Bacillus tequilensis strain 'UPMRB9' improves biochemical attributes and nutrient accumulation in different rice varieties under salinity stress

Salt-Tolerant Plant Growth-Promoting Bacteria (ST-PGPB): An Effective Strategy for Sustainable Food Production

Soil is the backbone of the agricultural economy of any country. Soil salinity refers to the higher concentration of soluble salts in the soil. Soil salinity is a ruinous abiotic stress that has emerged as a threatening issue for food security. High salt concentration causes an ionic imbalance that hampers water uptake, affecting photosynthesis and other metabolic processes, ultimately resulting in inferior seed germination and stunted plant growth. A wide range of strategies have been adopted to mitigate the harmful effects of salinity such as efficient irrigation techniques, soil reclamation, habitat restoration, flushing, leaching or using salt-tolerant crops, but all the methods have one or more limitations. An alternative and effective strategy is the exploitation of salt-tolerant plant growth-promoting bacteria (ST-PGPB) to mitigate salt stress and improve crop productivity. ST-PGPB can survive in salinity-tainted environments and perform their inherent plant growth-promoting and biocontrol functions effectively. Additionally, ST-PGPB can rescue plants via stress-responsive mechanisms including production of growth regulators, maintenance of osmotic balance, aminocyclopropane-1-carboxylate (ACC) deaminase activity, exopolysaccharides (EPS) activity, improvement in photosynthesis activity, synthesis of compatible solutes, antioxidant activity and regulation of salt overly sensitive (SOS) signaling pathway. Several well-known ST-PGPB, specifically Azospirillum, Bacillus, Burkholderia, Enterobacter, Pseudomonas and Pantoea, are used as bioinoculants to improve the growth of different crops. The application of ST-PGPB allows plants to cope with salt stress by boosting their defense mechanisms. This review highlights the impact of salinity stress on plant growth and the potential of ST-PGPB as a biofertilizer to improve crop productivity under salt stress.

Trichoderma and Bacillus multifunctional allies for plant growth and health in saline soils: recent advances and future challenges

Saline soils pose significant challenges to global agricultural productivity, hindering crop growth and efficiency. Despite various mitigation strategies, the issue persists, underscoring the need for innovative and sustainable solutions. One promising approach involves leveraging microorganisms and their plant interactions to reclaim saline soils and bolster crop yields. This review highlights pioneering and recent advancements in utilizing multi-traits Trichoderma and Bacillus species as potent promoters of plant growth and health. It examines the multifaceted impacts of saline stress on plants and microbes, elucidating their physiological and molecular responses. Additionally, it delves into the role of ACC deaminase in mitigating plant ethylene levels by Trichoderma and Bacillus species. Although there are several studies on Trichoderma-Bacillus, much remains to be understood about their synergistic relationships and their potential as auxiliaries in the phytoremediation of saline soils, which is why this work addresses these challenges.

Growth and protein response of rice plant with plant growth-promoting rhizobacteria inoculations under salt stress conditions

Soil salinity has been one of the significant barriers to improving rice production and quality. According to reports, Bacillus spp. can be utilized to boost plant development in saline soil, although the molecular mechanisms behind the interaction of microbes towards salt stress are not fully known. Variations in rice plant protein expression in response to salt stress and plant growth-promoting rhizobacteria (PGPR) inoculations were investigated using a proteomic method and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Findings revealed that 54 salt-responsive proteins were identified by mass spectrometry analysis (LC-MS/MS) with the Bacillus spp. interaction, and the proteins were functionally classified as gene ontology. The initial study showed that all proteins were labeled by mass spectrometry analysis (LC-MS/MS) with Bacillus spp. interaction; the proteins were functionally classified into six groups. Approximately 18 identified proteins (up-regulated, 13; down-regulated, 5) were involved in the photosynthetic process. An increase in the expression of eight up-regulated and two down-regulated proteins in protein synthesis known as chaperones, such as the 60 kDa chaperonin, the 70 kDa heat shock protein BIP, and calreticulin, was involved in rice plant stress tolerance. Several proteins involved in protein metabolism and signaling pathways also experienced significant changes in their expression. The results revealed that phytohormones regulated the manifestation of various chaperones and protein abundance and that protein synthesis played a significant role in regulating salt stress. This study also described how chaperones regulate rice salt stress, their different subcellular localizations, and the activity of chaperones.

Harnessing plant growth-promoting rhizobacteria, Bacillus subtilis and B. aryabhattai to combat salt stress in rice: a study on the regulation of antioxidant defense, ion homeostasis, and photosynthetic parameters

Introduction

The ongoing global expansion of salt-affected land is a significant factor, limiting the growth and yield of crops, particularly rice (Oryza sativa L). This experiment explores the mitigation of salt-induced damage in rice (cv BRRI dhan100) following the application of plant growth-promoting rhizobacteria (PGPR).

Methods

Rice seedlings, at five- and six-weeks post-transplanting, were subjected to salt stress treatments using 50 and 100 mM NaCl at seven-day intervals. Bacterial cultures consisting of endophytic PGPR (Bacillus subtilis and B. aryabhattai) and an epiphytic PGPR (B. aryabhattai) were administered at three critical stages: transplantation of 42-day-old seedlings, vegetative stage at five weeks post-transplantation, and panicle initiation stage at seven weeks post-transplantation.

Results

Salt stress induced osmotic stress, ionic imbalances, and oxidative damage in rice plants, with consequent negative effects on growth, decrease in photosynthetic efficiency, and changes in hormonal regulation, along with increased methylglyoxal (MG) toxicity. PGPR treatment alleviated salinity effects by improving plant antioxidant defenses, restoring ionic equilibrium, enhancing water balance, increasing nutrient uptake, improving photosynthetic attributes, bolstering hormone synthesis, and enhancing MG detoxification.

Discussion

These findings highlight the potential of PGPR to bolster physiological and biochemical functionality in rice by serving as an effective buffer against salt stress-induced damage. B. subtilis showed the greatest benefits, while both the endophytic and epiphytic B. aryabhattai had commendable effects in mitigating salt stress-induced damage in rice plants.

Survival of beneficial microbes in liquid bioformulation and optimization of different carrier materials using RSM technique

Soil salinity in rice cultivation areas is considered a severely limiting factor that adversely affects the quantity and quality of rice production in wetlands. Recently, the alternative use of salt-tolerant plant growth-promoting rhizobacteria (PGPR) inhabiting extreme saline conditions has gained remarkable attention and had positive effects on soil and crops. Therefore, a study has been initiated to develop a liquid biofertilizer formulation from locally isolated multi-strain salt-tolerant PGPR strains such as Bacillus tequilensis and Bacillus aryabhattai, using glycerol (5 mM), trehalose (10 mM), and polyvinylpyrrolidone (PVP) at 1% as additives to prolong the shelf-life of the bacteria. After 3 months of incubation, the bacterial population in the trehalose-supplemented mixed strain was highest at 9.73×107 CFU/mL, followed by UPMRE6 and UPMRB9 at 9.40×107 CFU/mL and 8.50×107 CFU/mL respectively. The results showed that the optimal trehalose concentration successfully prolonged the shelf-life of bacteria with minimal cell loss. Validation of quadratic optimization by response surface methodology revealed that the cell density of the mixed strain was 4.278×107 log CFU/mL after 24 h. The precision ratio was 99.7% higher than the predicted value in the minimized medium formulation: 0.267 g/mL trehalose, 1% glycerol, at 120 rpm agitation using the data analysis tools of Design Expert software. The population study confirmed the better and longer survival of salt-tolerant PGPR fortified with 10 mM trehalose, which was considered the best liquid biofertilizer formulation. Moreover, the optimized trehalose-glycerol liquid formulation can be used commercially as it is cost-effective.

Variability in morpho-biochemical, photosynthetic pigmentation, enzymatic and quality attributes of potato for salinity stress tolerance

Salt stress has emerged as a growing global concern, exerting a significant impact on agricultural productivity. The challenges of salt stress on potatoes are crucial for ensuring food security and sustainable agriculture. To address this issue a pot trial was executed to evaluate the impacts of NaCl in the soil on the growth, photosynthetic pigments, and quality attributes of potato, plants were grown in soil spiked with various concentrations of NaCl (0, 1, 3, 5, 7 g kg-1 of soil). Results revealed that salt stress have negative impacts on the growth, biomass, photosynthesis and quality attributes of potato. Lower level of salt stress 1 g kg-1 of soil improved the fresh and dry biomass of leaves (78.70 and 47.74%) and tubers (86.04 and 88.92%) as compared to control, respectively. Higher levels of salt stress (7 g kg-1) increased lipid peroxidation in leaves and improved the enzymatic antioxidants. It was observed that enzyme activities i.e., SOD (134.97%), POD (101.02%), and CAT (28.87%) increased in leaves and are inversely related to the NaCl concentration. The combination of reduction in chlorophyll contents and soluble sugars resulted in lower levels of quality attributes i.e., amylose (68.90%) and amylopectin (16.70%) of potato. Linear relationship in growth, biomass and physiological attributes showed the strong association with increased salt stress. Furthermore, the PCA-heatmap synergy offers identifying clusters of co-regulated attributes, which pinpoint the physiological responses that exhibit the strongest correlation with increasing salt stress levels. Findings indicate that potato can be grown successfully with (1 g kg-1 of NaCl in soil) without negative impacts on plant quality. Furthermore, this study contributes valuable insights into the complexities of salt stress on potato plants and provides a foundation for developing strategies to enhance their resilience in salt-affected environments.

Paired growth of cultivated and halophytic wild rice under salt stress induces bacterial endophytes and gene expression responses

Introduction

Utilizing salt-affected marginal lands in coastal regions can help meet the growing demand for rice. We explored a nature-based solution involving wild halophytic rice (O. coarctata, Oc) and commercial rice BRRI Dhan 67 (O. sativa, Os) grown in close proximity to each other under salt stress.

Methods

This was to investigate whether a paired planting strategy could help complement rice growth and yield under stress. We also investigated the gene expression and endophytic bacterial profiles of both Os and Oc in unpaired and paired conditions without and with salt.

Results

Paired plants exhibited lower salt damage indicators such as smaller reduction in plant height, electrolyte leakage and chlorophyll loss, as well as higher K+/Na+ ratio under saline stress. Some of the 39 endophytic bacteria in the mutualism experiment were unique to Oc and transferred to Os when paired. Differentially expressed genes in leaves of paired Os versus unpaired Os were 1097 (994 up-regulated, 101 down-regulated) without salt and 893 (763 up-regulated, 130 down-regulated) under salt stress. The presence of Oc plants under salt stress influenced major biological processes in Os, including oxidative stress; chitinase activity; phenylalanine catabolic process and response to ABA. Protein binding and serine/threonine kinase activity were primarily affected in molecular function. The downregulated WRKY transcription factor 22 in paired conditions under salt stress played a role in the MAPK signaling pathway, reducing respiratory cell death. The upregulated auxin-responsive protein IAA18 gene, involved in hormone signaling and cell enlargement, was present only in paired plants.

Discussion

Our findings therefore, offer insights into developing more effective cultivation strategies for sustainable rice production.

Assessing the role of ACC deaminase-producing bacteria in alleviating salinity stress and enhancing zinc uptake in plants by altering the root architecture of French bean (Phaseolus vulgaris) plants

MAIN CONCLUSION

The consortium inoculation with strains R1 and R4 modified the root system to boost seedling growth, increase the zinc content of French bean pods, and reduce salinity stress. The present study demonstrated the effect of two 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing plant growth-promoting rhizobacteria (Pantoea agglomerans R1 and Pseudomonas fragi R4) alone and consortia on the root system development, French bean growth, and zinc content as well as salinity stress tolerance. Both the strains were characterized for ACC utilization activity (426.23 and 380.54 nmol α-ketobutyrate mg protein^-1 h^-1), indole acetic acid (IAA) production, phosphate solubilization, ammonia, hydrogen cyanide (HCN), and siderophore production. The strains exhibited zinc solubilization in both plate and broth assays with zinc oxide and zinc carbonate as zinc sources as validated by atomic absorption spectroscopy (AAS). Single or combined inoculations with the selected strains significantly modulated the architectural and morphological traits of the root system of French bean plants. Furthermore, the application of R1and R4 consortia has enhanced zinc content in roots (60.83 mg kg^-1), shoots (15.41 mg kg^-1), and pods (30.04 mg kg^-1) of French bean plants grown in ZnCO₃ amended soil. In another set of pot experiments, the consortium bacterization has significantly enhanced length as well as fresh and dry biomass of roots and shoots of the French bean plant under saline stress conditions. Additionally, inoculation with ACC-degrading rhizobacterial strains has increased chlorophyll and carotenoid contents, osmoprotectant content, and antioxidative enzyme (catalase and peroxidase) activity in comparison to their counterparts exposed to salt treatments only. Current findings suggested ACC deaminase-producing rhizobacterial strains hold the potential to improve root architecture which in turn promotes plant growth under salt-stressed conditions as well as enhances micronutrient concentration in host plants.

Humic Acid-Amended Formulation Improves Shelf-Life of Plant Growth-Promoting Rhizobacteria (PGPR) Under Laboratory Conditions

Plant growth-promoting rhizobacteria (PGPR) is a soil bacterium that positively impacts soil and crops. These microbes invade plant roots, promote plant growth, and improve crop yield production. Bacillus subtilis is a type of PGPR with a short shelf-life due to its structural and cellular components, with a non-producing resistance structure (spores). Therefore, optimum formulations must be developed to prolong the bacterial shelf-life by adding humic acid (HA) as an amendment that could benefit the microbes by providing shelter and carbon sources for bacteria. Thus, a study was undertaken to develop a biofertilizer formulation from locally isolated PGPR, using HA as an amendment. Four doses of HA (0, 0.01, 0.05, and 0.1%) were added to tryptic soy broth (TSB) media and inoculated with B. subtilis (UPMB10), Bacillus tequilensis (UPMRB9) and the combination of both strains. The shelf-life was recorded, and viable cells count and optical density were used to determine the bacterial population and growth trend at monthly intervals and endospores detection using the malachite green staining method. After 12 months of incubation, TSB amended with 0.1% HA recorded the highest bacterial population significantly with inoculation of UPMRB9, followed by mixed strains and UPMB10 at 1.8x107 CFUmL-1, 2.8x107 CFUmL-1and 8.9x106 CFUmL-1, respectively. Results showed that a higher concentration of HA has successfully prolonged the bacterial shelf-life with minimal cell loss. Thus, this study has shown that the optimum concentration of humic acid can extend the bacterial shelf-life and improve the quality of a biofertilizer.

Effects of multiple halotolerant rhizobacteria on the tolerance, growth, and yield of rice plants under salt stress

Halotolerant bacteria get adapted to a saline environment through modified physiological/structural characteristics and may provide stress tolerance along with enhanced growth to the host plants by different direct and indirect mechanisms. This study reports on multiple halotolerant plant growth-promoting rhizobacteria isolated from the coastal soils in Bangladesh, in fields where the halophytic wild rice Oryza coarctata is endemic. The aim was to find halotolerant bacteria for potential use as biofertilizer under normal/salt-stressed conditions. In this study, eight different strains were selected from a total of 20 rhizobacterial isolates from the saline-prone regions of Debhata and Satkhira based on their higher salt tolerance. 16S rRNA gene sequencing results of the rhizobacterial strains revealed that they belonged to Halobacillus, Bacillus, Acinetobactor, and Enterobactor genera. A total of ten halotolerant rhizobacteria (the other 2 bacteria were previously isolated and already reported as beneficial for rice growth) were used as both single inoculants and in combinations and applied to rice growing in pots. To investigate their capability to improve rice growth, physiological parameters such as shoot and root length and weight, chlorophyll content at the seedling stage as well as survival and yield at the reproductive stage were measured in the absence or presence (in concentration 40 or 80 mmol/L) of NaCl and in the absence or presence of the rhizobacteria. At the reproductive stage, only 50% of the uninoculated plants survived without setting any grains in 80 mmol/L NaCl in contrast to 100% survival of the rice plants inoculated with a combination of the rhizobacteria. The combined halotolerant rhizobacterial inoculations showed significantly higher chlorophyll retention as well as yield under the maximum NaCl concentration applied compared to application of single species. Thus, the use of a combination of halotolerant rhizobacteria as bioinoculants for rice plants under moderate salinity can synergistically alleviate the effects of stress and promote rice growth and yield.

Engineering of a newly isolated Bacillus tequilensis BL01 for poly-γ-glutamic acid production from citric acid

BACKGROUND

Poly γ-glutamic acid (γ-PGA) is a promising biopolymer for various applications. For glutamic acid-independent strains, the titer of γ-PGA is too low to meet the industrial demand. In this study, we isolated a novel γ-PGA-producing strain, Bacillus tequilensis BL01, and multiple genetic engineering strategies were implemented to improve γ-PGA production.

RESULTS

First, the one-factor-at-a-time method was used to investigate the influence of carbon and nitrogen sources and temperature on γ-PGA production. The optimal sources of carbon and nitrogen were sucrose and (NH₄)₂SO₄ at 37 °C, respectively. Second, the sucA, gudB, pgdS, and ggt genes were knocked out simultaneously, which increased the titer of γ-PGA by 1.75 times. Then, the titer of γ-PGA increased to 18.0 ± 0.3 g/L by co-overexpression of the citZ and pyk genes in the mutant strain. Furthermore, the γ-PGA titer reached 25.3 ± 0.8 g/L with a productivity of 0.84 g/L/h and a yield of 1.50 g of γ-PGA/g of citric acid in fed-batch fermentation. It should be noted that this study enables the synthesis of low (1.84 × 10⁵ Da) and high (2.06 × 10⁶ Da) molecular weight of γ-PGA by BL01 and the engineering strain.

CONCLUSION

The application of recently published strategies to successfully improve γ-PGA production for the new strain B. tequilensis BL01 is reported. The titer of γ-PGA increased 2.17-fold and 1.32-fold compared with that of the wild type strain in the flask and 5 L fermenter. The strain shows excellent promise as a γ-PGA producer compared with previous studies. Meanwhile, different molecular weights of γ-PGA were obtained, enhancing the scope of application in industry.

Microbiome-metabolome analysis directed isolation of rhizobacteria capable of enhancing salt tolerance of Sea Rice 86

Soil salinization has been recognized as one of the main factors causing the decrease of cultivated land area and global plant productivity. Application of salt tolerant plants and improvement of plant salt tolerance are recognized as the major routes for saline soil restoration and utilization. Sea rice 86 (SR86) is known as a rice cultivar capable of growing in saline soil. Genome sequencing and transcriptome analysis of SR86 have been conducted to explore its salt tolerance mechanisms while the contribution of rhizobacteria is underexplored. In the present study, we examined the rhizosphere bacterial diversity and soil metabolome of SR86 seedlings under different salinity to understand their contribution to plant salt tolerance. We found that salt stress could significantly change rhizobacterial diversity and rhizosphere metabolites. Keystone taxa were identified via co-occurrence analysis and the correlation analysis between keystone taxa and rhizosphere metabolites indicated lipids and their derivatives might play an important role in plant salt tolerance. Further, four plant growth promoting rhizobacteria (PGPR), capable of promoting the salt tolerance of SR86, were isolated and characterized. These findings might provide novel insights into the mechanisms of plant salt tolerance mediated by plant-microbe interaction, and promote the isolation and application of PGPR in the restoration and utilization of saline soil.

Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.

Recent Advances in Bacterial Amelioration of Plant Drought and Salt Stress

Simple Summary

Salt and drought stress cause enormous crop losses worldwide. Several different approaches may be taken to address this problem, including increased use of irrigation, use of both traditional breeding and genetic engineering to develop salt-tolerant and drought-resistant crop plants, and the directed use of naturally occurring plant growth-promoting bacteria. Here, the mechanisms used by these plant growth-promoting bacteria are summarized and discussed. Moreover, recently reported studies of the effects that these organisms have on the growth of plants in the laboratory, the greenhouse, and the field under high salt and/or drought conditions is discussed in some detail. It is hoped that by understanding the mechanisms that these naturally occurring plant growth-promoting bacteria utilize to overcome damaging environmental stresses, it may be possible to employ these organisms to increase future agricultural productivity.

Abstract

The recent literature indicates that plant growth-promoting bacteria (PGPB) employ a range of mechanisms to augment a plant’s ability to ameliorate salt and drought stress. These mechanisms include synthesis of auxins, especially indoleacetic acid, which directly promotes plant growth; synthesis of antioxidant enzymes such as catalase, superoxide dismutase and peroxidase, which prevents the deleterious effects of reactive oxygen species; synthesis of small molecule osmolytes, e.g., trehalose and proline, which structures the water content within plant and bacterial cells and reduces plant turgor pressure; nitrogen fixation, which directly improves plant growth; synthesis of exopolysaccharides, which protects plant cells from water loss and stabilizes soil aggregates; synthesis of antibiotics, which protects stress-debilitated plants from soil pathogens; and synthesis of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which lowers the level of ACC and ethylene in plants, thereby decreasing stress-induced plant senescence. Many of the reports of overcoming these plant stresses indicate that the most successful PGPB possess several of these mechanisms; however, the involvement of any particular mechanism in plant protection is nearly always inferred and not proven.