VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Effects of combined microplastics and heavy metals pollution on terrestrial plants and rhizosphere environment: A review

Microplastics (MPs) can enter the soil environment through industry, agricultural production and daily life sources. Their interaction with heavy metals (HMs) poses a significant threat to a variety of terrestrial ecosystems, including agricultural ones, thereby affecting crop quality and threatening human health. This review initially addresses the impact of single and combined contamination with MPs and HMs on soil environment, including changes in soil physicochemical properties, microbial community structure and diversity, fertility, enzyme activity and resistance genes, as well as alterations in heavy metal speciation. The article further explores the effects of this pollution on the growth characteristics of terrestrial plants, such as plant biomass, antioxidant systems, metabolites and photosynthesis. In general, the combined contaminants tend to significantly affect soil environment and terrestrial plant growth, i.e., the impact of combined contaminants on plants weight ranged from -87.5% to 4.55%. Similarities and differences in contamination impact levels stem from the variations in contaminant types, sizes and doses of contaminants and the specific plant growth environments. In addition, MPs can not only infiltrate plants directly, but also significantly affect the accumulation of HMs in terrestrial plants. The heavy metals concentration in plants under the treatment of MPs were 70.26%-36.80%. The co-occurrence of these two pollution types can pose a serious threat to crop productivity and safety. Finally, this study proposes suggestions for future research aiming to address current gaps in knowledge, raises awareness about the impact of combined MPs + HMs pollution on plant growth and eco-environmental security.

Endophytic fungal community of Rosa damascena Mill. as a promising source of indigenous biostimulants: Elucidating its spatial distribution, chemical diversity, and ecological functions

The role of endophytes in maintaining healthy plant ecosystems and holding promise for agriculture and food security is deeply appreciated. In the current study, we determine the community structure, spatial distribution, chemical diversity, and ecological functions of fungal endophytes of Rosa damascena growing in the North-Western Himalayas. Culture-dependent methods revealed that R. damascena supported a rich endophyte diversity comprising 32 genera and 68 OTUs. The diversity was governed by climate, altitude, and tissue type. Species of Aspergillus, Cladosporium, Penicillium, and Diaporthe were the core endophytes of the host plant consisting of 48.8% of the endophytes collectively. The predominant pathogen of the host was Alternaria spp., especially A. alternata. GC-MS analyses affirmed the production of diverse arrays of volatile organic compounds (VOC) by individual endophytes. Among the primary rose oil components, Diaporthe melonis RDE257, and Periconia verrucosa RDE85 produced phenyl ethyl alcohol (PEA) and benzyl alcohol (BA). The endophytes displayed varied levels of plant growth-promoting, colonization, and anti-pathogenic traits. Between the selected endophytes, P. verrucosa and D. melonis significantly potentiated plant growth and the flavonoids and chlorophyll content in the host. The potential of these two endophytes and their metabolites PEA and BA was confirmed on Nicotiana tabacum. The treatments of the metabolites and individual endophytes enhanced the growth parameters in the model plant significantly. The results imply that P. verrucosa and D. melonis are potential plant growth enhancers and their activity may be partially due to the production of PEA and BA. Thus, R. damascena harbors diverse endophytes with potential applications in disease suppression and host growth promotion. Further investigations at the molecular level are warranted to develop green endophytic agents for sustainable cultivation of R. damascena and biocontrol of leaf spot disease.

Differential roles of Cassia tora 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase in trade-off between plant growth and drought tolerance

Due to global climate change, drought is emerging as a major threat to plant growth and agricultural productivity. Abscisic acid (ABA) has been implicated in plant drought tolerance, however, its retarding effects on plant growth cannot be ignored. The reactions catalyzed by 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) proteins are critical steps within the isoprenoid biosynthesis in plants. Here, five DXS (CtDXS1-5) and two DXR (CtDXR1-2) genes were identified from Cassia tora genome. Based on multiple assays including the phylogeny, cis-acting element, expression pattern, and subcellular localization, CtDXS1 and CtDXR1 genes might be potential candidates controlling the isoprenoid biosynthesis. Intriguingly, CtDXS1 transgenic plants resulted in drought tolerance but retardant growth, while CtDXR1 transgenic plants exhibited both enhanced drought tolerance and increased growth. By comparison of β-carotene, chlorophyll, abscisic acid (ABA) and gibberellin 3 (GA3) contents in wild-type and transgenic plants, the absolute contents and (or) altered GA3/ABA levels were suggested to be responsible for the balance between drought tolerance and plant growth. The transcriptome of CtDXR1 transgenic plants suggested that the transcript levels of key genes, such as DXS, 9-cis-epoxycarotenoid dioxygenases (NCED), ent-kaurene synthase (KS) and etc, involved with chlorophyll, β-carotene, ABA and GA3 biosynthesis were induced and their contents increased accordingly. Collectively, the trade-off effect induced by CtDXR1 was associated with redesigning architecture in phytohormone homeostasis and thus was highlighted for future breeding purposes.

Co-evolution within the plant holobiont drives host performance

Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.

Fungal volatiles have physiological properties

All fungi emit mixtures of volatile organic compounds (VOCs) during growth. The qualitative and quantitative composition of these volatile mixtures vary with the species of fungus, the age of the fungus, and the environmental parameters attending growth. In nature, fungal VOCs are found as combinations of alcohols, aldehydes, acids, ethers, esters, ketones, terpenes, thiols and their derivatives, and are responsible for the characteristic odors associated with molds, mushrooms and yeasts. One of the single most common fungal volatiles is 1-octen-3-ol also known as "mushroom alcohol" or "matsutake alcohol." Many volatiles, including 1-octen-3-ol, serve as communication agents and display biological activity as germination inhibitors, plant growth retardants or promoters, and as semiochemicals ("infochemicals") in interactions with arthropods. Volatiles are understudied and underappreciated elements of the chemical lives of fungi. This review gives a brief introduction to fungal volatiles in hopes of raising awareness of the physiological importance of these gas phase fungal metabolites to encourage mycologists and other biologists to stop "throwing away the head space."

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

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

Toward the Analysis of Volatile Organic Compounds from Tomato Plants (Solanum lycopersicum L.) Treated with Trichoderma virens or/and Botrytis cinerea

Gray mold caused by Botrytis cinerea causes significant losses in tomato crops. B. cinerea infection may be halted by volatile organic compounds (VOCs), which may exhibit fungistatic activity or enhance the defense responses of plants against the pathogen. The enhanced VOC generation was observed in tomato (Solanum lycopersicum L.), with the soil-applied biocontrol agent Trichoderma virens (10⁶ spores/1 g soil), which decreased the gray mold disease index in plant leaves at 72 hpi with B. cinerea suspension (1 × 10⁶ spores/mL). The tomato leaves were found to emit 100 VOCs, annotated and putatively annotated, assigned to six classes by the headspace GCxGC TOF-MS method. In Trichoderma-treated plants with a decreased grey mold disease index, the increased emission or appearance of 2-hexenal, (2E,4E)-2,4-hexadienal, 2-hexyn-1-ol, 3,6,6-trimethyl-2-cyclohexen-1-one, 1-octen-3-ol, 1,5-octadien-3-ol, 2-octenal, octanal, 2-penten-1-ol, (Z)-6-nonenal, prenol, and acetophenone, and 2-hydroxyacetophenone, β-phellandrene, β-myrcene, 2-carene, δ-elemene, and isocaryophyllene, and β-ionone, 2-methyltetrahydrofuran, and 2-ethyl-, and 2-pentylfuran, ethyl, butyl, and hexyl acetate were most noticeable. This is the first report of the VOCs that were released by tomato plants treated with Trichoderma, which may be used in practice against B. cinerea, although this requires further analysis, including the complete identification of VOCs and determination of their potential as agents that are capable of the direct and indirect control of pathogens.

Pepper growth promotion and biocontrol against Xanthomonas euvesicatoria by Bacillus cereus and Bacillus thuringiensis formulations

Background

Bacillus genus has been used in horticultural crops as a biocontrol agent against insect pests, microbial phytopathogens, and plant growth-promoting bacteria (PGPB), representing an alternative to agrochemicals. In particular, B. cereus (Bc) and B. thuringiensis (Bt) have been studied for their fungicidal and insecticidal activities. However, their use as biofertilizer formulations and biocontrol agents against phytopathogenic bacteria is limited.

Objective

To evaluate Bc and Bt formulations as PGPB and biocontrol agents against the bacterial spot agent Xanthomonas euvesicatoria (Xe) in greenhouse-grown chili peppers.

Methods

Bc and Bt isolates obtained from soil samples were identified and characterized using conventional biochemical and multiplex PCR identification methods. Bioassays to determine Bc and Bt isolates potential as PGPB were evaluated on chili pepper seedlings in seedbeds. In addition, formulations based on Bc (F-BC26 and F-BC08) and Bt (F-BT24) strains were assessed as biofertilizers on pepper, under controlled conditions. Furthermore, in vitro antagonism assays were performed by confronting Bc and Bt isolate formulations against Xe isolates in direct (foliage) and indirect (resistance induction) phytopathogen biocontrol assays on pepper plants, which were grown under controlled conditions for 15 d after formulations treatment.

Results

Isolates were identified as Bc and Bt. Formulations significantly improved pepper growth in seedbeds and pots, whereas in vitro bioassays demonstrated the bactericidal effect of Bc and Bt strains against Xe isolates. Furthermore, assays showed significant plant protection by F-BC26, F-BC08, and F-BT24 formulated strains against Xe.

Conclusion

Results indicated that F-BT24 and F-BC26 isolates formulations promoted pepper growth and protected it against Xanthomonas euvesicatoria.

Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition

Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R² ≥ 0.5) while upregulated genes are under natural selection pressure (R² ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length.

Perfume Guns: Potential of Yeast Volatile Organic Compounds in the Biological Control of Mycotoxin-Producing Fungi

Pathogenic fungi in the genera Alternaria, Aspergillus, Botrytis, Fusarium, Geotrichum, Gloeosporium, Monilinia, Mucor, Penicillium, and Rhizopus are the most common cause of pre- and postharvest diseases of fruit, vegetable, root and grain commodities. Some species are also able to produce mycotoxins, secondary metabolites having toxic effects on human and non-human animals upon ingestion of contaminated food and feed. Synthetic fungicides still represent the most common tool to control these pathogens. However, long-term application of fungicides has led to unacceptable pollution and may favour the selection of fungicide-resistant mutants. Microbial biocontrol agents may reduce the incidence of toxigenic fungi through a wide array of mechanisms, including competition for the ecological niche, antibiosis, mycoparasitism, and the induction of resistance in the host plant tissues. In recent years, the emission of volatile organic compounds (VOCs) has been proposed as a key mechanism of biocontrol. Their bioactivity and the absence of residues make the use of microbial VOCs a sustainable and effective alternative to synthetic fungicides in the management of postharvest pathogens, particularly in airtight environments. In this review, we will focus on the possibility of applying yeast VOCs in the biocontrol of mycotoxigenic fungi affecting stored food and feed.

Microbial Volatile Organic Compounds: An Alternative for Chemical Fertilizers in Sustainable Agriculture Development

Microorganisms are exceptional at producing several volatile substances called microbial volatile organic compounds (mVOCs). The mVOCs allow the microorganism to communicate with other organisms via both inter and intracellular signaling pathways. Recent investigation has revealed that mVOCs are chemically very diverse and play vital roles in plant interactions and microbial communication. The mVOCs can also modify the plant's physiological and hormonal pathways to augment plant growth and production. Moreover, mVOCs have been affirmed for effective alleviation of stresses, and also act as an elicitor of plant immunity. Thus, mVOCs act as an effective alternative to various chemical fertilizers and pesticides. The present review summarizes the recent findings about mVOCs and their roles in inter and intra-kingdoms interactions. Prospects for improving soil fertility, food safety, and security are affirmed for mVOCs application for sustainable agriculture.

Volatile organic compounds shape belowground plant-fungi interactions

Volatile organic compounds (VOCs), a bouquet of chemical compounds released by all life forms, play essential roles in trophic interactions. VOCs can facilitate a large number of interactions with different organisms belowground. VOCs-regulated plant-plant or plant-insect interaction both below and aboveground has been reported extensively. Nevertheless, there is little information about the role of VOCs derived from soilborne pathogenic fungi and beneficial fungi, particularly mycorrhizae, in influencing plant performance. In this review, we show how plant VOCs regulate plant-soilborne pathogenic fungi and beneficial fungi (mycorrhizae) interactions. How fungal VOCs mediate plant-soilborne pathogenic and beneficial fungi interactions are presented and the most common methods to collect and analyze belowground volatiles are evaluated. Furthermore, we suggest a promising method for future research on belowground VOCs.

Determination of Reactive Oxygen or Nitrogen Species and Novel Volatile Organic Compounds in the Defense Responses of Tomato Plants against Botrytis cinerea Induced by Trichoderma virens TRS 106

In the present study, Trichoderma virens TRS 106 decreased grey mould disease caused by Botrytis cinerea in tomato plants (S. lycopersicum L.) by enhancing their defense responses. Generally, plants belonging to the ‘Remiz’ variety, which were infected more effectively by B. cinerea than ‘Perkoz’ plants, generated more reactive molecules such as superoxide (O₂⁻) and peroxynitrite (ONOO⁻), and less hydrogen peroxide (H₂O₂), S-nitrosothiols (SNO), and green leaf volatiles (GLV). Among the new findings, histochemical analyses revealed that B. cinerea infection caused nitric oxide (NO) accumulation in chloroplasts, which was not detected in plants treated with TRS 106, while treatment of plants with TRS 106 caused systemic spreading of H₂O₂ and NO accumulation in apoplast and nuclei. SPME-GCxGC TOF-MS analysis revealed 24 volatile organic compounds (VOC) released by tomato plants treated with TRS 106. Some of the hexanol derivatives, e.g., 4-ethyl-2-hexynal and 1,5-hexadien-3-ol, and salicylic acid derivatives, e.g., 4-hepten-2-yl and isoamyl salicylates, are considered in the protection of tomato plants against B. cinerea for the first time. The results are valuable for further studies aiming to further determine the location and function of NO in plants treated with Trichoderma and check the contribution of detected VOC in plant protection against B. cinerea.

Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned?

The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.

Neocosmospora rubicola, a stem rot disease in potato: Characterization, distribution and management

Potato (Solanum tuberosum L.) is one of the most important crops in maintaining global food security. Plant stand and yield are affected by production technology, climate, soil type, and biotic factors such as insects and diseases. Numerous fungal diseases including Neocosmospora rubicola, causing stem rot, are known to have negative effects on potato growth and yield quality. The pathogen is known to stunt growth and cause leaf yellowing with grayish-black stems. The infectivity of N. rubicola across a number of crops indicates the need to search for appropriate management approaches. Synthetic pesticides application is a major method to mitigate almost all potato diseases at this time. However, these pesticides significantly contribute to environmental damage and continuous use leads to pesticide resistance by pathogens. Consumers interest in organic products have influenced agronomists to shift toward the use of biologicals in controlling most pathogens, including N. rubicola. This review is an initial effort to carefully examine current and alternative approaches to control N. rubicola that are both environmentally safe and ecologically sound. Therefore, this review aims to draw attention to the N. rubicola distribution and symptomatology, and sustainable management strategies for potato stem rot disease. Applications of plant growth promoting bacteria (PGPB) as bioformulations with synthetic fertilizers have the potential to increase the tuber yield in both healthy and N. rubicola infested soils. Phosphorus and nitrogen applications along with the PGPB can improve plants uptake efficiency and reduce infestation of pathogen leading to increased yield. Therefore, to control N. rubicola infestation, with maximum tuber yield benefits, a pre-application of the biofertilizer is shown as a better option, based on the most recent studies. With the current limited information on the disease, precise screening of the available resistant potato cultivars, developing molecular markers for resistance genes against N. rubicola will assist to reduce spread and virulence of the pathogen.

Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health

Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.

Plant growth-promoting and non-promoting rhizobacteria from avocado trees differentially emit volatiles that influence growth of Arabidopsis thaliana

Microbial volatile organic compounds (mVOCs) play important roles in inter- and intra-kingdom interactions, and they are also important as signal molecules in physiological processes acting either as plant growth-promoting or negatively modulating plant development. We investigated the effects of mVOCs emitted by PGPR vs non-PGPR from avocado trees (Persea americana) on growth of Arabidopsis thaliana seedlings. Chemical diversity of mVOCs was determined by SPME-GC-MS; selected compounds were screened in dose-response experiments in A. thaliana transgenic lines. We found that plant growth parameters were affected depending on inoculum concentration. Twenty-six compounds were identified in PGPR and non-PGPR with eight of them not previously reported. The VOCs signatures were differential between those groups. 4-methyl-2-pentanone, 1-nonanol, 2-phenyl-2-propanol and ethyl isovalerate modified primary root architecture influencing the expression of auxin- and JA-responsive genes, and cell division. Lateral root formation was regulated by 4-methyl-2-pentanone, 3-methyl-1-butanol, 1-nonanol and ethyl isovalerate suggesting a participation via JA signalling. Our study revealed the differential emission of volatiles by PGPR vs non-PGPR from avocado trees and provides a general view about the mechanisms by which those volatiles influence plant growth and development. Rhizobacteria strains and mVOCs here reported are promising for improvement the growth and productivity of avocado crop.

Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases

Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world's population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30-70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered.

Priming Seeds with Indole and (Z)-3-Hexenyl Acetate Enhances Resistance Against Herbivores and Stimulates Growth

A striking feature of plant ecology is the ability of plants to detect and respond to environmental cues such as herbivore-induced plant volatiles (HIPVs) by priming or directly activating defenses against future herbivores. However, whether seeds also respond to compounds that are common constituents of HIPV blends and initiate future plant resistance is unknown. Considering that seeds depend on other environmental cues to determine basic survival traits such as germination timing, we predicted that seeds exposed to synthetic constituents of HIPV blends would generate well-defended plants. We investigated the effect of seed exposure to common volatiles on growth, reproduction, and resistance characteristics in the model plants Arabidopsis thaliana and Medicago truncatula using herbivores from two feeding guilds. After seed scarification and vernalization, we treated seeds with one of seven different plant-derived volatile compounds for 24 h. Seeds were then germinated and the resulting plants were assayed for growth, herbivore resistance, and expression of inducible defense genes. Of all the synthetic volatiles tested, indole specifically reduced both beet armyworm growth on A. thaliana and pea aphid fecundity on M. truncatula. The induction of defense genes was not affected by seed exposure to indole in either plant species, indicating that activation of direct resistance rather than inducible resistance is the mechanism by which seed priming operates. Moreover, neither plant species showed any negative effect of seed exposure to any synthetic volatile on vegetative and reproductive growth. Rather, M. truncatula plants derived from seeds exposed to (Z)-3-hexanol and (Z)-3-hexenyl acetate grew larger compared to controls. Our results indicate that seeds are sensitive to specific volatiles in ways that enhance resistance profiles with no apparent costs in terms of growth. Seed priming by HIPVs may represent a novel ecological mechanism of plant-to-plant interactions, with broad potential applications in agriculture and seed conservation.

Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions

Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.

Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions

Sustainable agriculture demands the balanced use of inorganic, organic, and microbial biofertilizers for enhanced plant productivity and soil fertility. Plant growth-enhancing rhizospheric bacteria can be an excellent biotechnological tool to augment plant productivity in different agricultural setups. We present an overview of microbial mechanisms which directly or indirectly contribute to plant growth, health, and development under highly variable environmental conditions. The rhizosphere microbiomes promote plant growth, suppress pathogens and nematodes, prime plants immunity, and alleviate abiotic stress. The prospective of beneficial rhizobacteria to facilitate plant growth is of primary importance, particularly under abiotic and biotic stresses. Such microbe can promote plant health, tolerate stress, even remediate soil pollutants, and suppress phytopathogens. Providing extra facts and a superior understanding of microbial traits underlying plant growth promotion can stir the development of microbial-based innovative solutions for the betterment of agriculture. Furthermore, the application of novel scientific approaches for facilitating the design of crop-specific microbial biofertilizers is discussed. In this context, we have highlighted the exercise of "multi-omics" methods for assessing the microbiome's impact on plant growth, health, and overall fitness via analyzing biochemical, physiological, and molecular facets. Furthermore, the role of clustered regularly interspaced short palindromic repeats (CRISPR) based genome alteration and nanotechnology for improving the agronomic performance and rhizosphere microbiome is also briefed. In a nutshell, the paper summarizes the recent vital molecular processes that underlie the different beneficial plant-microbe interactions imperative for enhancing plant fitness and resilience under-challenged agriculture.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

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.

Action mechanisms of small microbial volatile compounds in plants

Microorganisms communicate with plants by exchanging chemical signals throughout the phytosphere. Before direct contact with plants occurs, beneficial microorganisms emit a plethora of volatile compounds that promote plant growth and photosynthesis as well as developmental, metabolic, transcriptional, and proteomic changes in plants. These compounds can also induce systemic drought tolerance and improve water and nutrient acquisition. Recent studies have shown that this capacity is not restricted to beneficial microbes; it also extends to phytopathogens. Plant responses to microbial volatile compounds have frequently been associated with volatile organic compounds with molecular masses ranging between ~ 45Da and 300Da. However, microorganisms also release a limited number of volatile compounds with molecular masses of less than ~45Da that react with proteins and/or act as signaling molecules. Some of these compounds promote photosynthesis and growth when exogenously applied in low concentrations. Recently, evidence has shown that small volatile compounds are important determinants of plant responses to microbial volatile emissions. However, the regulatory mechanisms involved in these responses remain poorly understood. This review summarizes current knowledge of biochemical and molecular mechanisms involved in plant growth, development, and metabolic responses to small microbial volatile compounds.

Efficiency of microbial bio-agents as elicitors in plant defense mechanism under biotic stress: A review

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MBCAs played beneficial role to protect plants from harmful pathogens to control plant diseases.

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MBCAs also support in plant growth promotion and stress tolerance.

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MBCAs act as elicitors to induce a signal to stimulate the plant defense mechanism against pathogens.

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Reticine A-induced hypersensitive reaction, systemic accumulation of H₂O₂ and salicylic acid.

Numerous harmful microorganisms and insect pests have the ability to cause plant infections or damage, which is mostly controlled by toxic chemical agents. These chemical compounds and their derivatives exhibit hazardous effects on habitats and human life too. Hence, there's a need to develop novel, more effective and safe bio-control agents. A variety of microbes such as viruses, bacteria, and fungi possess a great potential to fight against phytopathogens and thus can be used as bio-control agents instead of harmful chemical compounds. These naturally occurring microorganisms are applied to the plants in order to control phytopathogens. Moreover, practicing them appropriately for agriculture management can be a way towards a sustainable approach. The MBCAs follow various modes of action and act as elicitors where they induce a signal to activate plant defense mechanisms against a variety of pathogens. MBCAs control phytopathogens and help in disease suppression through the production of enzymes, antimicrobial compounds, antagonist activity involving hyper-parasitism, induced resistance, competitive inhibition, etc. Efficient recognition of pathogens and prompt defensive response are key factors of induced resistance in plants. This resistance phenomenon is pertaining to a complex cascade that involves an increased amount of defensive proteins, salicylic acid (SA), or induction of signaling pathways dependent on plant hormones. Although, there's a dearth of information about the exact mechanism of plant-induced resistance, the studies conducted at the physiological, biochemical and genetic levels. These studies tried to explain a series of plant defensive responses triggered by bio-control agents that may enhance the defensive capacity of plants. Several natural and recombinant microorganisms are commercially available as bio-control agents that mainly include strains of Bacillus, Pseudomonads and Trichoderma. However, the complete understanding of microbial bio-control agents and their interactions at cellular and molecular levels will facilitate the screening of effective and eco-friendly bio-agents, thereby increasing the scope of MBCAs. This article is a comprehensive review that highlights the importance of microbial agents as elicitors in the activation and regulation of plant defense mechanisms in response to a variety of pathogens.

PGPR in Agriculture: A Sustainable Approach to Increasing Climate Change Resilience

Growing environmental concerns are potentially narrowing global yield capacity of agricultural systems. Climate change is the most significant problem the world is currently facing. To meet global food demand, food production must be doubled by 2050; over exploitation of arable lands using unsustainable techniques might resolve food demand issues, but they have negative environmental effects. Current crop production systems are a major reason for changing global climate through diminishing biodiversity, physical and chemical soil degradation, and water pollution. The over application of fertilizers and pesticides contribute to climate change through greenhouse gas emissions (GHG) and toxic soil depositions. At this crucial time, there is a pressing need to transition to more sustainable crop production practices, ones that concentrate more on promoting sustainable mechanisms, which enable crops to grow well in resource limited and environmentally challenging environments, and also develop crops with greater resource use efficiency that have optimum sustainable yields across a wider array of environmental conditions. The phytomicrobiome is considered as one of the best strategies; a better alternative for sustainable agriculture, and a viable solution to meet the twin challenges of global food security and environmental stability. Use of the phytomicrobiome, due to its sustainable and environmentally friendly mechanisms of plant growth promotion, is becoming more widespread in the agricultural industry. Therefore, in this review, we emphasize the contribution of beneficial phytomicrobiome members, particularly plant growth promoting rhizobacteria (PGPR), as a strategy to sustainable improvement of plant growth and production in the face of climate change. Also, the roles of soil dwelling microbes in stress amelioration, nutrient supply (nitrogen fixation, phosphorus solubilization), and phytohormone production along with the factors that could potentially affect their efficiency have been discussed extensively. Lastly, limitations to expansion and use of biobased techniques, for instance, the perspective of crop producers, indigenous microbial competition and regulatory approval are discussed. This review largely focusses on the importance and need of sustainable and environmentally friendly approaches such as biobased/PGPR-based techniques in our agricultural systems, especially in the context of current climate change conditions, which are almost certain to worsen in near future.

Basidiomycetes Are Particularly Sensitive to Bacterial Volatile Compounds: Mechanistic Insight Into the Case Study of Pseudomonas protegens Volatilome Against Heterobasidion abietinum

Volatile organic compounds (VOCs) play an important role in the communication among organisms, including plants, beneficial or pathogenic microbes, and pests. In vitro, we observed that the growth of seven out of eight Basidiomycete species tested was inhibited by the VOCs of the biocontrol agent Pseudomonas protegens strain CHA0. In the Ascomycota phylum, only some species were sensitive (e.g., Sclerotinia sclerotiorum, Botrytis cinerea, etc.) but others were resistant (e.g., Fusarium oxysporum f. sp. cubense, Verticillium dahliae, etc.). We further discovered that CHA0 as well as other ten beneficial or phytopathogenic bacterial strains were all able to inhibit Heterobasidion abietinum, which was used in this research as a model species. Moreover, such an inhibition occurred only when bacteria grew on media containing digested proteins like peptone or tryptone (e.g., Luria-Bertani agar or LBA). Also, the inhibition co-occurred with a pH increase of the agar medium where the fungus grew. Therefore, biogenic ammonia originating from protein degradation by bacteria was hypothesized to play a major role in fungus inhibition. Indeed, when tested as a synthetic compound, it was highly toxic to H. abietinum (effective concentration 50% or EC₅₀ = 1.18 M; minimum inhibitory concentration or MIC = 2.14 M). Using gas chromatography coupled to mass spectrometry (GC/MS), eight VOCs were found specifically emitted by CHA0 grown on LBA compared to the bacterium grown on potato dextrose agar (PDA). Among them, two compounds were even more toxic than ammonia against H. abietinum: dimethyl trisulfide had EC₅₀ = 0.02 M and MIC = 0.2 M, and 2-ethylhexanol had EC₅₀ = 0.33 M and MIC = 0.77 M. The fungus growth inhibition was the result of severe cellular and sub-cellular alterations of hyphae occurring as early as 15 min of exposure to VOCs, as evidenced by transmission and scanning electron microscopy observations. Transcriptome reprogramming of H. abietinum induced by CHA0’s VOCs pointed out that detrimental effects occurred on ribosomes and protein synthesis while the cells tried to react by activating defense mechanisms, which required a lot of energy diverted from the growth and development (fitness cost).

Plant volatiles as cues and signals in plant communication

Volatile organic compounds are important mediators of mutualistic interactions between plants and their physical and biological surroundings. Volatiles rapidly indicate competition or potential threat before these can take place, and they regulate and coordinate adaptation responses in neighbouring plants, fine-tuning them to match the exact stress encountered. Ecological specificity and context-dependency of plant-plant communication mediated by volatiles represent important factors that determine plant performance in specific environments. In this review, we synthesise the recent progress made in understanding the role of plant volatiles as mediators of plant interactions at the individual and community levels, highlighting the complexity of the plant receiver response to diverse volatile cues and signals and addressing how specific responses shape plant growth and survival. Finally, we outline the knowledge gaps and provide directions for future research. The complex dialogue between the emitter and receiver based on either volatile cues or signals determines the outcome of information exchange, which shapes the communication pattern between individuals at the community level and determines their ecological implications at other trophic levels.

Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

BACKGROUND

Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity.

RESULTS

The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes.

CONCLUSIONS

Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.

Fungal volatiles emitted by members of the microbiome of desert plants are diverse and capable of promoting plant growth

Fungi represent a group of eukaryotic microorganisms that are an important part of the plant microbiome. They produce a vast array of metabolites, including fungal volatile organic compounds (fVOCs). However, the diversity and biological activities of fVOCs emitted by the mycobiota of plants native to arid and semi-arid environments remain under-explored. We characterized the chemical diversity of fVOCs produced by 22 representative members of the microbiome of agaves and cacti using SPME-GC-MS. We further tested the effects of pure compounds on the growth and development of Arabidopsis thaliana and host plants. Members of the Sordariomycetes (nine strains), Eurotiomycetes (three), Dothideomycetes (eight), Saccharomycetes (one) and Mucoromycetes (one) were included in our study. We identified 94 fungal organic volatiles classified into nine chemical classes. Terpenes showed the greatest chemical diversity, followed by alcohols and aliphatic compounds. We discovered that camphene and benzyl benzoate, together with the widely distributed and already tested benzyl alcohol, 2-phenylethyl alcohol and 3-methyl-1-butanol, improved plant growth and development of A. thaliana, Agave tequilana and Agave salmiana. Our studies on the fungal VOCs from desert plants underscore an untapped chemical diversity with promising biotechnological applications.

Engineering disease resistant plants through CRISPR-Cas9 technology

Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.

Rhizobial Volatiles: Potential New Players in the Complex Interkingdom Signaling With Legumes

Bacteria release a wide range of volatile compounds that play important roles in intermicrobial and interkingdom communication. Volatile metabolites emitted by rhizobacteria can promote plant growth and increase plant resistance to both biotic and abiotic stresses. Rhizobia establish beneficial nitrogen-fixing symbiosis with legume plants in a process starting with a chemical dialog in the rhizosphere involving various diffusible compounds. Despite being one of the most studied plant-interacting microorganisms, very little is known about volatile compounds produced by rhizobia and their biological/ecological role. Evidence indicates that plants can perceive and respond to volatiles emitted by rhizobia. In this perspective, we present recent data that open the possibility that rhizobial volatile compounds have a role in symbiotic interactions with legumes and discuss future directions that could shed light onto this area of investigation.

Volatiles from soil-borne fungi affect directional growth of roots

Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.

Beneficial features of plant growth-promoting rhizobacteria for improving plant growth and health in challenging conditions: A methodical review

New eco-friendly approaches are required to improve plant biomass production. Beneficial plant growth-promoting (PGP) bacteria may be exploited as excellent and efficient biotechnological tools to improve plant growth in various - including stressful - environments. We present an overview of bacterial mechanisms which contribute to plant health, growth, and development. Plant growth promoting rhizobacteria (PGPR) can interact with plants directly by increasing the availability of essential nutrients (e.g. nitrogen, phosphorus, iron), production and regulation of compounds involved in plant growth (e.g. phytohormones), and stress hormonal status (e.g. ethylene levels by ACC-deaminase). They can also indirectly affect plants by protecting them against diseases via competition with pathogens for highly limited nutrients, biocontrol of pathogens through production of aseptic-activity compounds, synthesis of fungal cell wall lysing enzymes, and induction of systemic responses in host plants. The potential of PGPR to facilitate plant growth is of fundamental importance, especially in case of abiotic stress, where bacteria can support plant fitness, stress tolerance, and/or even assist in remediation of pollutants. Providing additional evidence and better understanding of bacterial traits underlying plant growth-promotion can inspire and stir up the development of innovative solutions exploiting PGPR in times of highly variable environmental and climatological conditions.

Modes of Action of Microbial Biocontrol in the Phyllosphere

A fast-growing field of research focuses on microbial biocontrol in the phyllosphere. Phyllosphere microorganisms possess a wide range of adaptation and biocontrol factors, which allow them to adapt to the phyllosphere environment and inhibit the growth of microbial pathogens, thus sustaining plant health. These biocontrol factors can be categorized in direct, microbe-microbe, and indirect, host-microbe, interactions. This review gives an overview of the modes of action of microbial adaptation and biocontrol in the phyllosphere, the genetic basis of the mechanisms, and examples of experiments that can detect these mechanisms in laboratory and field experiments. Detailed insights in such mechanisms are key for the rational design of novel microbial biocontrol strategies and increase crop protection and production. Such novel biocontrol strategies are much needed, as ensuring sufficient and consistent food production for a growing world population, while protecting our environment, is one of the biggest challenges of our time.

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.

Bacteria from native soil in combination with arbuscular mycorrhizal fungi augment wheat yield and biofortification

Plant growth promoting bacteria (PGPB) have been used to enhance crop productivity. The effect of native PGPB and arbuscular mycorrhizal (AM) fungi in combination on wheat yield, biofortification and soil enzymatic activity is a relatively unexplored area. Twenty seven bacterial isolates from three different soils were characterized for their plant growth promoting traits. A total of three native and five non-native bacteria were used with and without arbuscular mycorrhizal (AM) fungi in an open greenhouse pot experiment with two wheat varieties to evaluate their effect on wheat yield, nutrient uptake, and soil health parameters. Wheat plants subjected to native PGPB (CP4) (Bacillus subtilis) and AM fungi treatment gave the best results with reference to macronutrient (nitrogen and phosphorus), micronutrient (iron and zinc) content in wheat grains and yield-related parameters, including thousand grain weight, number of grains per spike and total tillers per plant in both wheat cultivars. Treatment with CP4 and CP4 plus AM fungi enhanced total chlorophyll in wheat leaves indicating higher photosynthetic activity. Significant improvement in soil health-related parameters, including soil organic matter and dehydrogenase activity, was observed. Significant correlation among grain yield-related parameters, nutrient enhancement, and soil health parameters was observed in PGPB and AM fungi treated plants, especially HD-3086. These results provide a roadmap for utilizing native PGPB and AM fungi for enhancing wheat production in Punjab state of India and exploring their utility in other parts of the country with different soil and environmental conditions.

Dimethyl disulfide exerts antifungal activity against Sclerotinia minor by damaging its membrane and induces systemic resistance in host plants

Microbial volatile compounds (MVCs) significantly influence the growth of plants and phytopathogens. However, the practical application of MVCs at the field level is limited by the fact that the concentrations at which these compounds antagonize the pathogens are often toxic for the plants. In this study, we investigated the effect of dimethyl disulfide (DMDS), one of the MVCs produced by microorganisms, on the fitness of tomato plants and its fungicidal potential against a fungal phytopathogen, Sclerotinia minor. DMDS showed strong fungicidal and plant growth promoting activities with regard to the inhibition of mycelial growth, sclerotia formation, and germination, and reduction of disease symptoms in tomato plants infected with S. minor. DMDS exposure significantly upregulated the expression of genes related to growth and defense against the pathogen in tomato. Especially, the overexpression of PR1 and PR5 suggested the involvement of the salicylic acid pathway in the induction of systemic resistance. Several morphological and ultrastructural changes were observed in the cell membrane of S. minor and the expression of ergosterol biosynthesis gene was significantly downregulated, suggesting that DMDS damaged the membrane, thereby affecting the growth and pathogenicity of the fungus. In conclusion, the tripartite interaction studies among pathogenic fungus, DMDS, and tomato revealed that DMDS played roles in antagonizing pathogen as well as improving the growth and disease resistance of tomato. Our findings provide new insights into the potential of volatile DMDS as an effective tool against sclerotial rot disease.

Airborne medicine: bacterial volatiles and their influence on plant health

Like most other eukaryotes, plants do not live alone but in close association with a diverse microflora. These plant-associated microbes contribute to plant health in many different ways, ranging from modulation of hormonal pathways to direct antibiosis of plant pathogens. Over the last 15 yr, the importance of volatile organic compounds as mediators of mutualistic interactions between plant-associated bacteria and their hosts has become evident. This review summarizes current knowledge concerning bacterial volatile-mediated plant protection against abiotic and biotic stresses. It then discusses the translational potential of such metabolites or of their emitters for sustainable crop protection, the possible ways to harness this potential, and the major challenges still preventing us from doing so. Finally, the review concludes with highlighting the most pressing scientific gaps that need to be filled in order to enable a better understanding of: the molecular mechanisms underlying the biosynthesis of bacterial volatiles; the complex regulation of bacterial volatile emission in natural communities; the perception of bacterial volatiles by plants; and the modes of actions of bacterial volatiles on their host.

Bioinoculant capability enhancement through metabolomics and systems biology approaches

Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene product can be changed for engineered microbial inoculants. We have also described various modern biotechnological tools like constraint-based modeling, OptKnock, flux balance analysis and modeling of the biological network for enhancing the bioinoculant capability. These fluxes give the fascinating perception of the metabolic network in the absence of comprehensive kinetic information. These tools also help in the stimulation of the metabolic networks by incorporation of enzyme-encoding genes. The present review explains the use of systems biology and gene-editing tools for improving the capability of bioinoculants. Moreover, this review also emphasizes on the challenges and future perspective of systems biology and its multidisciplinary facets.

An overview on improvement of crop productivity in saline soils by halotolerant and halophilic PGPRs

Salinity of water and soil are of the most important factors limiting the production of crops. Moreover, with the increasing population of the planet and saline fields worldwide there is no choice but to use saline soil and water in the near future. Therefore, to increase plant growth under saline stress condition, provision of sustainable and environmentally friendly management for the use of saline water and soil resources is necessary. The development of saline resistant plants is a potent approach to solve this problem. Generally, soil salinity negatively affects the plant growth through ion toxicity, oxidative stress, osmotic stress and ethylene generation. In recent years, scientists through genetic engineering techniques, which are based on molecular and physiological characteristics of plants, have made salt tolerance plants. However, the validation of the present technique is restricted to laboratory condition and it is not easily applied in the agronomy research under field environment. Another option would be to isolate and utilize salinity resistant microorganisms from the rhizosphere of halophyte plants, namely plant growth-promoting rhizobacteria (PGPR). The mechanisms of these bacteria includes; ACC-deaminase and exopolysachared production, osmolite accumulation, antioxidant system activation, ion hemostasis and etc. In this review, we will discuss mechanisms of PGPR in producing tolerate plants under salt stress and how to improve the plant-microbe interactions in future for increasing agricultural productivity to feed all of the world's people.

Induced Systemic Resistance (ISR) and Fe Deficiency Responses in Dicot Plants

Plants develop responses to abiotic stresses, like Fe deficiency. Similarly, plants also develop responses to cope with biotic stresses provoked by biological agents, like pathogens and insects. Some of these responses are limited to the infested damaged organ, but other responses systemically spread far from the infested organ and affect the whole plant. These latter responses include the Systemic Acquired Resistance (SAR) and the Induced Systemic Resistance (ISR). SAR is induced by pathogens and insects while ISR is mediated by beneficial microbes living in the rhizosphere, like bacteria and fungi. These root-associated mutualistic microbes, besides impacting on plant nutrition and growth, can further boost plant defenses, rendering the entire plant more resistant to pathogens and pests. In the last years, it has been found that ISR-eliciting microbes can induce both physiological and morphological responses to Fe deficiency in dicot plants. These results suggest that the regulation of both ISR and Fe deficiency responses overlap, at least partially. Indeed, several hormones and signaling molecules, like ethylene (ET), auxin, and nitric oxide (NO), and the transcription factor MYB72, emerged as key regulators of both processes. This convergence between ISR and Fe deficiency responses opens the way to the use of ISR-eliciting microbes as Fe biofertilizers as well as biopesticides. This review summarizes the progress in the understanding of the molecular overlap in the regulation of ISR and Fe deficiency responses in dicot plants. Root-associated mutualistic microbes, rhizobacteria and rhizofungi species, known for their ability to induce morphological and/or physiological responses to Fe deficiency in dicot plant species are also reviewed herein.

Bioinoculants for Bioremediation Applications and Disease Resistance: Innovative Perspectives

Soil microbial species that act as PGPR or bioinoculants have the capability of improving plant health and promoting its growth. They facilitate plants for uptake nutrients from their surroundings. They provide resistivity to pathogenic pests and also play many roles in the bioremediation process. Bioremediation is the biological approach for the elimination of toxic contaminants by the approach of beneficial microbes. By the consortium of beneficial microbes and plant, a large number of heavy metal and organic contaminants can be controlled. With this advancement of bioremediation, microbial species that act as bioinoculants also help in the enhancement of induced systemic resistance (ISR) and their consortium triggers it by controlling SA, JA, ET and hormonal signaling pathways. Here, this review discusses the progress made on these areas and how the beneficial microbes that act as bioinoculants towards triggering bioremediation and ISR mechanism.