Insights into the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, the pathogen Botrytis cinerea and their plant host

Identification and application of an endophytic fungus Arcopilus aureus from Panax notoginseng against crop fungal disease

Endophytic fungi are important microbial resources for developing novel antibacterial and antifungal drugs to prevent and control crop diseases. Panax notoginseng has been used as a Chinese medicinal herb for a long time, as it has various bioactivities. However, information on endophytic fungi isolated from Panax notoginseng is rare. In this study, an endophytic fungus known as SQGX-6, which was later identified as the golden hair fungus Arcopilus aureus, was isolated from Panax notoginseng. SQGX-6 was extracted using ethyl acetate, and the active components of the fungus were identified using ultra-performance liquid chromatography-mass spectrometry (UHPLC-MS). The antifungal and antioxidant activities of the extract were determined and evaluated in vitro and in vivo. SQGX-6 and its extract inhibited the growth of Corn stalk rot (Fusarium graminearum), Corn southern leaf blight (Helminthosporium maydis), and Tomato gray mold (Botrytis cinerea) in vitro. The free radical scavenging rates for 2,2-Diphenyl-1-pyridinyl hydrazide (DPPH) radical scavenging activity, 3-Ethylbenzothiazoline-6-Sulfonic Acid Radical scavenging (ABTS) activity were also downregulated by the SQGX-6 extract. In vivo, the SQGX-6 extract inhibited the mycelial growth rates of the three aforementioned fungi and downregulated malondialdehyde (MDA) content and upregulated peroxidase (POD) and phenylalanine ammonia-lyase (PAL) content in fruits, leading to significant reduction in damage to cherry tomatoes caused by Botrytis cinerea. UHPLC-MS was performed to identify various active substances, including Alkaloids, Azoles, Benzofurans, Coumarins, Flavonoids, Organic acids, Phenols, and plant growth regulators contained in the extract. These results suggested that the endophytic fungus SQGX-6 of Panax notoginseng and its extract have excellent antifungal and antioxidant activities, and thus, it is an important microbial resource for the developing novel drugs against plant fungal infections.

Biocontrol Potential of Beneficial Fungus Aureobasidium pullulans Against Botrytis cinerea and Colletotrichum acutatum

Biological control is a promising approach to reduce plant diseases caused by fungal pathogens and ensure high productivity in horticultural production. In the present study, we evaluated the biocontrol potential and underlying mechanisms of the beneficial fungus Aureobasidium pullulans against Botrytis cinerea and Colletotrichum acutatum, casual agents of gray mold and anthracnose diseases in strawberry. Notably, this is the first time that A. pullulans has been tested against C. acutatum in strawberry. A. pullulans strains (AP-30044, AP-30273, AP-53383, and AP-SLU6) showed significant variation in terms of growth and conidia production. An inverse relationship was found between the growth and conidiation rate, suggesting a trade-off between resource allocation for growth and conidial production. Dual plate co-culturing assays showed that mycelial growth of B. cinerea and C. acutatum was reduced by up to 35 and 18%, respectively, when challenged with A. pullulans compared with control treatments. Likewise, culture filtrates of A. pullulans showed varying levels of antifungal activity against B. cinerea and C. acutatum, reducing the mycelial biomass by up to 90 and 72%, respectively. Furthermore, milk powder plate assays showed that A. pullulans produced substantial amounts of extracellular proteases, which are known to degrade fungal cuticle. Ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) analyses revealed that A. pullulans produced exophilins, liamocins, and free fatty acids known to have antifungal properties. A. pullulans shows high potential for successful biological control of strawberry diseases and discuss opportunities for further optimization of this beneficial fungus.

Isolation, purification, and identification of antifungal protein produced by Bacillus subtilis SL-44 and anti-fungal resistance in apple

Apple anthracnose is a fruit fungal disease that is currently recognized as one of the most severe threats to apples worldwide. In this study, antifungal protein from Bacillus subtilis SL-44 was isolated, purified, identified, and applied for Colletotrichum gloeosporioides control. The antagonistic experiment showed that SL-44 had an excellent broad spectrum against plant pathogenic fungi. The optimal fermentation conditions were as follows: initial pH was 7, inoculum volume was 2%, and rotational speed was 180 r/min. The optimized yield of antifungal protein increased by 45.83% compared with that before. The crude protein was isolated and purified by (NH₄)₂SO₄ precipitation, DEAE-Sepharose Fast Flow, and Sephadex G-100 column chromatography. LC-MS analyzed that antifungal protein was likely to be a novel protein with a molecular weight of 42 kDa. The mechanism revealed that the antifungal protein may disrupt the cell wall structure of C. gloeosporioides and function as its antifungal action. Additionally, antifungal protein significantly alleviated the size of the lesion to more than 70% in the apple infection protection test. In conclusion, antifungal protein has remarkable potential in developing fungicides for the biological control of apple anthracnose. HIGHLIGHTS: 1. B. subtilis SL-44 had broad-spectrum antagonism against plant pathogenic fungi. 2. The optimal fermentation conditions for extracting antifungal protein were optimized. 3. The antifungal protein is a novel protein with a molecular weight of 42 kDa. 4. The mechanism of antifungal protein may disrupt the cell wall structure of C. gloeosporioides.

Abundant bacteria and fungi attached to airborne particulates in vegetable plastic greenhouses

The proliferation of modern vegetable plastic greenhouses (VPGS) supplies more and more vegetables for food all over the world. The airborne bacteria and fungi induce more exposure opportunities for workers toiling in confined plastic greenhouses. Culture-independent approaches by qPCR and high-throughput sequencing technology were used to study the airborne particulates microbiota in typic VPGS in Shandong, a large base of vegetables in China. The result revealed the mean airborne bacteria concentrations reached 1.67 × 10³ cells/m³ (PM_2.5) and 2.38 × 10³ cells/m³ (PM₁₀), and the mean airborne fungal concentrations achieved 1.49 × 10² cells/m³ (PM_2.5) and 3.19 × 10² cells/m³ (PM₁₀) in VPGS. The predominant bacteria in VPGS included Ralstonia, Alcanivorax, Pseudomonas, Bacillus, and Acinetobacter. Botrytis, Alternaria, Fusarium, Sporobolomyces, and Cladosporium were frequently detected fungal genera in VPGS. A higher Chao1 of bacteria in PM₁₀ was significantly different from PM_2.5 in VPGS. The potential pathogens in VPGS include Raltonia picketti, Acinetobacter lwoffii, Bacillus anthracis, Botrytis cinerea, and Cladosporium sphaerospermum. The network analysis indicated that airborne microbiota was associated with soil microbiota which was affected by anthropologic activities. The predicted gene functions revealed that bacterial function mainly involved metabolism, neurodegenerative diseases, and fungal trophic mode dominated by Pathotroph-Saprotroph in VPGS. These findings unveiled airborne microbiomes in VPGS so that a strategy for improving air quality can be applied to safeguard health and vegetation.

Treatment with organic manure inoculated with a biocontrol agent induces soil bacterial communities to inhibit tomato Fusarium wilt disease

Introduction

Organic manure, plant growth-promoting microorganisms, and biocontrol agents are widely used to sustainably control soil-borne diseases. However, how and whether organic manure inoculated with biocontrol agents alters soil microbiota and reduces disease severity is poorly understood.

Methods

Here, we examined changes to the soil microbial community, soil properties, and incidence of Fusarium wilt disease in response to several fertilization regimes. Specifically, we studied the effects of inorganic chemical fertilization (CF), organic manure fertilization (OF), and Erythrobacter sp. YH-07-inoculated organic manure fertilization (BF) on the incidence of Fusarium wilt in tomato across three seasons.

Results

BF-treated soils showed increased microbial abundance, richness, and diversity compared to other treatments, and this trend was stable across seasons. BF-treated soils also exhibited a significantly altered microbial community composition, including increased abundances of Bacillus, Altererythrobacter, Cryptococcus, and Saprospiraceae, and decreased abundances of Chryseolinea and Fusarium. Importantly, BF treatment significantly suppressed the incidence of Fusarium wilt in tomato, likely due to direct suppression by Erythrobacter sp. YH-07 and indirect suppression through changes to the microbial community composition and soil properties.

Discussion

Taken together, these results suggest that Erythrobacter sp. YH-07-inoculated organic manure is a stable and sustainable soil amendment for the suppression of Fusarium wilt diseases.

Rhizospheric microorganisms: The gateway to a sustainable plant health

Plant health is essential for food security, and constitutes a major predictor to safe and sustainable food systems. Over 40% of the global crops' productions are lost to pests, insects, diseases, and weeds, while the routinely used chemical-based pesticides to manage the menace also have detrimental effects on the microbial communities and ecosystem functioning. The rhizosphere serves as the microbial seed bank where microorganisms transform organic and inorganic substances in the rhizosphere into accessible plant nutrients as plants harbor diverse microorganisms such as fungi, bacteria, nematodes, viruses, and protists among others. Although, the pathogenic microbes initiate diseases by infiltrating the protective microbial barrier and plants' natural defense systems in the rhizosphere. Whereas, the process is often circumvented by the beneficial microorganisms which antagonize the pathogens to instill disease resistance. The management of plant health through approaches focused on disease prevention is instrumental to attaining sustainable food security, and safety. Therefore, an in-depth understanding of the evolving and succession of root microbiomes in response to crop development as discussed in this review opens up new-fangled possibilities for reaping the profit of beneficial root–microbiomes' interactions toward attaining sustainable plant health.

Response of Fusarium pseudograminearum to Biocontrol Agent Bacillus velezensis YB-185 by Phenotypic and Transcriptome Analysis

The use of biological control agents (BCAs) is a promising alternative control measure for Fusarium crown rot (FCR) of wheat caused by Fusarium pseudograminearum. A bacterial strain, YB-185, was isolated from the soil of wheat plants with FCR and identified as Bacillus velezensis. YB-185 exhibited strong inhibition of F. pseudograminearum mycelial growth and conidial germination in culture. Seed treatment with YB-185 in greenhouse and field resulted in reductions in disease by 66.1% and 57.6%, respectively, along with increased grain yield. Microscopy of infected root tissues confirmed that YB-185 reduced root invasion by F. pseudograminearum. RNA-seq of F. pseudograminearum during co-cultivation with B. velezensis YB-185 revealed 5086 differentially expressed genes (DEGs) compared to the control. Down-regulated DEGs included genes for glucan synthesis, fatty acid synthesis, mechanosensitive ion channels, superoxide dismutase, peroxiredoxin, thioredoxin, and plant-cell-wall-degrading enzymes, whereas up-regulated DEGs included genes for chitin synthesis, ergosterol synthesis, glutathione S-transferase, catalase, and ABC transporters. In addition, fungal cell apoptosis increased significantly, as indicated by TUNEL staining, and the scavenging rate of 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical cation (ABTS·+) in the fungus significantly decreased. Thus, F. pseudograminearum may be trying to maintain normal cell functions by increasing cell wall and membrane synthesis, antioxidant and anti-stress responses, detoxification of bacterial antimicrobial compounds, and transportation of damaging compounds from its cells. However, cell death and free radical accumulation still occurred, indicating that the responses were insufficient to prevent cell damage. Bacillus velezensis YB-185 is a promising BCA against FCR that acts by directly damaging F. pseudograminearum, thus reducing its ability to colonize roots and produce symptoms.

Three strategies of transgenic manipulation for crop improvement

Heterologous expression of exogenous genes, overexpression of endogenous genes, and suppressed expression of undesirable genes are the three strategies of transgenic manipulation for crop improvement. Up to 2020, most (227) of the singular transgenic events (265) of crops approved for commercial release worldwide have been developed by the first strategy. Thirty-eight of them have been transformed by synthetic sequences transcribing antisense or double-stranded RNAs and three by mutated copies for suppressed expression of undesirable genes (the third strategy). By the first and the third strategies, hundreds of transgenic events and thousands of varieties with significant improvement of resistance to herbicides and pesticides, as well as nutritional quality, have been developed and approved for commercial release. Their application has significantly decreased the use of synthetic pesticides and the cost of crop production and increased the yield of crops and the benefits to farmers. However, almost all the events overexpressing endogenous genes remain at the testing stage, except one for fertility restoration and another for pyramiding herbicide tolerance. The novel functions conferred by the heterologously expressing exogenous genes under the control of constitutive promoters are usually absent in the recipient crops themselves or perform in different pathways. However, the endogenous proteins encoded by the overexpressing endogenous genes are regulated in complex networks with functionally redundant and replaceable pathways and are difficult to confer the desirable phenotypes significantly. It is concluded that heterologous expression of exogenous genes and suppressed expression by RNA interference and clustered regularly interspaced short palindromic repeats-cas (CRISPR/Cas) of undesirable genes are superior to the overexpression of endogenous genes for transgenic improvement of crops.

Root Transcriptional and Metabolic Dynamics Induced by the Plant Growth Promoting Rhizobacterium (PGPR) Bacillus subtilis Mbi600 on Cucumber Plants

Bacillus subtilis MBI600 is a commercialized plant growth-promoting bacterial species used as a biocontrol agent in many crops, controlling various plant pathogens via direct or indirect mechanisms. In the present study, a detailed transcriptomic analysis of cucumber roots upon response to the Bs MBI600 strain is provided. Differentially expressed genes (DEGs) analysis showed altered gene expression in more than 1000 genes at 24 and 48 h post-application of Bs MBI600. Bs MBI600 induces genes involved in ISR and SAR signaling. In addition, genes involved in phytohormone production and nutrient availability showed an upregulation pattern, justifying the plant growth promotion. Biocontrol ability of Bs MBI600 seems also to be related to the activation of defense-related genes, such as peroxidase, endo-1,3(4)-beta-glucanase, PR-4, and thaumatin-like. Moreover, KEGG enriched results showed that differentially expressed genes were classified into biocontrol-related pathways. To further investigate the plant's response to the presence of PGPR, a profile of polar metabolites of cucumber treated with Bs MBI600 was performed and compared to that of untreated plants. The results of the current study gave insights into the mechanisms deployed by this biocontrol agent to promote plant resistance, helping to understand the molecular interactions in this system.

A novel chicory fructanase can degrade common microbial fructan product profiles and displays positive cooperativity

Fructan metabolism in bacteria and plants relies on fructosyltransferases and fructanases. Plant fructanases (fructan exohydrolase, FEH) only hydrolyse terminal fructose residues. Levan (β-2,6 linkages) is the most abundant fructan type in bacteria. Dicot fructan accumulators, such as chicory (Cichorium intybus), accumulate inulin (β-2,1 linkages), harbouring several 1-FEH isoforms for their degradation. Here, a novel chicory fructanase with high affinity for levan was characterized, providing evidence that such enzymes widely occur in higher plants. It is adapted to common microbial fructan profiles, but has low affinity towards chicory inulin, in line with a function in trimming of microbial fructans in the extracellular environment. Docking experiments indicate the importance of an N-glycosylation site close to the active site for substrate specificity. Optimal pH and temperature for levan hydrolysis are 5.0 and 43.7 °C, respectively. Docking experiments suggested multiple substrate binding sites and levan-mediated enzyme dimerization, explaining the observed positive cooperativity. Alignments show a single amino acid shift in the position of a conserved DXX(R/K) couple, typical for sucrose binding in cell wall invertases. A possible involvement of plant fructanases in levan trimming is discussed, in line with the emerging 'fructan detour' concepts, suggesting that levan oligosaccharides act as signalling entities during plant-microbial interactions.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene

Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of α-pinene, β-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, β-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to β-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to β-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression   strain displayed an increased tolerance to β-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.

Phytostimulation and biocontrol potential of Gram-positive endospore-forming Bacilli

The spore-forming Bacillus and Paenibacillus species represent the phyla of beneficial bacteria for application as agricultural inputs in form of effective phytostimulators, biofertilizers, and biocontrol agents. The members of the genera Bacillus and Paenibacillus isolated from several ecological habitats are been thoroughly dissected for their effective application in the development of sustainable and eco-friendly agriculture. Numerous Bacillus and Paenibacillus species are reported as plant growth-promoting bacteria influencing the health and productivity of the food crops. This review narrates the mechanisms utilized by these species to enhance bioavailability and/or facilitate the acquisition of nutrients by the host plant, modulate plant hormones, stimulate host defense and stress resistance mechanisms, exert antagonistic action against soil and airborne pathogens, and alleviate the plant health. The mechanisms employed by Bacillus and Paenibacillus are seldom mutually exclusive. The comprehensive and systematic exploration of the aforementioned mechanisms in conjunction with the field investigations may assist in the exploration and selection of an effective biofertilizer and a biocontrol agent. This review aims to gather and discuss the literature citing the applications of Bacillus and Paenibacillus in the management of sustainable agriculture.