Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation

Exploring the dynamics of ISR signaling in maize upon seed priming with plant growth promoting actinobacteria isolated from tea rhizosphere of Darjeeling

Plant growth-promoting rhizobacteria (PGPR) offer an eco-friendly alternative to agrochemicals for better plant growth and development. Here, we evaluated the plant growth promotion abilities of actinobacteria isolated from the tea (Camellia sinensis) rhizosphere of Darjeeling, India. 16 S rRNA gene ribotyping of 28 isolates demonstrated the presence of nine different culturable actinobacterial genera. Assessment of the in vitro PGP traits revealed that Micrococcus sp. AB420 exhibited the highest level of phosphate solubilization (i.e., 445 ± 2.1 µg/ml), whereas Kocuria sp. AB429 and Brachybacterium sp. AB440 showed the highest level of siderophore (25.8 ± 0.1%) and IAA production (101.4 ± 0.5 µg/ml), respectively. Biopriming of maize seeds with the individual actinobacterial isolate revealed statistically significant growth in the treated plants compared to controls. Among them, treatment with Paenarthrobacter sp. AB416 and Brachybacterium sp. AB439 exhibited the highest shoot and root length. Biopriming has also triggered significant enzymatic and non-enzymatic antioxidative defense reactions in maize seedlings both locally and systematically, providing a critical insight into their possible role in the reduction of reactive oxygen species (ROS) burden. To better understand the role of actinobacterial isolates in the modulation of plant defense, three selected actinobacterial isolates, AB426 (Brevibacterium sp.), AB427 (Streptomyces sp.), and AB440 (Brachybacterium sp.) were employed to evaluate the dynamics of induced systemic resistance (ISR) in maize. The expression profile of five key genes involved in SA and JA pathways revealed that bio-priming with actinobacteria (Brevibacterium sp. AB426 and Brachybacterium sp. AB440) preferably modulates the JA pathway rather than the SA pathway. The infection studies in bio-primed maize plants resulted in a delay in disease progression by the biotrophic pathogen Ustilago maydis in infected maize plants, suggesting the positive efficacy of bio-priming in aiding plants to cope with biotic stress. Conclusively, this study unravels the intrinsic mechanisms of PGPR-mediated ISR dynamics in bio-primed plants, offering a futuristic application of these microorganisms in the agricultural fields as an eco-friendly alternative.

Impact of Rhizospheric Microbiome on Rice Cultivation

The rhizosphere niche is extremely important for the overall growth and development of plants. Evidently, it is necessary to understand the complete mechanism of plant microbe interactions of the rhizosphere for sustainable and low input productivity. To meet the increasing global food demand, rice (Oryza sativa L.) agriculture seeks optimal conditions. The unique oxic-anoxic interface of rice-growing soil has invited divergent microbes with dynamic biogeochemical cycles. This review provides the systematic analysis of microbes associated with the major biogeochemical cycles with the aim to generate better management strategies of rhizospheric microbiome in the field of rice agriculture. For instance, several methanogenic and methanotrophic bacteria in the rice rhizosphere make an equilibrium for methane concentration in the environment. The carbon sequestration in paddy soil is again done through many rhizospheric microorganisms that can directly assimilate CO2 with their photoautotrophic mode of nutrition. Also the phosphate solubilizing microbes remain to be the most important keys for the PGPR activity of the paddy ecosystem. In addition, rhizospheric microbiome remain crucial in degradation and solubilization of organo-sulfur and insoluble inorganic sulfides which can be taken by the plants. Further, this review elucidates on the advantages of using metagenomic and metaproteomic approaches as an alternative of traditional approaches to understand the overall metabolic pathways operational in paddy-field. These knowledges are expected to open new possibilities for designing the balanced microbiome used as inoculum for intensive farming and will eventually lead to exert positive impacts on rice cultivation.

Characterization of soybean chitinase genes induced by rhizobacteria involved in the defense against Fusarium oxysporum

Rhizobacteria are capable of inducing defense responses via the expression of pathogenesis-related proteins (PR-proteins) such as chitinases, and many studies have validated the functions of plant chitinases in defense responses. Soybean (Glycine max) is an economically important crop worldwide, but the functional validation of soybean chitinase in defense responses remains limited. In this study, genome-wide characterization of soybean chitinases was conducted, and the defense contribution of three chitinases (GmChi01, GmChi02, or GmChi16) was validated in Arabidopsis transgenic lines against the soil-borne pathogen Fusarium oxysporum. Compared to the Arabidopsis Col-0 and empty vector controls, the transgenic lines with GmChi02 or GmChi16 exhibited fewer chlorosis symptoms and wilting. While GmChi02 and GmChi16 enhanced defense to F. oxysporum, GmChi02 was the only one significantly induced by Burkholderia ambifaria. The observation indicated that plant chitinases may be induced by different rhizobacteria for defense responses. The survey of 37 soybean chitinase gene expressions in response to six rhizobacteria observed diverse inducibility, where only 10 genes were significantly upregulated by at least one rhizobacterium and 9 genes did not respond to any of the rhizobacteria. Motif analysis on soybean promoters further identified not only consensus but also rhizobacterium-specific transcription factor-binding sites for the inducible chitinase genes. Collectively, these results confirmed the involvement of GmChi02 and GmChi16 in defense enhancement and highlighted the diverse inducibility of 37 soybean chitinases encountering F. oxysporum and six rhizobacteria.

Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato

The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.

Controlling Tomato Fusarium Wilt Disease through Bacillus thuringiensis-Mediated Defense Primining

Background

Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. lycopersici (Fol) (Sacc.) W.C. Snyder and H.N. Hans is one of the most prevalent and devastating diseases of tomato plants (Solanum lycoprsicum L.) that leads to a severe reduction in crop yield almost worldwide.

Objective

Evaluation of biocontrol potential of Bacillus thuringiensis (Bt) isolate IBRC-M11096, against Fol in tomato through primin.

Materials and Methods

qRT-PCR technique was applied to analyze the effect of the strain on the hormonal defensive pathways; transcriptional responses of jasmonic acid (COI1, Pin2) and salicylic acid (NRP1 and PR1) pathway genes in Bt-treated plants following inoculation of Fol as compared to the plants only challenged with Fol. Also, the potential of the bacterial strain as a biocontrol agent was studied by evaluating growth indices and area under disease progress curve (AUDPC).

Results

The transcription of both defensive hormonal pathway genes (COI1, Pin2, NPR1, PR1) increased due to bacterial priming. The bacterial priming reduced the AUDPC compared to the inoculation with only Fol. The strain reduced the disease symptoms, and compared to the plants only challenged with the fungus, the bacterial strain significantly raised shoot dry and fresh weights and root dry weight.

Conclusion

Priming with the Bt strain led to improved shoot and root growth indices, reduced AUDPC, and fortified responses of both JA and SA hormonal pathways. However, further full-span studies are required to judge the efficacy of the bacterial strain in the biological control of tomato fusarium wilt under field conditions.

Biocontrol potential of Pseudomonas protegens ML15 against Botrytis cinerea causing gray mold on postharvest tomato (Solanum lycopersicum var. cerasiforme)

Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15's role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.

Biofortification of Broccoli Microgreens (Brassica oleracea var. italica) with Glucosinolates, Zinc, and Iron through the Combined Application of Bio- and Nanofertilizers

There is a severe need to develop a sustainable, affordable, and nutritious food supply system. Broccoli microgreens have attracted attention due to their rich nutritional content and abundant bioactive compounds, constituting an important opportunity to feed the ever-increasing population and fight global health problems. This study aimed to measure the impact of the combined application of biofertilizers and zinc and iron nanofertilizers on plant growth and the biofortification of glucosinolates (GLSs) and micronutrients in broccoli microgreens. Biofertilizers were based on plant growth-promoting (PGP) bacterial consortia previously isolated and characterized for multiple PGP traits. Nanofertilizers consisted of ZnO (77 nm) and γ-Fe2O3 (68 nm) nanoparticles synthesized with the coprecipitation method and functionalized with a Pseudomonas species preparation. Treatments were evaluated under seedbed conditions. Plant growth parameters of plant height (37.0-59.8%), leaf diameter (57.6-81.1%) and fresh weight (112.1-178.0%), as well as zinc (122.19-363.41%) and iron contents (55.19-161.57%), were mainly increased by nanoparticles subjected to the functionalization process with Pseudomonas species and uncapped NPs applied together with the biofertilizer treatment. Regarding GLSs, eight compounds were detected as being most positively influenced by these treatments. This work demonstrated the synergistic interactions of applying ZnO and γ-Fe2O3 nanofertilizers combined with biofertilizers to enhance plant growth and biofortify micronutrients and glucosinolates in broccoli microgreens.

Epigenetic Control of Plant Response to Heavy Metals

Plants are sessile organisms that must adapt to environmental conditions, such as soil characteristics, by adjusting their development during their entire life cycle. In case of low-distance seed dispersal, the new generations are challenged with the same abiotic stress encountered by the parents. Epigenetic modification is an effective option that allows plants to face an environmental constraint and to share the same adaptative strategy with their progeny through transgenerational inheritance. This is the topic of the presented review that reports the scientific progress, up to date, gained in unravelling the epigenetic response of plants to soil contamination by heavy metals and metalloids, collectively known as potentially toxic elements. The effect of the microbial community inhabiting the rhizosphere is also considered, as the evidence of a transgenerational transfer of the epigenetic status that contributes to the activation in plants of response mechanisms to soil pollution.

'A plant's major strength in rhizosphere': the plant growth promoting rhizobacteria

Human activities, industrialization and civilization have deteriorated the environment which eventually has led to alarming effects on plants and animals by heightened amounts of chemical pollutants and heavy metals in the environment, which create abiotic stress. Environmental conditions like drought, salinity, diminished macro-and micro-nutrients also contribute in abiotic stress, resulting in decrement of survival and growth of plants. Presence of pathogenic and competitive microorganisms, as well as pests lead to biotic stress and a plant alone can not defend itself. Thankfully, nature has rendered plant's rhizosphere with plant growth promoting rhizobacteria which maintain an allelopathic relationship with host plant to defend the plant and let it flourish in abiotic as well as biotic stress situations. This review discusses the mechanisms behind increase in plant growth via various direct and indirect traits expressed by associated microorganisms in the rhizosphere, along with their current scenario and promising future for sustainable agriculture. It also gives details of ten such bacterial species, viz. Acetobacter, Agrobacterium, Alcaligenes, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Enterobacter and Frankia, whose association with the host plants is famed for enhancing plant's growth and survival.

Insights into the Biocontrol Function of a Burkholderia gladioli Strain against Botrytis cinerea

Pathogenic fungi are the main cause of yield loss and postharvest loss of crops. In recent years, some antifungal microorganisms have been exploited and applied to prevent and control pathogenic fungi. In this study, an antagonistic bacteria KRS027 isolated from the soil rhizosphere of a healthy cotton plant from an infected field was identified as Burkholderia gladioli by morphological identification, multilocus sequence analysis, and typing (MLSA-MLST) and physiobiochemical examinations. KRS027 showed broad spectrum antifungal activity against various phytopathogenic fungi by secreting soluble and volatile compounds. KRS027 also has the characteristics of plant growth promotion (PGP) including nitrogen fixation, phosphate, and potassium solubilization, production of siderophores, and various enzymes. KRS027 is not only proven safe by inoculation of tobacco leaves and hemolysis test but also could effectively protect tobacco and table grapes against gray mold disease caused by Botrytis cinerea. Furthermore, KRS027 can trigger plant immunity by inducing systemic resistance (ISR) activated by salicylic acid- (SA), jasmonic acid- (JA), and ethylene (ET)-dependent signaling pathways. The extracellular metabolites and volatile organic compounds (VOCs) of KRS027 affected the colony extension and hyphal development by downregulation of melanin biosynthesis and upregulation of vesicle transport, G protein subunit 1, mitochondrial oxidative phosphorylation, disturbance of autophagy process, and degrading the cell wall of B. cinerea. These results demonstrated that B. gladioli KRS027 would likely become a promising biocontrol and biofertilizer agent against fungal diseases, including B. cinerea, and would promote plant growth. IMPORTANCE Searching the economical, eco-friendly and efficient biological control measures is the key to protecting crops from pathogenic fungi. The species of Burkholderia genus are widespread in the natural environment, of which nonpathogenic members have been reported to have great potential for biological control agents and biofertilizers for agricultural application. Burkholderia gladioli strains, however, need more study and application in the control of pathogenic fungi, plant growth promotion, and induced systemic resistance (ISR). In this study, we found that a B. gladioli strain KRS027 has broad spectrum antifungal activity, especially in suppressing the incidence of gray mold disease caused by Botrytis cinerea, and can stimulate plant immunity response via ISR activated by salicylic acid- (SA), jasmonic acid- (JA), and ethylene (ET)-dependent signaling pathways. These results indicate that B. gladioli KRS027 may be a promising biocontrol and biofertilizer microorganism resource in agricultural applications.

Oxidative Status of Medicago truncatula Seedlings after Inoculation with Rhizobacteria of the Genus Pseudomonas, Paenibacillus and Sinorhizobium

An increasing number of scientists working to raise agricultural productivity see the potential in the roots and the soil adjacent to them, together with a wealth of micro-organisms. The first mechanisms activated in the plant during any abiotic or biotic stress concern changes in the oxidative status of the plant. With this in mind, for the first time, an attempt was made to check whether the inoculation of seedlings of the model plant Medicago truncatula with rhizobacteria belonging to the genus Pseudomonas (P. brassicacearum KK5, P. corrugata KK7), Paenibacillus borealis KK4 and a symbiotic strain Sinorhizobium meliloti KK13 would change the oxidative status in the days following inoculation. Initially, an increase in H₂O₂ synthesis was observed, which led to an increase in the activity of antioxidant enzymes responsible for regulating hydrogen peroxide levels. The main enzyme involved in the reduction of H₂O₂ content in the roots was catalase. The observed changes indicate the possibility of using the applied rhizobacteria to induce processes related to plant resistance and thus to ensure protection against environmental stress factors. In the next stages, it seems reasonable to check whether the initial changes in the oxidative state affect the activation of other pathways related to plant immunity.

PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops

Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.

A Bacillus licheniformis Glycoside Hydrolase 43 Protein Is Recognized as a MAMP

Glycoside hydrolases from pathogens have often been reported as inducers of immune responses. However, the roles of glycoside hydrolase from plant-growth-promoting rhizobacteria (PGPR) in the resistance of plants against pathogens is not well studied. In this study, we identified a glycoside hydrolase 43 protein, H1AD43, produced by Bacillus licheniformis BL06 that can trigger defense responses, including cell death. Ion-exchange and size-exclusion chromatography were used for separation, and the amino acid sequence was identified by mass spectrometry. The recombinant protein generated by prokaryotic expression was able to elicit a hypersensitive response (HR) in Nicotiana benthamiana and trigger early defense responses, including reactive oxygen species (ROS) burst, callose accumulation, and the induction of defense genes. In addition, the protein could induce resistance in N. benthamiana, in which it inhibited infection by Phytophthora capsici Leonian and tobacco mosaic virus-green fluorescent protein (TMV-GFP) expression. H1AD43 thus represents a microbe-associated molecular pattern (MAMP) of PGPR that induces plant disease resistance and may provide a new method for the biological control of plant disease.

Profiling of Volatile Organic Compounds from Four Plant Growth-Promoting Rhizobacteria by SPME–GC–MS: A Metabolomics Study

The rhizosphere microbiome is a major determinant of plant health. Plant-beneficial or plant growth-promoting rhizobacteria (PGPR) influence plant growth, plant development and adaptive responses, such as induced resistance/priming. These new eco-friendly choices have highlighted volatile organic compounds (biogenic VOCs) as a potentially inexpensive, effective and efficient substitute for the use of agrochemicals. Secreted bacterial VOCs are low molecular weight lipophilic compounds with a low boiling point and high vapor pressures. As such, they can act as short- or long-distance signals in the rhizosphere, affecting competing microorganisms and impacting plant health. In this study, secreted VOCs from four PGPR strains (Pseudomonas koreensis (N19), Ps. fluorescens (N04), Lysinibacillus sphaericus (T19) and Paenibacillus alvei (T22)) were profiled by solid-phase micro-extraction gas chromatography mass spectrometry (SPME–GC–MS) combined with a multivariate data analysis. Metabolomic profiling with chemometric analyses revealed novel data on the composition of the secreted VOC blends of the four PGPR strains. Of the 121 annotated metabolites, most are known as bioactives which are able to affect metabolism in plant hosts. These VOCs belong to the following classes: alcohols, aldehydes, ketones, alkanes, alkenes, acids, amines, salicylic acid derivatives, pyrazines, furans, sulfides and terpenoids. The results further demonstrated the presence of species-specific and strain-specific VOCs, characterized by either the absence or presence of specific VOCs in the different strains. These molecules could be further investigated as biomarkers for the classification of an organism as a PGPR and selection for agricultural use.