Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium

Harnessing bacterial endophytes for environmental resilience and agricultural sustainability

In the current era of environmental disasters and the necessity of sustainable development, bacterial endophytes have gotten attention for their role in improving agricultural productivity and ecological sustainability. This review explores the multifaceted contributions of bacterial endophytes to plant health and ecosystem sustainability. Bacterial endophytes are invaluable sources of bioactive compounds, promising breakthroughs in medicine and biotechnology. They also serve as natural biocontrol agents, reducing the need for synthetic fertilizers and fostering environmentally friendly agricultural practices. It provides eco-friendly solutions that align with the necessity of sustainability since they can improve pest management, increase crop resilience, and facilitate agricultural production. This review also underscores bacterial endophytes' contribution to promoting sustainable and green industrial productions. It also presented how incorporating these microorganisms into diverse industrial sectors can harmonize humankind with ecological stability. The potential of bacterial endophytes has been largely untapped, presenting an opportunity for pioneering advancements in sustainable industrial applications. Their importance caught attention as they provided innovative solutions to the challenging problems of the new era. This review sheds light on the remarkable potential of bacterial endophytes in various industrial sectors. Further research is imperative to discover their multifaceted potential. It will be essential to delve deeper into their mechanisms, broaden their uses, and examine their long-term impacts.

Bacillus tequilensis influences metabolite production in tomato and restores soil microbial diversity during Fusarium oxysporum infection

This study evaluates cellular damage, metabolite profiling, and defence-related gene expression in tomato plants and soil microflora during Fusarium wilt disease after treatment with B. tequilensis PBE-1. Histochemical analysis showed that PBE-1 was the primary line of defence through lignin deposition and reduced cell damage. GC-MS revealed that PBE-1 treatment ameliorated stress caused by F. oxysporum infection. PBE-1 also improved transpiration, photosynthesis, and stomatal conductance in tomato. qRT-PCR suggested that the defence-related genes FLS2, SERK, NOS, WRKYT, NHO, SAUR, and MYC2, which spread infection, were highly upregulated during F. oxysporum infection, but either downregulated or expressed normally in PBE-1 + P treated plants. This indicates that the plant not only perceives the bio-control agent as a non-pathogen entity but its presence in normal metabolism and gene expression within the host plant is maintained. The study further corroborated findings that application of PBE-1 does not cause ecological disturbances in the rhizosphere. Activity of soil microflora across four treatments, measured by Average Well Colour Development (AWCD), showed continuous increases from weeks 1 to 4 post-pathogen infection, with distinct substrate usage patterns like tannic and fumaric acids impacting microbial energy source utilization and diversity. Principal Component Analysis (PCA) and diversity indices like McIntosh, Shannon, and Simpson further illustrated significant microbial community shifts over the study period. In conclusion, our findings demonstrate that B. tequilensis PBE-1 is an ideal bio-agent for field application during Fusarium wilt disease management in tomato.

Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture

Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Ochrobactrum sp. NBRISH6 Inoculation Enhances Zea mays Productivity, Mitigating Soil Alkalinity and Plant Immune Response

Intensifying sodic land characterized by high alkaline pH is an incipient environmental hazard-limiting agricultural potential. In this study, we investigated the effects of plant growth-promoting bacteria Ochrobactrum sp. strain NBRISH6 on the growth and physiology of maize (Zea mays L.) grown under alkaline stress at two soil pH levels. Additionally, we also studied the effects of NBRISH6 on soil fertility parameters. A greenhouse experiment was designed using two live soils (pH 8.2 and 10.2) in earthen pots using maize as a host. Results revealed a significant increase in plant growth and a decrease in defense enzymes in both soil types due to NBRISH6 inoculation as compared to non-treated control. Furthermore, activities of all soil enzymes along with bacterial diversity increased in NBRISH6 treatment under normal as well as stressed conditions. In addition, field evaluation of NBRISH6 inoculation using maize was carried out under normal and alkaline conditions, which resulted in significant enhancement of all vegetative parameters as compared to respective controls. Therefore, the study suggested that Ochrobactrum sp. NBRISH6 can be used to develop a bioinoculant formulation to ameliorate abiotic stresses and enhanced crop productivity.

Comparative transcriptome analysis reveals the phosphate starvation alleviation mechanism of phosphate accumulating Pseudomonas putida in Arabidopsis thaliana

Phosphate starvation is one of the major factors limiting plant productivity globally. Soil microflora with an inherent trait of phosphate accumulation directly influences soil phosphorus level by regulating its labile form in soil solution. However, the detailed mechanism involved during their interaction with plants under phosphate deficient conditions is still unexplored. Hence, to dissect these complex gene regulatory networks, transcriptome analysis of A. thaliana roots grown under phosphate starved conditions in presence of phosphate accumulating bacteria (Pseudomonas putida; RAR) was performed. Plants grown under phosphate starved conditions showed upregulation of phosphate starvation responsive genes associated with cell biogenesis, stress, photosynthesis, senescence, and cellular transport. Inoculation of RAR upregulated genes linked to defense, cell wall remodeling, and hormone metabolism in stressed plants. Gene ontology analysis indicated the induction of S-glycoside, glucosinolate, and glycosinolate metabolic processes in RAR inoculated plants under phosphate stressed conditions. Further, protein-protein interaction analysis revealed upregulation of root development, cation transport, anion transport, sulfur compound metabolic process, secondary metabolic process, cellular amino metabolic process, and response to salicylic acid in RAR inoculated plants under phosphate starved conditions. These results indicate the potential role of phosphate accumulating bacteria in alleviating phosphate starvation in plants by involving multiple pathways.

Mitigation of arsenic toxicity in rice by the co-inoculation of arsenate reducer yeast with multifunctional arsenite oxidizing bacteria

The study aimed to explicate the role of microbial co-inoculants for the mitigation of arsenic (As) toxicity in rice. Arsenate (AsV) reducer yeast Debaryomyces hansenii NBRI-Sh2.11 (Sh2.11) with bacterial strains of different biotransformation potential was attempted to develop microbial co-inoculants. An experiment to test their efficacy (yeast and bacterial strains) on plant growth and As uptake was conducted under a stressed condition of 20 mg kg-1 of arsenite (AsIII). A combination of Sh2.11 with an As(III)-oxidizer, Citrobacter sp. NBRI-B5.12 (B5.12), resulted in ∼90% decrease in grain As content as compared to Sh2.11 alone (∼40%). Reduced As accumulation in rice roots under co-treated condition was validated with SEM-EDS analysis. Enhanced As expulsion in the selected combination under in vitro conditions was found to be correlated with higher As content in the soil during their interaction with plants. Selected co-inoculant mediated enhanced nutrient uptake in association with better production of indole acetic acid (IAA) and gibberellic acid (GA) in shoot, support microbial co-inoculant mediated better biomass under stressful condition. Boosted defense response in association with enhanced glutathione-S-transferase (GST) and glutathione reductase (GR), activities under in vitro and in vivo conditions were observed. These results indicated that the As(III) oxidizer-B5.12 accelerated the As detoxification property of the As(V) reducer-Sh2.11. Henceforth, the results confer that the coupled reduction-oxidation process of the co-inoculant reduces the accumulation of As in rice grain. These co-inoculants can be further developed for field trials to achieve higher biomass with alleviated As toxicity in rice.

Transcriptional landscape of Brachypodium distachyon roots during interaction with Bacillus velezensis strain B26

Plant growth promoting rhizobacteria (PGPR) communicate with plants through roots. The molecular mechanism by which plants and PGPR respond to each other is not very well known. In the current study, we did RNA sequence analysis of Brachypodium distachyon Bd21-3 roots inoculated with PGPR, Bacillus velezensis strain B26. From our list of differentially expressed genes, we concentrated on transcripts that have a high possibility of participating in plant-PGPR interaction. Transcripts associated to the hormone signalling pathway were differentially expressed. We identified the upregulation of various transcripts linked to ion transporters. Reduction in expression of defense signalling genes indicated that B26 suppresses the plant defense mechanisms to begin successful interaction with roots. Transcripts associated with lignin branch of the phenylpropanoid pathway were upregulated as well, leading to more accumulation of lignin in the cell wall which enhances mechanical strength of plants. Overall, this study is an excellent resource for investigating associations between plant-PGPR interactions.

Potential of methyltransferase containing Pseudomonas oleovorans for abatement of arsenic toxicity in rice

Arsenic (As) has become natural health hazard for millions of people across the world due to its distribution in the food chain. Naturally, it is present in different oxidative states of inorganic [As(V) and As(III)] and organic (DMA, MMA and TMA) forms. Among different mitigation approaches, microbe mediated mitigation of As toxicity is an effective and eco-friendly approach. The present study involves the characterization of bacterial strains containing arsenite methyltransferase (Pseudomonas oleovorans, B4.10); arsenate reductase (Sphingobacterium puteale, B4.22) and arsenite oxidase (Citrobacter sp., B5.12) activity with plant growth promoting (PGP) traits. Efficient reduction of grain As content by 61 % was observed due to inoculation of methyltransferase containing B4.10 as compared to B4.22 (47 %) and B5.12 (49 %). Reduced bioaccumulation of As in root (0.339) and shoot (0.166) in presence of B4.10 was found to be inversely related with translocation factor for Mn (3.28), Fe (0.073), and Se (1.82). Bioaccumulation of these micro elements was found to be associated with the modulated expression of different mineral transporters (OsIRT2, OsFRO2, OsTOM1, OsSultr4;1, and OsZIP2) in rice shoot. Improved dehydrogenase (407 %), and β-glucosidase (97 %) activity in presence of P. oleovorans (B4.10) as compared to arsenate reductase (198 and 50 %), and arsenite oxidase (134 and 69 %) containing bacteria was also observed. Our finding confers the potential of methyltransferase positive P. oleovorans (B4.10) for As stress amelioration. Reduced grain As uptake was found to be mediated by improved plant growth and nutrient uptake associated with enhanced soil microbial activity.

Azotobacter chroococcum and Pseudomonas putida enhance pyrroloquinazoline alkaloids accumulation in Adhatoda vasica hairy roots by biotization

Adhatoda vasica is used in the treatment of cold, cough, chronic bronchitis, asthma, diarrhea, and dysentery. The biological activities of this species are attributed with the presence of alkaloids, triterpenoids, and flavonoids. Agrobacterium rhizogenes-mediated transformation of A. vasica, produces pyrroloquinazoline alkaloids, was achieved by infecting leaf discs with strain ATCC15834. The bacterial strain infected 82.7% leaf discs and 5-7 hairy root initials were developed from the cut edges of leaf discs. In this study, seven strains of Azotobacter chroococcum and five strains of Pseudomonas putida were used for the biotization of hairy roots. Plant growth-promoting rhizobacteria (PGPR) develops symbiotic association with roots of plants and increases the growth parameters of plants. PGPR (A. chroococcum and P. putida) increased the profiles of nitrogenase and acid phosphatase enzymes, biomass, dry matter contents, anthranilate synthase activity and accumulation of pyrroloquizoline alkaloids in the biotized hairy roots. Both enzymes (nitrogenase and acid phosphatase) maintain sufficient supply of nitrogen and dissolved phosphorus to the cells of hairy roots therefore, the levels of anthranilate synthase activity and pyrroloquinazoline alkaloids are increased. Total seven pyrroloquinazoline alkaloids (vasicine, vasicinone, vasicine acetate, 2-acetyl benzyl amine, vasicinolone, deoxyvasicine and vasicol) were identified from the biotized hairy roots of A. vasica. In our study, biotization increased the profiles of pyrroloquinazoline alkaloids therefore, this strategy may be used in increasing the production of medicinally important secondary metabolites in other plant species also. Our hypothetical model demonstrates that P. putida cell surface receptors receive root exudates by attaching on hairy roots. After attachment, the bacterial strain penetrates in the biotized hairy roots. This endophytic interaction stimulates acid phosphatase activity in the cells of biotized hairy roots. The P. putida plasmid gene (ppp1) expression led to the synthesis of acid phosphatase in cytosol. The enzyme enhances phosphorus availability as well as induces the formation of phosphoribosyl diphosphate. Later, phosphoribosyl diphosphate metabolizes to tryptophan and finally tryptophan converts to anthranilic acid. The synthesized anthranilic acid used in the synthesis of alkaloids in A. vasica.

Dissection of Paenibacillus polymyxa NSY50-Induced Defense in Cucumber Roots against Fusarium oxysporum f. sp. cucumerinum by Target Metabolite Profiling

Simple Summary

Plant growth-promoting rhizobacteria (PGPR) have significant potential to enhance the tolerance of biotic and abiotic stresses and the productivity of crops. However, the mechanism of PGPR in improving plant resistance to pathogens is unclear. Recently, the newly isolated Paenibacillus polymyxa strain NSY50 was shown to considerably suppress the Fusarium wilt of cucumber plants. This study was carried out to explore the underlying mechanism of NSY50 in improving plant resistance to pathogen invasion via target metabolite profiling, and the results indicated that strain NSY50 was able to alleviate Fusarium wilt stress by activating GSH metabolism and improving redox balance. Our research findings enable a deeper understanding of P. polymyxa NSY50-induced enhanced defense against F. oxysporum in cucumber.

Abstract

To gain insights into the roles of beneficial PGPR in controlling soil-borne disease, we adopted a metabolomics approach to investigate the beneficial impacts of P. polymyxa NSY50 on cucumber seedling roots under the pathogen of Fusarium oxysporum f. sp. cucumerinum (FOC). We found that NSY50 pretreatment (NSY50 + FOC) obviously reduced the production of reactive oxygen species (ROS). Untargeted metabolomic analysis revealed that 106 metabolites responded to NSY50 and/or FOC inoculation. Under FOC stress, the contents of root osmotic adjustment substances, such as proline and betaine were significantly increased, and dehydroascorbic acid and oxidized glutathione (GSH) considerably accumulated. Furthermore, the contents of free amino acids such as tryptophan, phenylalanine, and glutamic acid were also significantly accumulated under FOC stress. Similarly, FOC stress adversely affected glycolysis and the tricarboxylic acid cycles and transferred to the pentose phosphate pathway. Conversely, NSY50 + FOC better promoted the accumulation of α-ketoglutaric acid, ribulose-5-phosphate, and 7-phosphosodiheptanone compared to FOC alone. Furthermore, NSY50 + FOC activated GSH metabolism and increased GSH synthesis and metabolism-related enzyme activity and their encoding gene expressions, which may have improved redox homoeostasis, energy flow, and defense ability. Our results provide a novel perspective to understanding the function of P. polymyxa NSY50, accelerating the application of this beneficial PGPR in sustainable agricultural practices.

Harnessing plant microbiome for mitigating arsenic toxicity in sustainable agriculture

Heavy metal toxicity has become an impediment to agricultural productivity, which presents major human health concerns in terms of food safety. Among them, arsenic (As) a non-essential heavy metal has gained worldwide attention because of its noxious effects on agriculture and public health. The increasing rate of global warming and anthropogenic activities have promptly exacerbated As levels in the agricultural soil, thereby causing adverse effects to crop genetic and phenotypic traits and rendering them vulnerable to other stresses. Conventional breeding and transgenic approaches have been widely adapted for producing heavy metal resilient crops; however, they are time-consuming and labor-intensive. Hence, finding new mitigation strategies for As toxicity would be a game-changer for sustainable agriculture. One such promising approach is harnessing plant microbiome in the era of 'omics' which is gaining prominence in recent years. The use of plant microbiome and their cocktails to combat As metal toxicity has gained widespread attention, because of their ability to metabolize toxic elements and offer an array of perquisites to host plants such as increased nutrient availability, stress resilience, soil fertility, and yield. A comprehensive understanding of below-ground plant-microbiome interactions and their underlying molecular mechanisms in exhibiting resilience towards As toxicity will help in identifying elite microbial communities for As mitigation. In this review, we have discussed the effect of As, their accumulation, transportation, signaling, and detoxification in plants. We have also discussed the role of the plant microbiome in mitigating As toxicity which has become an intriguing research frontier in phytoremediation. This review also provides insights on the advancements in constructing the beneficial synthetic microbial communities (SynComs) using microbiome engineering that will facilitate the development of the most advanced As remedial tool kit in sustainable agriculture.

Pseudomonas putida and its close relatives: mixing and mastering the perfect tune for plants

Abstract

Plant growth–promoting rhizobacteria (PGPR) are a group of microorganisms of utmost interest in agricultural biotechnology for their stimulatory and protective effects on plants. Among the various PGPR species, some Pseudomonas putida strains combine outstanding traits such as phytohormone synthesis, nutrient solubilization, adaptation to different stress conditions, and excellent root colonization ability. In this review, we summarize the state of the art and the most relevant findings related to P. putida and its close relatives as PGPR, and we have compiled a detailed list of P. putida sensu stricto, sensu lato, and close relative strains that have been studied for their plant growth–promoting characteristics. However, the mere in vitro analysis of these characteristics does not guarantee correct plant performance under in vivo or field conditions. Therefore, the importance of studying adhesion and survival in the rhizosphere, as well as responses to environmental factors, is emphasized. Although numerous strains of this species have shown good performance in field trials, their use in commercial products is still very limited. Thus, we also analyze the opportunities and challenges related to the formulation and application of bioproducts based on these bacteria.

Key points

•The mini-review updates the knowledge on Pseudomonas putida as a PGPR.

• Some rhizosphere strains are able to improve plant growth under stress conditions.

• The metabolic versatility of this species encourages the development of a bioproduct.

Alleviative mechanisms of silicon solubilizing Bacillus amyloliquefaciens mediated diminution of arsenic toxicity in rice

Silicon (Si) has gained considerable attention for its utility in improved plant health under biotic and abiotic stresses through alteration of physiological and metabolic processes. Its interaction with arsenic (As) has been the compelling area of research amidst heavy metal toxicity. However, microbe mediated Si solubilization and their role for reduced As uptake is still an unexplored domain. Foremost role of Bacillus amyloliquefaciens (NBRISN13) in impediment of arsenite (AsIII) translocation signifies our work. Reduced grain As content (52-72%) during SN13 inoculation under feldspar supplementation (Si+SN+As) highlight the novel outcome of our study. Upregulation of Lsi1, Lsi2 and Lsi3genes in Si+SN+As treated rice plants associated with restricted As translocation, frames new propositions for future research on microbemediated reduced As uptake through increased Si transport. In addition to low As accumulation, alleviation of oxidative stress markers by modulation of defense enzyme activities and differential accumulation of plant hormones was found to be associated with improved growth and yield. Thus, our findings confer the potential role of microbe mediated Si solubilization in mitigation of As stress to restore plant growth and yield.

Functional Genetic Diversity and Plant Growth Promoting Potential of Polyphosphate Accumulating Bacteria in Soil

Polyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation.

IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.

Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes

Plant beneficial microorganisms improve the health and growth of the associated plants. Application of beneficial microbes triggers an enhanced resistance state, also termed as induced systemic resistance (ISR), in the host, against a broad range of pathogens. Upon the activation of ISR, plants employ long-distance systemic signaling to provide protection for distal tissue, inducing rapid and strong immune responses against pathogens invasions. The transmission of ISR signaling was commonly regarded to be a jasmonic acid- and ethylene-dependent, but salicylic acid-independent, transmission. However, in the last decade, the involvement of both salicylic acid and jasmonic acid/ethylene signaling pathways and the regulatory roles of small RNA in ISR has been updated. In this review, the plant early recognition, responsive reactions, and the related signaling transduction during the process of the plant-beneficial microbe interaction was discussed, with reflection on the crucial regulatory role of small RNAs in the beneficial microbe-mediated ISR.

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

Simple Summary

Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses.

Abstract

Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.

Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives

In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.

The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion

The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.

An OsNAM gene plays important role in root rhizobacteria interaction in transgenic Arabidopsis through abiotic stress and phytohormone crosstalk

Overexpression of Bacillus amyloliquefaciens SN13-responsive OsNAM gene in Arabidopsis reveals its important role in beneficial plant and plant growth promoting rhizobacteria interaction by conferring stress tolerance and phytohormone modulation. Salinity is one of the major constraints that affect crop development and yield. Plants respond and adapt to salt stress via complex mechanisms that involve morpho-physiological, biochemical, and molecular changes. The expression of numerous genes is known to alter during various abiotic stresses and impart stress tolerance. Recently, some known rhizospheric microbes have also been used to mitigate the effects of abiotic stresses; however, the molecular basis of such interactions remains elusive. Therefore, the present investigation was aimed to elucidate the plant growth-promoting rhizobacteria (PGPR; Bacillus amyloliquefaciens-SN13) -induced crosstalk among salinity and phytohormones in OsNAM-overexpressed Arabidopsis plants. Transgenic plants showed increased germination percentage compared to wild-type (WT) seeds under 100 mM of NaCl. Phenotypic data showed increased root length, rosette diameter, leaf size, and biomass in transgenics than WT plants. Transgenic plants can also better maintain membrane integrity and osmolyte concentration under salinity as compared to WT. Further, gene expression analysis of AP2/ERF, GST, ERD4, and ARF2 genes showed differential expression and their positive modulation in transgenic Arabidopsis exposed to salt stress in the presence of SN13 as compared to uninoculated WT. Modulation in IAA, ABA, and GA content in inoculated plants showed the more pronounced positive effects of SN13 on transgenic plants that supported our findings on Arabidopsis-SN13 interaction. Overall, the study concludes that SN13 positively modulated expression of stress-responsive genes under salinity and alter phytohormones levels in OsNAM-overexpressed plants suggesting its extensive role in cross-talk among salinity and phytohormones in response to PGPR.

Improving soybean growth under arsenic stress by inoculation with native arsenic-resistant bacteria

Certain metal (loid)-resistant bacteria that inhabit the rhizosphere have shown to improve plant growth and tolerance under toxic metal stress. In this study, we tested if six native, arsenic-resistant and plant growth promoting bacteria (PGPB) were able to enhance soybean (Glycine max L.) growth and modulate arsenic (As) uptake. As a previous work, we tested all single isolates and all possible binary combinations without arsenic stress to identify the combinations that would have the greatest plant growth promoting effect. In this study, a screening assay was performed with only five inoculation options selected after first stage (Pseudomonas sp. AW4, Pseudomonas sp. AW6, AW4+AW6, Rhodococcus sp. AW3+Pseudomonas sp. AW5 and Enterobacter sp. AW1+AW6). In both stages, inoculation was implemented by imbibition of soybean seeds with bacterial suspensions, and plant growth was carried out in pots using perlite as substrate in a chamber with controlled conditions. In the third stage, we performed similar assays, under As stress, using the three most promising inoculation options (AW4, AW6 and AW3+AW5). Treatments were performed by irrigation with 25 μM arsenite (As3+), 25 μM arsenate (As5+), 25 μM equimolar As3+/As5+ solution or water (control). Biometric and biochemical parameters indicated that inoculation with Pseudomonas sp. AW4 significantly promoted soybean growth under As3+/As5+ treatment and did not modified As accumulation pattern. Further field studies are needed to determine if some of these inoculation options are useful to improve in situ soybean growth under arsenic stress and could become a tool for the development of sustainable agriculture in As-impacted environments.

Impact of seed-transmitted endophytic bacteria on intra- and inter-cultivar plant growth promotion modulated by certain sets of metabolites in rice crop

Exploring the beneficial interactions between plant and endophytes could be an effective strategy in the implementation of sustainable agricultural practices to enhance crop productivity. In this study, we aimed to evaluate holistically the plant growth promoting (PGP) abilities rendered by seed-transmitted endophytic bacteria isolated from in vitro grown calli of two rice cultivars. Nine bacterial endophytes, designated as PB001-PB009, were isolated and identified at the genus level through 16S rRNA gene sequence analysis. Biochemical investigations disclosed that they possess several PGP traits, such as phosphate solubilization, indole acetic acid biosynthesis, ammonia production, nitrogen fixation, amylase production and siderophore production. Results in gnotobiotic conditions revealed an increase in fresh weight, dry weight, root length and shoot length of seedlings germinated from endophyte-primed seeds than the control (uninoculated) set in a non-host and two host rice cultivars. In net house experiments, plants germinated from Micrococcus sp. PB001, Pseudomonas sp. PB002, Methylobacterium sp. PB005 and Methylorubrum sp. PB009 primed seeds showed an increase of upto 34.06 %, 38.77 %, 182.87 %, 16.59 % and 33.52 % in chlorophyll content, number of tillers/plant, number of grains/plant, grain size and grain weight, respectively than control plant sets in the non-host rice cultivar, further validating inter-cultivar PGP abilities of these endophytes. Metabolite profiling unfolded the abundance of few metabolites that are involved in pathways associated with PGP traits, in seedlings germinated from the endophyte-primed seeds. Together, the study documents the effect of seed-transmitted endophytic bacteria on intra- and inter-cultivar PGP by modulating certain sets of metabolites in rice plant, and is promising in developing bioinoculant formulations employing these selected endophytes for enhancement of rice productivity.

High-Throughput Sequencing and Expression Analysis Suggest the Involvement of Pseudomonas putida RA-Responsive microRNAs in Growth and Development of Arabidopsis

Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of Arabidopsis upon P. putida RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in Arabidopsis, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

Omics-Based Mechanistic Insight Into the Role of Bioengineered Nanoparticles for Biotic Stress Amelioration by Modulating Plant Metabolic Pathways

Bioengineered silver nanoparticles can emerge as a facile approach to combat plant pathogen, reducing the use of pesticides in an eco-friendly manner. The plants' response during tripartite interaction of plant, pathogen, and nanoparticles remains largely unknown. This study demonstrated the use of bioengineered silver nanoparticles in combating black spot disease caused by necrotrophic fungus Alternaria brassicicola in Arabidopsis thaliana via foliar spray. The particles reduced disease severity by 70-80% at 5 μg/ml without showing phytotoxicity. It elicited plant immunity by a significant reduction in reactive oxygen species (ROS), decreases in stress enzymes by 0.6-19.8-fold, and emergence of autophagy. Comparative plant proteomics revealed 599 proteins expressed during the interaction, where 117 differential proteins were identified. Among different categories, proteins involved in bioenergy and metabolism were most abundant (44%), followed by proteins involved in plant defense (20%). Metabolic profiling by gas chromatography-mass spectroscopy yielded 39 metabolite derivatives in non-polar fraction and 25 in the polar fraction of plant extracts. It was observed that proteins involved in protein biogenesis and early plant defense were overexpressed to produce abundant antimicrobial metabolites and minimize ROS production. Bioengineered silver nanoparticles performed dual functions to combat pathogen attack by killing plant pathogen and eliciting immunity by altering plant defense proteome and metabolome.

Prescience of endogenous regulation in Arabidopsis thaliana by Pseudomonas putida MTCC 5279 under phosphate starved salinity stress condition

Phosphorus (P) availability and salinity stress are two major constraints for agriculture productivity. A combination of salinity and P starvation is known to be more deleterious to plant health. Plant growth promoting rhizobacteria are known to ameliorate abiotic stress in plants by increasing the availability of different nutrients. However, interaction mechanisms of plant grown under salinity and P stress condition and effect of beneficial microbe for stress alleviation is still obscure. Earlier we reported the molecular insight of auxin producing, phosphate solubilising Pseudomonas putida MTCC 5279 (RAR) mediated plant growth promotion in Arabidopsis thaliana. In present study new trait of proline and phosphatase production of RAR and its impact on modulation of physiological phenomenon under phosphate starved-salinity stress condition in A. thaliana has been investigated. Different physiological and molecular determinants under RAR- A. thaliana interaction showed that auxin producing RAR shows tryptophan dependence for growth and proline production in ATP dependant manner under salinity stress. However, under P deprived conditions growth and proline production are independent of tryptophan. RAR mediated lateral root branching and root hair density through modulation of abscisic acid signalling was observed. Acidic phosphatase activity under P starved and salinity stress condition was majorly modulated along with ROS metabolism and expression of stress responsive/phosphate transporter genes. A strong correlation of different morpho-physiological factor with RAR + salt conditions, showed We concluded that enhanced adverse effect of salinity with unavailability of P was dampened in presence of P. putida MTCC 5279 (RAR) in A. thaliana, though more efficiently salinity stress conditions. Therefore, alleviation of combined stress of salinity induced phosphate nutrient deficiency by inoculation of beneficial microbe, P. putida MTCC 5279 offer good opportunities for enhancing the agricultural productivity.

Metabolite profiling reveals a complex response of plants to application of plant growth-promoting endophytic bacteria

Endophytic bacteria have been explored for their role in plant growth promotion, however, not much has been explored in cucumber. The metabolomic response of plants to application of such microbes also remains largely unknown. Thus, we investigated the application of endophytic bacteria to cucumber to infer their role in plant growth promotion and document metabolome response. The lowest healthy leaf-stalks were sampled from four differently sourced cucumber plants, and endophytic bacteria were isolated after surface disinfection. Initial plant growth-promoting (PGP) screening was performed to identify PGP strains out of numerous isolates, and five strains (Strains 4=Curtobacterium spp., 72=Brevibacillus spp., 167=Paenibacillus spp., 193=Bacillus spp., and 227=Microbacterium spp.) were selected based on their contribution to root growth compared with the control. The selected strains were further evaluated in pot experiments, axenic PGP trait assays, and metabolomic analysis. Results revealed that the selected isolates possessed different qualitative characteristics among indole acetic acid, siderophore production, phosphate solubilization, and 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and nifH genes, and all isolates significantly enhanced plant growth in both pot experiments compared with the uninoculated control and fertilizer control. Metabolomic profiling revealed that both strains affected the plant metabolomes compared with the uninoculated control. Around 50 % of the metabolites explored had higher concentrations in either or both bacteria-applied plants compared with the uninoculated control. Differences were observed in both strains' regulation of metabolites, although both enhanced root growth near equally. Overall, endophytic bacteria significantly enhanced plant growth and tended to produce or induce release of certain metabolites within the plant endosphere.

The reduction of selenium(IV) by boreal Pseudomonas sp. strain T5-6-I - Effects on selenium(IV) uptake in Brassica oleracea

Selenium (Se) is an essential micronutrient but toxic when taken in excessive amounts. Therefore, understanding the metabolic processes related to selenium uptake and bacteria-plant interactions coupled with selenium metabolism are of high importance. We cultivated Brassica oleracea with the previously isolated heterotrophic aerobic Se(IV)-reducing Pseudomonas sp. T5-6-I strain to better understand the phenomena of bacteria-mediated Se(IV) reduction on selenium availability to the plants. B. oleracea grown on Murashige and Skoog medium (MS-salt agar) with and without of Pseudomonas sp. were amended with Se(IV)/⁷⁵Se(IV), and selenium transfer into plants was studied using autoradiography and gamma spectroscopy. XANES was in addition used to study the speciation of selenium in the B. oleracea plants. In addition, the effects of Se(IV) on the protein expression in B. oleracea was studied using HPLC-SEC. TEM and confocal microscopy were used to follow the bacterial/Se-aggregate accumulation in plants and the effects of bacterial inoculation on root-hair growth. In the tests using ⁷⁵Se(IV) on average 130% more selenium was translocated to the B. oleracea plants grown with Pseudomonas sp. compared to the plants grown with selenium, but without Pseudomonas sp.. In addition, these bacteria notably increased root hair density. Changes in the protein expression of B. oleracea were observed on the ∼30-58 kDa regions in the Se(IV) treated samples, probably connected e.g. to the oxidative stress induced by Se(IV) or expression of proteins connected to the Se(IV) metabolism. Based on the XANES measurements, selenium appears to accumulate in B. oleracea mainly in organic C-Se-H and C-Se-C bonds with and without bacteria inoculation. We conclude that the Pseudomonas sp. T5-6-I strain seems to contribute positively to the selenium accumulation in plants, establishing the high potential of Se⁰-producing bacteria in the use of phytoremediation and biofortification of selenium.

A comparative evaluation towards the potential of Klebsiella sp. and Enterobacter sp. in plant growth promotion, oxidative stress tolerance and chromium uptake in Helianthus annuus (L.)

Prevalence of metal pollutants exerts negative effects on human health and environment, thus propounding an urgent need for a safer substitute. This study was conducted to compare the chromium bioremediation and plant growth promotion ability of two bacterial strains, Klebsiella sp. strain CPSB4 (MH266218) and Enterobacter sp. strain CPSB49 (MH532567), isolated from the rhizospheric soils. A pot scale experiment was setup with Helianthus annuus (L.) as a test plant to compare the efficiency of both isolates in enhancement of plant growth, nutrients uptake, anti-oxidative enzymes production, lipid peroxidation, and chromium bioremediation. Inoculation of strains, CPSB4 and CPSB49 enhanced plant biomass, plant growth, nutrient uptake, anti-oxidative enzymes, and chromium bioremediation, while reduction in lipid peroxidation was observed compared to uninoculated control under chromium stress. The maximum increase in plant growth and nutrient uptake was found in treatments inoculated with CPSB49, while maximum chromium uptake by sunflower was observed in treatments inoculated with CPSB4. Moreover, an increase in anti-oxidative enzyme production and decrease in lipid peroxidation was observed on inoculation of the selected strains. Thus, the strains Klebsiella sp. and Enterobacter sp. can be effectively used in chromium bioremediation and plant growth promotion under chromium stress conditions.

PGPR-induced OsASR6 improves plant growth and yield by altering root auxin sensitivity and the xylem structure in transgenic Arabidopsis thaliana

Plant-growth-promoting rhizobacteria (PGPR) improve plant growth by altering the root architecture, although the mechanisms underlying this alteration have yet to be unravelled. Through microarray analysis of PGPR-treated rice roots, a large number of differentially regulated genes were identified. Ectopic expression of one of these genes, OsASR6 (ABA STRESS RIPENING6), had a remarkable effect on plant growth in Arabidopsis. Transgenic lines over-expressing OsASR6 had larger leaves, taller inflorescence bolts and greater numbers of siliques and seeds. The most prominent effect was observed in root growth, with the root biomass increasing four-fold compared with the shoot biomass increase of 1.7-fold. Transgenic OsASR6 over-expressing plants showed higher conductance, transpiration and photosynthesis rates, leading to an ˜30% higher seed yield compared with the control. Interestingly, OsASR6 expression led to alterations in the xylem structure, an increase in the xylem vessel size and altered lignification, which correlated with higher conductance. OsASR6 is activated by auxin and, in turn, increases auxin responses and root auxin sensitivity, as observed by the increased expression of auxin-responsive genes, such as SAUR32 and PINOID, and the key auxin transcription factor, ARF5. Collectively, these phenomena led to an increased root density. The effects of OsASR6 expression largely mimic the beneficial effects of PGPRs in rice, indicating that OsASR6 activation may be a key factor governing PGPR-mediated changes in rice. OsASR6 is a potential candidate for the manipulation of rice for improved productivity.

Impact of Pseudomonas putida RRF3 on the root transcriptome of rice plants: Insights into defense response, secondary metabolism and root exudation

Pseudomonas putida is widely used as a biocontrol agent, however, mechanisms by which it initiates the plants' defense response remains obscure. To gain an insight into the molecular changes that occur in plants upon plant growth-promoting rhizobacteria colonization, root transcriptome analysis by using a microarray was performed in rice using P. putida RRF3 (a rice rhizosphere isolate). Data analysis revealed a differential regulation of 61 transcripts (48 h post-treatment), of which, majority corresponded to defense response, cell wall modification and secondary metabolism. Seven genes encoding salicylic acid (SA) responsive pathogenesis-related proteins were up-regulated significantly (fold change ranges from 1 to 4), which suggests that RRF3 has a profound impact on a SA-mediated defense signaling mechanism in rice. Investigations performed at later stages of RRF3 colonization by real-time polymerase chain reaction and high-performance liquid chromatography (HPLC) analysis confirmed the above results, demonstrating RRF3 as a potent biocontrol agent. Further, the impact of RRF3 colonization on root exudation, in particular, exudation of SA was investigated by HPLC. However, analysis revealed RRF3 to have a negative impact on root exudation of SA. Overall, this study shows that P. putida RRF3 immunizes the rice plants by re-organizing the root transcriptome to stimulate plant defense responses ('priming'), and simultaneously protects itself from the primed plants by altering the rhizosphere chemical constituents.

Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress

The Bacillus amyloliquefaciens-SN13 and model crop rice (Oryza sativa) were chosen to understand the complex regulatory networks that govern plant-PGPR interaction under salt stress. During stress, inoculation with SN13 significantly increased biomass, relative water content, proline and total soluble sugar in rice while decreased lipid peroxidation and electrolyte leakage. Extensive alterations in gene expression were also observed in rice root transcriptome under stress in the presence of SN13. Rhizobacteria induced changes in expression of a considerable number of photosynthesis, hormone, and stress-responsive genes, in addition to cell-wall and lipid metabolism-related genes under salt stress as compared to salt stress or SN13 inoculation alone, indicating its potential role in reducing the harmful effects of salinity. To validate RNA-seq data, qRT-PCR was performed for selected differentially expressed genes representing various functional categories including metabolism, regulation, stress-response, and transporters. Results indicate qualitative and quantitative differences between roots responses to SN13 under stressed and unstressed conditions. Functional expressions of OsNAM and OsGRAM in yeast showed enhanced tolerance to various abiotic stresses, indicating crucial SN13-rice interaction in imparting beneficial effects under stress. This is first detailed report on understanding molecular mechanism underlying beneficial plant-microbe interaction in any economically important model crop plant under abiotic stress.

Systems Biology of Plant-Microbiome Interactions

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific, posing an obstacle to their general application. Remarkably, many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions, including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.

The Recruitment Model of Metabolic Evolution: Jasmonate-Responsive Transcription Factors and a Conceptual Model for the Evolution of Metabolic Pathways

Plants produce a vast array of structurally diverse specialized metabolites with various biological activities, including medicinal alkaloids and terpenoids, from relatively simple precursors through a series of enzymatic steps. Massive metabolic flow through these pathways usually depends on the transcriptional coordination of a large set of metabolic, transport, and regulatory genes known as a regulon. The coexpression of genes involved in certain metabolic pathways in a wide range of developmental and environmental contexts has been investigated through transcriptomic analysis, which has been successfully exploited to mine the genes involved in various metabolic processes. Transcription factors are DNA-binding proteins that recognize relatively short sequences known as cis-regulatory elements residing in the promoter regions of target genes. Transcription factors have positive or negative effects on gene transcription mediated by RNA polymerase II. Evolutionarily conserved transcription factors of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) and basic helix-loop-helix (bHLH) families have been identified as jasmonate (JA)-responsive transcriptional regulators of unrelated specialized pathways in distinct plant lineages. Here, I review the current knowledge and propose a conceptual model for the evolution of metabolic pathways, termed "recruitment model of metabolic evolution." According to this model, structural genes are repeatedly recruited into regulons under the control of conserved transcription factors through the generation of cognate cis-regulatory elements in the promoters of these genes. This leads to the adjustment of catalytic activities that improve metabolic flow through newly established passages.

Heavy Metal Stress, Signaling, and Tolerance Due to Plant-Associated Microbes: An Overview

Several anthropogenic activities including mining, modern agricultural practices, and industrialization have long-term detrimental effect on our environment. All these factors lead to increase in heavy metal concentration in soil, water, and air. Soil contamination with heavy metals cause several environmental problems and imparts toxic effect on plant as well as animals. In response to these adverse conditions, plants evolve complex molecular and physiological mechanisms for better adaptability, tolerance, and survival. Nowadays conventional breeding and transgenic technology are being used for development of metal stress resistant varieties which, however, are time consuming and labor intensive. Interestingly the use of microbes as an alternate technology for improving metal tolerance of plants is gaining momentum recently. The use of these beneficial microorganisms is considered as one of the most promising methods for safe crop-management practices. Interaction of plants with soil microorganisms can play a vital role in acclimatizing plants to metalliferous environments, and can thus be explored to improve microbe-assisted metal tolerance. Plant-associated microbes decrease metal accumulation in plant tissues and also help to reduce metal bioavailability in soil through various mechanisms. Nowadays, a novel phytobacterial strategy, i.e., genetically transformed bacteria has been used to increase remediation of heavy metals and stress tolerance in plants. This review takes into account our current state of knowledge of the harmful effects of heavy metal stress, the signaling responses to metal stress, and the role of plant-associated microbes in metal stress tolerance. The review also highlights the challenges and opportunities in this continued area of research on plant-microbe-metal interaction.

Enhanced Cellular Internalization: A Bactericidal Mechanism More Relative to Biogenic Nanoparticles than Chemical Counterparts

Biogenic synthesis of silver nanoparticles for enhanced antimicrobial activity has gained a lot of momentum making it an urgent need to search for a suitable biocandidate which could be utilized for efficient capping and shaping of silver nanoparticles with enhanced bactericidal activity utilizing its secondary metabolites. Current work illustrates the enhancement of antimicrobial efficacy of silver nanoparticles by reducing and modifying their surface with antimicrobial metabolites of cell free filtrate of Trichoderma viride (MTCC 5661) in comparison to citrate stabilized silver nanoparticles. Nanoparticles were characterized by visual observations, UV-visible spectroscopy, zetasizer, and transmission electron microscopy (TEM). Synthesized particles were monodispersed, spherical in shape and 10-20 nm in size. Presence of metabolites on surface of biosynthesized silver nanoparticles was observed by gas chromatography-mass spectroscopy (GC-MS), energy dispersive X-ray analysis (EDAX), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). The antimicrobial activity of both silver nanoparticles was tested against Shigella sonnei, Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) by growth inhibition curve analysis and colony formation unit assay. Further, it was noted that internalization of biosynthesized nanoparticles inside the bacterial cell was much higher as compared to citrate stabilized particles which in turn lead to higher production of reactive oxygen species. Increase in oxidative stress caused severe damage to bacterial membrane enhancing further uptake of particles and revoking other pathways for bacterial disintegration resulting in complete and rapid death of pathogens as evidenced by fluorescein diacetate/propidium iodide dual staining and TEM. Thus, study reveals that biologically synthesized silver nanoarchitecture coated with antimicrobial metabolites of T. viride was more potent than their chemical counterpart in killing of pathogenic bacteria.

Bacillus amyloliquefaciens Confers Tolerance to Various Abiotic Stresses and Modulates Plant Response to Phytohormones through Osmoprotection and Gene Expression Regulation in Rice

Being sessile in nature, plants have to withstand various adverse environmental stress conditions including both biotic and abiotic stresses. Comparatively, abiotic stresses such as drought, salinity, high temperature, and cold pose major threat to agriculture by negatively impacting plant growth and yield worldwide. Rice is one of the most widely consumed staple cereals across the globe, the production and productivity of which is also severely affected by different abiotic stresses. Therefore, several crop improvement programs are directed toward developing stress tolerant rice cultivars either through marker assisted breeding or transgenic technology. Alternatively, some known rhizospheric competent bacteria are also known to improve plant growth during abiotic stresses. A plant growth promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens NBRI-SN13 (SN13) was previously reported by our lab to confer salt stress tolerance to rice seedlings. However, the present study investigates the role of SN13 in ameliorating various abiotic stresses such as salt, drought, desiccation, heat, cold, and freezing on a popular rice cv. Saryu-52 under hydroponic growth conditions. Apart from this, seedlings were also exogenously supplied with abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA) and ethephon (ET) to study the role of SN13 in phytohormone-induced stress tolerance as well as its role in abiotic and biotic stress cross-talk. All abiotic stresses and phytohormone treatments significantly affected various physiological and biochemical parameters like membrane integrity and osmolyte accumulation. SN13 also positively modulated stress-responsive gene expressions under various abiotic stresses and phytohormone treatments suggesting its multifaceted role in cross-talk among stresses and phytohormones in response to PGPR. To the best of our knowledge, this is the first report on detailed analysis of plant growth promotion and stress alleviation by a PGPR in rice seedlings subjected to various abiotic stresses and phytohormone treatments for 0, 1, 3, 10, and 24 h.

Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil

Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.

Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress

Plant growth promoting rhizobacteria (PGPR) hold promising future for sustainable agriculture. Here, we demonstrate a carotenoid producing halotolerant PGPR Dietzia natronolimnaea STR1 protecting wheat plants from salt stress by modulating the transcriptional machinery responsible for salinity tolerance in plants. The expression studies confirmed the involvement of ABA-signalling cascade, as TaABARE and TaOPR1 were upregulated in PGPR inoculated plants leading to induction of TaMYB and TaWRKY expression followed by stimulation of expression of a plethora of stress related genes. Enhanced expression of TaST, a salt stress-induced gene, associated with promoting salinity tolerance was observed in PGPR inoculated plants in comparison to uninoculated control plants. Expression of SOS pathway related genes (SOS1 and SOS4) was modulated in PGPR-applied wheat shoots and root systems. Tissue-specific responses of ion transporters TaNHX1, TaHAK, and TaHKT1, were observed in PGPR-inoculated plants. The enhanced gene expression of various antioxidant enzymes such as APX, MnSOD, CAT, POD, GPX and GR and higher proline content in PGPR-inoculated wheat plants contributed to increased tolerance to salinity stress. Overall, these results indicate that halotolerant PGPR-mediated salinity tolerance is a complex phenomenon that involves modulation of ABA-signalling, SOS pathway, ion transporters and antioxidant machinery.

Pseudomonas putida attunes morphophysiological, biochemical and molecular responses in Cicer arietinum L. during drought stress and recovery

Drought is one of the most important abiotic stresses that adversely affect plant growth and yield potential. However, some drought resistant rhizosphere competent bacteria are known to improve plant health and promote growth during abiotic stresses. Present study showed the role of Pseudomonas putida MTCC5279 (RA) in ameliorating drought stress on cv. BG-362 (desi) and cv. BG-1003 (kabuli) chickpea cultivars under in vitro and green house conditions. Polyethylene glycol-induced drought stress severely affected seed germination in both cultivars which was considerably improved on RA-inoculation. Drought stress significantly affected various growth parameters, water status, membrane integrity, osmolyte accumulation, ROS scavenging ability and stress-responsive gene expressions, which were positively modulated upon application of RA in both chickpea cultivars. Quantitative real-time (qRT)-PCR analysis showed differential expression of genes involved in transcription activation (DREB1A and NAC1), stress response (LEA and DHN), ROS scavenging (CAT, APX, GST), ethylene biosynthesis (ACO and ACS), salicylic acid (PR1) and jasmonate (MYC2) signalling in both chickpea cultivars exposed to drought stress and recovery in the presence or absence of RA. The observations imply that RA confers drought tolerance in chickpea by altering various physical, physiological and biochemical parameters, as well as by modulating differential expression of at least 11 stress-responsive genes. To the best of our knowledge, this is the first report on detailed analysis of plant growth promotion and stress alleviation in one month old desi and kabuli chickpea subjected to drought stress for 0, 1, 3 and 7 days and recovery in the presence of a PGPR.

Synergistic effect of Pseudomonas putida and Bacillus amyloliquefaciens ameliorates drought stress in chickpea (Cicer arietinum L.)

Two plant growth promoting rhizobacteria (PGPR) Pseudomonas putida NBRIRA and Bacillus amyloliquefaciens NBRISN13 with ability to tolerate abiotic stress along with multiple PGP traits like ACC deaminase activity, minerals solubilisation, hormones production, biofilm formation, siderophore activity were evaluated for their synergistic effect to ameliorate drought stress in chickpea. Earlier we have reported both the strains individually for their PGP attributes and stress amelioration in host plants. The present study explains in detail the possibilities and benefits of utilizing these 2 PGPR in consortium for improving the chickpea growth under control and drought stressed condition. In vitro results clearly demonstrate that both the PGPR strains are compatible to each other and their synergistic growth enhances the PGP attributes. Greenhouse experiments were conducted to evaluate the effect of inoculation of both strains individually and consortia in drought tolerant and sensitive cultivars (BG362 and P1003). The growth parameters were observed significantly higher in consortium as compared to individual PGPR. Colonization of both PGPR in chickpea rhizosphere has been visualized by using gfp labeling. Apart from growth parameters, defense enzymes, soil enzymes and microbial diversity were significantly modulated in individually PGPR and in consortia inoculated plants. Negative effects of drought stress has been ameliorated and apparently seen by higher biomass and reversal of stress indicators in chickpea cultivars treated with PGPR individually or in consortia. Findings from the present study demonstrate that synergistic application has better potential to improve plant growth promotion under drought stress conditions.

Unraveling Aspects of Bacillus amyloliquefaciens Mediated Enhanced Production of Rice under Biotic Stress of Rhizoctonia solani

Rhizoctonia solani is a necrotrophic fungi causing sheath blight in rice leading to substantial loss in yield. Excessive and persistent use of preventive chemicals raises human health and environment safety concerns. As an alternative, use of biocontrol agents is highly recommended. In the present study, an abiotic stress tolerant, plant growth promoting rhizobacteria Bacillus amyloliquefaciens (SN13) is demonstrated to act as a biocontrol agent and enhance immune response against R. solani in rice by modulating various physiological, metabolic, and molecular functions. A sustained tolerance by SN13 primed plant over a longer period of time, post R. solani infection may be attributed to several unconventional aspects of the plants' physiological status. The prolonged stress tolerance observed in presence of SN13 is characterized by (a) involvement of bacterial mycolytic enzymes, (b) sustained maintenance of elicitors to keep the immune system induced involving non-metabolizable sugars such as turanose besides the known elicitors, (c) a delicate balance of ROS and ROS scavengers through production of proline, mannitol, and arabitol and rare sugars like fructopyranose, β-D-glucopyranose and myoinositol and expression of ferric reductases and hypoxia induced proteins, (d) production of metabolites like quinazoline and expression of terpene synthase, and (e) hormonal cross talk. As the novel aspect of biological control this study highlights the role of rare sugars, maintenance of hypoxic conditions, and sucrose and starch metabolism in B. amyloliquefaciens (SN13) mediated sustained biotic stress tolerance in rice.

Metabolite profiling reveals abiotic stress tolerance in Tn5 mutant of Pseudomonas putida

Pseudomonas is an efficient plant growth–promoting rhizobacteria (PGPR); however, intolerance to drought and high temperature limit its application in agriculture as a bioinoculant. Transposon 5 (Tn5) mutagenesis was used to generate a stress tolerant mutant from a PGPR Pseudomonas putida NBRI1108 isolated from chickpea rhizosphere. A mutant NBRI1108T, selected after screening of nearly 10,000 transconjugants, exhibited significant tolerance towards high temperature and drought. Southern hybridization analysis of EcoRI and XhoI restricted genomic DNA of NBRI1108T confirmed that it had a single Tn5 insertion. The metabolic changes in the polar and non-polar extracts of NBRI1108 and NBRI1108T were examined using ¹H, ³¹P nuclear magnetic resonance (NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS). Thirty six chemically diverse metabolites consisting of amino acids, fatty acids and phospholipids were identified and quantified. Insertion of Tn5 influenced amino acid and phospholipid metabolism and resulted in significantly higher concentration of aspartic acid, glutamic acid, glycinebetaine, glycerophosphatidylcholine (GPC) and putrescine in NBRI1108T as compared to that in NBRI1108. The concentration of glutamic acid, glycinebetaine and GPC increased by 34%, 95% and 100%, respectively in the NBRI1108T as compared to that in NBRI1108. High concentration of glycerophosphatidylethanolamine (GPE) and undetected GPC in NBRI1108 indicates that biosynthesis of GPE may have taken place via the methylation pathway of phospholipid biosynthesis. However, high GPC and low GPE concentration in NBRI1108T suggest that methylation pathway and phosphatidylcholine synthase (PCS) pathway of phospholipid biosynthesis are being followed in the NBRI1108T. Application of multivariate principal component analysis (PCA) on the quantified metabolites revealed clear variations in NBRI1108 and NBRI1108T in polar and non-polar metabolites. Identification of abiotic stress tolerant metabolites from the NBRI1108T suggest that Tn5 mutagenesis enhanced tolerance towards high temperature and drought. Tolerance to drought was further confirmed in greenhouse experiments with maize as host plant, where NBRI1108T showed relatively high biomass under drought conditions.