Proteomics provides insights into biological pathways altered by plant growth promoting bacteria and arbuscular mycorrhiza in sorghum grown in marginal soil

Comparative effects of Serendipita indica and a mix of arbuscular mycorrhizal fungi on the growth, photosynthetic capacity, and proteomics of Schinus terebinthifolius Raddi

MAIN CONCLUSION

Both, Serendipita indica and AMF, show promise as sustainable biofertilizers for reforestation, improving nutrient uptake and stress tolerance, despite contrasting effects on photosynthetic capacity and biomass allocation. Reclaiming degraded areas is essential for biodiversity conservation and enhancing ecosystem services enhancement, especially when using native species. This study investigated Schinus terebinthifolius Raddi, a native Brazilian species, and its compatibility with plant growth-promoting microorganisms (PGPM), including an endophytic fungus (Serendipita indica) and a consortium of arbuscular mycorrhizal fungi (AMF), to identify effective strategies for reforestation in nutrient-poor environments. We observed growth stimulation by both PGPMs; however, S. indica primarily enhanced root weight, whereas AMF improved shoot weight. S. indica's positive effects on root systems could be attributed to increased auxin levels and altered root architecture, which are critical for seedling establishment in reforestation programs. In terms of nutritional status, both treatments increased the content of most nutrients, with higher micronutrient contents in the shoots and higher macronutrient content in roots of inoculated plants. Despite AMF's role in enhancing photosynthesis, plants inoculated with these fungi showed reduced photosynthetic capacity traits, possibly due to lower leaf nitrogen content. The proteomic analysis of Schinus terebinthifolius leaf extracts revealed that, despite the upregulation of several proteins associated with the photosynthetic apparatus in response to S. indica treatment, no enhancement in photosynthetic capacity was observed. We also found several proteins related to oxidative stress in plants inoculated with both fungi, indicating a greater tolerance to adverse environmental conditions. These findings underscore the potential of both, S. indica and AMF, as sustainable alternatives to chemical fertilizers in reforestation efforts, enhancing seedling quality and survival in nutrient-poor soils.

H2 O2 , NO, and H2 S networks during root development and signalling under physiological and challenging environments: Beneficial or toxic?

Hydrogen peroxide (H₂ O₂ ) is a reactive oxygen species (ROS) and a key modulator of the development and architecture of the root system under physiological and adverse environmental conditions. Nitric oxide (NO) and hydrogen sulphide (H₂ S) also exert myriad functions on plant development and signalling. Accumulating pieces of evidence show that depending upon the dose and mode of applications, NO and H₂ S can have synergistic or antagonistic actions in mediating H₂ O₂ signalling during root development. Thus, H₂ O₂ -NO-H₂ S crosstalk might essentially impart tolerance to elude oxidative stress in roots. Growth and proliferation of root apex involve crucial orchestration of NO and H₂ S-mediated ROS signalling which also comprise other components including mitogen-activated protein kinase, cyclins, cyclin-dependent kinases, respiratory burst oxidase homolog (RBOH), and Ca²⁺ flux. This assessment provides a comprehensive update on the cooperative roles of NO and H₂ S in modulating H₂ O₂ homoeostasis during root development, abiotic stress tolerance, and root-microbe interaction. Furthermore, it also analyses the scopes of some fascinating future investigations associated with strigolactone and karrikins concerning H₂ O₂ -NO-H₂ S crosstalk in plant roots.

The Role of Plant Growth-Promoting Microorganisms (PGPMs) and Their Feasibility in Hydroponics and Vertical Farming

There are many reasons for the increase in hydroponics/soil-free systems in agriculture, and these systems have now advanced to the form of vertical farming. The sustainable use of space, the reduction in water use compared to soil-based agriculture, the lack of pesticides, the ability to control nutrient inputs, and the implementation of user-friendly technology for environmental control and harvesting are all factors that have made the global market for vertical farming predicted to reach more than USD 10.02 billion by 2027. By comparison, soil-based agriculture consumes 20 times more water, and some agricultural practices promote soil deterioration and cause environmental pollution. Plant growth-promoting microorganisms (PGPMs) have been used extensively in traditional agriculture to enhance plant growth, environmental stress tolerance, and the efficacy of phytoremediation in soil-based farming. Due to the controlled atmosphere in hydroponics and vertical farms, there is strong potential to maximize the use of PGPMs. Here, we review the leveraging of plant growth-promoting microorganism mechanisms in hydroponics and vertical farming. We recommend a synchronized PGPM treatment using a biostimulant extract added to the hydroponic medium while also pre-treating seeds or seedlings with a microbial suspension for aquaponic and aeroponic systems.

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.

Microbial Biostimulants as Response to Modern Agriculture Needs: Composition, Role and Application of These Innovative Products

An increasing need for a more sustainable agriculturally-productive system is required in order to preserve soil fertility and reduce soil biodiversity loss. Microbial biostimulants are innovative technologies able to ensure agricultural yield with high nutritional values, overcoming the negative effects derived from environmental changes. The aim of this review was to provide an overview on the research related to plant growth promoting microorganisms (PGPMs) used alone, in consortium, or in combination with organic matrices such as plant biostimulants (PBs). Moreover, the effectiveness and the role of microbial biostimulants as a biological tool to improve fruit quality and limit soil degradation is discussed. Finally, the increased use of these products requires the achievement of an accurate selection of beneficial microorganisms and consortia, and the ability to prepare for future agriculture challenges. Hence, the implementation of the microorganism positive list provided by EU (2019/1009), is desirable.

What Did We Learn From Plant Growth-Promoting Rhizobacteria (PGPR)-Grass Associations Studies Through Proteomic and Metabolomic Approaches?

Plant growth stimulation by microorganisms that interact in a mutually beneficial manner remains poorly understood. Understanding the nature of plant-bacteria interactions may open new routes for plant productivity enhancement, especially cereal crops consumed by humans. Proteomic and metabolomic analyses are particularly useful for elucidating these mechanisms. A complete depiction of these mechanisms will prompt researchers to develop more efficient plant-bacteria associations. The success of microorganisms as biofertilizers may replace the current massive use of chemical fertilizers, mitigating many environmental and economic issues. In this review, we discuss the recent advances and current state of the art in proteomics and metabolomics studies involving grass-bacteria associations. We also discuss essential subjects involved in the bacterial plant-growth promotion, such, nitrogen fixation, plant stress, defense responses, and siderophore production.

Pseudomonas fluorescens promote photosynthesis, carbon fixation and cadmium phytoremediation of hyperaccumulator Sedum alfredii

Plant growth-promoting bacteria (PGPB) can promote photosynthesis and biomass production of hyperaccumulators, achieving enhanced phytoremediation efficiency of cadmium (Cd). A better understanding of the mechanisms controlling photosynthesis of hyperaccumulating plants by PGPB is necessary for developing strategies that promote the practical phytoextraction of Cd-polluted soils. In this study, chlorophyll fluorescence, gas exchange, and transcriptome sequencing were conducted to evaluate the physiological and transcriptional changes on photosynthesis and carbon fixation in hyperaccumulator Sedum alfredii after inoculation with PGPB Pseudomonas fluorescens. The results showed that bacterial inoculation significantly enhanced maximum quantum yield of PS II (Fv/Fm), effective quantum yield of PS II (ΦPSII), photochemical quenching (qP) and chlorophyll concentration, while reduced non-photochemical quenching (NPQ) of S. alfredii. Further, inoculation resulted in an increased net photosynthetic rates (Pn), intercellular CO₂ concentration (Ci), transpiration rate (Tr) and stomatal conductance (Gs) of the studied plant. At the transcriptional level, 70 photosynthetic genes and 42 C4-pathway carbon fixation related genes were significantly up-regulated in response to inoculation, which could be the reason for enhanced photosynthesis and dry biomass. To sum up, this P. fluorescens strain can simultaneously promote growth and Cd uptake of S. alfredii, which can be a promising bacterial agent applied to Cd phytoremediation practices.

Proteomic analysis and interactions network in leaves of mycorrhizal and nonmycorrhizal sorghum plants under water deficit

For understanding the water deficit stress mechanism in sorghum, we conducted a physiological and proteomic analysis in the leaves of Sorghum bicolor L. Moench (a drought tolerant crop model) of non-colonized and colonized plants with a consortium of arbuscular mycorrhizal fungi. Physiological results indicate that mycorrhizal fungi association enhances growth and photosynthesis in plants, under normal and water deficit conditions. 2D-electrophoresis profiles revealed 51 differentially accumulated proteins in response to water deficit, of which HPLC/MS successfully identified 49. Bioinformatics analysis of protein–protein interactions revealed the participation of different metabolic pathways in nonmycorrhizal compared to mycorrhizal sorghum plants under water deficit. In noninoculated plants, the altered proteins are related to protein synthesis and folding (50S ribosomal protein L1, 30S ribosomal protein S10, Nascent polypeptide-associated complex subunit alpha), coupled with multiple signal transduction pathways, guanine nucleotide-binding beta subunit (Rack1) and peptidyl-prolyl-cis-trans isomerase (ROC4). In contrast, in mycorrhizal plants, proteins related to energy metabolism (ATP synthase-24kDa, ATP synthase β), carbon metabolism (malate dehydrogenase, triosephosphate isomerase, sucrose-phosphatase), oxidative phosphorylation (mitochondrial-processing peptidase) and sulfur metabolism (thiosulfate/3-mercaptopyruvate sulfurtransferase) were found. Our results provide a set of proteins of different metabolic pathways involved in water deficit produced by sorghum plants alone or associated with a consortium of arbuscular mycorrhizal fungi isolated from the tropical rain forest Los Tuxtlas Veracruz, México.

Plant Growth Promoting Rhizobacteria (PGPR) Regulated Phyto and Microbial Beneficial Protein Interactions

Plant Growth Promoting Rhizobacteria (PGPR) influence plants’ physiological characteristics, metabolites, pathways and proteins via alteration of corresponding gene expression. In the current study, a total of 42 upregulated uncharacterized sorghum bicolor root proteins influenced by PGPR were subjected to different analyses: phylogenetic tree, protein functional network, sequences similarity network (SSN), Genome Neighborhood Network (GNN) and motif analysis. The screen for homologous bacterial proteins to uncover associated protein families and similar proteins in non-PGPRs was identified. The sorghum roots’ uncharacterized protein sequences analysis indicated the existence of two protein categories, the first being related to phytobeneficial protein family associated with DNA regulation such as Sulfatase, FGGY_C, Phosphodiesterase or stress tolerance such as HSP70. The second is associated with bacterial transcriptional regulators such as FtsZ, MreB_Mbl and DNA-binding transcriptional regulators, as well as the AcrR family, which existed in PGPR and non PGPR. Therefore, Plant Growth-Promoting Rhizobacteria (PGPR) regulated phytobeneficial traits through reciprocal protein stimulation via microbe plant interactions, both during and post colonization.

Nutrient enhancement of chickpea grown with plant growth promoting bacteria in local soil of Bathinda, Northwestern India

Plant growth promoting bacteria (PGPB) enhance crop productivity as part of green technology to reduce the use of chemical fertilizers. They also have the capability to enhance macro- and micronutrient content of plants. In the present study, PGPB isolates belonging to Pseudomonas citronellis (PC), Pseudomonas sp. RA6, Serratia sp. S2, Serratia marcescens CDP13, and Frateuria aurantia (Symbion-K) were tested on two chickpea varieties, PBG1 and PBG5 grown for 30 days in local soil from Bathinda region in Northwestern India. PC and CDP13 were found to be better chickpea growth stimulators compared to the commercial Symbion-K based on shoot length and biomass. Most PGPB enhanced macro- and micronutrients in shoots to varying degrees compared to the control. PBG5 gave better response compared to PBG1 with reference to plant growth attributes and enhancement of the macronutrients, calcium, nitrogen and phosphorus and micronutrients, boron, copper, iron, and zinc. PBG5 is a high yielding variety with better resistance compared to PBG1. Overall, PGPB isolated from the local soil and PGPB from other parts of India were shown to be useful for enhancement of nutrient content and plant growth.

Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent

Powdery mildew (PM) is considered a major cause of yield losses and reduced quality in cucumber worldwide, but the molecular basis of PM resistance remains poorly understood. A segment substitution line, namely, SSL508-28, was developed with dominant PM resistance in the genetic background of PM-susceptible cucumber inbred line D8. The substituted segment contains 860 genes. An iTRAQ-based comparative proteomic technology was used to map the proteomes of PM-inoculated and untreated (control) D8 and SSL508-28. The number of differentially regulated proteins (DRPs) in SSL508-28 was almost three times higher than that in D8. Fourteen DRPs were located in the substituted segment interval. Comparative gene expression analysis revealed that nodulin-related protein 1 (NRP1) may be a good candidate for PM resistance. Gene Ontology enrichment analysis showed that DRPs functioning in tetrapyrrole biosynthetic process, sulfur metabolic process and cell redox homeostasis were specifically enriched in the resistant line SSL508-28. DRPs categorized in the KEGG term photosynthesis increased in both lines upon PM infection, suggesting that the strategies used by cucumber may be different from those used by other crops to react to PM attacks at the initial stage. The measurement of hydrogen peroxide and superoxide anion production and net photosynthetic rate were consistent with the changes in protein abundance, suggesting that the proteomic results were reliable. There was a poor correlation between DRPs measured by iTRAQ and the corresponding gene expression changes measured by RNA-seq with the same experimental design. Taken together, these findings improve the understanding of the molecular mechanisms underlying the response of cucumber to PM infection.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.