Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects

Crop productivity is affected by environmental and genetic factors. Microbes that are beneficial to plants are used to enhance the crop yield and are alternatives to chemical fertilizers and pesticides. Pseudomonas and Bacillus species are the predominant plant growth-promoting bacteria. The spore-forming ability of Bacillus is distinguished from that of Pseudomonas, and members of this genus also survive for a long time under unfavorable environmental conditions. Bacillus spp. secrete several metabolites that trigger plant growth and prevent pathogen infection. Limited studies have been conducted to understand the physiological changes that occur in crops in response to Bacillus spp. to provide protection against adverse environmental conditions. This review describes the current understanding of Bacillus-induced physiological changes in plants as an adaptation to abiotic and biotic stresses. During water scarcity, salinity and heavy metal accumulate in soil, and Bacillus spp. produce exopolysaccharides and siderophores, which prevent the movement of toxic ions and adjust the ionic balance and water transport in plant tissues while controlling the pathogenic microbial population. In addition, the synthesis of indole-3-acetic acid, gibberellic acid and 1-aminocyclopropane-1-carboxylate (ACC) deaminase by Bacillus regulates the intracellular phytohormone metabolism and increases plant stress tolerance. Cell-wall-degrading substances, such as chitosanase, protease, cellulase, glucanase, lipopeptides and hydrogen cyanide, from Bacillus spp. damage the pathogenic bacteria, fungi, nematodes, viruses and pests to control their populations in plants and agricultural lands. The normal plant metabolism is affected by unfavorable environmental stimuli, which suppress crop growth and yield. Abiotic and biotic stress factors that have detrimental effects on crops are mitigated by Bacillus-induced physiological changes, including the regulation of water transport, nutrient up-take and the activation of the antioxidant and defense systems. Bacillus association stimulates plant immunity against stresses by altering stress-responsive genes, proteins, phytohormones and related metabolites. This review describes the beneficial effect of Bacillus spp. on crop plants, which improves plant productivity under unfavorable climatic conditions, and the current understanding of the mitigation mechanism of Bacillus spp. in stress-tolerant and/or stress-resistant plants.

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Bacillus: A Biological Tool for Crop Improvement through Bio-Molecular Changes in Adverse Environments.

Root-associated bacterial communities play a vital role in maintaining health of the plant host. These communities exist in complex relationships, where composition and abundance of community members is dependent on a number of factors such as local soil chemistry, plant genotype and phenotype, and perturbations in the surrounding abiotic environment. One common perturbation, drought, has been shown to have drastic effects on bacterial communities, yet little is understood about the underlying causes behind observed shifts in microbial abundance. As drought may affect root bacterial communities both directly by modulating moisture availability, as well as indirectly by altering soil chemistry and plant phenotypes, we provide a synthesis of observed trends in recent studies and discuss possible directions for future research that we hope will provide for more knowledgeable predictions about community responses to future drought events.

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Drought Stress and Root-Associated Bacterial Communities.

Plant roots support complex microbial communities that can influence plant growth, nutrition, and health. While extensive characterizations of the composition and spatial compartmentalization of these communities have been performed in different plant species, there is relatively little known about the impact of abiotic stresses on the root microbiota. Here, we have used rice as a model to explore the responses of root microbiomes to drought stress. Using four distinct genotypes, grown in soils from three different fields, we tracked the drought-induced changes in microbial composition in the rhizosphere (the soil immediately surrounding the root), the endosphere (the root interior), and unplanted soils. Drought significantly altered the overall bacterial and fungal compositions of all three communities, with the endosphere and rhizosphere compartments showing the greatest divergence from well-watered controls. The overall response of the bacterial microbiota to drought stress was taxonomically consistent across soils and cultivars and was primarily driven by an enrichment of multiple Actinobacteria and Chloroflexi, as well as a depletion of several Acidobacteria and Deltaproteobacteria While there was some overlap in the changes observed in the rhizosphere and endosphere communities, several drought-responsive taxa were compartment specific, a pattern likely arising from preexisting compositional differences, as well as plant-mediated processes affecting individual compartments. These results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in restructuring of root microbial communities and suggest the possibility that constituents of the altered plant microbiota might contribute to plant survival under extreme environmental conditions.IMPORTANCE With the likelihood that changes in global climate will adversely affect crop yields, the potential role of microbial communities in enhancing plant performance makes it important to elucidate the responses of plant microbiomes to environmental variation. By detailed characterization of the effect of drought stress on the root-associated microbiota of the crop plant rice, we show that the rhizosphere and endosphere communities undergo major compositional changes that involve shifts in the relative abundances of a taxonomically diverse set of bacteria in response to drought. These drought-responsive microbes, in particular those enriched under water deficit conditions, could potentially benefit the plant as they could contribute to tolerance to drought and other abiotic stresses, as well as provide protection from opportunistic infection by pathogenic microbes. The identification and future isolation of microbes that promote plant tolerance to drought could potentially be used to mitigate crop losses arising from adverse shifts in climate.

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Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

Root exudates are a pathway for plant-microbial communication and play a key role in ecosystem response to environmental change. Here, we collate recent evidence that shows that plants of different growth strategies differ in their root exudation, that root exudates can select for beneficial soil microbial communities, and that drought affects the quantity and quality of root exudation. We use this evidence to argue for a central involvement of root exudates in plant and microbial response to drought and propose a framework for understanding how root exudates influence ecosystem form and function during and after drought. Specifically, we propose that fast-growing plants modify their root exudates to recruit beneficial microbes that facilitate their regrowth after drought, with cascading impacts on their abundance and ecosystem functioning. We identify outstanding questions and methodological challenges that need to be addressed to advance and solidify our comprehension of the importance of root exudates in ecosystem response to drought.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.16223

Plant root exudation under drought: implications for ecosystem functioning.

Drought is a major limiting factor of crop productivity worldwide and its incidence is predicted to increase under climate change. Drought adaptation of cool-season grasses is thus a major challenge to secure the agricultural productivity under current and future climate conditions. Endophytes are non-pathogenic plant-associated bacteria that can play an important role in conferring resistance and improving plant tolerance to drought. In this study, the effect of inoculation of the bacterial endophyte Bacillus subtilis strain B26 on growth, water status, photosynthetic activity and metabolism of timothy (Phleum pratense L.) subjected to drought stress was investigated under controlled conditions. Under both drought-stress and non-stressed conditions, strain B26 successfully colonized the internal tissues of timothy and had a positive impact on plant growth. Exposure of inoculated plant to a 8-wk drought-stress led to significant increase in shoot and root biomass by 26.6 and 63.8%, and in photosynthesis and stomatal conductance by 55.2 and 214.9% respectively, compared to non-inoculated plants grown under similar conditions. There was a significant effect of the endophyte on plant metabolism; higher levels of several sugars, notably sucrose and fructans and an increase of key amino acids such as, asparagine, glutamic acid and glutamine were recorded in shoots and roots of colonized plants compared to non-colonized ones. The accumulation of the non-protein amino acid GABA in shoots of stressed plants and in roots of stressed and unstressed plants was increased in the presence of the endophyte. Taken together, our results indicate that B. subtilis B26 improves timothy growth under drought stress through the modification of osmolyte accumulation in roots and shoots. These results will contribute to the development of a microbial agent to improve the yield of grass species including forage crops and cereals exposed to environmental stresses.

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Alleviation of Drought Stress and Metabolic Changes in Timothy (Phleum pratense L.) Colonized with Bacillus subtilis B26.

Plant growth-promoting bacteria (PGB) induce positive effects in plants, for instance, increased growth and reduced abiotic stresses susceptibility. The mechanisms by which these bacteria impact the host plant are numerous, diverse and often specific. Here, we studied the agronomical, molecular and biochemical effects of the endophytic PGB Bacillus subtilis B26 on the full life cycle of Brachypodium distachyon Bd21, an established model species for functional genomics in cereal crops and temperate grasses. Inoculation of Brachypodium with B. subtilis strain B26 increased root and shoot weights, accelerated growth rate and seed yield as compared to control plants. B. subtilis strain B26 efficiently colonized the plant and was recovered from roots, stems and blades as well as seeds of Brachypodium, indicating that the bacterium is able to migrate, spread systemically inside the plant, establish itself in the aerial plant tissues and organs, and is vertically transmitted to seeds. The presence of B. subtilis strain B26 in the seed led to systemic colonization of the next generation of Brachypodium plants. Inoculated Brachypodium seedlings and mature plants exposed to acute and chronic drought stress minimized the phenotypic effect of drought compared to plants not harbouring the bacterium. Protection from the inhibitory effects of drought by the bacterium was linked to upregulation of the drought-response genes, DREB2B-like, DHN3-like and LEA-14-A-like and modulation of the DNA methylation genes, MET1B-like, CMT3-like and DRM2-like, that regulate the process. Additionally, total soluble sugars and starch contents increased in stressed inoculated plants, a biochemical indication of drought tolerance. In conclusion, we show a single inoculation of Brachypodium with a PGB affected the whole growth cycle of the plant, accelerating its growth rates, shortening its vegetative period, and alleviating drought stress effects. These effects are relevant to grasses and cereal crops.

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Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass Brachypodium distachyon Colonized by Bacillus subtilis B26.

Encapsulation of Lactobacillus casei ATCC 393 cells and evaluation of their survival after freeze-drying, storage and under gastrointestinal conditions

Plant growth promoting bacteria (PGPB) represent a wide variety of soil and endophytic bacteria that have the ability to promote growth or to protect against stress of its host plant. Encapsulation of PGPB, using vegetable proteins instead of animal or petroleum-derived polymers, is a new technology to crop production and protection. Pea protein isolates (PPI) alginate capsules were synthesized and used for the protection and delivery of Bacillus subtilis B26 as plant inoculum for agricultural applications. The capsules provided a protective site to B26 strain allowing good survival, between 45 to 50%, after 112 days of incubation at different temperatures. The loaded microcapsules sustained a large population of bacteria, up to 8.3 LogCFUg-1 of soil after 3 weeks post application. The soil concentration stabilized to 7.3 Log CFUg-1 after 8 weeks post application. Capsules loaded with B26, once incorporated in the soil, successfully colonized test plants, and cell numbers inside plant tissues were sustained at 3.5 and 3.3 Log 7.3 CFUg-1 in the root and the shoot respectively. These results indicate that PPIalginate technology represents a good choice for commercial application of B. subtilis B26 in agriculture.

https://www.longdom.org/open-access/pea-protein-alginate-encapsulated-bacillus-subtilis-b26-a-plant-biostimulantprovides-controlled-release-and-increased-storage-survival-jbfbp-1000157.pdf

Pea Protein Alginate Encapsulated Bacillus subtilis B26, a Plant Biostimulant,Provides Controlled Release and Increased Storage Survival

A method of increasing drought resistance of a plant, the method comprising applying a Bacillus methylotrophicus or a composition thereof (i) to the plant or to a part of the plant; and/or (ii) to an area around the plant or plant part, in an amount effective to produce an increased drought resistance in the plant as compared to the drought stress resistance of the plant in the absence of said application of Bacillus methylotrophicus or composition, is described. A biologically pure culture of a 1-aminocyclopropane-l-carboxylate (ACC) deaminase deficient Bacillus methylotrophicus bacterium strain, or a mutant thereof able to induce drought resistance in a plant are also described.

François Gagné-Bourque

Papers

Alleviation of Drought Stress and Metabolic Changes in Timothy (Phleum pratense L.) Colonized with Bacillus subtilis B26.

Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass Brachypodium distachyon Colonized by Bacillus subtilis B26.

Encapsulation of Lactobacillus casei ATCC 393 cells and evaluation of their survival after freeze-drying, storage and under gastrointestinal conditions

Pea Protein Alginate Encapsulated Bacillus subtilis B26, a Plant Biostimulant,Provides Controlled Release and Increased Storage Survival

A bacillus methylotrophicus strain and method of using the strain to increase drought resistance in a plant