Epsc Involved in the Encoding of Exopolysaccharides Produced by Bacillus amyloliquefaciens FZB42 Act to Boost the Drought Tolerance of Arabidopsis thaliana

Structure characterization and immunological activity of capsular polysaccharide from live and heat-killed Lacticaseibacillus paracasei 6235

Capsular polysaccharide (CPS) as a probiotic component has the ability to regulate the function of the host's immune system. However, how the structure and function of heat-killed CPS are altered remains unclear. In the present study, CPS were isolated and purified from live (LCPS) and heat-killed (HCPS) Lacticaseibacillus paracasei 6235. The differences in structure and immunomodulation between LCPS and HCPS were compared and analyzed. The results demonstrate that after heat killed, the molecular weight of CPS decreased from 23.4 kDa to 17.5 kDa, with the disappearance of galactosamine in the monosaccharide composition, and changes in the microstructure. Methylation analysis and nuclear magnetic resonance analysis revealed that the LCPS and HCPS are similar in structure, which main units of →3,4)-α-D-Glcp-(1→4)-α-D-Galp-(1→3)-β-L-Rhap-(1→6)-β-D-Galp-(1→, and repeating units of →3,4)-α-D-Glcp-(1→, →3)-β-L-Rhap-(1→, and →4)-α-D-Galp-(1→ residues. Furthermore, both LCPS and HCPS significantly downregulated the expression of pro-inflammatory cytokines in RAW264.7 cells induced by LPS. Specifically, HCPS reduced the levels of IL-6 and IL-1β by 79.38 % and 88.42 %, respectively, compared to LCPS. Concurrently, both LCPS and HCPS effectively mitigated inflammatory responses through the NF-κB and MAPK signaling pathways. Moreover, compared to LCPS, HCPS increased the protein expression levels of NF-κB/p-NF-κB and IκB/p-IκB by 26.14 % and 28.92 %, respectively. These results suggest that CPS has a role in modulating immune responses and that HCPS is more effective. This study can be further developed into new products related to postbiotics.

Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions

Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.

Exopolysaccharide is required by Paraburkholderia phytofirmans PsJN to confer drought-stress tolerance in pea

Paraburkholderia phytofirmans PsJN is a plant symbiotic bacterium that can colonize a broad spectrum of plant hosts and frequently shows beneficial effects on plant growth. Exopolysaccharide (EPS) is known to be important in plant-bacteria interactions. Previously, we reported that EPS is required for PsJN to survive from drought stress and colonize in pea (Pisum sativum) under drought condition. However, whether EPS is necessary for PsJN to promote plant growth remains unknown. In this work, a comparative study was conducted between the wild-type PsJN and its ∆bceQ mutant that lacks EPS to investigate the role of EPS in PsJN to confer drought-stress tolerance on pea plant. Our results showed that wild type PsJN, but not the ∆bceQ mutant, promoted pea seed germination and seedlings growth under drought stress. Pea plants inoculated with the wild type PsJN had a higher level of drought tolerance, as shown by a better vegetative growth and enhanced nodule formation, than plants inoculated with the ∆bceQ mutant. Moreover, EPS plays a role in the plant colonization under drought stress, because the ∆bceQ mutant was unable to colonize pea seeds and roots as effectively as the wild type PsJN. Further, expression of the EPS biosynthesis genes in the bceOVN operon of the wild type PsJN was induced by the presence of glucose. Overall, this study demonstrated that PsJN can promote pea plant growth under drought conditions and EPS is required for PsJN to confer beneficial effects to host plant.

Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions

Soil salinity negatively affects microbial communities, soil fertility, and agricultural productivity and has become a major agricultural problem worldwide. Plant growth-promoting rhizobacteria (PGPR) with salt tolerance can benefit plant growth under saline conditions and diminish the negative effects of salt stress on plants. In this study, we aimed to understand the salt-tolerance mechanism of Paenibacillus polymyxa at the genetic and metabolic levels and elucidate the mechanism of strain SC2 in promoting maize growth under saline conditions. Under salt stress, we found that strain SC2 promoted maize seedling growth, which was accompanied by a significant upregulation of genes encoding for the biosynthesis of peptidoglycan, polysaccharide, and fatty acid, the metabolism of purine and pyrimidine, and the transport of osmoprotectants such as trehalose, glycine betaine, and K+ in strain SC2. To further enhance the salt resistance of strain SC2, three mutants (SC2-11, SC2-13, and SC2-14) with higher capacities for salt resistance and exopolysaccharide synthesis were obtained via atmospheric and room-temperature plasma mutagenesis. In saline-alkaline soil, the mutants showed better promoting effect on maize seedlings than wild-type SC2. The fresh weight of maize seedlings was increased by 68.10% after treatment with SC2-11 compared with that of the control group. The transcriptome analysis of maize roots demonstrated that SC2 and SC2-11 could induce the upregulation of genes related to the plant hormone signal transduction, starch and sucrose metabolism, reactive oxygen species scavenging, and auxin and ethylene signaling under saline-alkaline stress. In addition, various transcription factors, such as zinc finger proteins, ethylene-responsive-element-binding protein, WRKY, myeloblastosis proteins, basic helix-loop-helix proteins, and NAC proteins, were up-regulated in response to abiotic stress. Moreover, the microbial community composition of maize rhizosphere soil after inoculating with strain SC2 was varied from the one after inoculating with mutant SC2-11. Our results provide new insights into the various genes involved in the salt resistance of strain SC2 and a theoretical basis for utilizing P. polymyxa in saline-alkaline environments.

Exopolysaccharides from agriculturally important microorganisms: Conferring soil nutrient status and plant health

A wide variety of microorganisms secretes extracellular polymeric substances or commonly known as exopolysaccharides (EPS), which have been studied to influence plant growth via various mechanisms. EPS-producing microorganisms have been found to have positive effects on plant health such as by facilitating nutrient entrapment in the soil, or by improving soil quality, especially by helping in mitigating various abiotic stress conditions. The various types of microbial polysaccharides allow for the compartmentalization of the microbial community enabling them to endure undressing stress conditions. With the growing population, there is a constant need for developing sustainable agriculture where we could use various PGPR to help the plant cope with various stress conditions and simultaneously enhance the crop yield. These polysaccharides have also found application in various sectors, especially in the biomedical fields, manifesting their potential to act as antitumor drugs, play a significant role in immune evasion, and reveal various therapeutic potentials. These constitute high levels of bioactive polysaccharides which possess a wide range of implementation starting from industrial applications to novel food applications. In this current review, we aim at presenting a comprehensive study of how these microbial extracellular polymeric substances influence agricultural productivity along with their other commercial applications.

Granular bacterial inoculant alters the rhizosphere microbiome and soil aggregate fractionation to affect phosphorus fractions and maize growth

The constraint of phosphorus (P) fixation on crop production in alkaline calcareous soils can be alleviated by applying bioinoculants. However, the impact of bacterial inoculants on this process remains inadequately understood. Here, a field study was conducted to investigate the effect of a high-concentration, cost-effective, and slow-release granular bacterial inoculant (GBI) on maize (Zea mays L.) plant growth. Additionally, we explored the effects of GBI on rhizosphere soil aggregate physicochemical properties, rhizosphere soil P fraction, and microbial communities within aggregates. The outcomes showed a considerable improvement in plant growth and P uptake upon application of the GBI. The application of GBI significantly enhanced the AP, phoD gene abundance, alkaline phosphatase activity, inorganic P fractions, and organic P fractions in large macroaggregates. Furthermore, GBI impacted soil aggregate fractionation, leading to substantial alterations in the composition of fungal and bacterial communities. Notably, key microbial taxa involved in P-cycling, such as Saccharimonadales and Mortierella, exhibited enrichment in the rhizosphere soil of plants treated with GBI. Overall, our study provides valuable insight into the impact of GBI application on microbial distributions and P fractions within aggregates of alkaline calcareous soils, crucial for fostering healthy root development and optimal crop growth potential. Subsequent research endeavors should delve into exploring the effects of diverse GBIs and specific aggregate types on P fraction and community composition across various soil profiles.

Choreographing root architecture and rhizosphere interactions through synthetic biology

Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

Fostering plant growth performance under drought stress using rhizospheric microbes, their gene editing, and biochar

Stress due to drought lowers crop yield and frequently leads to a rise in food scarcity. Plants' intricate metabolic systems enable them to tolerate drought stress, but they are unable to handle it well. Adding some external, environmentally friendly supplements can boost plant growth and productivity when it comes to drought-stressed plants. In order to prevent the detrimental effects of drought in agricultural regions, environmentally friendly practices must be upheld. Plant growth-promoting rhizobacteria (PGPR) can exhibit beneficial phytostimulation, mineralization, and biocontrol activities under drought stress. The significant impact of the PGPR previously reported has not been accepted as an effective treatment to lessen drought stress. Recent studies have successfully shown that manipulating microbes can be a better option to reduce the severity of drought in plants. In this review, we demonstrate how modifying agents such as biochar, PGPR consortia, PGPR, and mycorrhizal fungi can help overcome drought stress responses in crop plants. This article also discusses CRISPR/Cas9-modifiable genes, increase plant's effectiveness in drought conditions, and increase plant resistance to drought stress. With an eco-friendly approach in mind, there is a need for practical management techniques having potential prospects based on an integrated strategy mediated by CRISPR-Cas9 editing, PGPR, which may alleviate the effects of drought stress in crops and aid in achieving the United Nation Sustainable Development Goals (UN-SDGs-2030).

Exploring the mechanism of exopolysaccharides in mitigating cadmium toxicity in rice through analyzing the changes of antioxidant system

Recently, exopolysaccharides (EPS) were found to alleviate cadmium (Cd) toxicity to crops by regulating the antioxidant system, but the mechanism remains unclear. Herein, by quantitative and transcriptomic approaches, a systematical map of the changes in the antioxidant system was drawn to dissected the underlying mechanism. The results demonstrated that the ascorbate-glutathione cycle (ASA-GSH cycle) is a major contributor. Specifically, compared to the control, the rice exposed to Cd exhibited a significant increase in the GSH pool (about 9-fold at 7 d), but a continuous decrease in the ASA pool (only 15.42% remained at 15 d) and an excessive accumulation of reactive oxygen species (ROS). Interestingly, with the addition of EPS, the increase of the GSH pool significantly slowed down (decreased by 180.18% at 7 d, compared to the Cd-stressed treatment), and the ASA pool remained high (consistently above 70.00% of the control group). ROS also maintained at a good level. Moreover, the activities of enzymatic antioxidants showed the similar trend. By RNA-Seq analysis, multiple genes enriched in ASA-GSH related pathway were screened (such as OsRBOHB, OsGST, OsPOD) for further study. This study provides a foundation for EPS application in agriculture, which also establishes a better way for analyzing antioxidant system.

Epigenetic and Hormonal Modulation in Plant-Plant Growth-Promoting Microorganism Symbiosis for Drought-Resilient Agriculture

Plant growth-promoting microorganisms (PGPMs) have emerged as valuable allies for enhancing plant growth, health, and productivity across diverse environmental conditions. However, the complex molecular mechanisms governing plant-PGPM symbiosis under the climatic hazard of drought, which is critically challenging global food security, remain largely unknown. This comprehensive review explores the involved molecular interactions that underpin plant-PGPM partnerships during drought stress, thereby offering insights into hormonal regulation and epigenetic modulation. This review explores the challenges and prospects associated with optimizing and deploying PGPMs to promote sustainable agriculture in the face of drought stress. In summary, it offers strategic recommendations to propel research efforts and facilitate the practical implementation of PGPMs, thereby enhancing their efficacy in mitigating drought-detrimental effects in agricultural soils.

Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention

KEY MESSAGE

The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.

Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation

Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.

Role of microbial inoculants as bio fertilizers for improving crop productivity: A review

The world's population is increasing and is anticipated to spread 10 billion by 2050, and the issue of food security is becoming a global concern. To maintain global food security, it is essential to increase crop productivity under changing climatic conditions. Conventional agricultural practices frequently use artificial/chemical fertilizers to enhance crop productivity, but these have numerous negative effects on the environment and people's health. To address these issues, researchers have been concentrating on substitute crop fertilization methods for many years, and biofertilizers as a crucial part of agricultural practices are quickly gaining popularity all over the globe. Biofertilizers are living formulations made of indigenous plant growth-promoting rhizobacteria (PGPR) which are substantial, environment-friendly, and economical biofertilizers for amassing crop productivity by enhancing plant development either directly or indirectly, and are the renewable source of plant nutrients and sustainable agronomy. The review aims to provide a comprehensive overview of the current knowledge on microbial inoculants as biofertilizers, including their types, mechanisms of action, effects on crop productivity, challenges, and limitations associated with the use of microbial inoculants. In this review, we focused on the application of biofertilizers to agricultural fields in plant growth development by performing several activities like nitrogen fixation, siderophore production, phytohormone production, nutrient solubilization, and facilitating easy uptake by crop plants. Further, we discussed the indirect mechanism of PGPRs, in developing induced system resistance against pest and diseases, and as a biocontrol agent for phytopathogens. This review article presents a brief outline of the ideas and uses of microbial inoculants in improving crop productivity as well as a discussion of the challenges and limitations to use microbial inoculants.

Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants

Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.

Transcriptional Response and Plant Growth Promoting Activity of Pseudomonas fluorescens DR397 under Drought Stress Conditions

Drought is one of the most vulnerable factors that affect crop productivity. Little is known about plant-associated microbiomes and their functional roles in assisting plant growth under drought. We investigated the genetic and transcriptomic characteristics of opportunistic beneficial microorganisms that selectively alleviate stress through plant-bacteria interactions under drought. Pseudomonas fluorescens DR397 was isolated from the drought-prone rhizospheric soil of soybean and showed high metabolic activity at -1.25 Mpa. The genome of DR397 possesses several genes related to the synthesis of compatible solutes (choline and glycine-betaine), exopolysaccharides (alginate and cellulose), and secretion systems (type II, III, IV, and VI), as well as genes related to plant growth promotion (indole-3-acetic acid, transketolase, and thiamine phosphate synthesis). The expression of these genes was significantly upregulated (8- to 263-fold change) only under drought conditions with plant root exudate treatment, whereas subtle transcriptomic changes were observed under solely root exudate treatment. When DR397 was placed on both legume cultivars (Pisum sativum and Phaseolus vulgaris), growth was hardly affected under well-watered conditions, but the shoot and root growths were increased by up from 62.0% to 149.1% compared with the control group under drought conditions. These results provide fundamental insight on the plant-bacterial interactions that alleviate plant stress as an important ecological strategy for improving drought tolerance. IMPORTANCE Drought is a serious abiotic stress on plants as wells as the microbes that coexist with plants, which significantly lowers their fitness. The plant-bacterial interaction is an important strategy to enhance their fitness under drought. However, many knowledge gaps still exist in our understanding of transcriptomic features of bacteria interacting with plant under drought. Here, by investigating the transcriptomic profiles and pot cultivation with legume, we show that the interactions of Pseudomonas fluorescens DR397 with plants change with drought. We, therefore, provide a fundamental evidence of a hidden hero in the soil that promote plant fitness from external stress.

Plant Growth-Promoting Rhizobacteria Eliminate the Effect of Drought Stress in Plants: A Review

Plants evolve diverse mechanisms to eliminate the drastic effect of biotic and abiotic stresses. Drought is the most hazardous abiotic stress causing huge losses to crop yield worldwide. Osmotic stress decreases relative water and chlorophyll content and increases the accumulation of osmolytes, epicuticular wax content, antioxidant enzymatic activities, reactive oxygen species, secondary metabolites, membrane lipid peroxidation, and abscisic acid. Plant growth-promoting rhizobacteria (PGPR) eliminate the effect of drought stress by altering root morphology, regulating the stress-responsive genes, producing phytohormones, osmolytes, siderophores, volatile organic compounds, and exopolysaccharides, and improving the 1-aminocyclopropane-1-carboxylate deaminase activities. The use of PGPR is an alternative approach to traditional breeding and biotechnology for enhancing crop productivity. Hence, that can promote drought tolerance in important agricultural crops and could be used to minimize crop losses under limited water conditions. This review deals with recent progress on the use of PGPR to eliminate the harmful effects of drought stress in traditional agriculture crops.

Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato

Bacillus cereus sensu lato is a group of bacteria of medical and agricultural importance in different ecological niches and with controversial taxonomic relationships. Studying the composition of non-coding RNAs (ncRNAs) in several bacterial groups has been an important tool for identifying genetic information and better understanding genetic regulation towards environment adaptation. However, to date, no comparative genomics study of ncRNA has been performed in this group. Thus, this study aimed to identify and characterize the set of ncRNAs from 132 strains of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis to obtain an overview of the diversity and distribution of these genetic elements in these species. We observed that the number of ncRNAs differs in the chromosomes of the three species, but not in the plasmids, when species or phylogenetic clusters were compared. The prevailing functional/structural category was Cis-reg and the most frequent class was Riboswitch. However, in plasmids, the class Group II intron was the most frequent. Also, nine ncRNAs were selected for validation in the strain B. thuringiensis 407 by RT-PCR, which allowed to identify the expression of the ncRNAs. The wide distribution and diversity of ncRNAs in the B. cereus group, and more intensely in B. thuringiensis, may help improve the abilities of these species to adapt to various environmental changes. Further studies should address the expression of these genetic elements in different conditions.

Bacillus amyloliquefaciens Rescues Glycyrrhizic Acid Loss Under Drought Stress in Glycyrrhiza uralensis by Activating the Jasmonic Acid Pathway

Drought is a major factor limiting the production of the perennial medicinal plant Glycyrrhiza uralensis Fisch. (Fabaceae) in Northwest China. In this study, 1-year-old potted plants were inoculated with the strain Bacillus amyloliquefaciens FZB42, using a gradient of concentrations (CFU), to test for microbe-induced host tolerance to drought condition treatments in a greenhouse experiment. At the concentration of 10⁸ CFU ml^-1, FZB42 had significant growth-promoting effect on G. uralensis: the root biomass was 1.52, 0.84, 0.94, and 0.38 times that under normal watering and mild, moderate, and severe drought stress conditions, respectively. Under moderate drought, the positive impact of FZB42 on G. uralensis growth was most pronounced, with both developing axial and lateral roots strongly associated with indoleacetic acid (IAA) accumulation. An untargeted metabolomic analysis and physiological measurements of mature roots revealed that FZB42 improved the antioxidant system of G. uralensis through the accumulation of proline and sucrose, two osmotic adjustment solutes, and by promoting catalase (CAT) activity under moderate drought stress. Furthermore, significantly higher levels of total flavonoids, liquiritin, and glycyrrhizic acid (GA), the pharmacologically active substances of G. uralensis, were found in the roots of inoculated plants after FZB42 inoculation under all imposed drought conditions. The jasmonic acid (JA) content, which is closely related to plant defense responses and secondary metabolites' production, was greatly increased in roots after the bacterial inoculations, indicating that FZB42 activated the JA pathway. Taken together, our results demonstrate that inoculation with FZB42 alleviates the losses in production and pharmacological metabolites of G. uralensis caused by drought via the JA pathway's activation. These results provide a developed prospect of a microbial agent to improve the yield and quality of medical plants in arid and semi-arid regions.

Bacterial Inoculant and Sucrose Amendments Improve the Growth of Rheum palmatum L. by Reprograming Its Metabolite Composition and Altering Its Soil Microbial Community

Rheum palmatum L. is an important traditional Chinese medicinal herb now in demand worldwide. Recently, the theoretical framework suggested that sucrose triggers colonization of PGPM (plant growth-promoting microbes) in the rhizosphere, but their interactions on the plant remain largely unknown. Here, we applied three concentrations of both Bacillus amyloliquefaciens EZ99 inoculant (1.0 × 10⁵, 1.0 × 10⁶, and 1.0 × 10⁷ colony-forming units (CFU)/mL, denoted as LB, MB, and HB, respectively) and sucrose (0.15, 1.5, and 15 g/L, denoted as LS, MS, and HS, respectively) to investigate their co-effects on R. palmatum in a field experiment. The results showed that LB + MS (1.0 × 10⁵ CFU/mL Bacillus + 1.5 g/L sucrose) and LB + LS (1.0 × 10⁵ CFU/mL Bacillus + 0.15 g/L sucrose) treatments significantly increased root fresh weight (p ≤ 0.05). Metabolite analysis revealed that the treatment LB + LS significantly increased the relative content of major active components in rhubarb, namely anthraquinones and phenolic compounds, by 1.5% and 2.3%. Although high sucrose addition increased the activities of certain soil enzymes, the LB + LS treatment significantly increased total potassium (TK), whereas it decreased available potassium (AK), which facilitated the potassium utilization in rhizosphere soil. Furthermore, rhizosphere microbiomes revealed that fungal diversity was augmented in LB + LS treatment, in which the common causative fungal pathogen Fusarium spp. showed an effective suppression. Additionally, the redundancy analysis and Spearman correlations revealed a positive relationship of Sphingomonas associated with change in potassium bioavailability. Altogether, our findings suggest that the combined application of a bacterial inoculant and sucrose can improve the growth and quality of R. palmatum, and stimulate uptake of plant nutrients that contribute to alter the microbial community for biocontrol potential. Hence, this work not only has broad application prospects across economical plants, but also emphasizes agroecological practices for sustainable agriculture.

Architecture and physico-chemical properties of Bacillus amyloliquefaciens L-17 pellicle formed at the air-liquid interface

Bacillus amyloliquefaciens is a ubiquitous soil and plant-associated bacterial species which shows structural and adaptative responses to the environment. This present paper explores the ability of the strain L-17 to form subaerial biofilms on a liquid surface. Hydrophobic and non-wetting properties were observed for the rough top biofilm layer in contact with the air, which are quite different to the hydrophilic properties which were observed for the smooth biofilm layer in contact with the liquid. Both pellicle interfaces were visualized by scanning electron microscopy revealing a complex three-dimensional architecture composed of exopolymers organized in stacked fibrous network or sheet-like structures in the vicinity of the subaerial surface. Disruption of the extracellular matrix by combining physical and chemical treatments indicated that both loosely and tightly bound polysaccharides were found as major components of this complex pellicle. Proteins were also involved in the aggregation and cohesion of the matrix as multi extraction steps were needed to recover some tightly bounded proteins. This was confirmed by applying protease treatment which was able to significantly disrupt the pellicle. Overall results underline the ability of B. amyloliquefaciens L-17 to survive on air-liquid interfaces. This feature offers an interesting strategy to escape aquatic environments and develop aerial biofilm in response to environmental changes involving wet-dry cycles.

Bacterial Exopolysaccharides: Insight into Their Role in Plant Abiotic Stress Tolerance

Various abiotic stressors like drought, salinity, temperature, and heavy metals are major environmental stresses that affect agricultural productivity and crop yields all over the world. Continuous changes in climatic conditions put selective pressure on the microbial ecosystem to produce exopolysaccharides. Apart from soil aggregation, exopolysaccharide (EPS) production also helps in increasing water permeability, nutrient uptake by roots, soil stability, soil fertility, plant biomass, chlorophyll content, root and shoot length, and surface area of leaves while also helping maintain metabolic and physiological activities during drought stress. EPS-producing microbes can impart salt tolerance to plants by binding to sodium ions in the soil and preventing these ions from reaching the stem, thereby decreasing sodium absorption from the soil and increasing nutrient uptake by the roots. Biofilm formation in high-salinity soils increases cell viability, enhances soil fertility, and promotes plant growth and development. The third environmental stressor is presence of heavy metals in the soil due to improper industrial waste disposal practices that are toxic for plants. EPS production by soil bacteria can result in the biomineralization of metal ions, thereby imparting metal stress tolerance to plants. Finally, high temperatures can also affect agricultural productivity by decreasing plant metabolism, seedling growth, and seed germination. The present review discusses the role of exopolysaccharide-producing plant growth-promoting bacteria in modulating plant growth and development in plants and alleviating extreme abiotic stress condition. The review suggests exploring the potential of EPS-producing bacteria for multiple abiotic stress management strategies.

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance

Global increase in water scarcity is a serious problem for sustaining crop productivity. The lack of water causes the degeneration of the photosynthetic apparatus, an imbalance in key metabolic pathways, an increase in free radical generation as well as weakens the root architecture of plants. Drought is one of the major stresses that directly interferes with the osmotic status of plant cells. Abscisic acid (ABA) is known to be a key player in the modulation of drought responses in plants and involvement of both ABA-dependent and ABA-independent pathways have been observed during drought. Concomitantly, other phytohormones such as auxins, ethylene, gibberellins, cytokinins, jasmonic acid also confer drought tolerance and a crosstalk between different phytohormones and transcription factors at the molecular level exists. A number of drought-responsive genes and transcription factors have been utilized for producing transgenic plants for improved drought tolerance. Despite relentless efforts, biotechnological advances have failed to design completely stress tolerant plants until now. The root microbiome is the hidden treasure that possesses immense potential to revolutionize the strategies for inducing drought resistance in plants. Root microbiota consist of plant growth-promoting rhizobacteria, endophytes and mycorrhizas that form a consortium with the roots. Rhizospheric microbes are proliferous producers of phytohormones, mainly auxins, cytokinin, and ethylene as well as enzymes like the 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides that help to induce systemic tolerance against drought. This review, therefore focuses on the major mechanisms of plant-microbe interactions under drought-stressed conditions and emphasizes the importance of drought-tolerant microbes for sustaining and improving the productivity of crop plants under stress.

The Effects of Plant-Associated Bacterial Exopolysaccharides on Plant Abiotic Stress Tolerance

Plant growth-promoting rhizobacteria (PGPR) are beneficial soil microorganisms that can stimulate plant growth and increase tolerance to biotic and abiotic stresses. Some PGPR are capable of secreting exopolysaccharides (EPS) to protect themselves and, consequently, their plant hosts against environmental fluctuations and other abiotic stresses such as drought, salinity, or heavy metal pollution. This review focuses on the enhancement of plant abiotic stress tolerance by bacterial EPS. We provide a comprehensive summary of the mechanisms through EPS to alleviate plant abiotic stress tolerance, including salinity, drought, temperature, and heavy metal toxicity. Finally, we discuss how these abiotic stresses may affect bacterial EPS production and its role during plant-microbe interactions.

Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments

Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.

Induction of Salt Tolerance in Arabidopsis thaliana by Volatiles From Bacillus amyloliquefaciens FZB42 via the Jasmonic Acid Signaling Pathway

Previously, we showed that Bacillus amyloliquefaciens FZB42 can confer salt tolerance in plants by root inoculation under salt stress condition, and the FZB42 volatile organic compounds (VOCs) promoted plant growth and development under non-salt stress condition. In the present study, we investigated the mechanism that allows FZB42 VOCs to confer salt tolerance in Arabidopsis without colonization of plant roots. We found that FZB42 VOCs significantly increased the biomass of Arabidopsis and also maintained the leaf chlorophyll content under salt stress condition. Physiological tests showed that the plant anti-oxidation system was activated by FZB42 VOCs, where higher peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD) activities were detected in plants exposed to FZB42 VOCs compared with non-exposed plants. In addition, FZB42 VOCs increased the leaf total soluble sugars (TSS) content but decreased the proline content compared with the non-exposed plants. Moreover, FZB42 VOCs significantly decreased the Na⁺ contents of the whole plants and induced the expression of genes (NHX1; Na⁺/H⁺ exchanger 1 and HKT1; high-affinity K⁺ transporter 1) that function to alleviate Na⁺ toxicity. Furthermore, analysis of mutants with defects in specific hormone pathways showed that FZB42 VOCs induced salt tolerance in plants by modulating jasmonic acid (JA) signaling, which was confirmed by the up-regulation of JA synthesis, defense-related genes, and JA biosynthesis inhibitor tests. The results of this study provide new insights into the molecular mechanism related to the interactions between plant growth-promoting rhizobacteria and plants under salt stress condition.

Biocontrol and plant growth-promoting potentiality of bacteria isolated from compost extract

The use of compost extracts is steadily increasing, offering an attractive way for plant growth enhancement and disease management replacing chemical pesticides. In this study, potential mechanisms involved in plant growth promotion and suppressive activity against fungal diseases, of a compost extract produced from poultry manure/olive husk compost, were investigated. Results of physico-chemical and microbiological investigations showed high ability to reduce Fusarium oxysporum, Alternaria alternata, Aspergillus niger and Botrytis cinerea growth. The suppressive ability detected using confrontation test and the phytostimulatory effect tested on tomato seeds were related mainly to its microbial population content. Among 150 bacterial strains, isolated from the compost extract, 13 isolates showed antifungal activity against the four tested plant pathogenic fungi. Their identification based on 16S rRNA gene sequence revealed they belonged to different species of the genus Bacillus, Alcaligenes, Providencia and Ochrobactrum. When tested for their ability to produce cell wall degradation enzymes using specific media, the majority of the 13 isolates were shown to synthesize proteases, lipases and glucanases. Similarly, the best part of them showed positive reaction for plant growth promoting substances liberation, biosurfactant production and biofilm formation. In vivo tests were carried out using tomato seeds and fruits and proved that 92% of strains improved tomato plants vigor indexes when compared to the control and 6 among them were able to reduce decay severity caused by B. cinerea over 50%. Principal component analysis showed an important correlation between in vitro and in vivo potentialities and that Bacillus siamensis CEBZ11 strain was statistically the most effective strain in protecting tomato plants from gray mould disease. This study revealed the selected strains would be useful for plant pathogenic fungi control and plant growth promotion.

Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains

The application of biocontrol biopesticides based on plant growth-promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences' Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140. KEY POINTS: • Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140. • Identification of genetic determinants responsible for PGPR activities. • Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.

Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction

Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world’s population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.

Bacillus amyloliquefaciens LZ04 improves the resistance of Arabidopsis thaliana to high calcium stress and the potential role of lncRNA-miRNA-mRNA regulatory network in the resistance

Bacillus amyloliquefaciens is a non-pathogenic and plant growth-promoting rhizobacterium that enhances plant resistance to drought and diseases. Arabidopsis thaliana is a multipurpose model plant for exploring microorganism-plant interactions and a crucial vegetal tool for molecular research. Non-coding RNAs are RNA molecules involved in the regulation of various biological functions and constitute a research hotspot in the field of plant biology. In this study, the effect of B. amyloliquefaciens treatment on the resistance of A. thaliana to high calcium stress was analyzed. The transcriptome sequencing of A. thaliana roots under four treatment conditions was performed to screen differentially expressed lncRNAs, mRNAs and miRNAs. Functional analysis was also performed to understand the potential mechanism by which B. amyloliquefaciens-regulated lncRNAs, miRNAs and mRNAs affect the resistance of A. thaliana to high calcium stress. The results indicated that B. amyloliquefaciens treatment increased the resistance of A. thaliana to high calcium stress. A set of differentially expressed lncRNAs, mRNAs and miRNAs were screened between the high calcium and control group on one hand, and high calcium and high calcium + B. amyloliquefaciens groups on the other hand. Functional analysis indicated that the differentially expressed mRNAs and miRNA were involved in various biological functions and that transcriptional dysregulation caused by high calcium stress involves metabolic processes rather than defense responses. Conclusively, B. amyloliquefaciens may improve the resistance of A. thaliana to high calcium stress via a lncRNA-miRNA-mRNA regulatory network. These findings will contribute to the development of agriculture in karst regions with high calcium content.

Bacillus subtilis strain GOT9 confers enhanced tolerance to drought and salt stresses in Arabidopsis thaliana and Brassica campestris

Soil is a primary source of water and inorganic nutrients vital for plant growth. In particular, the rhizosphere, a microecological region around the plant roots, is enriched with root exudates that enable beneficial microbial communities to form. Plant growth-promoting rhizobacteria (PGPR) are rhizosphere bacteria that contribute to the improvement of plant growth through diverse physiological mechanisms. Identifying PGPR is beneficial for agriculture because their use can effectively increase the productivity of plants without the harmful side effects of chemical fertilizers. To further enrich the pool of PGPR that contribute to abiotic stress resistance in plants, we screened roughly 491 bacteria that had previously been isolated in soil from Gotjawal in Jeju island, South Korea. Among several candidates, the application of Bacillus subtilis strain GOT9, led to the enhancement of drought and salt stress tolerance in Arabidopsis. In agreement with the increased stress tolerance phenotypes, its application resulted in increases in the transcripts of various drought stress- and salt stress-inducible genes in the absence or presence of the stresses. Furthermore, the treatment resulted in improved lateral root growth and development in Arabidopsis. GOT9 also led to enhanced tolerance against drought and salt stresses and to upregulation of drought-inducible genes in Brassica, a closely related crop to Arabidopsis. Taken together, these results show that GOT9 could be utilized as a biotic resource that effectively minimizes damage to plants from environmental stresses.

Biofilms Positively Contribute to Bacillus amyloliquefaciens 54-induced Drought Tolerance in Tomato Plants

Drought stress is a major obstacle to agriculture. Although many studies have reported on plant drought tolerance achieved via genetic modification, application of plant growth-promoting rhizobacteria (PGPR) to achieve tolerance has rarely been studied. In this study, the ability of three isolates, including Bacillus amyloliquefaciens 54, from 30 potential PGPR to induce drought tolerance in tomato plants was examined via greenhouse screening. The results indicated that B. amyloliquefaciens 54 significantly enhanced drought tolerance by increasing survival rate, relative water content and root vigor. Coordinated changes were also observed in cellular defense responses, including decreased concentration of malondialdehyde and elevated concentration of antioxidant enzyme activities. Moreover, expression levels of stress-responsive genes, such as lea, tdi65, and ltpg2, increased in B. amyloliquefaciens 54-treated plants. In addition, B. amyloliquefaciens 54 induced stomatal closure through an abscisic acid-regulated pathway. Furthermore, we constructed biofilm formation mutants and determined the role of biofilm formation in B. amyloliquefaciens 54-induced drought tolerance. The results showed that biofilm-forming ability was positively correlated with plant root colonization. Moreover, plants inoculated with hyper-robust biofilm (ΔabrB and ΔywcC) mutants were better able to resist drought stress, while defective biofilm (ΔepsA-O and ΔtasA) mutants were more vulnerable to drought stress. Taken altogether, these results suggest that biofilm formation is crucial to B. amyloliquefaciens 54 root colonization and drought tolerance in tomato plants.

Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.

Abiotic stress resistance, plant growth promotion and antifungal potential of halotolerant bacteria from a Tunisian solar saltern

The uses of halotolerant bacteria isolated from naturally saline habitats have the potential to be useful crop protection agents for plants in stressful conditions. These beneficial microbes generate several plant growth regulators and bioactive molecules, which enhance plant protection from adversities, such as plant pathogens, salts and metals stresses. In this study, 15 halotolerant bacterial strains endowed with important antimicrobial activities were isolated from Sfax solar saltern (Tunisia). All of these strains were characterized by biochemical and molecular tools aiming to investigate their in-vitro and in-vivo antifungal potentialities, plant growth promotion capabilities and metal tolerance abilities under saline stress condition. The 16S rRNA gene sequencing showed that the isolated strains were affiliated to different phylum and three species were described for the first time as plant growth promoting strains (Idiomarina zobelli FMH6v, Nesterenkonia halotolerans FMH10 and Halomonas janggokensis FMH54). The tested strains exhibited several potentialities: to tolerate high salt and heavy metal concentrations, to produce biosurfactants, exopolysaccharides and extracellular hydrolytic enzymes, to form biofilms and to liberate plant promoting substances. Eight strains were able to protect tomatoes fruits from the proliferation of the fungal disease caused by Botrytis cinerea and six strains improved plant vigor indexes. Principal component analysis showed an important correlation between in-vitro and in-vivo potentialities and two strains Bacillus velezensis FMH2 and Bacillus subtilis subsp. spizizenii FMH45 were statistically considered as the most effective strains in protecting plants from fungal pathogens attack and promoting the growth of tomatoes seedlings under saline and multi heavy-metals stress conditions.