Proteomic analysis reveals that tomato interaction with plant growth promoting bacteria is highly determined by ethylene perception

A plant's perception of growth-promoting bacteria and their metabolites

Many recent studies have highlighted the importance of plant growth-promoting (rhizo)bacteria (PGPR) in supporting plant's development, particularly under biotic and abiotic stress. Most focus on the plant growth-promoting traits of selected strains and the latter's effect on plant biomass, root architecture, leaf area, and specific metabolite accumulation. Regarding energy balance, plant growth is the outcome of an input (photosynthesis) and several outputs (i.e., respiration, exudation, shedding, and herbivory), frequently neglected in classical studies on PGPR-plant interaction. Here, we discuss the primary evidence underlying the modifications triggered by PGPR and their metabolites on the plant ecophysiology. We propose to detect PGPR-induced variations in the photosynthetic activity using leaf gas exchange and recommend setting up the correct timing for monitoring plant responses according to the specific objectives of the experiment. This research identifies the challenges and tries to provide future directions to scientists working on PGPR-plant interactions to exploit the potential of microorganisms' application in improving plant value.

Uncovering the Role of Hormones in Enhancing Antioxidant Defense Systems in Stressed Tomato (Solanum lycopersicum) Plants

Tomato is one of the most important fruits worldwide. It is widely consumed due to its sensory and nutritional attributes. However, like many other industrial crops, it is affected by biotic and abiotic stress factors, reducing its metabolic and physiological processes. Tomato plants possess different mechanisms of stress responses in which hormones have a pivotal role. They are responsible for a complex signaling network, where the antioxidant system (enzymatic and non-enzymatic antioxidants) is crucial for avoiding the excessive damage caused by stress factors. In this sense, it seems that hormones such as ethylene, auxins, brassinosteroids, and salicylic, jasmonic, abscisic, and gibberellic acids, play important roles in increasing antioxidant system and reducing oxidative damage caused by different stressors. Although several studies have been conducted on the stress factors, hormones, and primary metabolites of tomato plants, the effect of endogenous and/or exogenous hormones on the secondary metabolism is still poorly studied, which is paramount for tomato growing management and secondary metabolites production. Thus, this review offers an updated overview of both endogenous biosynthesis and exogenous hormone application in the antioxidant system of tomato plants as a response to biotic and abiotic stress factors.

A non-K+-solubilizing PGPB (Bacillus megaterium) increased K+ deprivation tolerance in Oryza sativa seedlings by up-regulating root K+ transporters

Potassium is one of the principal macronutrients required by all plants, but its mobility is restricted between soil compartments. Numerous studies have shown that Plant Growth Promoting Bacteria (PGPB) can facilitate nutrient uptake. The present work examined the effects of the PGPB (Bacillus megaterium) on rice plants subjected to potassium deprivation. To study only direct effects of B. megaterium, we first checked its lack of capacity to solubilize soil K. Rice plants were provided with 1.5 mM K (100%) or 0.015 mM K (1%) and growth related parameters, nutrient concentrations and gene expression of K⁺ transporters were determined. After two weeks, the 1% K treatment reduced growth of non-inoculated plants by about 50% compared with the 100% K treatment. However, there was no effect of reduced K nutrition on growth of inoculated plants. The reduction in growth in non-inoculated plants was accompanied by a similar reduction in K⁺ concentration in both roots and leaves and an overall 80% reduction of the plant potassium concentrations. In inoculated plants a 50% reduction occurred only in leaves. The expression of the K⁺ transporters HKT1;1, 1;2, 1;5, 2;2, 2;3 and 2;4 was up-regulated by the inoculation of B. megaterium under K deprivation conditions, explaining their higher K tissue concentrations and growth. Thus, the bacterial strain improved plant potassium nutrition without affecting K⁺ availability in the soil. The results demonstrate the potential of this bacteria for using as a biofertilizer to reduce the amount of potassium fertilizers to be applied in the field.

Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato

The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.

Sugarcane Root Transcriptome Analysis Revealed the Role of Plant Hormones in the Colonization of an Endophytic Diazotroph

Some sugarcane germplasms can absorb higher amounts of nitrogen via atmospheric nitrogen fixation through the bacterial diazotrophs. Most endophytic diazotrophs usually penetrate through the root, colonize inside the plant, and fix the nitrogen. To assess the plant’s bacterial association during root colonization, strain GXS16 was tagged with a plasmid-bear green fluorescent protein (GFP) gene. The results demonstrated that the strain can colonize roots all the way to the maturation zone. The strain GXS16 showed maximum nitrogenase enzyme activity at pH 8 and 30°C, and nitrogenase activity is less affected by different carbon sources. Further, strain GXS16 colonization response was investigated through plant hormones analysis and RNAseq. The results showed that the bacterial colonization gradually increased with time, and the H₂O₂ and malondialdehyde (MDA) content significantly increased at 1 day after inoculation. There were no substantial changes noticed in proline content, and the ethylene content was detected initially, but it decreased with time. The abscisic acid (ABA) content showed significant increases of 91.9, 43.9, and 18.7%, but conversely, the gibberellin (GA₃) content decreased by 12.9, 28.5, and 45.2% at 1, 3, and 5 days after inoculation, respectively. The GXS16 inoculation significantly increased the activities of catalase (CAT), superoxide dismutase (SOD), polyphenol oxidase (PPO), ascorbate peroxidase (APX), and glutathione reductase (GR) at different timepoint. In contrast, the peroxisome (POD) activity had no changes detected during the treatment. In the case of RNAseq analysis, 2437, 6678, and 4568 differentially expressed genes (DEGs) were identified from 1, 3, and 5 days inoculated root samples, and 601 DEGs were shared in all samples. The number or the expression diversity of DEGs related to ethylene was much higher than that of ABA or GA, which indicated the critical role of ethylene in regulating the sugarcane roots response to GXS16 inoculation.

Wheat grain proteomic and protein-metabolite interactions analyses provide insights into plant growth promoting bacteria-arbuscular mycorrhizal fungi-wheat interactions

Proteomic, protein-protein and protein-metabolite interaction analyses in wheat inoculated with PGPB and AMF identified key proteins and metabolites that may have a role in enhancing yield and biofortification. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) have an impact on grain yield and nutrition. This dynamic yet complex interaction implies a broad reprogramming of the plant's metabolic and proteomic activities. However, little information is available regarding the role of native PGPB and AMF and how they affect the plant proteome, especially under field conditions. Here, proteomic, protein-protein and protein-metabolite interaction studies in wheat triggered by PGPB, Bacillus subtilis CP4 either alone or together with AMF under field conditions was carried out. The dual inoculation with native PGPB (CP4) and AMF promoted the differential abundance of many proteins, such as histones, glutenin, avenin and ATP synthase compared to the control and single inoculation. Interaction study of these differentially expressed proteins using STRING revealed that they interact with other proteins involved in seed development and abiotic stress tolerance. Furthermore, these interacting proteins are involved in carbon fixation, sugar metabolism and biosynthesis of amino acids. Molecular docking predicted that wheat seed storage proteins, avenin and glutenin interact with secondary metabolites, such as trehalose, and sugars, such as xylitol. Mapping of differentially expressed proteins to KEGG pathways showed their involvement in sugar metabolism, biosynthesis of secondary metabolites and modulation of histones. These proteins and metabolites can serve as markers for improving wheat-PGPB-AMF interactions leading to higher yield and biofortification.

Endoplasmic reticulum-related E3 ubiquitin ligases: Key regulators of plant growth and stress responses

Accumulating evidence has revealed that the ubiquitin proteasome system plays fundamental roles in the regulation of diverse cellular activities in eukaryotes. The ubiquitin protein ligases (E3s) are central to the proteasome system because of their ability to determine its substrate specificity. Several studies have demonstrated the essential role of a group of ER (endoplasmic reticulum)-localized E3s in the positive or negative regulation of cell homeostasis. Most ER-related E3s are conserved between plants and mammals, and a few plant-specific components have been reported. In this review, we summarize the functions of ER-related E3s in plant growth, ER-associated protein degradation and ER-phagy, abiotic and biotic stress responses, and hormone signaling. Furthermore, we highlight several questions that remain to be addressed and suggest directions for further research on ER-related E3 ubiquitin ligases.

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

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

Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem

Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.

Deciphering plant-microbe crosstalk through proteomics studies

Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

Role of Pea LTPs and Abscisic Acid in Salt-Stressed Roots

Lipid transfer proteins (LTPs) are a class of small, cationic proteins that bind and transfer lipids and play an important role in plant defense. However, their precise biological role in plants under adverse conditions including salinity and possible regulation by stress hormone abscisic acid (ABA) remains unknown. In this work, we studied the localization of LTPs and ABA in the roots of pea plants using specific antibodies. Presence of LTPs was detected on the periphery of the cells mainly located in the phloem. Mild salt stress (50 mM NaCI) led to slowing plant growth and higher immunostaining for LTPs in the phloem. The deposition of suberin in Casparian bands located in the endoderma revealed with Sudan III was shown to be more intensive under salt stress and coincided with the increased LTP staining. All obtained data suggest possible functions of LTPs in pea roots. We assume that these proteins can participate in stress-induced pea root suberization or in transport of phloem lipid molecules. Salt stress increased ABA immunostaining in pea root cells but its localization was different from that of the LTPs. Thus, we failed to confirm the hypothesis regarding the direct influence of ABA on the level of LTPs in the salt-stressed root cells.

Influence of PGPB Inoculation on HSP70 and HMA3 Gene Expression in Switchgrass under Cadmium Stress

This study aimed to evaluate the gene expression of HSP70 and HMA3 in the switchgrass inoculated with plant-growth-promoting-bacteria (PGPB) under cadmium (Cd) stress and to observe the benefit of PGPB in plant growth and development. Plants were grown in hydroponic culture and treated with PGPB inoculants: Pseudomonas grimontii, Pantoea vagans, Pseudomonas veronii, and Pseudomonas fluorescens with the strains Bc09, So23, E02, and Oj24, respectively. The experimental results revealed that HSP70 and HMA3 genes expressed highly in the PGPB-inoculated plants under Cd stress. In addition, the expression of HSP70 and HMA3 genes was considerably higher in the first two days after successive four-day exposure of Cd in plants compared to the last two days of exposure. Increased biomass and indole-3-acetic-acid production with reduced Cd accumulation were observed in the PGPB-inoculated plants under Cd stress compared to the Cd-control plants. These PGPB, with their beneficial mechanisms, protect plants by modifying the gene expression profile that arises during Cd-toxic conditions and increased the healthy biomass of switchgrass. This demonstrates there is a correlation among the growth parameters under Cd stress. The PGPB in this study may help to intensify agriculture by triggering mechanisms to encourage plant growth and development under heavy metal stress.

Optimization of Cultural Conditions for Bacillus megaterium Cultured in Agaricus bisporus Industrial Wastewater

The aim of this study was to optimize the cultural conditions for Bacillus megaterium using Agaricus bisporus industrial wastewater as nature culture through response surface methodology. In our present study, we analyzed the total number of living B. megaterium in the fermentation broth using multispectral imaging flow cytometry. Plackett-Burman design was applied to evaluate the effects of six variables, namely, initial pH, industrial wastewater solubility, rotating speed, culture temperature, inoculum size, and loading volume. Loading volume, initial pH, and culture temperature were found to influence the biomass of B. megaterium significantly and were further optimized by Box-Behnken design. After verification test, the optimum fermentation conditions of B. megaterium using the A. bisporus processing wastewater as nature culture media were obtained as follows: initial pH of 7.4, culture temperature of 25°C, loading volume of 40 mL/250 mL, culture time of 24 h, industrial wastewater solubility of 1%, rotating speed of 200 rpm, and inoculum size of 8%. The predicted optimum model's value was 8.88 × 10⁸ Obj/mL and the average experimental value was 9.03 ± 0.02 × 10⁸ Obj/mL, which met the national microbial fertilizers' standard. Furthermore, the field experiment results showed that the fermentation broth of B. megaterium could significantly improve the yield of Spinacia oleracea L.

Host-specific proteomic and growth analysis of maize and tomato seedlings inoculated with Azospirillum brasilense Sp7

Azospirillum brasilense Sp7 (Sp7) is a diazotrophic, free-living plant growth-promoting rhizobacterium (PGPR) that is increasingly used for its ability to reduce stress and improve nutrient uptake by plants. To test the hypothesis that Sp7 interacts differently with the primary metabolism in C₃ and C₄ plants, differential proteomics were employed to study weekly protein expression in Sp7-treated maize (Zea mays cv. B73) and tomato (Solanum lycopersicum cv. Boludo) seedlings. Plant and root growth parameters were also monitored. Protein changes were most striking at the four-leaf stage (T1) for both species. Proteins related to metabolism and redox homeostasis were most abundant in tomato at T1, but later, plants experienced inhibited Calvin-Benson (CB) cycle and chloroplast development, indicating that photosynthetic proteins were damaged by reactive oxygen species (ROS). In maize, Sp7 first increased ROS-scavenging enzymes and decreased those related to metabolism, which ultimately reduced photoinhibition at later sampling times. Overall, the early interaction with maize is more complex and beneficial because the photosynthetic aparatus is protected by the C₄ mechanism, thereby improving the interaction of the PGPR with maize. Better seedling emergence and vigor were observed in inoculated maize compared to tomato. This study provides an integrated perspective on the Sp7 strain-specific interactions with young C₃ and C₄ plants to modulate primary metabolism and photosynthesis.

Molecular Insights into the Involvement of a Never Ripe Receptor in the Interaction Between Two Beneficial Soil Bacteria and Tomato Plants Under Well-Watered and Drought Conditions

Management of plant growth-promoting bacteria (PGPB) can be implemented to deal with sustainable intensification of agriculture. Ethylene is an essential component for plant growth and development and in response to drought. However, little is known about the effects of bacterial inoculation on ethylene transduction pathway. Thus, the present study sought to establish whether ethylene perception is critical for growth induction by two different PGPB strains under drought conditions and the analysis of bacterial effects on ethylene production and gene expression in tomatoes (Solanum lycopersicum). The ethylene-insensitive never ripe (nr) and its isogenic wild-type (wt) cv. Pearson line were inoculated with either Bacillus megaterium or Enterobacter sp. strain C7 and grown until the attainment of maturity under both well-watered and drought conditions. Ethylene perception is crucial for B. megaterium. However, it is not of prime importance for Enterobacter sp. strain C7 PGPB activity under drought conditions. Both PGPB decreased the expression of ethylene-related genes in wt plants, resulting in stress alleviation, while only B. megaterium induced their expression in nr plants. Furthermore, PGPB inoculation affected transcriptomic profile dependency on strain, genotype, and drought. Ethylene sensitivity determines plant interaction with PGPB strains. Enterobacter sp. strain C7 could modulate amino-acid metabolism, while nr mutation causes a partially functional interaction with B. megaterium, resulting in higher oxidative stress and loss of PGPB activity.

Phosphorus concentration coordinates a respiratory bypass, synthesis and exudation of citrate, and the expression of high-affinity phosphorus transporters in Solanum lycopersicum

Plants exhibit respiratory bypasses (e.g., the alternative oxidase [AOX]) and increase the synthesis of carboxylates in their organs (leaves and roots) in response to phosphorus (P) deficiency, which increases P uptake capacity. They also show differential expression of high-affinity inorganic phosphorus (Pi) transporters, thus avoiding P toxicity at a high P availability. The association between AOX and carboxylate synthesis was tested in Solanum lycopersicum plants grown at different soil P availability, by using plants grown under P-sufficient and P-limiting conditions and by applying a short-term (24 hr) P-sufficient pulse to plants grown under P limitation. Tests were also performed with plants colonized with arbuscular mycorrhizal fungi, which increased plant P concentration under reduced P availability. The in vivo activities of AOX and cytochrome oxidase were measured together with the concentration of carboxylates and the P concentration in plant organs. Gene transcription of Pi transporters (LePT1 and LePT2) was also studied. A coordinated response between plant P concentration with these traits was observed, indicating that a sufficient P availability in soil led to a suppression of both AOX activity and synthesis of citrate and a downregulation of the transcription of genes encoding high-affinity Pi transporters, presumably to avoid P toxicity.