Plant Growth‐Promoting Rhizobacteria and Bacterial Biocontrol Agents in Tomato Disease Management: Mechanisms, Applications, and Omics Perspectives

Because of swift climate change, drought is a primary environmental factor that substantially diminishes plant productivity. Furthermore, the increased use of chemical fertilizers has given rise to numerous environmental problems and health risks. Presently, there is a transition towards biofertilizers to enhance crops' yield, encompassing medicinal and aromatic varieties. This study aimed to explore the impacts of plant growth-promoting rhizobacteria (PGPR), both independently and in conjunction with arbuscular mycorrhizal fungi (AMF), on various morphological, physiological, and phytochemical characteristics of Dracocephalum kotschyi Boiss. This experimentation took place under different irrigation conditions. The irrigation schemes encompassed well watering (WW), mild water stress (MWS), and severe water stress (SWS). The study evaluated the effects of various biofertilizers, including AMF, PGPR, and the combined application of both AMF and PGPR (AMF + PGPR), compared to a control group where no biofertilizers were applied. The findings of the study revealed that under water-stress conditions, the dry yield and relative water content of D. kotschyi Boiss. experienced a decline. However, the application of AMF, PGPR, and AMF + PGPR led to an enhancement in dry yield and relative water content compared to the control group. Among the treatments, the co-application of AMF and PGPR in plants subjected to well watering (WW) exhibited the tallest growth (65 cm), the highest leaf count (187), and the most elevated chlorophyll a (0.59 mg g-1 fw) and b (0.24 mg g-1 fw) content. Regarding essential oil production, the maximum content (1.29%) and yield (0.13 g plant -1) were obtained from mild water stress (MWS) treatment. The co-application of AMF and PGPR resulted in the highest essential oil content and yield (1.31% and 0.15 g plant-1, respectively). The analysis of D. kotschyi Boiss. essential oil identified twenty-six compounds, with major constituents including geranyl acetate (11.4-18.88%), alpha-pinene (9.33-15.08%), Bis (2-Ethylhexyl) phthalate (8.43-12.8%), neral (6.80-9.32%), geranial (9.23-11.91%), and limonene (5.56-9.12%). Notably, the highest content of geranyl acetate, geranial, limonene, and alpha-pinene was observed in plants subjected to MWS treatment following AMF + PGPR application. Furthermore, the co-application of AMF, PGPR, and severe water stress (SWS) notably increased the total soluble sugar (TSS) and proline content. In conclusion, the results indicate that the combined application of AMF and PGPR can effectively enhance the quantity and quality of essential oil in D. kotschyi Boiss., particularly when the plants are exposed to water deficit stress conditions.

An experiment was conducted to study the compatibility of copper hydroxide (Kocide 3000) with bacterial and fungal biocontrol agents under in vitro conditions.Bacterial biocontrol agents viz., Pseudomonas fluorescens and Bacillus subtilis were compatible with copper hydroxide (Kocide 3000) even at a high concentration of 300 ppm.Fungal biocontrol agent, Trichoderma viride was inhibited by copper hydroxide at a concentration above 2500 ppm.The fungal biocontrol agent was highly compatible with the fungicide than the bacterial biocontrol agents.

The expanding human population necessitates more food production, but this must be done in the face of worsening climate change and a limiting supply of farmland. Today's challenge is to increase agricultural production demand while lowering the use of synthetic chemical fertilisers and pesticides. Growing need for agricultural production while reducing the usage of synthetic chemical fertilisers and pesticides has become a major problem in recent years. Plant growth-promoting rhizobacteria (PGPR) plays a vital part in the agriculture industry's sustainability. PGPR has been shown to be an ecologically friendly method of improving agricultural yields by stimulating plant development via a direct or indirect process. PGPR regulates hormonal and nutritional balance, induces resistance against plant diseases, and solubilizes nutrients for easier absorption by plants, among other things. Furthermore, PGPR exhibits both synergistic and antagonistic interactions with microorganisms in the rhizosphere and in bulk soil, which improves plant growth rate indirectly. PGPR regularly establish mutualistic interactions with host plants related to nutrient absorption (N fixation, P and K solubilization, and siderophore production), enhanced stress resistance (abiotic and biotic), and regulation of plant development and physiology through signal compound production, including phytohormones and specific inter-organism signal compounds, could be used as a more sustainable agricultural approach. Root exudates, which are released into the rhizosphere by host plants as a reduced carbon supply for phytomicrobiome members, also aid in providing a stable environment for microbe development. Given the benefits of PGPR in terms of biofertilization, biocontrol, and bioremediation, all of which have a favourable impact on crop yield and ecosystem functioning, its use in agriculture should be encouraged. With the advancement of technology in the establishment of effective research and development, PGPR utilisation will undoubtedly become a reality and will be helpful in critical processes that assure the stability and productivity of agro-ecosystems, bringing us to a perfect agricultural system.

Background: Collar rot is an important disease of lentil in India and causes significant yield loss annually. Considering the recent focus on the development and use of environmentally feasible management strategies, the objectives of the study was to identify resistant sources and evaluation of native antagonists as well as plant growth promoting rhizobacteria (PGPRs) in yield improvement and disease management of lentil. Methods: Eleven popular lentil varieties were screened for resistance/susceptibility reaction against collar rot in vivo. The efficacy of two bacterial and fungal biocontrol agents (BCAs) was tested against a virulent isolate of Sclerotium rolfsii. Four PGPRs were also evaluated to study their influence on the growth parameters as well as their ability to manage S. rolfsii. Result: Three genotypes were found to be tolerant, four genotypes were moderately susceptible, while four genotypes were highly susceptible. Among the BCAs, the highest average inhibition % was observed in treatment with Bacillus sp. Among the PGPR treatments, Rhizobium in combination with phosphate solubilizing bacteria and Trichoderma or Bacillus was the most effective in controlling the collar rot when used as seed treatment and hence can be used for disease management.

Among the biotic stresses, plant pathogens can reduce yield crop which affected potential loss to crop productivity. Plant growth-promoting rhizobacteria (PGPR) can help plants to be resistant against biotic stress via direct antagonism to pathogens or by induction of systemic resistance to pathogens. The presence of high levels of nutrients exuded from various roots of most plants can support bacterial growth and metabolism as well as maintain health of the plant in the growth process. PGPR promote plant growth due to their abilities in phytohormone production, nitrogen fixation, and phosphorus solubilization; produce several substances which are related to pathogen control, i.e., exhibiting competition with plant pathogens, synthesis of antibiotics, antifungal metabolites and defense enzymes, and secretion of iron-chelating siderophores; and trigger induced systemic resistance (ISR) via methyl jasmonate and methyl salicylate in plants. The ISR resembles pathogen-induced systemic acquired resistance (SAR) through the salicylic acid-dependent SAR pathway under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. The use of PGPR combinations of different mechanisms of action, i.e., induced resistance and antagonistic PGPR, might be useful in formulating inoculants leading to a more efficient use for biological control strategies to improve crop productivity. Many PGPR have been isolated from the tissues of many plants, and various species of bacteria, i.e., Azotobacter, Azospirillum, Alcaligenes, Arthrobacter, Bacillus, Burkholderia, Enterobacter, Klebsiella, Pseudomonas, and Serratia, have been reported to control several diseases and enhance plant growth. PGPR belonging to the genera Pseudomonas and Bacillus are also well known for their antagonistic effects and their ability to trigger ISR. An increasingly successful study to reduce disease severity is the use of bacteria, namely, Bacillus subtilis, P. fluorescens, Serratia, and the fungus Trichoderma. Tea and rice plants are cultivated in Indonesia predominantly in Java and Sumatra islands. Major constraints of cultivation include low fertility of soils, poor input management, low germination, and high susceptibility to the diseases. The strategies employed by PGPR provide promising approaches to alter agricultural crops and plantation practices toward sustainable environmental development. Research has been conducted to know the effect of PGPR on tea plant growth that can work optimally as a biological fertilizer and plant-induced resistance to suppress blister blight (Exobasidium vexans Massee), a major disease in tea plantation that can decrease yield loss up to 50%. Individual PGPR strains for in vitro broad-spectrum pathogen suppression and production of several physiological/biochemical activities related to plant growth promotion have been screened. Numerous bacterial isolates have been found to function both as biofertilizers and biological control agents, namely, Chryseobacterium sp. AzII-1, Acinetobacter sp., Alcaligenes sp. E5, Bacillus E65, and Burkholderia E76. Study about synergism among bacteria has been carried out in the laboratory test using four combinations, i.e., (a) Chryseobacterium sp. AzII-1 + Acinetobacter sp., (b) Chryseobacterium sp. AzII-1 + Alcaligenes sp. E5, (c) Chryseobacterium sp. AzII-1 + Bacillus E65, and (d) Chryseobacterium sp. AzII-1 + Burkholderia E76. All bacterial combinations had a synergistic effect. It was shown that the bacterial population was not significantly different with the average of the total bacterial population (4.62 × 108 CFU/ml). The effect of bacterial combinations to blister blight and plant growth under a tea nursery trial revealed that combination of Chryseobacterium sp. AzII-1 75% + Alcaligenes sp. E5 25% could increase the growth of tea plant and suppress the intensity of blister blight up to 1.27%. The disease intensity of blister blight decreased in all treatments under field trial, while the Acinetobacter sp. treatment in tea shoots was 17.26% higher than the control. PGPR have also been isolated from cultivated rice. Serratia SKM, Burkholderia E76, and Bacillus E65 have the potential for controlling rice diseases and induce plant growth promotion. Under in vitro antagonistic assay, it was shown that these isolates could suppress effectively the growth of rice pathogens Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB). Kaolin formulation of these three isolates was evaluated as a foliar application on rice. PGPR application under experimental plots resulted in enhancement of rice growth and yield, with the yield increment on cv. Sintanur being 12.8 percent higher compared with control (cv. Ciherang). Based on PGPR application technology which is demonstrated in farmers’ plots, the severity of BB disease was reduced to 76.8 percent compared with the untreated plot. The farmers were convinced with the beneficial effects of PGPR on both plant growth and yield and reduction of BB disease incidence. PGPR technologies have the potential to reduce agrochemical application. They can also be exploited as low in input and environmentally friendly for sustainable plant management. PGPR is highly diverse, and in this review, we focus on PGPR in plant growth promotion, as well as understanding the role of PGPR in crop protection.

Novel plant growth promoting rhizobacteria—Prospects and potential

Chapter 13 - Nanoemulsion formulations with plant growth promoting rhizobacteria (PGPR) for sustainable agriculture

Global agriculture currently suffers from pollution caused by the widespread use of chemical fertilizers and pesticides. These agrochemicals, when consumed in food, can harm human health (e.g. increasing risks of cancer and thyroid disorders) and damage the environment by reducing soil fertility, among other effects. Thus, there is a high demand for biological agents, such as microorganisms, that could partially or fully replace these agrochemicals.Plant growth-promoting rhizobacteria (PGPR) are promising in this regard, as they can enhance plant growth and productivity sustainably. These bacteria promote plant growth and development through both direct and indirect mechanisms. Directly, PGPR increase plant growth by making phosphorus, nitrogen, and other essential minerals more available to plants, as well as by regulating plant hormone levels. Indirectly, PGPR inhibit pathogenic microbes that otherwise hinder plant growth and development, for instance, through the production of siderophores. In addition, PGPR show synergistic and antagonistic interactions with microorganisms within the rhizosphere and beyond in bulk soil, which indirectly boosts plant growth rate. Studies indicate that PGPR can improve plant health and yield across a variety of plant species, under both favourable and challenging conditions. As a result, PGPR have the potential to reduce the global reliance on harmful agricultural chemicals that disrupt environmental health. Additionally, the demand for PGPR as biofertilizers and biopesticides is growing globally, further highlighting their potential as powerful alternatives in sustainable agriculture. Numerous bacteria act as PGPRs, which have been described in the literature as effective in enhancing plant growth. In order to improve the efficacy of PGPRs, it is important to study their characteristics and mode of application since there is a gap between their mode of action (mechanism) for plant growth and their role as biofertilizers.

Bacterial biocontrol agents are much smaller in size and do not have long lifecycle as the fungi. They multiply rapidly and increase in population by several folds within a few hours. The morphological characteristics of bacterial cells are less variable. Hence, biological, biochemical, physiological, immunological and genomic characteristics are determined for reliable and precise identification and meaningful classification of the bacterial biocontrol agents, capable of suppressing the development of crop diseases caused by microbial pathogens. Metabolic fingerprinting, fatty acid methyl esters (FAME) analysis and nucleic acid-based techniques are more frequently applied than the isolation-based methods which are less consistent and time-consuming, for the identification of bacterial BCAs. Many species of plant growth-promoting rhizobacteria (PGPR) have been reported to be efficient biocontrol agent of crop diseases. Spore formers such as Bacillus spp. are considered to be preferable to Pseudomonas spp., because of their longer survivability, even in adverse environmental conditions. Various techniques have been employed to assess the biocontrol potential of the bacterial BCAs in laboratory assays and under greenhouse and field conditions, where they are expected to interact with microbial pathogens. Some of the actinomycetes like Streptomyces spp. have been shown to be effective biocontrol agents against soilborne pathogens infecting several crops.

Chapter 6 - Plant growth promoting rhizobacteria (PGPR): an overview for sustainable agriculture and development

The cashew tree (Anacardium occidentale L.) is of vital importance to the Ivorian economy. Côte d’Ivoire is first world producer. However, its cultivation faces several constraints linked to anthracnose. The aim of this study was to assess the efficacy of two formulated bacterial biocontrol agents against anthracnose of cashew. To this end, in vitro confrontation tests were carried out against Colletotrichum gloeosporioides with two previously formulated bacterial biopesticides. Biocontrol tests were then carried out against anthracnose in greenhouses and cashew plantations. The results showed that the two bacterial biocontrol agents tested controlled in vitro the proliferation of Colletotrichum gloeosporioides responsible for anthracnose and significantly reduced the disease severity index on cashew seedlings in the greenhouse. In vitro, inhibition rates ranging from 70.16±6.9 to 72.65±6.5% were observed on the mycelial growth of Colletotrichum gloeosporioides. In the greenhouse and in cashew plantations, a sharp reduction in the anthracnose severity index was observed. In the greenhouse, anthracnose reduction rates by the two bacterial biocontrol agents ranged from 62.80 ± 5.2% to 85.95 ± 2.8%. In cashew plantations, the reduction rates varied from 42.24 to 41.05%. In view of the above, these two bacterial biocontrol agents could be used for biological control of cashew anthracnose in Côte d'Ivoire.

Under green revolution practices, the imbalanced use of chemical fertilizers and pesticides causes a negative impact on soil health due to the loss of soil microbial flora and fauna. To overcome this negative impact of the green revolution and to increase sustainable agricultural production without damaging further agricultural lands, the only alternative and effective means is to reduce the use of chemicals in agriculture specifically for plant nutrition and plant protection. Under sustainable agricultural practices, plant growth-promoting rhizobacteria (PGPR) can be effective tools to increase productivity while ensuring sustainability in agriculture. PGPR colonize the rhizosphere zone and help in promoting plant growth and development by regulating nutrient acquisition, modulation of plant hormones, and ameliorating various negative effects of various pathogens. PGPR also help sustain the plant growth productivity and significantly increase soil fertility and health under different biotic and abiotic stresses. As per the literature, many studies prove to increase agriculture productivity due to the use of PGPR as eco-friendly microbial inoculants for promoting plant growth attaributes through various direct and indirect mechanisms. The mechanisms of PGPR include biological nitrogen fixation, phytohormones production, Phosphate, potassium, and zinc solubilization, siderophores production, and secretion of other secondary metabolites (phenolic compounds (phenylpropanoids and flavonoids)) that enhance crop productivity and control phytopathogens. Therefore, this chapter focuses on a detailed description of PGPR keeping in view their functional mechanisms as eco-friendly approaches to increase productivity and enhance soil fertility. PGPR can be used as an eco-friendly, socially acceptable, and cost-effective technology for challenges in the future.KeywordsPGPRProductivitySoil fertility and healthRhizosphereSustainable agriculture

Soil bacteria beneficial to plant growth usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. The mechanisms of PGPR-mediated enhancement of crop growth includes (i) a symbiotic and associative nitrogen fixation; (ii) solubilization and mineralization of other nutrients; (iii) production of hormones e.g. auxin i.e. indole acetic acid (IAA), abscisic acid (ABA), gibberellic acid and cytokinins; (iv) production of ACC-deaminase to reduce the level of ethylene in crop roots thus enhancing root length and density; (v) ability to produce antagonistic siderophores, s-1-3-glucanase, chitinases, antibiotics, fluorescent pigment and cyanide against pathogens and (vi) enhanced resistance to drought and oxidative stresses by producing water soluble vitamins niacin, thiamine, riboflavin, biotin and pantothenic acid. Increased crop production through biocontrol is an indirect mechanism of PGPR that results in suppression of soil born deleterious microorganisms. Biocontrol mechanisms involved in pathogen suppression by PGPR include substrate competition, antibiotic production, and induced systemic resistance in the host. PGPR can play an essential role in helping plants to establish and grow in nutrient deficient conditions. Their use in agriculture can favour a reduction in agro-chemical use and support ecofriendly crop production. Trials with rhizosphere-associated plant growth-promoting P-solubilizing and N2-fixing microorganisms indicated yield increase in rice, wheat, sugar cane, maize, sugar beet, legumes, canola, vegetables and conifer species. A range of beneficial bacteria including strains of Herbaspirillum, Azospirillum and Burkholderia are closely associated with rhizosphere of rice crops. Common bacteria found in the maize rhizosphere are Azospirillum sp., Klebsiella sp., Enterobacter sp., Rahnella aquatilis, Herbaspirillum seropedicae, Paenibacillus azotofixans, and Bacillus circulans. Similarly, strains of Azotobacter, Azorhizobium, Azospirillum, Herbaspirillum, Bacillus and Klebsiella can supplement the use of urea-N in wheat production either by BNF or growth promotion. The commonly present PGPR in sugarcane plants are Azospirillum brasilense, Azospirillum lipoferum, Azospirillum amazonense, Acetobacter diazotrophicus, Bacillus tropicalis, Bacillus borstelensis, Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. Symbiotic N2-fixing bacteria collectively known as Rhizobia are currently classified into six genera; Rhizobium, Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium and Sinorhizobium and 91 species. Their inoculation may increase nodulation and N2-fixation in legumes. All these Rhizobiumn spp. can minimize chemical N fertilizers by BNF, but only if conditions for expression of N2-fixing activity and subsequent transfer of N to plants are favourable. In this Chapter, PGPR role has been discussed in the process of crop growth promotion, their mechanisms of action and their importance in crop production on sustainable basis.

An experiment was conducted to study the compatibility of azoxystrobin 23 SC with bacterial and fungal biocontrol agents and insecticides under in vitro and glass house conditions, respectively. Bacterial biocontrol agents viz., Pseudomonas fluorescens and Bacillus subtilis were compatible with azoxystrobin 23 SC even at a high concentration of 300 ppm whereas fungal biocontrol agent Trichoderma viride was inhibited by azoxystrobin 23 SC at a concentration above 15 ppm. Among the four insecticides tested for compatibility, all insecticides were physically compatible with azoxystrobin 23 SC at 125, 250 and 500 g ai ha -1 whereas dichlorvos was biologically incompatible even at the lowest concentration tested.

The role of PGPR in nutrient cycling, soil structure improvement, and soil pH modification. Traditional agriculture relies heavily on chemical inputs, which pose significant threats to the environment and deplete natural resources. The environmental challenges posed by chemical-based agriculture and emphasize the urgent need for sustainable alternatives in the face of climate change. Plant Growth-Promoting Rhizobacteria (PGPR) are beneficial soil microorganisms that enhance plant growth through various direct and indirect mechanisms, offering a sustainable approach to improving soil fertility and crop productivity. PGPR have emerged as a sustainable alternative, fostering plant development, and enhancing stress resilience. A comprehensive understanding of the underlying signalling pathways and stress management mechanisms is essential to maximizing their potential. Plant health has been demonstrated, nutrient uptake has improved, and environmental stress has been reduced with the help of PGPR. PGPR facilitate nitrogen fixation, phosphorus and potassium solubilization, and organic matter decomposition, enhancing nutrient availability and promoting plant growth. Their ability to produce exopolysaccharides contributes to soil aggregation, improving soil structure and water retention. Additionally, PGPR modifies rhizosphere pH, enhancing nutrient solubility and availability. PGPR also promote crop yield by enhancing root and shoot growth, improving seed germination, and increasing stress tolerance against drought, salinity, and heavy metal contamination. PGPR provides effective biocontrol against pathogens through antibiosis, competition, and induced systemic resistance (ISR), contributing to improved crop resilience. Despite their potential, several challenges hinder the widespread adoption of PGPR, including inconsistent field performance, limited shelf-life, compatibility issues with native soil microbiota, and regulatory barriers. Emerging approaches such as genetic engineering, multi-strain consortia, and nano-formulations are being developed to enhance PGPR efficacy and stability under diverse environmental conditions. Integrating PGPR with organic and chemical fertilizers presents a promising strategy for achieving higher yields while minimizing environmental impact. Research should focus on understanding PGPR-plant signalling pathways, optimizing formulation techniques, and developing policies to promote their commercial use. Collaborative efforts between researchers, industries, and policymakers are essential to enhance the application of PGPR in sustainable agriculture. Widespread adoption of PGPR-based technologies could significantly contribute to global food security, environmental sustainability, and the reduction of chemical inputs in agriculture. The potential of PGPR as a valuable tool for enhancing agricultural productivity through environmentally friendly practices. Future research should focus on developing efficient, cost-effective formulations and enhancing collaboration between researchers, policymakers, and industries to ensure global food security and environmental sustainability.