Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.

https://www.pnas.org/content/pnas/115/22/E5213.full.pdf

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

Fungi are an understudied, biotechnologically valuable group of organisms. Due to 
the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential.

The amazing potential of fungi: 50 ways we can exploit fungi industrially

s Background Impressive progress was made in the last decade in development, registration and commercialization of biocontrol products based on yeast to manage postharvest pathogens of fruit. To successfully inhibit the pathogen infection and development, several possible mechanisms operate in a tritrophic host-pathogen-antagonist interaction system. Scope and Approach The current reviews focuses on the recent knowledge on the mechanisms by which yeast biocontrol agents (BCAs) interact with pathogens and fruit tissues. The main mechanisms of action explored include antibiosis, mycoparasitism, production of lytic enzymes, induced resistance, competition for limiting nutrients and space, and the role of oxidative stress. Omics techniques can provide a powerful tool to study complex fruit host-pathogen-antagonist-native microflora interactions. Key Findings and Conclusions Various aspects relevant to mechanisms of action of yeast antagonists have been discussed, including unique environment of surface wounds, iron competition, biofilm formation, cell wall degrading enzymes, and involvement of oxidative stress. Outstanding advancement in molecular and omics technologies revolutionized the research about the physiological status of BCAs and the global effect of the application of BCAs on the transcriptome and/or proteome of fruit. Microbial communities on plant surfaces could impact disease control through their interactions with host plants, pathogens, and BCAs, in a quadritrophic interaction system, hence microbiome research opens new research opportunities. The complex modes of action make antagonistic performance and efficacy more dependent on production, formulation, packing, application, and storage. A deep understanding of the mode of action is essential to develop appropriate formulation and methods of application.

Development of biocontrol products for postharvest diseases of fruit: The importance of elucidating the mechanisms of action of yeast antagonists

Fungal volatile organic compounds: A review with emphasis on their biotechnological potential

Antibiotics are low-molecular-mass products of secondary metabolism, nonessential for the growth of producing organisms, but very important for human health. They have unusual structures and are most often formed during the late growth phase of the producing microorganisms. Their production arises from intracellular intermediates, which are condensed into more complex structures through defined biochemical pathways. Their synthesis can be influenced by manipulating the type and concentration of nutrients formulating the culture media. Among them, the effect of the carbon source has been the subject of continuous studies for both industry and research groups. Glucose and other carbohydrates have been reported to interfere with antibiotic synthesis and this effect depends on the rapid utilization of the preferred carbon source. Different mechanisms have been described in bacteria and fungi to explain the negative effects of carbon catabolites on antibiotic production. They show important differences depending on the microbe being considered. Their understanding and manipulation have been useful for both perfecting fermentation conditions to produce anti-infectives and for strain improvement. To improve the production of antibiotics, carbon source repression can be decreased or abolished by mutations resulting in antimetabolite resistance. Enzymes reported as regulated by the carbon source have been used as targets for strain improvement. During the last few years, important advances have been reported elucidating the essential aspects of carbon source regulation on antibiotic production at biochemical and molecular levels. The aim of this review is to describe these advances, giving special emphasis to those reported for the genus Streptomyces.

/pdf/carbon-source-regulation-of-antibiotic-production-228qr7jl56.pdf

Carbon source regulation of antibiotic production

Aims: To isolate and identify antioomycete substances from Fusarium oxysporum EF119 against Phytophthora infestans and to investigate their antimicrobial activities against various plant pathogenic bacteria, oomycetes and true fungi.



Methods and Results:  Two antioomycete substances were isolated from liquid cultures of F. oxysporum EF119, which shows a potent disease control efficacy against tomato late blight caused by P. infestans. They were identified as bikaverin and fusaric acid by mass and nuclear magnetic resonance spectral analyses. They inhibited the mycelial growth of plant pathogenic oomycetes and fungi. Fusaric acid also effectively suppressed the cell growth of various plant pathogenic bacteria, but bikaverin was virtually inactive. Treatment with bikaverin at 300 μg ml−1 suppressed the development of tomato late blight by 71%. Fusaric acid provided effective control against tomato late blight and wheat leaf rust over 67% at concentrations more than 100 μg ml−1.



Conclusions:  Both bikaverin and fusaric acid showed in vitro and in vivo antioomycete activity against P. infestans.



Significance and Impact of the Study: Fusarium oxysporum EF119 producing both bikaverin and fusaric acid may be used as a biocontrol agent against tomato late blight caused by P. infestans.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2672.2007.03581.x

Bikaverin and fusaric acid from Fusarium oxysporum show antioomycete activity against Phytophthora infestans.

Aims: To characterize the volatile antifungal compound produced by Oxyporus latemarginatus EF069 and to examine in vitro and in vivo fumigation activity of the fungus.



Methods and Results:  An antifungal volatile-producing strain, O. latemarginatus EF069 inhibited the mycelial growth of Alternaria alternata, Botrytis cinerea, Colletotrichum gloeosporioides, Fusarium oxysporum f. sp. lycopersici, and Rhizoctonia solani by mycofumigation. An antifungal volatile compound was isolated from the hexane extract of wheat bran–rice hull cultures of O. latemarginatus EF069 by repeated silica gel column chromatography and identified as 5-pentyl-2-furaldehyde (PTF). The purified PTF inhibited mycelial growth of R. solani in a dose-dependent manner. The mycofumigation with solid cultures of EF069 also reduced effectively the development of postharvest apple decay caused by B. cinerea and Rhizoctonia root rot of moth orchid caused by R. solani.



Conclusions: Oxyporus latemarginatus EF069 showed in vitro and in vivo fumigation activity against plant pathogenic fungi by producing 5-pentyl-2-furaldehyde.



Significance and Impact of the Study: Oxyporus latemarginatus EF069 producing an antifungal volatile compound may be used as a biofumigant for the control of fungal plant diseases.

https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2672.2008.04087.x

Mycofumigation with Oxyporus latemarginatus EF069 for control of postharvest apple decay and Rhizoctonia root rot on moth orchid

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Bikaverin and fusaric acid from Fusarium oxysporum show antioomycete activity against Phytophthora infestans.

Mycofumigation with Oxyporus latemarginatus EF069 for control of postharvest apple decay and Rhizoctonia root rot on moth orchid