Pseudozyma aphidis Induces Salicylic-Acid-Independent Resistance to Clavibacter michiganensis in Tomato Plants

High-quality genome resource of a basidiomycetous yeast, Moesziomyces antarcticus isolate RS1, isolated from rice seed

Moesziomyces antarcticus (anamorph: Pseudozyma antarctica) is a basidiomycetous yeast in the Ustilaginaceae family and is a core member of the rice seed microbiome. M. antarcticus RS1 was isolated from surface-sterilized rice seeds. This 18.287 Mb draft genome of M. antarcticus RS1 is comprised of a 60.8% GC content and 6,817 protein-coding genes.

Inactivation of tomato WAT1 leads to reduced susceptibility to Clavibacter michiganensis through downregulation of bacterial virulence factors

Tomato bacterial canker caused by Clavibacter michiganensis (Cm) is considered to be one of the most destructive bacterial diseases of tomato. To date, no resistance to the pathogen has been identified. While several molecular studies have identified (Cm) bacterial factors involved in disease development, the plant genes and mechanisms associated with susceptibility of tomato to the bacterium remain largely unknown. Here, we show for the first time that tomato gene SlWAT1 is a susceptibility gene to Cm. We inactivated the gene SlWAT1 through RNAi and CRISPR/Cas9 to study changes in tomato susceptibility to Cm. Furthermore, we analysed the role of the gene in the molecular interaction with the pathogen. Our findings demonstrate that SlWAT1 functions as an S gene to genetically diverse Cm strains. Inactivation of SlWAT1 reduced free auxin contents and ethylene synthesis in tomato stems and suppressed the expression of specific bacterial virulence factors. However, CRISPR/Cas9 slwat1 mutants exhibited severe growth defects. The observed reduced susceptibility is possibly a result of downregulation of bacterial virulence factors and reduced auxin contents in transgenic plants. This shows that inactivation of an S gene may affect the expression of bacterial virulence factors.

Modes of Action of Biocontrol Agents and Elicitors for sustainable Protection against Bacterial Canker of Tomato

Tomato is one of the world’s most commonly grown and consumed vegetables. However, it can be attacked by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm), which causes bacterial canker on tomato plants, resulting in significant financial losses in field production and greenhouses worldwide. The current management strategies rely principally on the application of various chemical pesticides and antibiotics, which represent a real danger to the environment and human safety. Plant growth-promoting rhizobacteria (PGPR) have emerged as an attractive alternative to agrochemical crop protection methods. PGPR act through several mechanisms to support plant growth and performance, while also preventing pathogen infection. This review highlights the importance of bacterial canker disease and the pathogenicity of Cmm. We emphasize the application of PGPR as an ecological and cost-effective approach to the biocontrol of Cmm, specifying the complex modes of biocontrol agents (BCAs), and presenting their direct/indirect mechanisms of action that enable them to effectively protect tomato crops. Pseudomonas and Bacillus are considered to be the most interesting PGPR species for the biological control of Cmm worldwide. Improving plants’ innate defense mechanisms is one of the main biocontrol mechanisms of PGPR to manage bacterial canker and to limit its occurrence and gravity. Herein, we further discuss elicitors as a new management strategy to control Cmm, which are found to be highly effective in stimulating the plant immune system, decreasing disease severity, and minimizing pesticide use.

Pseudozyma aphidis Suppresses Microbe-Associated Molecular Pattern (MAMP)-Triggered Callose Deposition and Can Penetrate Leaf Tissue

Beneficial microorganisms need to overcome the plant defense system to establish on or within plant tissues. Like pathogens, beneficial microbes can manipulate a plant's immunity pathways, first by suppressing and hiding to establish on the host and then by inducing resistance to protect the plant. In the current study, we demonstrated that although Pseudozyma aphidis can activate microbe-associated molecular pattern (MAMP)-associated genes, it does not activate MAMP-triggered callose deposition and can, moreover, suppress such deposition triggered by Flg22 or chitin. While MAMP-associated gene activation by P. aphidis was not dependent on salicylic acid, jasmonic acid, or ethylene signaling, suppression of MAMP-triggered callose deposition required the salicylic acid and jasmonic acid signaling factors JAR1-1 and E3 ubiquitin ligase COI1 yet did not rely on EIN2, NPR1, or the transcription factor JIN1/MYC2. We also demonstrated the ability of P. aphidis, known to be an epiphytic yeast-like organism, to penetrate the stomata and establish within plant tissues, as do endophytes. These results thus demonstrate the potential of P. aphidis to suppress MAMP-elicited defenses in order to establish on and within host plant tissues. IMPORTANCE Our study demonstrates the ability of P. aphidis to penetrate into plant tissues, where it avoids and overcomes plant defense systems in order to establish and subsequently protect the plant.

GmGSTU13 Is Related to the Development of Mosaic Symptoms in Soybean Plants Infected with Soybean Mosaic Virus

The leaves of soybean cultivar ZheA8901 show various symptoms (necrosis, mosaic, and symptomless) when infected with different strains of soybean mosaic virus (SMV). Based on a proteomic analysis performed with tandem mass tags (TMT), 736 proteins were differentially expressed from soybean samples that showed asymptomatic, mosaic, and necrosis symptoms induced by SMV strains SC3, SC7, and SC15, respectively. Among these, GmGSTU13 and ascorbate peroxidase (APX) were only upregulated in mosaic and symptomless leaves, respectively. The protein level of GmGSTU13 determined by western blot analysis was consistent with TMT analysis, and quantitative reverse transcriptase PCR analysis showed that GmGSTU13 mRNA levels in mosaic plants were 5.26- and 3.75-fold higher than those in necrotic and symptomless plants, respectively. Additionally, the expression of the viral coat protein (CP) gene was increased, and serious mosaic symptoms were observed in GmGSTU13-overexpressing plants inoculated with all three SMV strains. These results showed that GmGSTU13 is associated with the development of SMV-induced mosaic symptoms in soybean and that APX is upregulated in symptomless leaves at both the transcriptional and protein levels. In APX gene-silenced soybean plants, the relative expression of the viral CP gene was 1.50, 7.59, and 1.30 times higher than in positive control plants inoculated with the three SMV strains, suggesting that the upregulation of APX may be associated with lack of symptoms in soybean infected with SMV. This work provides a useful dataset for identifying key proteins responsible for symptom development in soybean infected with different SMV strains.

Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response

Bacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) is an economically important disease. To understand the host defense response to Cmm infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to Cmm showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with Cmm. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with Cmm. Furthermore, Cmm infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some Cmm-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against Cmm.

Pseudomonas entomophila 23S Produces a Novel Antagonistic Compound against Clavibacter michiganensis subsp. michiganensis, a Pathogen of Tomato Bacterial Canker

Biopesticides, which consist of antagonistic microorganisms, or the bioactive compounds they produce offer attractive alternatives to synthetic agrochemicals as a means of reducing plant diseases in crop production systems. In our previous study, a strain of Pseudomonas entomophila 23S was reported to have a strong antagonistic activity toward Clavibacter michiganensis subsp. michiganensis (Cmm), a pathogen of tomato bacterial canker disease, which causes serious damage to the tomato production industry. This study focused on purification and characterization of the anti-Cmm compound(s) produced by P. entomophila 23S. The cell-free supernatant was first subjected to butanol extraction, fractioned by solid-phase extraction (SPE), and purified by high-performance liquid-chromatography (HPLC). The semi-preparative purified compounds retained anti-Cmm activity. These compounds were then characterized by liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-HRMS/MS) and nuclear magnetic resonance (NMR). Two anti-Cmm compounds, C15H16N2O and C16H18N2O, were isolated by this procedure. From the LC/MS spectra, the compounds were predicted to have an isoquinoline ring, the presence of which was confirmed by NMR. The compounds differed with respect to the presence of a methyl group in a side chain. In addition, P. entomophila 23S grown in different culture media produced the greatest amounts of these anti-Cmm compounds when in Nutrient Broth (NB), where bacterial growth was the slowest. NB composition is more favorable in stimulating P. entomophila 23S to produce higher amounts of these anti-Cmm compounds.

Secretion-Based Modes of Action of Biocontrol Agents with a Focus on Pseudozyma aphidis

Plant pathogens challenge our efforts to maximize crop production due to their ability to rapidly develop resistance to pesticides. Fungal biocontrol agents have become an important alternative to chemical fungicides, due to environmental concerns related to the latter. Here we review the complex modes of action of biocontrol agents in general and epiphytic yeasts belonging to the genus Pseudozyma specifically and P. aphidis in particular. Biocontrol agents act through multiple direct and indirect mechanisms, which are mainly based on their secretions. We discuss the direct modes of action, such as antibiosis, reactive oxygen species-producing, and cell wall-degrading enzyme secretions which can also play a role in mycoparasitism. In addition, we discuss indirect modes of action, such as hyperbiotrophy, induced resistance and growth promotion based on the secretion of effectors and elicitors from the biocontrol agent. Due to their unique characteristics, epiphytic yeasts hold great potential for use as biocontrol agents, which may be more environmentally friendly than conventional pesticides and provide a way to reduce our dependency on fungicides based on increasingly expensive fossil fuels. No less important, the complex mode of action of Pseudozyma-based biocontrol agents can also reduce the frequency of resistance developed by pathogens to these agents.

Shaping the leaf microbiota: plant-microbe-microbe interactions

The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.

A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme

Plants are not only challenged by pathogenic organisms but also colonized by commensal microbes. The network of interactions these microbes establish with their host and among each other is suggested to contribute to the immune responses of plants against pathogens. In wild Arabidopsis thaliana populations, the oomycete pathogen Albugo laibachii plays an influential role in structuring the leaf phyllosphere. We show that the epiphytic yeast Moesziomyces bullatus ex Albugo on Arabidopsis, a close relative of pathogenic smut fungi, is an antagonistic member of the A. thaliana phyllosphere, which reduces infection of A. thaliana by A. laibachii. Combination of transcriptomics, reverse genetics, and protein characterization identified a GH25 hydrolase with lysozyme activity as a major effector of this microbial antagonism. Our findings broaden the understanding of microbial interactions within the phyllosphere, provide insights into the evolution of epiphytic basidiomycete yeasts, and pave the way for novel biocontrol strategies.

Biocontrol yeasts: mechanisms and applications

Yeasts occur in all environments and have been described as potent antagonists of various plant pathogens. Due to their antagonistic ability, undemanding cultivation requirements, and limited biosafety concerns, many of these unicellular fungi have been considered for biocontrol applications. Here, we review the fundamental research on the mechanisms (e.g., competition, enzyme secretion, toxin production, volatiles, mycoparasitism, induction of resistance) by which biocontrol yeasts exert their activity as plant protection agents. In a second part, we focus on five yeast species (Candida oleophila, Aureobasidium pullulans, Metschnikowia fructicola, Cryptococcus albidus, Saccharomyces cerevisiae) that are or have been registered for the application as biocontrol products. These examples demonstrate the potential of yeasts for commercial biocontrol usage, but this review also highlights the scarcity of fundamental studies on yeast biocontrol mechanisms and of registered yeast-based biocontrol products. Yeast biocontrol mechanisms thus represent a largely unexplored field of research and plentiful opportunities for the development of commercial, yeast-based applications for plant protection exist.

Pseudozyma aphidis activates reactive oxygen species production, programmed cell death and morphological alterations in the necrotrophic fungus Botrytis cinerea

Many types of yeast have been studied in the last few years as potential biocontrol agents against different phytopathogenic fungi. Their ability to control plant diseases is mainly through combined modes of action. Among them, antibiosis, competition for nutrients and niches, induction of systemic resistance in plants and mycoparasitism have been the most studied. In previous work, we have established that the epiphytic yeast Pseudozyma aphidis inhibits Botrytis cinerea through induced resistance and antibiosis. Here, we demonstrate that P. aphidis adheres to B. cinerea hyphae and competes with them for nutrients. We further show that the secreted antifungal compounds activate the production of reactive oxygen species and programmed cell death in B. cinerea mycelium. Finally, P. aphidis and its secreted compounds negatively affect B. cinerea hyphae, leading to morphological alterations, including hyphal curliness, vacuolization and branching, which presumably affects the colonization ability and infectivity of B. cinerea. This study demonstrates additional modes of action for P. aphidis and its antifungal compounds against the plant pathogen B. cinerea.

Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China

Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming. Based on the observed relative abundances, the phyla Bacteroidetes, Actinobacteria, TM7, and Basidiomycota were significantly increased on BCF-associated leaves compared with MBF leaves, while Acidobacteria and Ascomycota were significantly decreased. An ecological function prediction analysis based on metabolic processes indicated that BCF could accelerate nutrient (C, N, and S) cycling but may increase the risk of fungal-associated diseases. Our findings suggest that shifts in leaf-associated bacterial and fungal communities can be important indicators for the scientific management of BCF systems.

Foliar microbiome transplants confer disease resistance in a critically-endangered plant

There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was not effective in a closely related plant. Plant conservation efforts should strive to include foliar microbes as part of comprehensive management plans.

Foliar application of the leaf-colonizing yeast Pseudozyma churashimaensis elicits systemic defense of pepper against bacterial and viral pathogens

Yeast associates with many plant parts including the phyllosphere, where it is subject to harsh environmental conditions. Few studies have reported on biological control of foliar pathogens by yeast. Here, we newly isolated leaf-colonizing yeasts from leaves of field-grown pepper plants in a major pepper production area of South Korea. The yeast was isolated using semi-selective medium supplemented with rifampicin to inhibit bacterial growth and its disease control capacity against Xanthomonas axonopodis infection of pepper plants in the greenhouse was evaluated. Of 838 isolated yeasts, foliar spray of Pseudozyma churashimaensis strain RGJ1 at 108 cfu/mL conferred significant protection against X. axonopodis and unexpectedly against Cucumber mosaic virus, Pepper mottle virus, Pepper mild mottle virus, and Broad bean wilt virus under field conditions. Direct antagonism between strain RGJ1 and X. axonopodis was not detected from co-culture assays, suggesting that disease is suppressed via induced resistance. Additional molecular analysis of the induced resistance marker genes Capsicum annuum Pathogenesis-Related (CaPR) 4 and CaPR5 indicated that strain RGJ1 elicited plant defense priming. To our knowledge, this study is the first report of plant protection against bacterial and viral pathogens mediated by a leaf-colonizing yeast and has potential for effective disease management in the field.