Transcriptome Analysis of Induced Systemic Drought Tolerance Elicited by Pseudomonas chlororaphis O6 in Arabidopsis thaliana

Utilizing machine learning and bioinformatics analysis to identify drought-responsive genes affecting yield in foxtail millet

Drought stress is a major constraint on crop development, potentially causing huge yield losses and threatening global food security. Improving Crop's stress tolerance is usually associated with a yield penalty. One way to balance yield and stress tolerance is modification specific gene by emerging precision genome editing technology. However, our knowledge of yield-related drought-tolerant genes is still limited. Foxtail millet (Setaria italica) has a remarkable tolerance to drought and is considered to be a model C4 crop that is easy to engineer. Here, we have identified 46 drought-responsive candidate genes by performing a machine learning-based transcriptome study on two drought-tolerant and two drought-sensitive foxtail millet cultivars. A total of 12 important drought-responsive genes were screened out by principal component analysis and confirmed experimentally by qPCR. Significantly, by investigating the haplotype of these genes based on 1844 germplasm resources, we found two genes (Seita.5G251300 and Seita.8G036300) exhibiting drought-tolerant haplotypes that possess an apparent advantage in 1000 grain weight and main panicle grain weight without penalty in grain weight per plant. These results demonstrate the potential of Seita.5G251300 and Seita.8G036300 for breeding drought-tolerant high-yielding foxtail millet. It provides important insights for the breeding of drought-tolerant high-yielding crop cultivars through genetic manipulation technology.

Integrated Benefits to Agriculture with Trichoderma and Other Endophytic or Root-Associated Microbes

The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte-plant relationship and the fungi and bacteria involved. Their abilities to alleviate biotic (diseases and pests) and abiotic stresses (drought, salt, and flooding) to remediate pollution and increase photosynthetic capabilities will be described. Their mechanisms of action will be elucidated. These frequently result in increased plant yields. Finally, methods and practices for formulation and commercial use will be described.

Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana

AIMS

This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion.

METHODS AND RESULTS

Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4-5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 µg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 µg/ml nitrite), along with production of exopolysaccharides (125 ± 20 µg/ml) and auxin-like compounds (42.6 ± 0.05 µg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5-2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2-4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani.

CONCLUSIONS

P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.

IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

Meta-analysis of plant growth-promoting rhizobacteria interaction with host plants: implications for drought stress response gene expression

Introduction

The molecular and physiological mechanisms activated in plants during drought stress tolerance are regulated by several key genes with both metabolic and regulatory roles. Studies focusing on crop gene expression following plant growth-promoting rhizobacteria (PGPR) inoculation may help understand which bioinoculant is closely related to the induction of abiotic stress responses.

Methods

Here, we performed a meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to summarise information regarding plant-PGPR interactions, focusing on the regulation of nine genes involved in plant drought stress response. The literature research yielded 3,338 reports, of which only 41 were included in the meta-analysis based on the chosen inclusion criteria. The meta-analysis was performed on four genes (ACO, APX, ACS and DREB2); the other five genes (ERD15, MYB, MYC, acdS, WRKY) had an insufficient number of eligible articles.

Results

Forest plots obtained through each meta-analysis showed that the overexpression of ACO, APX, ACS and DREB2 genes was not statistically significant. Unlike the other genes, DREB2 showed statistically significant results in both the presence and absence of PGPR. Considering I2>75 %, the results showed a high heterogeneity among the studies included, and the cause for this was examined using subgroup analysis. Moreover, the funnel plot and Egger's test showed that the analyses were affected by strong publication bias.

Discussion

This study argues that the presence of PGPR may not significantly influence the expression of drought stress response-related crop genes. This finding may be due to high heterogeneity, lack of data on the genes examined, and significant publication bias.

Microbial interactions within beneficial consortia promote soil health

By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.

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.

Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain

Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.

Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM and IPD3 in Arabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

Enhancing Mechanisms of the Plant Growth-Promoting Bacterial Strain Brevibacillus sp. SR-9 on Cadmium Enrichment in Sweet Sorghum by Metagenomic and Transcriptomic Analysis

To explore the mechanism by which the plant growth-promoting bacterium Brevibacillus sp. SR-9 improves sweet sorghum tolerance and enriches soil cadmium (Cd) under pot conditions, the effect of strain SR-9 inoculation on the microbial community of sorghum rhizosphere soil was analyzed by metagenomics. Gene expression in sweet sorghum roots was analyzed using transcriptomics. The results showed that strain SR-9 promoted the growth of sweet sorghum and improved the absorption and enrichment of Cd in the plants. Compared with the uninoculated treatment, the aboveground part and root dry weight in strain SR-9 inoculated with sorghum increased by 21.09% and 17.37%, respectively, and the accumulation of Cd increased by 135% and 53.41%, respectively. High-throughput sequencing showed that strain SR-9 inoculation altered the rhizosphere bacterial community, significantly increasing the relative abundance of Actinobacteria and Firmicutes. Metagenomic analysis showed that after inoculation with strain SR-9, the abundance of genes involved in amino acid transport metabolism, energy generation and conversion, and carbohydrate transport metabolism increased. KEGG functional classification showed that inoculation with strain SR-9 increased the abundance of genes involved in soil microbial metabolic pathways in the rhizosphere soil of sweet sorghum and the activity of soil bacteria. Transcriptome analysis identified 198 upregulated differentially expressed genes in sweet sorghum inoculated with strain SR-9, including those involved in genetic information processing, biological system, metabolism, environmental information processing, cellular process, and human disease. Most of the annotated differentially expressed genes were enriched in the metabolic category and were related to pathways such as signal transduction, carbohydrate metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. This study showed that plant growth-promoting bacteria can alter the rhizosphere bacterial community composition, increasing the activity of soil bacteria and upregulating gene expression in sweet sorghum roots. The findings enhance our understanding of the microbiological and botanical mechanisms by which plant growth-promoting bacterial inoculation improves the remediation of heavy metals by sorghum.

Recent Developments in the Application of Plant Growth-Promoting Drought Adaptive Rhizobacteria for Drought Mitigation

Drought intensity that has increased as a result of human activity and global warming poses a serious danger to agricultural output. The demand for ecologically friendly solutions to ensure the security of the world's food supply has increased as a result. Plant growth-promoting rhizobacteria (PGPR) treatment may be advantageous in this situation. PGPR guarantees the survival of the plant during a drought through a variety of processes including osmotic adjustments, improved phytohormone synthesis, and antioxidant activity, among others and these mechanisms also promote the plant's development. In addition, new developments in omics technology have improved our understanding of PGPR, which makes it easier to investigate the genes involved in colonizing plant tissue. Therefore, this review addresses the mechanisms of PGPR in drought stress resistance to summarize the most current omics-based and molecular methodologies for exploring the function of drought-responsive genes. The study discusses a detailed mechanistic approach, PGPR-based bioinoculant design, and a potential roadmap for enhancing their efficacy in combating drought stress.

Advancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.

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.

Mechanistic Insights of Plant Growth Promoting Bacteria Mediated Drought and Salt Stress Tolerance in Plants for Sustainable Agriculture

Climate change has devastating effects on plant growth and yield. During ontogenesis, plants are subjected to a variety of abiotic stresses, including drought and salinity, affecting the crop loss (20-50%) and making them vulnerable in terms of survival. These stresses lead to the excessive production of reactive oxygen species (ROS) that damage nucleic acid, proteins, and lipids. Plant growth-promoting bacteria (PGPB) have remarkable capabilities in combating drought and salinity stress and improving plant growth, which enhances the crop productivity and contributes to food security. PGPB inoculation under abiotic stresses promotes plant growth through several modes of actions, such as the production of phytohormones, 1-aminocyclopropane-1-carboxylic acid deaminase, exopolysaccharide, siderophore, hydrogen cyanide, extracellular polymeric substances, volatile organic compounds, modulate antioxidants defense machinery, and abscisic acid, thereby preventing oxidative stress. These bacteria also provide osmotic balance; maintain ion homeostasis; and induce drought and salt-responsive genes, metabolic reprogramming, provide transcriptional changes in ion transporter genes, etc. Therefore, in this review, we summarize the effects of PGPB on drought and salinity stress to mitigate its detrimental effects. Furthermore, we also discuss the mechanistic insights of PGPB towards drought and salinity stress tolerance for sustainable agriculture.

Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions

In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.

The Role of Plant-Associated Bacteria, Fungi, and Viruses in Drought Stress Mitigation

Drought stress is an alarming constraint to plant growth, development, and productivity worldwide. However, plant-associated bacteria, fungi, and viruses can enhance stress resistance and cope with the negative impacts of drought through the induction of various mechanisms, which involve plant biochemical and physiological changes. These mechanisms include osmotic adjustment, antioxidant enzyme enhancement, modification in phytohormonal levels, biofilm production, increased water and nutrient uptake as well as increased gas exchange and water use efficiency. Production of microbial volatile organic compounds (mVOCs) and induction of stress-responsive genes by microbes also play a crucial role in the acquisition of drought tolerance. This review offers a unique exploration of the role of plant-associated microorganisms-plant growth promoting rhizobacteria and mycorrhizae, viruses, and their interactions-in the plant microbiome (or phytobiome) as a whole and their modes of action that mitigate plant drought stress.

Endophytic halotolerant Bacillus velezensis FMH2 alleviates salt stress on tomato plants by improving plant growth and altering physiological and antioxidant responses

Salinity stress has significant deleterious effects on agricultural lands and plant yields. Plants undergo a series of physiological and molecular changes to reduce salt-induced damage. However, these mechanisms remain insufficient. The inoculation of plant growth promoting bacteria to improve plant health under stress conditions offers promise. Bacillus velezensis FMH2 has been shown to protect tomato fruits against black mold disease and to improve seed tolerance to abiotic stresses. During this study, the major physiological and metabolic changes connected with FMH2 mitigation of abiotic stress tolerance in tomato plants were explored. In presence of different salt levels, FMH2 showed a high potentiality to colonize internal plant tissues and to produce several plant growth promoting metabolites such as siderophores, indole acetic acid, and hydrolytic enzymes. FMH2-treatment promoted plant growth (root structure, plant elongation, leaf emission, fresh and dry weights, water content, etc.) in absence as well as in presence of salt stress. FMH2 treatment decreased endogenous Na⁺ accumulation and increased K⁺ and Ca²⁺ uptake. Furthermore, B. velezensis FMH2-treatment improved chlorophyll contents, membrane integrity and phenol peroxidase concentrations, and reduced malondialdehyde and hydrogen peroxide levels under saline conditions with a significant salinity × strain interaction. The present study suggests the endophytic strain FMH2 involved different mechanisms and regulatory functions to enhance plant oxidative systems and regulate ion uptake mechanisms supporting both growth and stress management.

Plant Growth Promoting and Stress Mitigating Abilities of Soil Born Microorganisms

Abiotic stresses affect the plant growth in different ways and at different developmental stages that reduce the crop yields. The increasing world population continually demands more crop yields; therefore it is important to use low-cost technologies against abiotic stresses to increase crop productivity. Soil microorganisms survive in the soil associated with plants in extreme condition. It was demonstrated that these beneficial microorganisms promote plant growth and development under various stresses. The soil microbes interact with the plant through rhizospheric or endophytic association and promote the plant growth through different processes such as nutrients mobilization, disease suppression, and hormone secretions. The microorganisms colonized in the rhizospheric region and imparted the abiotic stress tolerance by producing 1-aminocyclopropane-1- carboxylate (ACC) deaminase, antioxidant, and volatile compounds, inducing the accumulation of osmolytes, production of exopolysaccharide, upregulation or downregulation of stress genes, phytohormones and change the root morphology. A large number of these rhizosphere microorganisms are now patented. In the present review, an attempt was made to throw light on the mechanism of micro-organism that operates during abiotic stresses and promotes plant survival and productivity.

Delineation of mechanistic approaches employed by plant growth promoting microorganisms for improving drought stress tolerance in plants

Drought stress is expected to increase in intensity, frequency, and duration in many parts of the world, with potential negative impacts on plant growth and productivity. The plants have evolved complex physiological and biochemical mechanisms to respond and adjust to water-deficient environments. The physiological and biochemical mechanisms associated with water-stress tolerance and water-use efficiency have been extensively studied. Besides these adaptive and mitigating strategies, the plant growth-promoting rhizobacteria (PGPR) play a significant role in alleviating plant drought stress. These beneficial microorganisms colonize the endo-rhizosphere/rhizosphere of plants and enhance drought tolerance. The common mechanism by which these microorganisms improve drought tolerance included the production of volatile compounds, phytohormones, siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase), accumulation of antioxidant, stress-induced metabolites such as osmotic solutes proline, alternation in leaf and root morphology and regulation of the stress-responsive genes. The PGPR is an easy and efficient alternative approach to genetic manipulation and crop enhancement practices because plant breeding and genetic modification are time-consuming and expensive processes for obtaining stress-tolerant varieties. In this review, we will elaborate on PGPR's mechanistic approaches in enhancing the plant stress tolerance to cope with the drought stress.

Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.

Environment and pathogens shape local and regional adaptations to climate change in the chocolate tree, Theobroma cacao L

Predicting the potential fate of a species in the face of climate change requires knowing the distribution of molecular adaptations across the geographic range of the species. In this work, we analysed 79 genomes of Theobroma cacao, an Amazonian tree known for the fruit from which chocolate is produced, to evaluate how local and regional molecular signatures of adaptation are distributed across the natural range of the species. We implemented novel techniques that incorporate summary statistics from multiple selection scans to infer selective sweeps. The majority of the molecular adaptations in the genome are not shared among populations. We show that ~71.5% of genes under selection also show significant associations with changes in environmental variables. Our results support the interpretation that these genes contribute to local adaptation of the populations in response to abiotic factors. We also found strong patterns of molecular adaptation in a diverse array of disease resistance genes (6.5% of selective sweeps), suggesting that differential adaptation to pathogens also contributes significantly to local adaptations. Our results are consistent with the interpretation that local selective pressures are more important than regional selective pressures in explaining adaptation across the range of a species.

Plant Growth-Promoting Rhizobacteria Isolated from Degraded Habitat Enhance Drought Tolerance of Acacia (Acacia abyssinica Hochst. ex Benth.) Seedlings

Drought stress (DS) is the most impacting global phenomenon affecting the ecological balance of a particular habitat. The search for potential plant growth-promoting rhizobacteria (PGPR) capable of enhancing plant tolerance to drought stress is needed. Thus, this study was initiated to evaluate the effect of inoculating Acacia abyssinica seedlings with PGPR isolated from rhizosphere soil of Ethiopia to enhance DS tolerance. The strains were selected based on in vitro assays associated with tolerance to drought and other beneficial traits such as salinity, acidity, temperature, heavy metal tolerances, biofilm formation, and exopolysaccharide (EPS) production. The strains with the best DS tolerance ability were selected for the greenhouse trials with acacia plants. The results indicate that out of 73 strains, 10 (14%) were completely tolerant to 40% polyethylene glycol. Moreover, 37% of the strains were strong biofilm producers, while 66 (90.41%) were EPS producers with a better production in the medium containing sucrose at 28 ± 2°C and pH 7 ± 0.2. Strains PS-16 and RS-79 showed tolerance to 11% NaCl. All the strains were able to grow in wider ranges of pH (4–10) and temperature (15–45°C) and had high tolerance to heavy metals. The inoculated bacterial strains significantly (p ≤ 0.05) increased root and shoot length and dry biomass of acacia plants. One of the strains identified as P. fluorescens strain FB-49 was outstanding in enhancing DS tolerance compared to the single inoculants and comparable to consortia. Stress-tolerant PGPR could be used to enhance acacia DS tolerance after testing other phytobeneficial traits.

Plant survival under drought stress: Implications, adaptive responses, and integrated rhizosphere management strategy for stress mitigation

In many regions of the world, the incidence and extent of drought spells are predicted to increase which will create considerable pressure on global agricultural yields. Most likely among all the abiotic stresses, drought has the strongest effect on soil biota and plants along with complex environmental effects on other ecological systems. Plants being sessile appears the least resilient where drought creates osmotic stress, limits nutrient mobility due to soil heterogeneity, and reduces nutrient access to plant roots. Drought tolerance is a complex quantitative trait controlled by many genes and is one of the difficult traits to study and characterize. Nevertheless, existing studies on drought have indicated the mechanisms of drought resistance in plants on the morphological, physiological, and molecular basis and strategies have been devised to cope with the drought stress such as mass screening, breeding, marker-assisted selection, exogenous application of hormones or osmoprotectants and or engineering for drought resistance. These strategies have largely ignored the role of the rhizosphere in the plant's drought response. Studies have shown that soil microbes have a substantial role in modulation of plant response towards biotic and abiotic stress including drought. This response is complex and involves alteration in host root system architecture through hormones, osmoregulation, signaling through reactive oxygen species (ROS), induction of systemic tolerance (IST), production of large chain extracellular polysaccharides (EPS), and transcriptional regulation of host stress response genes. This review focuses on the integrated rhizosphere management strategy for drought stress mitigation in plants with a special focus on rhizosphere management. This combinatorial approach may include rhizosphere engineering by addition of drought-tolerant bacteria, nanoparticles, liquid nano clay (LNC), nutrients, organic matter, along with plant-modification with next-generation genome editing tool (e.g., CRISPR/Cas9) for quickly addressing emerging challenges in agriculture. Furthermore, large volumes of rainwater and wastewater generated daily can be smartly recycled and reused for agriculture. Farmers and other stakeholders will get a proper knowledge-exchange and an ideal road map to utilize available technologies effectively and to translate the measures into successful plant-water stress management. The proposed approach is cost-effective, eco-friendly, user-friendly, and will impart long-lasting benefits on agriculture and ecosystem and reduce vulnerability to climate change.

Root-Bacteria Associations Boost Rhizosheath Formation in Moderately Dry Soil through Ethylene Responses

The rhizosheath is a layer of soil around the root that provides a favorable environment for soil microbe enrichment and root growth. Rice (Oryza sativa) roots form rhizosheaths under moderate soil drying (MSD) conditions, but how the rhizosheath forms associations with microbes is unclear. To investigate rice rhizosheath formation under MSD, we employed a multiphasic approach, integrating data from high-throughput sequencing and root-bacteria interactions. Rice roots formed a pronounced rhizosheath under MSD, but not under continuous flooding regimens. Plant growth-promoting rhizobacteria of the Enterobacteriaceae were enriched in rhizosheaths of two different rice varieties, 'Gaoshan 1' (drought tolerant) and 'Nipponbare' (drought sensitive). RNA-sequencing analysis revealed that the ethylene pathway was induced in the rhizosheath-root system under MSD. Enterobacter aerogenes, a bacterium isolated from the rhizosheath, degrades the ethylene precursor 1-aminocyclopropane-1-carboxylate, thereby increasing rhizosheath formation. Furthermore, a 1-aminocyclopropane-1-carboxylate deaminase-deficient mutant of E. aerogenes failed to enhance rice rhizosheath formation. Our results suggest that root-bacteria associations substantially contribute to rhizosheath formation in rice under MSD conditions by mechanisms that involve the ethylene response. These data inform strategies to reduce water consumption in rice production, one of the most water-intensive human activities.

Induction of drought tolerance in tomato upon the application of ACC deaminase producing plant growth promoting rhizobacterium Bacillus subtilis Rhizo SF 48

A total of ten 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing PGPR isolates were selected and evaluated for the induction of drought stress tolerance in tomato. Among the selected PGPR, maximum seed (laboratory) and plant growth promotion (greenhouse) was observed in tomato seeds bacterized with Bacillus subtilis Rhizo SF 48. The genomic study confirmed the presence of ACC deaminase gene in Rhizo SF 48 and the obtained sequence was deposited to the NCBI database with the Accession No. MK652706. The tomato plants grown upon treatment with Rhizo SF 48 significantly enhanced plant growth even after exposing to different levels of drought stress as compared to stress induced control plants. About 7.5% and 38% increase in RWC were observed in Rhizo SF 48 treated tomato plants grown under well-watered and stress conditions (S4) compared to their control plants, respectively. An increase of 0.76, 0.23 and 0.78 fold in proline, SOD and APX activity and a decrease of 0.3 fold in MDA and H2O2 contents were observed in Rhizo SF 48 treated plants compared to control plants grown under S4 conditions. The histo-chemical studies showed lower accumulations of H2O2 and superoxide anion in the leaves of Rhizo SF 48 treated plants under drought stress, which was in confirmation with the quantification results of H2O2 and SOD. The qRT-PCR studies on drought (Le25) and ethylene responsive factor (SlERF84) marker genes showed that a significant decrease of 0.75 and 0.81 folds, respectively in Le25 and SlERF84 accumulation was observed in Rhizo SF 48 treated plants compared to untreated plants grown under S4 conditions. From the results, it can be attributed that ACC deaminase producing Rhizo SF 48 was able to protect tomato plants against oxidative damage caused due to drought stress and enhanced plant growth promotion. It can be concluded that ACC deaminase producing Rhizo SF 48 can serve as a useful bio-inoculant for sustainable tomato production in arid and semi-arid regions with water deficit.

Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat

Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.

Microbes in Cahoots with Plants: MIST to Hit the Jackpot of Agricultural Productivity during Drought

Drought conditions marked by water deficit impede plant growth thus causing recurrent decline in agricultural productivity. Presently, research efforts are focussed towards harnessing the potential of microbes to enhance crop production during drought. Microbial communities, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) buddy up with plants to boost crop productivity during drought via microbial induced systemic tolerance (MIST). The present review summarizes MIST mechanisms during drought comprised of modulation in phytohormonal profiles, sturdy antioxidant defence, osmotic grapnel, bacterial exopolysaccharides (EPS) or AMF glomalin production, volatile organic compounds (VOCs), expression of fungal aquaporins and stress responsive genes, which alters various physiological processes such as hydraulic conductance, transpiration rate, stomatal conductivity and photosynthesis in host plants. Molecular studies have revealed microbial induced differential expression of various genes such as ERD15 (Early Response to Dehydration 15), RAB18 (ABA-responsive gene) in Arabidopsis, COX1 (regulates energy and carbohydrate metabolism), PKDP (protein kinase), AP2-EREBP (stress responsive pathway), Hsp20, bZIP1 and COC1 (chaperones in ABA signalling) in Pseudomonas fluorescens treated rice, LbKT1, LbSKOR (encoding potassium channels) in Lycium, PtYUC3 and PtYUC8 (IAA biosynthesis) in AMF inoculated Poncirus, ADC, AIH, CPA, SPDS, SPMS and SAMDC (polyamine biosynthesis) in PGPR inoculated Arabidopsis, 14-3-3 genes (TFT1-TFT12 genes in ABA signalling pathways) in AMF treated Solanum, ACO, ACS (ethylene biosynthesis), jasmonate MYC2 gene in chick pea, PR1 (SA regulated gene), pdf1.2 (JA marker genes) and VSP1 (ethylene-response gene) in Pseudomonas treated Arabidopsis plants. Moreover, the key role of miRNAs in MIST has also been recorded in Pseudomonas putida RA treated chick pea plants.

Overexpression of Chickpea Defensin Gene Confers Tolerance to Water-Deficit Stress in Arabidopsis thaliana

Plant defensins are mainly known for their antifungal activity. However, limited information is available regarding their function in abiotic stresses. In this study, a defensin gene, Ca-AFP, from Cicer arietinum, commonly known as chickpea, was cloned and transformed in Arabidopsis thaliana for its functional characterization under simulated water-deficit conditions. Under simulated water-deficit conditions (mannitol and polyethylene glycol-6000 induced), the transgenic A. thaliana plants had higher accumulation of the Ca-AFP transcript compared to that under non-stress condition and showed higher germination rate, root length, and biomass than the wild-type (WT) plants. To get further insights into the role of Ca-AFP in conferring tolerance to water-deficit stress, we determined various physiological parameters and found significant reduction in the transpiration rate and stomatal conductance whereas the net photosynthesis and water use efficiency was increased in the transgenic plants compared to that in the WT plants under water deficit conditions. The transgenic plants showed enhanced superoxide dismutase, ascorbate peroxidase, and catalase activities, had higher proline, chlorophyll, and relative water content, and exhibited reduced ion leakage and malondialdehyde content under water-deficit conditions. Overall, our results indicate that overexpression of Ca-AFP could be an efficient approach for conferring tolerance to water-deficit stress in plants.

Plant Host-Associated Mechanisms for Microbial Selection

Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome. In this review, we provide an overview of the current research into mechanisms employed by the plant host to select for and control its microbiome. We specifically review recent research that expands upon the role of keystone microbial species, phytohormones, and abiotic stress, and in how they relate to plant driven dynamic microbial structuring.

Protective effects of farnesol on a Rhizobium strain exposed to cadmium

Soil acts as a repository for many metals that human activity releases into the environment. Cadmium enters agricultural soils primarily from application of phosphate fertilizers and sewage sludge. Among soil bacteria, rhizobia have a great agronomic and environmental significance and are major contributors to a sustainable maintenance of soil fertility. However, the services that this group of microorganisms provides are affected by environmental constraints, such as Cd contamination. Bioactive compounds also influence soil microorganisms. Farnesol is a phytocompound with recognized bioactivity, inducing both beneficial and harmful effects. In this study, Rhizobium sp. strain E20-8 was exposed to sole or combined exposure to Cd and farnesol. Results showed that farnesol (25 and 200 µM) did not affect rhizobia; exposure to Cd (µM) inhibited rhizobia growth and induced several biomarkers of oxidative stress; exposure to the combination of farnesol and Cd reduced oxidative damage, and the highest concentration of farnesol tested reduced Cd accumulation and allowed a significant growth recovery. Farnesol protective effects on rhizobia exposed to Cd is novel information which can be used in the development of microbe-based environmental engineering strategies for restoration of metal contaminated areas.

Rhizosphere pseudomonads as probiotics improving plant health

Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin's effects on plants' xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.

Modulation of Spartina densiflora plant growth and metal accumulation upon selective inoculation treatments: A comparison of gram negative and gram positive rhizobacteria

Metal contamination of estuaries is a severe environmental problem, for which phytoremediation is gaining momentum. In particular, the associations between halophytes-autochthonous rhizobacteria have proven useful for metal phytostabilization in salt marshes. In this work, three bacterial strains (gram-negative and gram-positive) were used for Spartina densiflora inoculation. All three bacteria, particularly Pantoea strains, promoted plant growth and mitigated metal stress on polluted sediments, as revealed from functionality of the photosynthetic apparatus (PSII) and maintenance of nutrient balance. Pantoea strains did not significantly affect metal accumulation in plant roots, whereas the Bacillus strain enhanced it. Metal loading to shoots depended on particular elements, although in all cases it fell below the threshold for animal consumption. Our results confirm the possibility of modulating plant growth and metal accumulation upon selective inoculation, and the suitability of halophyte-rhizobacteria interactions as biotechnological tools for metal phytostabilization in salt marshes, preventing metal transfer to the food chain.

Soil memory as a potential mechanism for encouraging sustainable plant health and productivity

The unspecified components of plant-microbe and plant-microbiome associations in the rhizosphere are complex, but recent research is simplifying our understanding of these relationships. We propose that the strong association between hosts, symbionts, and pathogens could be simplified by the concept of soil memory, which explains how a plant could promote their fecundity and protect their offspring through tightly associated relationships with the soil. Although there are many questions surrounding the mechanisms of this phenomenon, recent research has exposed evidence of its existence. Along with evidence from observations and mechanisms related to soil memory, we report means to utilize our understanding as sustainable protection for agricultural crops and propose future research questions.

Nitric Oxide and Hydrogen Peroxide Production are Involved in Systemic Drought Tolerance Induced by 2R,3R-Butanediol in Arabidopsis thaliana

2R,3R-Butanediol, a volatile compound produced by certain rhizobacteria, is involved in induced drought tolerance in Arabidopsis thaliana through mechanisms involving stomatal closure. In this study, we examined the involvement of nitric oxide and hydrogen peroxide in induced drought tolerance, because these are signaling agents in drought stress responses mediated by abscisic acid (ABA). Fluorescence-based assays showed that systemic nitric oxide and hydrogen peroxide production was induced by 2R,3R-butanediol and correlated with expression of genes encoding nitrate reductase and nitric oxide synthase. Co-treatment of 2R,3R-butanediol with an inhibitor of nitrate reductase or an inhibitor of nitric oxide synthase lowered nitric oxide production and lessened induced drought tolerance. Increases in hydrogen peroxide were negated by co-treatment of 2R,3R-butanediol with inhibitors of NADPH oxidase, or peroxidase. These findings support the volatile 2R,3R-butanediol synthesized by certain rhizobacteria is an active player in induction of drought tolerance through mechanisms involving nitric oxide and hydrogen peroxide production.