Production of Plant-Associated Volatiles by Select Model and Industrially Important Streptomyces spp

Aerial signaling by plant-associated Streptomyces setonii WY228 regulates plant growth and enhances salt stress tolerance

Plant-associated streptomycetes play important roles in plant growth and development. However, knowledge of volatile-mediated crosstalk between Streptomyces spp. and plants remains limited. In this study, we investigated the impact of volatiles from nine endophytic Streptomyces strains on the growth and development of plants. One versatile strain, Streptomyces setonii WY228, was found to significantly promote the growth of Arabidopsis thaliana and tomato seedlings, confer salt tolerance, and induce early flowering and increased fruit yield following volatile treatment. Analysis of plant growth-promoting traits revealed that S. setonii WY228 could produce indole-3-acetic acid, siderophores, ACC deaminase, fix nitrogen, and solubilize inorganic phosphate. These capabilities were further confirmed through genome sequencing and analysis. Volatilome analysis indicated that the volatile organic compounds emitted from ISP-2 medium predominantly comprised sesquiterpenes and 2-ethyl-5-methylpyrazine. Further investigations showed that 2-ethyl-5-methylpyrazine and sesquiterpenoid volatiles were the primary regulators promoting growth, as confirmed by experiments using the terpene synthesis inhibitor phosphomycin, pure compounds, and comparisons of volatile components. Transcriptome analysis, combined with mutant and inhibitor studies, demonstrated that WY228 volatiles promoted root growth by activating Arabidopsis auxin signaling and polar transport, and enhanced root hair development through ethylene signaling activation. Additionally, it was confirmed that volatiles can stimulate plant abscisic acid signaling and activate the MYB75 transcription factor, thereby promoting anthocyanin synthesis and enhancing plant salt stress tolerance. Our findings suggest that aerial signaling-mediated plant growth promotion and abiotic stress tolerance represent potentially overlooked mechanisms of Streptomyces-plant interactions. This study also provides an exciting strategy for the regulation of plant growth and the improvement of horticultural crop yields within sustainable agricultural practices.

Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents

Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.

Actinomycete Potential as Biocontrol Agent of Phytopathogenic Fungi: Mechanisms, Source, and Applications

Synthetic fungicides have been the main control of phytopathogenic fungi. However, they cause harm to humans, animals, and the environment, as well as generating resistance in phytopathogenic fungi. In the last few decades, the use of microorganisms as biocontrol agents of phytopathogenic fungi has been an alternative to synthetic fungicide application. Actinomycetes isolated from terrestrial, marine, wetland, saline, and endophyte environments have been used for phytopathogenic fungus biocontrol. At present, there is a need for searching new secondary compounds and metabolites of different isolation sources of actinomycetes; however, little information is available on those isolated from other environments as biocontrol agents in agriculture. Therefore, the objective of this review is to compare the antifungal activity and the main mechanisms of action in actinomycetes isolated from different environments and to describe recent achievements of their application in agriculture. Although actinomycetes have potential as biocontrol agents of phytopathogenic fungi, few studies of actinomycetes are available of those from marine, saline, and wetland environments, which have equal or greater potential as biocontrol agents than isolates of actinomycetes from terrestrial environments.

Analysis of Streptomyces Volatilomes Using Global Molecular Networking Reveals the Presence of Metabolites with Diverse Biological Activities

Streptomyces species produce a wide variety of specialized metabolites, some of which are used for communication or competition for resources in their natural environments. In addition, many natural products used in medicine and industry are derived from Streptomyces, and there has been interest in their capacity to produce volatile organic compounds (VOCs) for different industrial and agricultural applications. Recently, a machine-learning workflow called MSHub/GNPS was developed, which enables auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data, molecular networking, and library search capabilities, but it has not been applied to Streptomyces volatilomes. In this study, 131 Streptomyces isolates from the island of Newfoundland were phylogenetically typed, and 37 were selected based on their phylogeny and growth characteristics for VOC analysis using both a user-guided (conventional) and an MSHub/GNPS-based approach. More VOCs were annotated by MSHub/GNPS than by the conventional method. The number of unknown VOCs detected by the two methods was higher than those annotated, suggesting that many novel compounds remain to be identified. The molecular network generated by GNPS can be used to guide the annotation of such unknown VOCs in future studies. However, the number of overlapping VOCs annotated by the two methods is relatively small, suggesting that a combination of analysis methods might be required for robust volatilome analysis. More than half of the VOCs annotated with high confidence by the two approaches are plant-associated, many with reported bioactivities such as insect behavior modulation. Details regarding the properties and reported functions of such VOCs are described. IMPORTANCE This study represents the first detailed analysis of Streptomyces volatilomes using MSHub/GNPS, which in combination with a routinely used conventional method led to many annotations. More VOCs could be annotated using MSHub/GNPS as compared to the conventional method, many of which have known antimicrobial, anticancer, and insect behavior-modulating activities. The identification of numerous plant-associated VOCs by both approaches in the current study suggests that their production could be a more widespread phenomenon by members of the genus, highlighting opportunities for their large-scale production using Streptomyces. Plant-associated VOCs with antimicrobial activities, such as 1-octen-3-ol, octanol, and phenylethyl alcohol, have potential applications as fumigants. Furthermore, many of the annotated VOCs are reported to influence insect behavior, alluding to a possible explanation for their production based on the functions of other recently described Streptomyces VOCs in dispersal and nutrient acquisition.

Antifungal volatile organic compounds from Streptomyces setonii WY228 control black spot disease of sweet potato

Volatile organic compounds (VOCs) produced by microorganisms are considered as promising environmental-safety fumigants for controlling postharvest diseases. Ceratocystis fimbriata, the pathogen of black spot disease, seriously affects the quality and yield of sweet potato in the field and postharvest. This study tested the effects of VOCs produced by Streptomyces setonii WY228 on the control of C. fimbriata in vitro and in vivo. The VOCs exhibited strong antifungal activity and significantly inhibited the growth of C. fimbriata. During the 20-days storage, VOCs fumigation significantly controlled the occurrence of pathogen, increased the content of antioxidant and defense-related enzymes and flavonoids, and boosted the starch content so as to maintain the quality of sweet potato. Headspace analysis showed that volatiles 2-ethyl-5-methylpyrazine and dimethyl disulfide significantly inhibited the mycelial growth and spore germination of C. fimbriata in a dose dependent manner. Fumigation with 100 μL/L 2-ethyl-5-methylpyrazine completely controlled the pathogen in vivo after 10-days storage. Transcriptome analysis showed that volatiles mainly downregulated the ribosomal synthesis genes and activated the proteasome system of pathogen in response to VOCs stress, while the genes related to spore development, cell membrane synthesis, mitochondrial function, as well as hydrolase and toxin synthesis were also downregulated, indicating that WY228-produced VOCs act diverse modes of action for pathogen control. Our study demonstrates that fumigation of sweet potato tuberous roots with S. setonii WY228 or use of formulations based on the VOCs is a promising new strategy to control sweet potato and other food and fruit pathogens during storage and shipment. Importance Black spot disease caused by Ceratocystis fimbriata has caused huge economic losses to worldwide sweet potato production. At present, the control of C. fimbriata mainly depends on toxic fungicides, and there is a lack of effective alternative strategies. The research on biological control of sweet potato black spot disease is also very limited. The development of efficient biocontrol technique against pathogens using microbial volatile organic compounds could be an alternative method to control this disease. Our study revealed the significant biological control effect of volatile organic compounds of Streptomyces setonii WY228 on black spot disease of postharvest sweet potato and the complex antifungal mechanism against C. fimbriata. Our data demonstrated that Streptomyces setonii WY228 and its volatile 2-ethyl-5-methylpyrazine could be candidate strain and compound for the creation of fumigants, and showed the important potential of biotechnology application in the field of food and agriculture.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.