanacearum infection in tomato. Increasing the number of phages in combinations decreased the incidence of disease by up to 80% in greenhouse and field experiments during a single crop season. The decreased incidence of disease was explained by a reduction in pathogen density and the selection for phage-resistant but slow-growing pathogen strains, together with enrichment for bacterial species that were antagonistic toward R. solanacearum. Phage treatment did not affect the existing rhizosphere microbiota. Specific phage combinations have potential as precision tools to control plant pathogenic bacteria.

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae , Bacillaceae , Gibberella , and Fusarium oxysporum , the healthy soil microbiome contained more Streptomyces Mirabilis , Bradyrhizobiaceae , Comamonadaceae , Mortierella , and nonpathogenic fungi of Fusarium . Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

It is important to study the response of plant pathogens to the antibiosis traits of biocontrol microbes to design the efficient biocontrol strategies. In this study, we evaluated the role of volatile organic compounds (VOCs) produced by a biocontrol strain Bacillus amyloliquefaciens SQR-9 on the growth and virulence traits of tomato wilt pathogen Ralstonia solanacearum (RS). The VOCs of SQR-9 significantly inhibited the growth of RS on agar medium and in soil. In addition, the VOCs significantly inhibited the motility traits, production of antioxidant enzymes and exopolysaccharides, biofilm formation and tomato root colonization by RS. The strain SQR-9 produced 22 VOCs, but only nine VOCs showed 1–11% antibacterial activity against RS in their corresponding amounts; however, the consortium of all VOCs showed 70% growth inhibition of RS. The proteomics analysis showed that the VOCs of SQR-9 downregulated RS proteins related to the antioxidant activity, virulence, carbohydrate and amino acid metabolism, protein folding and translation, while the proteins involved in the ABC transporter system, amino acid synthesis, detoxification of aldehydes and ketones, methylation, protein translation and folding, and energy transfer were upregulated. This study describes the significance and effectiveness of VOCs produced by a biocontrol strain against tomato wilt pathogen.

Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to Fusarium oxysporum f.sp. cucumerinum (Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of Comamonadaceae , a potential beneficial microbial group. Further validation demonstrated that Comamonadaceae can be “cultured” by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

Although silicon (Si) is not recognized as an essential element for general higher plants, it has beneficial effects on the growth and production of a wide range of plant species. Si is known to effectively mitigate various environmental stresses and enhance plant resistance against both fungal and bacterial pathogens. In this review, the effects of Si on plant-pathogen interactions are analyzed, mainly on physical, biochemical, and molecular aspects. In most cases, the Si-induced biochemical/molecular resistance during plant-pathogen interactions were dominated as joint resistance, involving activating defense-related enzymes activates, stimulating antimicrobial compound production, regulating the complex network of signal pathways, and activating of the expression of defense-related genes. The most previous studies described an independent process, however, the whole plant resistances were rarely considered, especially the interaction of different process in higher plants. Si can act as a modulator influencing plant defense responses and interacting with key components of plant stress signaling systems leading to induced resistance. Priming of plant defense responses, alterations in phytohormone homeostasis, and networking by defense signaling components are all potential mechanisms involved in Si-triggered resistance responses. This review summarizes the roles of Si in plant-microbe interactions, evaluates the potential for improving plant resistance by modifying Si fertilizer inputs, and highlights future research concerning the role of Si in agriculture.