From Rhizosphere to Endosphere: Conserved and Specialised Mechanisms of Plant Growth-Promoting Bacteria in Mediating Salt Tolerance.

The beneficial microbial-plant interaction plays important role in the soil health, crop growth and productivity. Plant growth promoting rhizobacteria (PGPR) are such beneficial microorganisms, which in association with plant roots not only promote their growth but also help in counteracting the detrimental effects of soil stresses. Salt stress is one such stress, frequently confronted by the plants. The present study aimed at isolation and identification of PGPR inhabiting the mungbean rhizosphere, testing them for salt (NaCl) tolerance and subsequently in salt-supplemented mungbean crop. For this purpose, two salt-tolerant bacterial strains belonging to genus Pantoea and Enterococcus, characterized for their P-solubilization ability, indole acetic acid and siderophore production were selected. These two PGPR were further evaluated for their effect on the salt-stressed mungbean plants, grown at two salt concentrations (5 and 10dS/m). The plants treated with the combination of PGPR showed better performance in growth (16-37%) and yield (22-32%), under salt stress, as compared with control. The increasing salt concentration was found to increase the membrane damage, Na+ concentration in the plants. PGPR treatments effectively reduced the Na+ concentration (17-41%), membrane damage (1.1-1.5 folds) and enhanced the antioxidants i.e. ascorbic acid (8-26%) and glutathione (10-30%) in salt-stressed plants, in comparison to uninoculated stressed plants. Overall, the results indicated that both PGPR were effective as stress mitigators however, in combination they showed relatively better improvement in growth, yield as well as oxidative parameters of the salt-affected plants. These findings about the effects of native salt-tolerant PGPR Pantoea and Enterococcus sp. in mungbean crop are novel.

ABSTRACTA novel plant growth-promoting rhizobacterium (PGPR), which was designated strain BY2G20, was isolated from saline-alkaline soil in Dongying, China. Strain BY2G20 can grow at a NaCl range from 0 to 7% and a pH range from 7 to 9 and can prevent the growth of the phytopathogen Ralstonia solanacearum. Based on its phenotypic and genomic characteristics and phylogenetic analysis, strain BY2G20 represents a novel species of the genus Metabacillus, for which the name Metabacillus dongyingensis sp. nov. is proposed. Comparative genomic analysis of strain BY2G20 with its closely related species exhibited a high level of evolutionary plasticity derived by horizontal gene transfer, which facilitated adaptative evolution. Different evolutionary constraints have operated on the diverse functions of BY2G20, with the gene adapted to saline-alkaline ecosystems experiencing functional constraints. We determined the genetic properties of saline-alkaline tolerance and plant growth promotion, such as cation-proton antiporters, cation transporters, osmoprotectant synthesis and transport, H+-transporting F1F0-ATPase, indole-3-acetic acid production, and secondary metabolite synthesis. We also evaluated the effects of strain BY2G20 on the growth of Zea mays L. (maize) under salt stress. The physiological parameters of maize such as plant height, stem diameter, dry biomass, and fresh biomass were significantly higher after inoculating strain BY2G20 under salt stress, indicating that inoculation with BY2G20 enhanced the growth of maize in saline areas. This study demonstrates that M. dongyingensis sp. nov. BY2G20 is a potential candidate for organic agriculture biofertilizers in saline-alkaline areas.IMPORTANCE Plant growth and yield are adversely affected by soil salinity. PGPRs can promote plant growth and enhance plant tolerance to salt stress. In this study, a saline-alkaline tolerant PGPR strain BY2G20 was isolated from the rhizosphere of Ulmus pumila in Dongying, China. Strain BY2G20 represents a novel species within the genus Metabacillus based on phenotypic, genomic, and phylogenetic analysis. Genomic components have undergone different functional constraints, and the disparity in the evolutionary rate may be associated with the adaptation to a specific niche. Genomic analysis revealed numerous adaptive features of strain BY2G20 to a saline-alkaline environment and rhizosphere, especially genes related to salt tolerance, pH adaptability, and plant growth promotion. Our work also exhibited that inoculation of strain BY2G20 enhanced the growth of maize under salt stress. This study demonstrates that PGPRs play an important role in stimulating salt tolerance in plants and can be used as biofertilizers to enhance the growth of crops in saline-alkaline areas.

Chapter 18 - Metabolic and genomic traits of PGPR in salinity stress

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.

Salinity stress poses a major obstacle to agricultural productivity. Employing plant growth-promoting rhizobacteria (PGPR) has attracted significant attention due to its potential to improve plant development in challenging conditions. Yet, additional investigation is essential to fully understand the potential of PGPR in mitigating salinity stress, especially in field applications. Hence, this study investigated the resistance mechanisms of soybean (Glycine max (L.) Merr.) under salt stress with PGPR application through a field experiment with four treatments: normal soybean planting (NN), normal planting + PGPR (NP), salt stress planting (SN), and salt stress planting + PGPR (SP). This research investigated how applying PGPR under salt stress influences soybean photosynthetic traits, osmotic regulation, rhizosphere microbial communities, and yield quality. The results demonstrated that salt stress enhanced leaf temperature and significantly reduced the leaf area index, SPAD value, stomatal conductance, photosynthetic rate, and transpiration rate of soybeans. Compared to SN treatment, SP treatment significantly improved the stomatal conductance, photosynthetic rate, and transpiration rate by 10.98%, 16.28%, and 35.59%, respectively. Salt stress substantially increased sodium (Na+) concentration and Na+/K+ ratio in leaves, roots, and grains while reducing potassium (K+) concentration in roots and leaves. Under salinity stress, PGPR application significantly minimized Na+ concentration in leaves and enhanced K⁺ concentration in leaves, roots, and grains by 47.05%, 25.72%, and 14.48%, respectively. PGPR application boosted carbon assimilation (starch synthesis) by enhancing the activities of sucrose synthase, fructokinase, and ADP-glucose pyrophosphorylase. It improved physiological parameters and increased soybean yield by 32.57% compared to SN treatment. Additionally, PGPR enhanced antioxidant enzyme activities, including glutathione reductase, peroxidase, ascorbate peroxidase, and monodehydroascorbate reductase, reducing oxidative damage from salt stress. Analysis of rhizosphere microbial communities revealed that PGPR application enriched beneficial bacterial phyla such as Bacteroidetes, Firmicutes, Nitrospirae, and Patescibacteria and fungal genera like Metarhizium. These microbial shifts likely contributed to improved nutrient cycling and plant–microbe interactions, further enhancing soybean resilience to salinity. This study demonstrates that PGPR enhances soybean growth, microbial diversity, and salt tolerance under salinity stress, while future efforts should optimize formulations, explore synergies, and scale up for sustainable productivity.

An important abiotic stressor that hinders plant growth, nutrient uptake, and global agricultural productivity is soil salinity. Among the different strategies to overcome the issue of salinity in agriculture sector, plant growth-promoting rhizobacteria (PGPR) have gained recognition as promising beneficial microbes that can improve plants’ response to biotic and abiotic stressors. The salinity tolerance and traits that promote plant growth of eight PGPR strains (RT1, RT2, RT3, RT4, RT5, RT7, and RT12) were evaluated in this study. During screening, one strain, RT12, had the highest plant growth-promoting activity and salt tolerance in the group. The strain when subjected to NaCl stress showed quantitative ACC-deaminase activity, in the presence of NaCl at various concentrations, demonstrating extraordinary tolerance to salt stress by withstanding doses of up to 3M NaCl. In order to further investigate the effects of salt stress on Brassica juncea (mustard), RT12, which was identified as Pseudomonas putida using 16s RNA sequencing, was inoculated. Two salt treatments (100 and 150 mM) were applied to the mustard variety ‘Mingora’ in a greenhouse. The results revealed that through ACC utilization, PGPR directly induced plant growth in salt-stressed mustard plants by lowering excess ethylene production. All plant parameters were negatively impacted by an increase in NaCl concentration in uninoculated plants. However, P. putida RT12 inoculation enhanced all growth parameters, antioxidant production, total soluble sugar (TSS), total protein (TP), proline, relative water content (RWC), chlorophyll contents, and nutrient uptake in salt-treated plants. The inoculation with P. putida also caused a marked decline in Na+ uptake and an increase in K+ uptake in the shoot. By maintaining a greater K+/Na+ ratio in the tissues of RT12-inoculated plants compared to controls, this change in ion uptake helped to maintain nutritional balance of the plants. The findings suggest that inoculating plants with ACC deaminase-producing PGPR, such as P. putida RT12, may boost growth and stress resistance.

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa)

Plant growth-promoting rhizobacteria (PGPR) have an important role in maintaining sustainable agricultural practices. Increased demand for crop production using minimal chemical fertilisers has become a great challenge for both researchers and farmers. This chapter focuses on the important classification of PGPR and their various commercial uses in promoting sustainable agricultural practices. PGPR are subdivided into three categories: plant growth-promoting bacteria (PGPB), biocontrol PGPB, and plant stress homeo-regulating bacteria (PSHB). PGPR produce secondary metabolites having biofertiliser activity such as the ability to fix nitrogen, phosphate solubilisation, potash mobilisation, and biocontrol of plants. There are various reports on using PGPR strains, Pseudomonas sp., and Bacillus sp. as biocontrol agents. Hence, this article focuses on summarising the PGPR as biofertiliser for agricultural sustainability.

This collection features four peer-reviewed literature reviews on plant growth-promoting rhizobacteria in agriculture. The first chapter considers the use of plant growth-promoting rhizobacteria (PGPR) as plant biostimulants in agriculture. It considers the benefits of PGPR, such as their ability to promote plant growth and productivity under both normal and abiotic-stressed induced environments. The chapter also looks towards PGPR application as a sustainable and efficient method to enhance crop production. The second chapter reviews recent research on the use of PGPR as biofertilizers to enhance root function and improve nutrient uptake, with emphasis on their effects on root architecture, metabolism and adaptation to abiotic stress. The third chapter explores the use of microbial bio-effectors and their ability to optimise the mineral nutrition of agricultural crops. The chapter also reviews the wealth of research on the mechanism of action, applications and efficacy of key plant growth-promoting microorganisms (PGPMs). The final chapter reviews the use of plant growth-promoting bacteria (PGPB) as a biocontrol agent against invertebrate pests. The chapter analyses the effects of PGPB species against these pest types and enlists a case study on the PGPB species Pseudomonas protegens to further demonstrate this.

To examine how to utilize the plant growth-promoting bacteria (PGPB) and plant growth-promoting rhizobacteria (PGPR) in ameliorating drought and salinity stress conditions in agriculture, a bibliometric analysis is hereby carried out, examining trends and patterns in scientific literature based on information collected from the Scopus database, including production from 2019 to 2024; this analysis focuses on terms associated with environmental issues, such as drought, salinity, climate change, as well as plant growth regulators; a consistent upward trend in publication is shown in this study to indicate increased interest in PGPR / PGPB and its potential application in alleviating several environmental stresses; important conclusions indicated that a significantly large increase was directed toward studies on how PGPR / PGPB interacts with the plant hormones-gibberellins, ABA, auxin, cytokinins, and ethylene; the association of PGPR / PGPB with plant hormones in agricultural research is gradually becoming important, especially when it is associated with crop yield enhancement and stress tolerance to adverse environmental conditions; the study gives some insights into a changing research trend besides presenting the importance of PGPR / PGPB in respect to sustainable agriculture practice and development of stress-tolerant plants.

The application of plant growth-promoting bacteria (PGPB) is vital for sustainable agriculture with continuous world population growth and an increase in soil salinity. Salinity is one of the severe abiotic stresses which lessens the productivity of agricultural lands. Plant growth-promoting bacteria are key players in solving this problem and can mitigate salinity stress. The highest of reported halotolerant Plant growth-promoting bacteria belonged to Firmicutes (approximately 50%), Proteobacteria (40%), and Actinobacteria (10%), respectively. The most dominant genera of halotolerant plant growth-promoting bacteria are Bacillus and Pseudomonas. Currently, the identification of new plant growth-promoting bacteria with special beneficial properties is increasingly needed. Moreover, for the effective use of plant growth-promoting bacteria in agriculture, the unknown molecular aspects of their function and interaction with plants must be defined. Omics and meta-omics studies can unreveal these unknown genes and pathways. However, more accurate omics studies need a detailed understanding of so far known molecular mechanisms of plant stress protection by plant growth-promoting bacteria. In this review, the molecular basis of salinity stress mitigation by plant growth-promoting bacteria is presented, the identified genes in the genomes of 20 halotolerant plant growth-promoting bacteria are assessed, and the prevalence of their involved genes is highlighted. The genes related to the synthesis of indole acetic acid (IAA) (70%), siderophores (60%), osmoprotectants (80%), chaperons (40%), 1-aminocyclopropane-1-carboxylate (ACC) deaminase (50%), and antioxidants (50%), phosphate solubilization (60%), and ion homeostasis (80%) were the most common detected genes in the genomes of evaluated halotolerant plant growth-promoting and salinity stress-alleviating bacteria. The most prevalent genes can be applied as candidates for designing molecular markers for screening of new halotolerant plant growth-promoting bacteria.

Soil salinization refers to the buildup of salts in soil to a level toxic to plants. The major factors that contribute to soil salinity are the quality, the amount and the type of irrigation water used. The presented review discusses the different sources and causes of soil salinity. The effect of soil salinity on biological processes of plants is also discussed in detail. This is followed by a debate on the influence of salt on the nutrient uptake and growth of plants. Salinity decreases the soil osmotic potential and hinders water uptake by the plants. Soil salinity affects the plants K uptake, which plays a critical role in plant metabolism due to the high concentration of soluble sodium (<TEX>$Na^+$</TEX>) ions. Visual symptoms that appear in the plants as a result of salinity include stunted plant growth, marginal leaf necrosis and fruit distortions. Different strategies to ameliorate salt stress globally include breeding of salt tolerant cultivars, irrigation to leach excessive salt to improve soil physical and chemical properties. As part of an ecofriendly means to alleviate salt stress and an increasing considerable attention on this area, the review then focuses on the different plant growth promoting bacteria (PGPB) mediated mechanisms with a special emphasis on ACC deaminase producing bacteria. The various strategies adopted by PGPB to alleviate various stresses in plants include the production of different osmolytes, stress related phytohormones and production of molecules related to stress signaling such as bacterial 1-aminocyclopropane-1-carboxylate (ACC) derivatives. The use of PGPB with ACC deaminase producing trait could be effective in promoting plant growth in agricultural areas affected by different stresses including salt stress. Finally, the review ends with a discussion on the various PGPB activities and the potentiality of facultative halophilic/halotolerant PGPB in alleviating salt stress.

Response of subterranean clover to dual inoculation with vesicular-arbuscular mycorrhizal fungi and a plant growth-promoting bacterium, Pseudomonas putida

Abiotic stresses such as salt and drought represent adverse environmental conditions that significantly damage plant growth and agricultural productivity. In this study, the mechanism of the plant growth-promoting rhizo-bacteria (PGPR)-stimulated tolerance against abiotic stresses has been explored. Results suggest that PGPR strains, Arthrobacter protophormiae (SA3) and Dietzia natronolimnaea (STR1), can facilitate salt stress tolerance in wheat crop, while Bacillus subtilis (LDR2) can provide tolerance against drought stress in wheat. These PGPR strains enhance photosynthetic efficiency under salt and drought stress conditions. Moreover, all three PGPR strains increase indole-3-acetic acid (IAA) content of wheat under salt and drought stress conditions. The SA3 and LDR2 inoculations counteracted the increase of abscisic acid (ABA) and 1-aminocyclopropane-1-carboxylate (ACC) under both salt and drought stress conditions, whereas STR1 had no significant impact on the ABA and ACC content. The impact of PGPR inoculations on these physiological parameters were further confirmed by gene expression analysis as we observed enhanced levels of the TaCTR1 gene in SA3-, STR1- and LDR2-treated wheat seedlings as compared to uninoculated drought and salt stressed plants. PGPR inoculations enhanced expression of TaDREB2 gene encoding for a transcription factor, which has been shown to be important for improving the tolerance of plants to abiotic stress conditions. Our study suggest that PGPR confer abiotic stress tolerance in wheat by enhancing IAA content, reducing ABA/ACC content, modulating expression of a regulatory component (CTR1) of ethylene signaling pathway and DREB2 transcription factor.

Salinity is one of the mostsevere abiotic stress in the world. Also, the irrigated lands have been treated with second salinity. Canola is one of the most important industrial crops for oil production all over the world which is affected by salinity. Salt stress causes imbalanced ion hemostasis (Na+ and K+) and interrupted mineral absorption in canola. Also, salinity stress leads to oxidative stress (production and accumulation of reactive oxygen species (ROS). Accumulation of ROS is extremely dangerous and lethal for plants. As a consequence, canola production is reduced under salinity stress. So, a suitable approach should be found to deal with salinity stress and prevent the loss of production oilseed. Plant growth-promoting rhizobacteria (PGPR) can colonize on the plant root surface and alleviate the salt stress effect by providing minerals like nitrogen, phosphate, and potassium. Also, they alleviate salt stress by phytohormones like auxin (IAA), cytokinin (CK), and abscisic acid (ABA). This study focus on physiological parameters like leaf area (LA), root length (RL), shoot length (SL), chlorophyll fluorescence indexes (Fv/Fm and Fv/F0), relative water content (RWC), electrolyte leakage index (ELI), photosynthesis pigments (chlorophyll a, b, and carotenoids), Na+, and K+; and biochemical parameters like malondialdehyde (MDA) content, hydrogen peroxide content (H2O2), total protein content, proline, antioxidant capacity, and antioxidant enzyme activities in canola through the inoculation with Enterobacter sp. S16-3 and Pseudomonas sp. C16-2O. This study showed that LA, RL, SL, chlorophyll fluorescence indexes, RWC were significantly increased and ELI was significantly decreased in bacteria inoculated treatments. Also, MDA, H2O2 were decreased, and antioxidant capacity, proline, and antioxidant enzymes were increased due to inoculation with these bacteria. Besides, the amount of K+ as an index of salinity tolerance significantly increased, and leaf Na+ content was significantly decreased.