Developing Actinobacterial Endophytes as Biocontrol Products for Fusarium pseudograminearum in Wheat

Antagonistic effects of Talaromyces muroii TM28 against Fusarium crown rot of wheat caused by Fusarium pseudograminearum

Fusarium crown rot (FCR) caused by Fusarium pseudograminearum is a serious threat to wheat production worldwide. This study aimed to assess the effects of Talaromyces muroii strain TM28 isolated from root of Panax quinquefolius against F. pseudograminearum. The strain of TM28 inhibited mycelial growth of F. pseudograminearum by 87.8% at 72 h, its cell free fermentation filtrate had a strong antagonistic effect on mycelial growth and conidial germination of F. pseudograminearum by destroying the integrity of the cell membrane. In the greenhouse, TM28 significantly increased wheat fresh weight and height in the presence of pathogen Fp, it enhanced the antioxidant defense activity and ameliorated the negative effects of F. pseudograminearum, including disease severity and pathogen abundance in the rhizosphere soil, root and stem base of wheat. RNA-seq of F. pseudograminearum under TM28 antagonistic revealed 2,823 differentially expressed genes (DEGs). Most DEGs related to cell wall and cell membrane synthesis were significantly downregulated, the culture filtrate of TM28 affected the pathways of fatty acid synthesis, steroid synthesis, glycolysis, and the citrate acid cycle. T. muroii TM28 appears to have significant potential in controlling wheat Fusarium crown rot caused by F. pseudograminearum.

Streptomyces and their specialised metabolites for phytopathogen control - comparative in vitro and in planta metabolic approaches

In the search for new crop protection microbial biocontrol agents, isolates from the genus Streptomyces are commonly found with promising attributes. Streptomyces are natural soil dwellers and have evolved as plant symbionts producing specialised metabolites with antibiotic and antifungal activities. Streptomyces biocontrol strains can effectively suppress plant pathogens via direct antimicrobial activity, but also induce plant resistance through indirect biosynthetic pathways. The investigation of factors stimulating the production and release of Streptomyces bioactive compounds is commonly conducted in vitro, between Streptomyces sp. and a plant pathogen. However, recent research is starting to shed light on the behaviour of these biocontrol agents in planta, where the biotic and abiotic conditions share little similarity to those of controlled laboratory conditions. With a focus on specialised metabolites, this review details (i) the various methods by which Streptomyces biocontrol agents employ specialised metabolites as an additional line of defence against plant pathogens, (ii) the signals shared in the tripartite system of plant, pathogen and biocontrol agent, and (iii) an outlook on new approaches to expedite the identification and ecological understanding of these metabolites under a crop protection lens.

Antagonistic Strain Bacillus halotolerans Jk-25 Mediates the Biocontrol of Wheat Common Root Rot Caused by Bipolaris sorokiniana

Common root rot caused by Bipolaris sorokiniana infestation in wheat is one of the main reasons for yield reduction in wheat crops worldwide. The bacterium strain JK-25 used in the current investigation was isolated from wheat rhizosphere soil and was later identified as Bacillus halotolerans based on its morphological, physiological, biochemical, and molecular properties. The strain showed significant antagonism to B. sorokiniana, Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia zeae. Inhibition of B. sorokiniana mycelial dry weight and spore germination rate by JK-25 fermentation supernatant reached 60% and 88%, respectively. The crude extract of JK-25 was found, by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), to contain the surfactin that exerted an inhibitory effect on B. sorokiniana. The disruption of mycelial cell membranes was observed under laser scanning confocal microscope (LSCM) after treatment of B. sorokiniana mycelium with the crude extract. The antioxidant enzyme activity of B. sorokiniana was significantly reduced and the oxidation product malondialdehyde (MDA) content increased after treatment with the crude extract. The incidence of root rot was significantly reduced in pot experiments with the addition of JK-25 culture fermentation supernatant, which had a significant biological control effect of 72.06%. Its ability to produce siderophores may help to promote wheat growth and the production of proteases and pectinases may also be part of the strain's role in suppressing pathogens. These results demonstrate the excellent antagonistic effect of JK-25 against B. sorokiniana and suggest that this strain has great potential as a resource for biological control of wheat root rot strains.

Baseline Sensitivity and Potential Resistance Mechanisms for Fusarium pseudograminearum to Fludioxonil

Fusarium crown rot (FCR), which is caused by Fusarium pseudograminearum, is one of the most important diseases affecting wheat production in the Huanghuai wheat-growing region of China. Although the phenylpyrrole fungicide fludioxonil is known to have a broad-spectrum activity against a wide range of plant pathogens, including F. pseudograminearum, it has not yet been registered for the control of FCR in China, and further research is needed to assess the biological characteristics and molecular mechanisms associated with fludioxonil resistance, and especially the potential for highly resistant isolates to emerge. The current study demonstrated that the baseline fludioxonil sensitivity of 61 F. pseudograminearum isolates collected from the Henan province of China during the summers of 2019 to 2021 conformed to a unimodal distribution with a mean effective concentration for 50% inhibition (EC₅₀) value of 0.021 ± 0.003 μg/ml, which indicated that none of the isolates exhibited natural resistance to fludioxonil. Nevertheless, four fludioxonil-resistant mutants were attained after repeated exposure to fludioxonil under laboratory conditions. All resistant mutants exhibited significantly lower growth rates on potato dextrose agar (PDA) and lower levels of sporulation and pathogenicity in wheat seedlings. In addition, the resistant mutants also exhibited less growth on PDA amended with either 0.5 M mannitol, 0.5 M glucose, 0.5 M MgCl₂, or 0.5 M NaCl, which indicated that they had greater sensitivity to osmotic stress. Molecular analysis of the proposed fludioxonil target protein FpOs1 indicated that the predicted sequences of the resistant mutants contained none of the characteristic amino acid changes previously associated with fludioxonil resistance in other species. Further investigation via quantitative real-time PCR analysis revealed that expression of the FpOs1 gene was significantly altered in the resistant mutants in both the absence and presence of fludioxonil. Meanwhile, plate assays found evidence of cross-resistance between fludioxonil and cyprodinil, as well as with the triazole fungicides tebuconazole and difenoconazole, but not with other commonly used fungicides including prochloraz, fluazinam, and carbendazim. Taken together, these results provide new insights into the mechanism and biological characteristics associated with fludioxonil resistance in F. pseudograminearum and indicate that fludioxonil could provide effective and sustained control of FCR during wheat production.

Bambara Groundnut Rhizobacteria Antimicrobial and Biofertilization Potential

Bambara groundnut, an underutilized crop has been proved to be an indigenous crop in Africa with the potential for food security. The rhizosphere of Bambara groundnut contains Rhizobacteria, with the ability to grow, adapt, and colonize their surroundings even in unfavorable conditions and have not been explored for their plant growth-promoting properties. The aim of this research was to determine the potential of rhizobacteria from Bambara groundnut soil samples as either biofertilizers or biocontrol agents or both to help provide sustainable agriculture in Africa and globally. Bambara groundnut rhizospheric soil samples were collected and analyzed for their chemical composition. Rhizobacteria isolates were cultured from the soil samples. Plant growth-promoting, antifungal activities and phylogenetic analysis using 16S rRNA were carried out on the isolates to identify the rhizobacteria. A 2-year field study planting was carried out to determine the effect of these rhizobacteria as biofertilizers for Bambara groundnut (Vigna subterranean). The study was carried out in a complete randomized block experimental design with three replications. All the isolates were able to produce ammonia and 1-aminocyclopropane-1-carboxylate, while 4.65, 12.28, and 27.91% produced hydrogen cyanide, indole acetic acid, and solubilized phosphate, respectively, making them important targets as biocontrol and biofertilizer agents. The field results revealed that treatment with rhizobacteria had significant results compared with the control. Characterization of selected isolates reveals their identity as B. amyloliquefaciens, B. thuringiensis, and Bacillus sp. These Bacillus isolates have proved to be plant growth-promoting agents that can be used as biofertilizers to enhance the growth of crops and consequent improved yield. This is the first time the rhizobacteria from the Bambara groundnut rhizosphere are applied as biofertilizer.

Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat

Simple Summary

Biological control of plant diseases caused by fungal pathogens using antagonistic microorganisms including Bacilli has been considered to be an effective and safe alternative to chemical fungicides. Fusarium crown rot of wheat is a serious fungal disease affecting yield and grain quality. In this study, a newly isolated strain of Bacillus subtilis YB-15 from soil of wheat rhizosphere significantly inhibited Fusarium crown rot as well as improved growth of wheat seedlings. Multiple potential biocontrol and growth-promoting attributes of Bacillus subtilis YB-15 were determined in vitro and according to the whole genome sequencing analysis. Overall, the results demonstrated that Bacillus subtilis YB-15 has great potential for practical application in controlling plant fungal diseases and improving plant growth.

Abstract

Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.

Phylogenetic affiliation of endophytic actinobacteria associated with selected orchid species and their role in growth promotion and suppression of phytopathogens

Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we investigated the culturable endophytic actinobacteria associated with ten epiphytic orchid species of Assam, India. 51 morphologically distinct actinobacteria were recovered from surface sterilized roots and leaves of orchids and characterized based on different PGP and antifungal traits. According to the 16S rRNA gene sequence, these isolates were divided into six families and eight genera, where Streptomyces was most abundant (n=29, 56.86%), followed by Actinomadura, Nocardia, Nocardiopsis, Nocardioides, Pseudonocardia, Microbacterium, and Mycolicibacterium. Regarding PGP characteristics, 25 (49.01%) isolates demonstrated phosphate solubilization in the range of 61.1±4.4 - 289.7±11.9 µg/ml, whereas 27 (52.94%) isolates biosynthesized IAA in the range of 4.0 ± 0.08 - 43.8 ± 0.2 µg/ml, and 35 (68.62%) isolates generated ammonia in the range of 0.9 ± 0.1 - 5.9 ± 0.2 µmol/ml. These isolates also produced extracellular enzymes, viz. protease (43.13%), cellulase (23.52%), pectinase (21.56%), ACC deaminase (27.45%), and chitinase (37.25%). Out of 51 isolates, 27 (52.94%) showed antagonism against at least one test phytopathogen. In molecular screening, most isolates with antifungal and chitinase producing traits revealed the presence of 18 family chitinase genes. Two actinobacterial endophytes, Streptomyces sp. VCLA3 and Streptomyces sp. RVRA7 were ranked as the best strains based on PGP and antifungal activity on bonitur scale. GC-MS examination of ethyl acetate extract of these potent strains displayed antimicrobial compound phenol, 2,4-bis-(1,1-dimethylethyl) as the major metabolite along with other antifungal and plant growth beneficial bioactive chemicals. SEM analysis of fungal pathogen F. oxysporum (MTCC 4633) affected by Streptomyces sp. VCLA3 revealed significant destruction in the spore structure. An in vivo plant growth promotion experiment with VCLA3 and RVRA7 on chili plants exhibited statistically significant (p<0.05) improvements in all of the evaluated vegetative parameters compared to the control. Our research thus gives insight into the diversity, composition, and functional significance of endophytic actinobacteria associated with orchids. This research demonstrates that isolates with multiple plant development and broad-spectrum antifungal properties are beneficial for plant growth. They may provide a viable alternative to chemical fertilizers and pesticides and a sustainable solution for chemical inputs in agriculture.

A Plant Stress-Responsive Bioreporter Coupled With Transcriptomic Analysis Allows Rapid Screening for Biocontrols of Necrotrophic Fungal Pathogens

Streptomyces are soil-borne Actinobacteria known to produce a wide range of enzymes, phytohormones, and metabolites including antifungal compounds, making these microbes fitting for use as biocontrol agents in agriculture. In this study, a plant reporter gene construct comprising the biotic stress-responsive glutathione S-transferase promoter GSTF7 linked to a luciferase output (GSTF7:luc) was used to screen a collection of Actinobacteria candidates for manipulation of plant biotic stress responses and their potential as biocontrol agents. We identified a Streptomyces isolate (KB001) as a strong candidate and demonstrated successful protection against two necrotrophic fungal pathogens, Sclerotinia sclerotiorum and Rhizoctonia solani, but not against a bacterial pathogen (Pseudomonas syringe). Treatment of Arabidopsis plants with either KB001 microbial culture or its secreted compounds induced a range of stress and defense response-related genes like pathogenesis-related (PR) and hormone signaling pathways. Global transcriptomic analysis showed that both treatments shared highly induced expression of reactive oxygen species and auxin signaling pathways at 6 and 24 h posttreatment, while some other responses were treatment specific. This study demonstrates that GSTF7 is a suitable marker for the rapid and preliminary screening of beneficial bacteria and selection of candidates with potential for application as biocontrols in agriculture, including the Streptomyces KB001 that was characterized here, and could provide protection against necrotrophic fungal pathogens.