Plant Growth-Promoting Rhizobacteria for Sustainable Agricultural Production

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Selective biotic stressors' action on seed germination: A review

In the realm of plant biology and agriculture, seed germination serves as a fundamental process with far-reaching implications for crop production and environmental health. This comprehensive review seeks to unravel the intricate web of interactions between some biotic stressors and seed germination, addressing the pertinent issue of how these stressors influence seed germination. Different chemicals produced by interacting plants (different parts), fungi, bacteria, or insects can either promote or inhibit seed germination. Releasing chemicals that modulate signaling pathways and cellular processes significantly disrupt essential cellular functions. This disruption leads to diverse germination outcomes, introducing additional layers of complexity to this regulatory landscape. The chemicals perturb enzyme activity and membrane integrity, imposing unique challenges on the germination process. Understanding the mechanisms- how allelochemicals, mycotoxins, or bacterial toxins affect seed germination or the modes of action holds promise for more sustainable agricultural practices, enhanced pest control, and improved environmental outcomes. In sum, this review contributes to a fundamental exposition of the pivotal role of biotic stressors in shaping the germination of seeds.

The role of drought response genes and plant growth promoting bacteria on plant growth promotion under sustainable agriculture: A review

Drought is a major stressor that poses significant challenges for agricultural practices. It becomes difficult to meet the global demand for food crops and fodder. Plant physiology, physico-chemistry and morphology changes in plants like decreased photosynthesis and transpiration rate, overproduction of reactive oxygen species, repressed shoot and root shoot growth and modified stress signalling pathways by drought, lead to detrimental impacts on plant development and output. Coping with drought stress requires a variety of adaptations and mitigation techniques. Crop yields could be effectively increased by employing plant growth-promoting rhizobacteria (PGPR), which operate through many mechanisms. These vital microbes colonise the rhizosphere of crops and promote drought resistance by producing exopolysaccharides (EPS), 1-aminocyclopropane-1-carboxylate (ACC) deaminase and phytohormones including volatile compounds. The upregulation or downregulation of stress-responsive genes causes changes in root architecture due to acquiring drought resistance. Further, PGPR induces osmolyte and antioxidant accumulation. Another key feature of microbial communities associated with crops includes induced systemic tolerance and the production of free radical-scavenging enzymes. This review is focused on detailing the role of PGPR in assisting plants to adapt to drought stress.

Microbial biofertilizers and algae-based biostimulant affect fruit yield characteristics of organic processing tomato

BACKGROUND

Microbial biofertilizers and algae-based biostimulants have been recognized for supporting sustainable agriculture. Field experiments were conducted in 2022 and 2023 growing seasons in an organic farm located in Ferrara (Italy) with the aim of evaluating plant growth-promoting microorganisms (PGPMs) and algae-based biostimulants (Biost) in tomato (Solanum lycopersicum L.). The experimental treatments were: (i) two microbial biofertilizers (PGPM_1, PGPM_2) and no inoculated plants (No_PGPM); and (ii) two algae-based biostimulant rates (0.5% (Biost_0.5%), 1.0% (Biost_1.0%)) and no application (No_Biost). PGPMs were applied at transplanting, while biostimulants at 15 and 30 days after transplanting. Treatments were replicated three times according to a split-plot experimental design. Plant characteristics were evaluated at 30 days after transplanting in No_Biost treatments. During tomato cultivation, soil plant analysis development (SPAD), nitrogen difference vegetation index (NDVI), leaf area index (LAI) and photosynthetic photon flux density (PPFD) were monitored. Tomato yield was determined.

RESULTS

PGPM_2 showed the highest shoot biomass (132.9 g plant-1), plant height (44.7 cm), leaf number (34.0 plant-1) and root biomass (9.22 g plant-1). Intermediate values were observed in PGPM_1, while all parameters were lower in No_PGPM. Both PGPMs achieved higher values of SPAD, NDVI, PPFD and LAI than No_PGPM. Biost_1.0% increased all measured growth parameters followed by Biost_0.5% and No_Biost, respectively. Tomato yield was the highest for PGPM_2-Biost_1.0% (67.2 t ha-1). PGPMs affected fruit size and sugar content, while biostimulants were associated with color and lycopene.

CONCLUSION

The application of microbial biofertilizers and algae-based biostimulants could be part of environment-friendly practice in organic farming. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Unearthing the soil-bacteria nexus to enhance potassium bioavailability for global sustainable agriculture: A mechanistic preview

Established as a plant macronutrient, potassium (K) substantially bestows plant growth and thus, global food production. It is absorbed by plants as potassium cation (K+) from soil solution, which is enriched through slow-release from soil minerals or addition of soluble fertilizers. Contribution of bioavailable K+ from soil is usually insignificant (< 2 %), although the earth's crust is rich in K-bearing minerals. However, K is fixed largely in interlayer spaces of K-bearing minerals, which can be released by K-solubilizing bacteria (KSB) such as Bacillus, Pseudomonas, Enterobacter, and Acidithiobacillus. The underlying mechanisms of K dissolution by KSB include acidolysis, ion exchange reactions, chelation, complexolysis, and release of various organic and inorganic acids such as citric, oxalic, acetic, gluconic, and tartaric acids. These acids cause disintegration of K-bearing minerals and bring K+ into soil solution that becomes available to the plants. Current literature review updates the scientific information about microbial species, factors, and mechanisms governing the bio-intrusion of K-bearing minerals. Moreover, it explores the potential of KSB not only for K-solubilization but also to enhance bioavailability of phosphorus, nitrogen, and micronutrients, as well as its other beneficial impact on plant growth. Thus, in the context of sustainable agricultural production and global food security, utilization of KSB may facilitate plant nutrient availability, conserve natural resources, and reduce environmental impacts caused by chemical fertilizers.

BioSolutions for Green Agriculture: Unveiling the Diverse Roles of Plant Growth-Promoting Rhizobacteria

The extensive use of chemical pesticides and fertilizers in conventional agriculture has raised significant environmental and health issues, including the emergence of resistant pests and pathogens. Plant growth-promoting rhizobacteria (PGPR) present a sustainable alternative, offering dual benefits as biofertilizers and biocontrol agents. This review delves into the mechanisms by which PGPR enhance plant growth, including nutrient solubilization, phytohormone production, and pathogen suppression. PGPR's commercial viability and application, particularly under abiotic stress conditions, are also examined. PGPR improves plant growth directly by enhancing nutrient uptake and producing growth-promoting substances and indirectly by inhibiting phytopathogens through mechanisms such as siderophore production and the secretion of lytic enzymes. Despite their potential, the commercialization of PGPR faces challenges, including strain specificity, formulation stability, and regulatory barriers. The review highlights the need for ongoing research to deepen our understanding of plant-microbe interactions and develop more robust PGPR formulations. Addressing these challenges will be crucial for integrating PGPR into mainstream agricultural practices and reducing reliance on synthetic agrochemicals. The successful adoption of PGPR could lead to more sustainable agricultural practices, promoting healthier crops and ecosystems.

Harnessing rhizobacteria: Isolation, identification, and antifungal potential against soil pathogens

Rhizobacteria play a crucial role in plant health by providing natural antagonism against soil-borne fungi. The use of rhizobacteria has been viewed as an alternative to the use of chemicals that could be useful for the integrated management of plant diseases and also increase yield in an environmentally friendly manner. However, there is limited understanding of the specific mechanisms by which rhizobacteria inhibit these pathogens and the diversity of rhizobacterial species involved. This study aims to isolate, identify, and characterize rhizobacteria with antagonistic activities against soil-borne fungi. Laboratory tests were carried out on isolated rhizobacteria to evaluate their inhibitory activity against Rhizoctonia solani, Pythium aphanidermatum and Macrophomina phaseolina. The selected bacteria were identified using the Vitek 2 compact system and 16S rRNA genes. Experiments were carried out to evaluate the plant growth promotion and biocontrol ability of these selected isolates. Out of 324 rhizobacteria isolates obtained from various plant species, twelve were chosen due to their strong (>50 %) wide-ranging antifungal activity against three significant phytopathogenic fungi species. According to the identification results, they belong to the following species: Aeribacillus pallidus ECC4, Alloiococcus otitis BRE6, Aneurinibacillus thermoaerophilus ECL1, A. thermoaerophilus SDV1, Bacillus halotolerans DMC8, B. megaterium SKE2, B. megaterium TNK1, B. subtilis NAS1, Enterobacter cloacae complex BZD3, Leclercia adecarboxylata DKS3, Paenibacillus polymyxa TRS4, and Staphylococcus lentus BZD2. Eleven isolates produced protease, six isolates produced chitinase, and seven isolates were highly effective in producing hydrogen cyanide. Ten isolates could fix nitrogen, while all isolates could produce potassium, indole-3-acetic acid, siderophore, and ammonia. These findings enhance our understanding of rhizobacterial biodiversity and their potential as biocontrol agents in sustainable agriculture.

Alleviated cadmium toxicity in wheat (Triticum aestivum L.) by the coactive role of zinc oxide nanoparticles and plant growth promoting rhizobacteria on TaEIL1 gene expression, biochemical and physiological changes

Cadmium (Cd) contamination in agricultural soil is a major global concern among the multitude of human health and food security. Zinc oxide nanoparticles (ZnO-NPs) and plant growth promoting rhizobacteria (PGPR) have been known to combat heavy metal toxicity in crops. Herein, the study intended to explore the interactive effect of treatments mediated by inoculation of PGPR and foliar applied ZnO-NPs to alleviate Cd induced phytotoxicity in wheat plants which is rarely investigated. For this purpose, TaEIL1 expression, morpho-physiological, and biochemical traits of wheat were examined. Our results revealed that Cd reduced growth and biomass, disrupted plant physiological and biochemical traits, and further expression patterns of TaEIL1. The foliar application of ZnO-NPs improved growth attributes, photosynthetic pigments, and gas exchange parameters in a dose-additive manner, and this effect was further amplified with a combination of PGPR. The combined application of ZnO-NPs (100 mg L-1) with PGPR considerably increased the catalase (CAT; 52.4%), peroxidase (POD; 57.4%), superoxide dismutase (SOD; 60.1%), ascorbate peroxidase (APX; 47.4%), leading to decreased malondialdehyde (MDA; 47.4%), hydrogen peroxide (H2O2; 38.2%) and electrolyte leakage (EL; 47.3%) under high Cd (20 mg kg-1) stress. Furthermore, results revealed a significant reduction in roots (56.3%), shoots (49.4%), and grains (59.4%) Cd concentration after the Combined treatment of ZnO-NPs and PGPR as compared to the control. Relative expression of TaEIL1 (two homologues) was evaluated under control (Cd 0), Cd, ZnO-NPs, PGPR, and combined treatments. Expression profiling revealed a differential expression pattern of TaEIL1 under different treatments. The expression pattern of TaEIL1 genes was upregulated under Cd stress but downregulated under combined ZnO-NPs and PGPR, revealing its crucial role in Cd stress tolerance. Inferentially, ZnO-NPs and PGPR showed significant potential to alleviate Cd toxicity in wheat by modulating the antioxidant defense system and TaEIL1 expression. By inhibiting Cd uptake, and facilitating their detoxification, this innovative approach ensures food safety and security.

Actinomycetes isolated from rhizosphere of wild Coffea arabica L. showed strong biocontrol activities against coffee wilt disease

Coffee, the second most traded commodity globally after petroleum and is the most exported cash crop of Ethiopia. However, coffee cultivation faces challenges due to fungal diseases, resulting in significant yield losses. The primary fungal diseases affecting coffee production include coffee berry disease, wilt disease (caused by Gibberella xylarioides), and coffee leaf rust. In this study, we aimed to isolate potentially antagonistic actinomycetes from the root rhizosphere of wild Coffea arabica plants in the Yayo coffee forest biosphere in southwestern Ethiopia. Soil samples were collected from the rhizosphere, and actinomycetes were selectively isolated and identified to the genus level by morphological, physiological, and biochemical characterization. These pure isolates were screened for their antagonistic activity against Gibberella xylarioides in vitro using a dual culturing method. Promising isolates demonstrating strong inhibition of fungal mycelial growth were further investigated through in vivo experiments using coffee seedlings. A total of 82 rhizobacteria were isolated. These isolates' inhibition of fungal mycelial growth varied from 0% to 83.3%. Among them, four isolates MUA26, MUA13, MUA52, and MUA14 demonstrated the highest percentage inhibition of fungal mycelial growth: 83.3%, 80%, 76.67%, and 73.3%, respectively. Seedlings inoculated with MUA13, MUA14, and MUA26 during the challenge inoculations (Rhizobacteria + Gibberella xylarioides) exhibited the lowest disease incidence compared to the infected fungi (P < 0.05). Notably, the seedlings inoculated with MUA26 demonstrated the highest disease control efficiency, reaching 83% (P < 0.05). MUA26 was found to produce extracellular enzymes, including chitinase, protease, and lipase, which acted as inhibitors. In summary, this study highlights that MUA26, among the actinomycete isolates, exhibited significant antagonistic activity against Gibberella xylarioides f.sp. coffea. Its efficacy in controlling coffee wilt disease, both in vitro and in vivo, positions it as a potential bioinoculant for managing coffee wilt disease.

Strengthen sunflowers resilience to cadmium in saline-alkali soil by PGPR-augmented biochar

In the center of the Nile Delta in Egypt, the Kitchener drain as the primary drainage discharges about 1.9 billion m3 per year of water, which comprises agricultural drainage (75 %), domestic water (23 %), and industrial water (2 %), to the Mediterranean Sea. Cadmium (Cd) stands out as a significant contaminant in this drain; therefore, this study aimed to assess the integration of biochar (0, 5, and 10 ton ha-1) and three PGPRs (PGPR-1, PGPR-2, and PGPR-3) to alleviate the negative impacts of Cd on sunflowers (Helianthus annuus L.) in saline-alkali soil. The treatment of biochar (10 ton ha-1) and PGPR-3 enhanced the soil respiration, dehydrogenase, nitrogenase, and phosphatase activities by 137 %, 129 %, 326 %, and 127 %, while it declined soil electrical conductivity and available Cd content by 31.7 % and 61.3 %. Also, it decreased Cd content in root, shoot, and seed by 55.3 %, 50.7 %, and 92.5 %, and biological concentration and translocation factors by 55 % and 5 %. It also declined the proline, lipid peroxidation, H2O2, and electrolyte leakage contents by 48 %, 94 %, 80 %, and 76 %, whereas increased the catalase, peroxidase, superoxide dismutase, and polyphenol oxidase activities by 80 %, 79 %, 61 %, and 116 %. Same treatment increased seed and oil yields increased by 76.1 % and 76.2 %. The unique aspect of this research is its investigation into the utilization of biochar in saline-alkali soil conditions, coupled with the combined application of biochar and PGPR to mitigate the adverse effects of Cd contamination on sunflower cultivation in saline-alkali soil.

Exploring the Organic Acid Secretion Pathway and Potassium Solubilization Ability of Pantoea vagans ZHS-1 for Enhanced Rice Growth

Soil potassium deficiency is a common issue limiting agricultural productivity. Potassium-solubilizing bacteria (KSB) show significant potential in mitigating soil potassium deficiency, improving soil quality, and enhancing plant growth. However, different KSB strains exhibit diverse solubilization mechanisms, environmental adaptability, and growth-promoting abilities. In this study, we isolated a multifunctional KSB strain ZHS-1, which also has phosphate-solubilizing and IAA-producing capabilities. 16S rDNA sequencing identified it as Pantoea vagans. Scanning electron microscopy (SEM) showed that strain ZHS-1 severely corroded the smooth, compact surface of potassium feldspar into a rough and loose state. The potassium solubilization reached 20.3 mg/L under conditions where maltose was the carbon source, sodium nitrate was the nitrogen source, and the pH was 7. Organic acid metabolism profiling revealed that strain ZHS-1 primarily utilized the EMP-TCA cycle, supplemented by pathways involving pantothenic acid, glyoxylic acid, and dicarboxylic acids, to produce large amounts of organic acids and energy. This solubilization was achieved through direct solubilization mechanisms. The strain also secreted IAA through a tryptophan-dependent metabolic pathway. When strain ZHS-1 was inoculated into the rhizosphere of rice, it demonstrated significant growth-promoting effects. The rice plants exhibited improved growth and root development, with increased accumulation of potassium and phosphorus. The levels of available phosphorus and potassium in the rhizosphere soil also increased significantly. Additionally, we observed a decrease in the relative abundance of Actinobacteria and Proteobacteria in the rice rhizosphere soil, while the relative abundance of genera associated with acid production and potassium solubilization, such as Gemmatimonadota, Acidobacteria, and Chloroflexi, as well as Cyanobacteria, which are beneficial to plant growth, increased. These findings contribute to a deeper understanding of the potassium solubilization mechanisms of strain ZHS-1 and highlight its potential as a plant growth-promoting rhizobacteria.

Unveiling the frontiers of potato disease research through bibliometric analysis

Research on potato diseases had been widely reported, but a systematic review of potato diseases was lacking. Here, bibliometrics was used to systematically analyze the progress of potato disease. The publications related to "potato" and "disease" were searched in the Web of Science (WOS) from 2014 to 2023. The results showed that a total of 2095 publications on potato diseases were retrieved, with the annual publication output increasing year by year at a growth rate of 8.52%. The main countries where publications were issued were the United States, China, and India. There was relatively close cooperation observed between China, the United States, and the United Kingdom in terms of international collaboration, while international cooperation by India was less extensive. Based on citation analysis and trending topics, potential future research directions include nanoparticles, which provides highly effective carriers for biologically active substances due to their small dimensions, extensive surface area, and numerous binding sites; machine learning, which facilitates rapid identification of relevant targets in extensive datasets, thereby accelerating the process of disease diagnosis and fungicide innovation; and synthetic communities composed of various functional microorganisms, which demonstrate more stable effects in disease prevention and control.

Recent trends in the phytoremediation of radionuclide contamination of soil by cesium and strontium: Sources, mechanisms and methods: A comprehensive review

This comprehensive review examines recent trends in phytoremediation strategies to address soil radionuclide contamination by cesium (Cs) and strontium (Sr). Radionuclide contamination, resulting from natural processes and nuclear-related activities such as accidents and the operation of nuclear facilities, poses significant risks to the environment and human health. Cs and Sr, prominent radionuclides involved in nuclear accidents, exhibit chemical properties that contribute to their toxicity, including easy uptake, high solubility, and long half-lives. Phytoremediation is emerging as a promising and environmentally friendly approach to mitigate radionuclide contamination by exploiting the ability of plants to extract toxic elements from soil and water. This review focuses specifically on the removal of 90Sr and 137Cs, addressing their health risks and environmental implications. Understanding the mechanisms governing plant uptake of radionuclides is critical and is influenced by factors such as plant species, soil texture, and physicochemical properties. Phytoremediation not only addresses immediate contamination challenges but also provides long-term benefits for ecosystem restoration and sustainable development. By improving soil health, biodiversity, and ecosystem resilience, phytoremediation is in line with global sustainability goals and environmental protection initiatives. This review aims to provide insights into effective strategies for mitigating environmental hazards associated with radionuclide contamination and to highlight the importance of phytoremediation in environmental remediation efforts.

The Co-Inoculation Effect on Triticum aestivum Growth with Synthetic Microbial Communities (SynComs) and Their Potential in Agrobiotechnology

The use of rhizospheric SynComs can be a new and sustainable strategy in the agrobiotechnology sector. The objective of this study was to create the most appropriate SynCom composition; examine the ability to dissolve natural rock phosphate (RP) from Morocco in liquid-modified NBRIP medium; determine organic acids, and phytohormones; and verify plant growth promoting and nutrition uptake effect in the pot experiments of winter wheat (Triticum aestivum). A total of nine different microorganisms were isolated, which belonged to three different genera: Bacillus, Pseudomonas, and Streptomyces. Out of the 21 treatments tested, four SynComs had the best phosphate-dissolving properties: IJAK-27+44+91 (129.17 mg L-1), IIBEI-32+40 (90.95 µg mL-1), IIIDEG-45+41 (122.78 mg L-1), and IIIDEG-45+41+72 (120.78 mg L-1). We demonstrate that these SynComs are capable of producing lactic, acetic, gluconic, malic, oxalic, citric acids, and phytohormones such as indole-3-acetic acid, zeatin, gibberellic acid, and abscisic acid. In pot experiments with winter wheat, we also demonstrated that the designed SynComs were able to effectively colonize the plant root rhizosphere and contributed to more abundant plant growth characteristics and nutrient uptake as uninoculated treatment or uninoculated treatment with superphosphate (NPK 0-19-0). The obtained results show that the SynCom compositions of IJAK-27+44+91, IIBEI-32+40, IIIDEG-45+41, and IIIDEG-45+41+72 can be considered as promising candidates for developing biofertilizers to facilitate P absorption and increase plant nutrition.

Beneficial effects of Bacillus mojavensis strain MTC-8 on plant growth, immunity and disease resistance against Magnaporthe oryzae

Rice blast, a prevalent and highly destructive rice disease that significantly impacts rice yield, is caused by the rice blast fungus. In the present study, a strain named MTC-8, identified as Bacillus mojavensis, was demonstrated has strong antagonistic activity against the rice blast fungus, Rhizoctonia solani, Ustilaginoidea virens, and Bipolaria maydis. The potential biocontrol agents were identified using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis and chromatography. Further investigations elucidated the inhibitory mechanism of the isolated compound and demonstrated its ability to suppress spore germination, alter hyphal morphology, disrupt cell membrane integrity, and induce defense-related gene expression in rice. MTC-8 promoted plant growth and may lead to the development of a biocontrol agent that meets agricultural standards. Overall, the Bacillus mojavensis MTC-8 strain exerted beneficial effects on plant growth, immunity and disease resistance against rice blast fungus. In this study, we isolated and purified a bioactive substance from fermentation broth, and the results provide a foundation for the development and application of biopesticides. Elucidation of the inhibitory mechanism against rice blast fungus provides theoretical support for the identification of molecular targets. The successful development of a biocontrol agent lays the groundwork for its practical application in agriculture.

Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit-like amidase mediates the degradation of insecticide flonicamid by Variovorax boronicumulans CGMCC 4969

The main metabolic product of the pyridinecarboxamide insecticide flonicamid, N-(4-trifluoromethylnicotinyl)glycinamide (TFNG-AM), has been shown to have very high mobility in soil, leading to its accumulation in the environment. Catabolic pathways of flonicamid have been widely reported, but few studies have focused on the metabolism of TFNG-AM. Here, the rapid transformation of TFNG-AM and production of the corresponding acid product N-(4-trifluoromethylnicotinoyl) glycine (TFNG) by the plant growth-promoting bacterium Variovorax boronicumulans CGMCC 4969 were investigated. With TFNG-AM at an initial concentration of 0.86 mmol/L, 90.70 % was transformed by V. boronicumulans CGMCC 4969 resting cells within 20 d, with a degradation half-life of 4.82 d. A novel amidase that potentially mediated this transformation process, called AmiD, was identified by bioinformatic analyses. The gene encoding amiD was cloned and expressed recombinantly in Escherichia coli, and the enzyme AmiD was characterized. Key amino acid residue Val154, which is associated with the catalytic activity and substrate specificity of signature family amidases, was identified for the first time by homology modeling, structural alignment, and site-directed mutagenesis analyses. When compared to wild-type recombinant AmiD, the mutant AmiD V154G demonstrated a 3.08-fold increase in activity toward TFNG-AM. The activity of AmiD V154G was greatly increased toward aromatic L-phenylalanine amides, heterocyclic TFNG-AM and IAM, and aliphatic asparagine, whereas it was dramatically lowered toward benzamide, phenylacetamide, nicotinamide, acetamide, acrylamide, and hexanamid. Quantitative PCR analysis revealed that AmiD may be a substrate-inducible enzyme in V. boronicumulans CGMCC 4969. The mechanism of transcriptional regulation of AmiD by a member of the AraC family of regulators encoded upstream of the amiD gene was preliminarily investigated. This study deepens our understanding of the mechanisms of metabolism of toxic amides in the environment, providing new ideas for microbial bioremediation.

Streptomyces N2A, an endophytic actinobacteria that promotes soybean growth and increases yield and seed quality under field conditions

Sustainable agriculture based on the use of soil-beneficial microbes such as plant growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCA) is gaining great consideration to reduce the use of agrochemicals for crop production. With this aim, in this study, a total of 78 actinobacteria were isolated from the rhizosphere and endosphere of soybean roots. Based on in vitro compatibility with Bradyrhizobium japonicum, the ability to produce phytohormones, siderophores, exo-enzymes, antifungal compounds and phosphate solubilization (PGPR traits), two endophytic strains, named N2A and N9, were selected to evaluate their effects on plant growth and development at greenhouse and field conditions. Greenhouse trials showed significantly promoted seedling emergence compared to control and the conventional fungicide treatment. Analysis of growth and development associated parameters at reproductive stages and maturity at greenhouse, but also and most importantly, in field experiments showed significant improvements. Plant biomass, node number, pod number, and consequently yield, were higher in plants previously treated with N2A and co-inoculated with B. japonicum compared to the conventional seed treatment. Furthermore, a significant increase in health status and vigor was observed for seeds harvested from the N2A-treated plants in relation to seeds obtained from the conventional treatment. Thus, we demonstrated that Streptomyces sp. N2A can replace traditional chemical fungicides to protect the seed during germination, allowing good implantation, but also, stimulating the growth and development of soybean crop increasing yield and seed quality at field conditions. Altogether, this supports the potential use of Streptomyces N2A as a PGPR for soybean crop production more efficiently and sustainably.

Plant growth-promoting rhizobacteria Pseudomonas aeruginosa HG28-5 improves salt tolerance by regulating Na+/K+ homeostasis and ABA signaling pathway in tomato

Salinity stress badly restricts the growth, yield and quality of vegetable crops. Plant growth-promoting rhizobacteria (PGPR) is a friendly and effective mean to enhance plant growth and salt tolerance. However, information on the regulatory mechanism of PGPR on vegetable crops in response to salt stress is still incomplete. Here, we screened a novel salt-tolerant PGPR strain Pseudomonas aeruginosa HG28-5 by evaluating the tomatoes growth performance, chlorophyll fluorescence index, and relative electrolyte leakage (REL) under normal and salinity conditions. Results showed that HG28-5 colonization improved seedling growth parameters by increasing the plant height (23.7%), stem diameter (14.6%), fresh and dry weight in the shoot (60.3%, 91.1%) and root (70.1%, 92.5%), compared to salt-stressed plants without colonization. Likewise, HG28-5 increased levels of maximum photochemical efficiency of PSII (Fv/Fm) (99.3%), the antioxidant enzyme activities as superoxide dismutase (SOD, 85.5%), peroxidase (POD, 35.2%), catalase (CAT, 20.6%), and reduced the REL (48.2%), MDA content (41.3%) and ROS accumulation in leaves of WT tomatoes under salt stress in comparison with the plants treated with NaCl alone. Importantly, Na+ content of HG28-5 colonized salt-stressed WT plants were decreased by15.5% in the leaves and 26.6% in the roots in the corresponding non-colonized salt-stressed plants, which may be attributed to the higher K+ concentration and SOS1, SOS2, HKT1;2, NHX1 transcript levels in leaves of colonized plants under saline condition. Interestingly, increased abscisic acid (ABA) content and upregulation of ABA pathway genes (ABA synthesis-related genes NCED1, NCED2, NCED4, NECD6 and signal genes ABF4, ABI5, and AREB) were observed in HG28-5 inoculated salt-stressed WT plants. ABA-deficient mutant (not) with NCED1 deficiency abolishes the effect of HG28-5 on alleviating salt stress in tomato, as exhibited by the substantial rise of REL and ROS accumulation and sharp drop of Fv/Fm in the leaves of not mutant plants. Notably, HG28-5 colonization enhances tomatoes fruit yield by 54.9% and 52.4% under normal and saline water irrigation, respectively. Overall, our study shows that HG28-5 colonization can significantly enhance salt tolerance and improved fruit yield by a variety of plant protection mechanism, including reducing oxidative stress, regulating plant growth, Na+/K+ homeostasis and ABA signaling pathways in tomato. The findings not only deepen our understanding of PGPR regulation plant growth and salt tolerance but also allow us to apply HG28-5 as a microbial fertilizer for agricultural production in high-salinity areas.

Exploring the biochemical dynamics in faba bean (Vicia faba L. minor) in response to Orobanche foetida Poir. parasitism under inoculation with different rhizobia strains

In Tunisia, Orobanche foetida Poir. is considered an important agricultural biotic constraint on faba bean (Vicia faba L.) production. An innovative control method for managing this weed in faba bean is induced resistance through inoculation by rhizobia strains. In this study, we explored the biochemical dynamics in V. faba L. minor inoculated by rhizobia in response to O. foetida parasitism. A systemic induced resistant reaction was evaluated through an assay of peroxidase (POX), polyphenol oxidase (PPO) and phenyl alanine ammonialyase (PAL) activity and phenolic compound and hydrogen peroxide (H2O2) accumulation in faba bean plants infested with O. foetida and inoculated with rhizobia. Two rhizobia strains (Mat, Bj1) and a susceptible variety of cultivar Badi were used in a co-culture Petri dish experiment. We found that Mat inoculation significantly decreased O. foetida germination and the number of tubercles on the faba bean roots by 87% and 88%, respectively. Following Bj1 inoculation, significant decreases were only observed in O. foetida germination (62%). In addition, Mat and Bj1 inoculation induced a delay in tubercle formation (two weeks) and necrosis in the attached tubercles (12.50% and 4.16%, respectively) compared to the infested control. The resistance of V. faba to O. foetida following Mat strain inoculation was mainly associated with a relatively more efficient enzymatic antioxidative response. The antioxidant enzyme activity was enhanced following Mat inoculation of the infected faba bean plant. Indeed, increases of 45%, 67% and 86% were recorded in the POX, PPO and PAL activity, respectively. Improvements of 56% and 12% were also observed in the soluble phenolic and H2O2 contents. Regarding inoculation with the Bj1 strain, significant increases were only observed in soluble phenolic and H2O2 contents and PPO activity (especially at 45 days after inoculation) compared to the infested control. These results imply that inoculation with the rhizobia strains (especially Mat) induced resistance and could bio-protect V. faba against O. foetida parasitism by inducing systemic resistance, although complete protectionwas not achieved by rhizobia inoculation. The Mat strain could be used as a potential candidate for the development of an integrated method for controlling O. foetida parasitism in faba bean.

Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium

Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.

Zinc oxide nanoparticles and Klebsiella sp. SBP-8 alleviates chromium toxicity in Brassica juncea by regulation of antioxidant capacity, osmolyte production, nutritional content and reduction in chromium adsorption

Heavy metals are one of the most damaging environmental toxins that hamper growth of plants. These noxious chemicals include lead (Pb), arsenic (As), nickel (Ni), cadmium (Cd) and chromium (Cr). Chromium is one of the toxic metal which induces various oxidative processes in plants. The emerging role of nanoparticles as pesticides, fertilizers and growth regulators have attracted the attention of various scientists. Current study was conducted to explore the potential of zinc oxide nanoparticles (ZnONPs) alone and in combination with plant growth promoting rhizobacteria (PGPR) Klebsiella sp. SBP-8 in Cr stress alleviation in Brassica juncea (L.). Chromium stress reduced shoot fresh weight (40%), root fresh weight (28%), shoot dry weight (28%) and root dry weight (34%) in B. juncea seedlings. Chromium stressed B. juncea plants showed enhanced levels of malondialdehyde (MDA), electrolyte leakage (EL), hydrogen peroxide (H2O2) and superoxide ion (O2• -). However, co-supplementation of ZnONPs and Klebsiella sp. SBP-8 escalated the activity of antioxidant enzymes i.e., superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) in B. juncea grown in normal and Cr-toxic soil. It is further proposed that combined treatment of ZnONPs and Klebsiella sp. SBP-8 may be useful for alleviation of other abiotic stresses in plants.

Promoting sustainable agriculture by exploiting plant growth-promoting rhizobacteria (PGPR) to improve maize and cowpea crops

Maize and cowpea are among the staple foods most consumed by most of the African population, and are of significant importance in food security, crop diversification, biodiversity preservation, and livelihoods. In order to satisfy the growing demand for agricultural products, fertilizers and pesticides have been extensively used to increase yields and protect plants against pathogens. However, the excessive use of these chemicals has harmful consequences on the environment and also on public health. These include soil acidification, loss of biodiversity, groundwater pollution, reduced soil fertility, contamination of crops by heavy metals, etc. Therefore, essential to find alternatives to promote sustainable agriculture and ensure the food and well-being of the people. Among these alternatives, agricultural techniques that offer sustainable, environmentally friendly solutions that reduce or eliminate the excessive use of agricultural inputs are increasingly attracting the attention of researchers. One such alternative is the use of beneficial soil microorganisms such as plant growth-promoting rhizobacteria (PGPR). PGPR provides a variety of ecological services and can play an essential role as crop yield enhancers and biological control agents. They can promote root development in plants, increasing their capacity to absorb water and nutrients from the soil, increase stress tolerance, reduce disease and promote root development. Previous research has highlighted the benefits of using PGPRs to increase agricultural productivity. A thorough understanding of the mechanisms of action of PGPRs and their exploitation as biofertilizers would present a promising prospect for increasing agricultural production, particularly in maize and cowpea, and for ensuring sustainable and prosperous agriculture, while contributing to food security and reducing the impact of chemical fertilizers and pesticides on the environment. Looking ahead, PGPR research should continue to deepen our understanding of these microorganisms and their impact on crops, with a view to constantly improving sustainable agricultural practices. On the other hand, farmers and agricultural industry players need to be made aware of the benefits of PGPRs and encouraged to adopt them to promote sustainable agricultural practices.

Endophytic Bacillus vallismortis and Bacillus tequilensis bacteria isolated from medicinal plants enhance phosphorus acquisition and fortify Brassica napus L. vegetative growth and metabolic content

Phosphorus fertilization imposes critical limitations on crop productivity and soil health. The aim of the present work is to explore the potential of two phosphate solubilizing bacteria (PSB) species in phosphorus supplementation of canola (Brassica napus L.). Out of 38 bacterial isolates obtained from nine medicinal plants, two bacterial strains (20P and 28P) were proved as the most potent for the in-vitro tricalcium phosphate solubilization test. These isolates verified their activity toward different enzymes as nitrogenase and alkaline phosphatase. Also, 20P and 28P gave a high amount of indole-3-acetic acid, 34.16 μg/ml and 35.20 μg/ml, respectively, and were positive for siderophores production as they detected moderate affinity for iron chelation. Molecular identification confirmed that strain 20P was Bacillus vallismortis and strain 28P was Bacillus tequilensis. A pot experiment was conducted to study the effect of four different phosphorus concentrations (0%, 50%, 75%, and 100% P) each alone and/or in combination with B. vallismortis, B. tequilensis, or both bacterial isolates on the vegetative growth and some physiological parameters of canola. The combined treatment of 50% phosphorus + (B. vallismortis + B. tequilensis) was generally the most effective with respect to shoot height, shoot dry mass, leaf area, photosynthetic pigment fractions, total sugar content, and accumulated NPK content. In contrast, the rhizosphere pH reached the minimum value under the same treatment. These findings highlighted the potential use of PSB (B. vallismortis and B. tequilensis) along with phosphorus fertilization as a safe sustainable tactic.

Impact of antagonistic endophytic bacteria on productivity of some economically important legumes

Understanding the interactions within and between endophytes and their hosts is still obscure. Investigating endophytic bacterial plant growth-promoting (PGP) traits and co-inoculation effects on legumes' performance is a candidate. Endophytic bacteria were isolated from Vicia sativa root nodules. Such endophytes were screened for their PGP traits, hydrolytic enzymes, and antifungal activities. Sterilized Vicia faba and Pisum sativum seedlings were co-inoculated separately with seven different endophytic bacterial combinations before being planted under sterilized conditions. Later on, several growth-related traits were measured. Eleven endophytes (six rhizobia, two non-rhizobia, and three actinomycetes) could be isolated, and all of them were indole-acetic-acid (IAA) producers, while seven isolates could solubilize phosphorus, whereas three, five, five, and four isolates could produce protease, cellulase, amylase, and chitinase, respectively. Besides, some of these isolates possessed powerful antifungal abilities against six soil-borne pathogenic fungi. Co-inoculation of tested plants with endophytic bacterial mixes (Rhizobiamix+Actinomix+non-Rhizobiamix), (Rhizobiamix+Actinomix), or (Rhizobiamix+non-Rhizobiamix) significantly improved the studied growth parameters (shoot, root fresh and dry weights, length and yield traits) compared to controls, whereas co-inoculated plants with (Rhizobiaalone), (non-Rhizobiamix), or (Actinomix) significantly recorded lower growth parameters. Five efficient endophytes were identified: Rhizobium leguminosarum bv. Viciae, Rhizobium pusense, Brevibacterium frigoritolerans, Streptomyces variabilis, and Streptomyces tendae. Such results suggested that these isolates could be utilized as biocontrols and biofertilizers to improve legumes productivity. Also, co-inoculation with different endophytic mixes is better than single inoculation, a strategy that should be commercially exploited.

Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment

Background

Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community.

Methods

In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods.

Results

The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community.

Discussion

Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.

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.

Progress in Microbial Fertilizer Regulation of Crop Growth and Soil Remediation Research

More food is needed to meet the demand of the global population, which is growing continuously. Chemical fertilizers have been used for a long time to increase crop yields, and may have negative effect on human health and the agricultural environment. In order to make ongoing agricultural development more sustainable, the use of chemical fertilizers will likely have to be reduced. Microbial fertilizer is a kind of nutrient-rich and environmentally friendly biological fertilizer made from plant growth-promoting bacteria (PGPR). Microbial fertilizers can regulate soil nutrient dynamics and promote soil nutrient cycling by improving soil microbial community changes. This process helps restore the soil ecosystem, which in turn promotes nutrient uptake, regulates crop growth, and enhances crop resistance to biotic and abiotic stresses. This paper reviews the classification of microbial fertilizers and their function in regulating crop growth, nitrogen fixation, phosphorus, potassium solubilization, and the production of phytohormones. We also summarize the role of PGPR in helping crops against biotic and abiotic stresses. Finally, we discuss the function and the mechanism of applying microbial fertilizers in soil remediation. This review helps us understand the research progress of microbial fertilizer and provides new perspectives regarding the future development of microbial agent in sustainable agriculture.

Utilizing the power of plant growth promoting rhizobacteria on reducing mineral fertilizer, improved yield, and nutritional quality of Batavia lettuce in a floating culture

In soilless cultivation, plants are grown with nutrient solutions prepared with mineral nutrients. Beneficial microorganisms are very important in plant nutrition. However, they are not present in soilless culture systems. In this study we investigated the impact of introducing Plant Growth Promoting Rhizobacteria (PGPR) as an alternative to traditional mineral fertilizer in hydroponic floating lettuce cultivation. By reducing mineral fertilizers at various ratios (20%, 40%, 60%, and 80%), and replacing them with PGPR, we observed remarkable improvements in multiple growth parameters. Applying PGPR led to significant enhancements in plant weight, leaf number, leaf area, leaf dry matter, chlorophyll content, yield, and nutrient uptake in soilles grown lettuce. Combining 80% mineral fertilizers with PGPR demonstrated a lettuce yield that did not significantly differ from the control treatment with 100% mineral fertilizers. Moreover, PGPR application improved the essential mineral concentrations and enhanced human nutritional quality, including higher levels of phenols, flavonoids, vitamin C, and total soluble solids. PGPR has potential as a sustainable substitute for synthetic mineral fertilizers in hydroponic floating lettuce cultivation, leading to environmentally friendly and nutritionally enriched farming.

Plant growth-promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions

Even though canola is one of the most important industrial crops worldwide, it has high nutrient requirements and is susceptible to pests and diseases. Therefore, natural methods are sought to support the development of these plants. One of those methods could be a plant growth-promoting rhizobacteria (PGPR) that have a beneficial effect on plant development. The aim of this study was a genomic comparison of two PGPR strains chosen based on their effect on canola growth: Peribacillus frigoritolerans 2RO30, which stimulated canola growth only in sterile conditions, and Pseudomonas sivasensis 2RO45, which promoted canola growth in both sterile and non-sterile conditions. First of all, six bacterial strains: RO33 (Pseudomonas sp.), RO37 (Pseudomonas poae), RO45 (Pseudomonas kairouanensis), 2RO30 (Peribacillus frigoritolerans), 2RO45 (Pseudomonas sivasensis), and 3RO30 (Pseudomonas migulae), demonstrating best PGP traits in vitro, were studied for their stimulating effect on canola growth under sterile conditions. P. frigoritolerans 2RO30 and P. sivasensis 2RO45 showed the best promoting effect, significantly improving chlorophyll content index (CCI) and roots length compared to the non-inoculated control and to other inoculated seedlings. Under non-sterile conditions, only P. sivasensis 2RO45 promoted the canola growth, significantly increasing CCI compared to the untreated control and to other inoculants. Genome comparison revealed that the genome of P. sivasensis 2RO45 was enriched with additional genes responsible for ACC deaminase (acdA), IAA (trpF, trpG), and siderophores production (fbpA, mbtH, and acrB) compared to 2RO30. Moreover, P. sivasensis 2RO45 showed antifungal effect against all the tested phytopathogens and harbored six more biosynthetic gene clusters (BGC), namely, syringomycin, pyoverdin, viscosin, arylpolyene, lankacidin C, and enterobactin, than P. frigoritolerans 2RO30. These BGCs are well known as antifungal agents; therefore, it can be assumed that these BGCs were responsible for the antifungal activity of P. sivasensis 2RO45 against all plant pathogens. This study is the first report describing P. sivasensis 2RO45 as a canola growth promoter, both under controlled and natural conditions, thus suggesting its application in improving canola yield, by improving nutrient availability, enhancing stress tolerance, and reducing environmental impact of farming practices.

Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat

The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.

Enhancing Water Status and Nutrient Uptake in Drought-Stressed Lettuce Plants (Lactuca sativa L.) via Inoculation with Different Bacillus spp. Isolated from the Atacama Desert

Drought is a major challenge for agriculture worldwide, being one of the main causes of losses in plant production. Various studies reported that some soil's bacteria can improve plant tolerance to environmental stresses by the enhancement of water and nutrient uptake by plants. The Atacama Desert in Chile, the driest place on earth, harbors a largely unexplored microbial richness. This study aimed to evaluate the ability of various Bacillus sp. from the hyper arid Atacama Desert in the improvement in tolerance to drought stress in lettuce (Lactuca sativa L. var. capitata, cv. "Super Milanesa") plants. Seven strains of Bacillus spp. were isolated from the rhizosphere of the Chilean endemic plants Metharme lanata and Nolana jaffuelii, and then identified using the 16s rRNA gene. Indole acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity were assessed. Lettuce plants were inoculated with Bacillus spp. strains and subjected to two different irrigation conditions (95% and 45% of field capacity) and their biomass, net photosynthesis, relative water content, photosynthetic pigments, nitrogen and phosphorus uptake, oxidative damage, proline production, and phenolic compounds were evaluated. The results indicated that plants inoculated with B. atrophaeus, B. ginsengihumi, and B. tequilensis demonstrated the highest growth under drought conditions compared to non-inoculated plants. Treatments increased biomass production and were strongly associated with enhanced N-uptake, water status, chlorophyll content, and photosynthetic activity. Our results show that specific Bacillus species from the Atacama Desert enhance drought stress tolerance in lettuce plants by promoting several beneficial plant traits that facilitate water absorption and nutrient uptake, which support the use of this unexplored and unexploited natural resource as potent bioinoculants to improve plant production under increasing drought conditions.

Effects of the application of microbiologically activated bio-based fertilizers derived from manures on tomato plants and their rhizospheric communities

Bio-based fertilizers (BBFs) recovered from animal manure are promising products to optimise resources recovery and generate high agricultural yields. However, their fertilization value may be limited and it is necessary to enrich BBFs with microbial consortia to enhance their fertilization value. Three specific microbial consortia were developed according to the characteristics of three different BBFs produced from manure (bio-dried solid fraction, solid fraction of digestate and biochar) to enhance plant growth and product quality. A greenhouse pot experiment was carried out with tomato plants grown with microbiologically activated BBFs applied either as N-organic fertilizers or as an organic amendment. A next generation sequencing analysis was used to characterise the development of each rhizospheric community. All the activated BBFs gave enhanced tomato yields (fresh and dry weight) compared with the non-activated treatments and similar to, or higher than, chemical fertilization. Concerning the tomato fruits' organoleptic quality, lycopene and carotenoids concentrations were improved by biological activation. Metagenomic analysis points at Trichoderma as the main driver of the positive effects, with the effects of added bacteria being negligible or limited at the early stages after fertilization. In the context of the circular economy, the activated BBFs could be used to replace synthetic fertilisers, reducing costs and environmental burdens and increasing production.

Isolation and evaluation of Qatari soil rhizobacteria for antagonistic potential against phytopathogens and growth promotion in tomato plants

Plant growth promoting rhizobacteria are a diverse group of microorganisms that enhance the growth of plants under various conditions. In this study, 55 isolates of endogenous rhizobacteria were collected from the rhizosphere of Avicennia marina, Suaeda vermiculata, Salsola soda, Anabasis setifera, Salicornia europaea, Arthrocnemum macrostachyum, Limonium axillare, Tetraena qatarensis, Aeluropus lagopoides, and Prosopis juliflora. The isolates were evaluated in-vitro for their antagonist potential against Fusarium oxysporum and Botrytis cinerea using the dual culture technique, where the maximum growth inhibition reached 49% and 57%, respectively. In-vivo evaluation was accomplished to determine the growth-promoting potential of the rhizobacteria under greenhouse conditions where the strain ANABR3 (Bacillus subtilis) showed the strongest growth-promoting effects. Further in-vivo testing regarding the effectiveness of rhizobacteria in the presence of the phytopathogen was also completed using the Hoagland medium. LEMR3 and SALIR5 (both identified as two strains of B. subtilis) supported the tomato seedlings to overcome the disease and significantly (p ≤ 0.05) increased above and belowground biomass compared to the control. Additionally, several characterizing tests were carried out on the selected strains, these strains were found to possess numerous features that promote plant growth directly and indirectly such as the production of IAA, HCN, hydrolytic enzymes, ACC deaminase, NH3, and some rhizobacteria were capable of phosphate solubilization. In conclusion, this study showed that local rhizobacterial isolates collected from arid lands possess valuable traits, making them promising bio-control agents and bio-fertilizers for agricultural purposes.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Potential Impacts of Certain N2-Fixing Bacterial Strains and Mineral N Doses for Enhancing the Growth and Productivity of Maize Plants

The enhancing effect of N2-fixing bacterial strains in the presence of mineral N doses on maize plants in pots and field trials was investigated. The OT-H1 of 10 isolates maintained the total nitrogen, nitrogenase activities, IAA production, and detection of NH3 in their cultures. In addition, they highly promoted the germination of maize grains in plastic bags compared to the remainder. Therefore, OT-H1 was subjected for identification and selected for further tests. Based on their morphological, cultural, and biochemical traits, they belonged to the genera Azotobacter. The genomic sequences of 16S rRNA were, thus, used to confirm the identification of the genera. Accordingly, the indexes of tree and similarity for the related bacterial species indicated that genera were exactly closely linked to Azotoacter salinestris strain OR512393. In pot (35 days) and field (120 days) trials, the efficiencies of both A. salinestris and Azospirillum oryzea SWERI 111 (sole/dual) with 100, 75, 50, and 25% mineral N doses were evaluated with completely randomized experimental design and three repetitions. Results indicated that N2-fixing bacteria in the presence of mineral N treatment showed pronounced effects compared to controls. A high value of maize plants was also noticed through increasing the concentration of mineral N and peaked at a dose of 100%. Differences among N2-fixing bacteria were insignificant and were observed for A. oryzea with different mineral N doses. Thus, the utilization of A. oryzea and A. salinestris in their dual mix in the presence of 75 followed by 50% mineral N was found to be the superior treatments, causing the enhancement of vegetative growth and grain yield parameters of maize plants. Additionally, proline and the enzyme activities of both polyphenol oxidase (PPO) and peroxidase (PO) of maize leaves were induced, and high protein contents of maize grains were accumulated due to the superior treatments. The utilization of such N2-fixing bacteria was, therefore, found to be effective at improving soil fertility and to be an environmentally safe strategy instead, or at least with low doses, of chemical fertilizers.

Synergistic action of Pseudomonas fluorescens with melatonin attenuates salt toxicity in mustard by regulating antioxidant system and flavonoid profile

Salt stress is an alarming abiotic stress that reduces mustard growth and yield. To attenuate salt toxicity effects, plant growth-promoting rhizobacteria (PGPR) offers a sustainable approach. Among the various PGPR, Pseudomonas fluorescens (P. fluorescens NAIMCC-B-00340) was chosen for its salt tolerance (at 100 mM NaCl) and for exhibiting various growth-promoting activities. Notably, P. fluorescens can produce auxin, which plays a role in melatonin (MT) synthesis. Melatonin is a pleiotropic molecule that acts as an antioxidant to scavenge reactive oxygen species (ROS), resulting in stress reduction. Owing to the individual role of PGPR and MT in salt tolerance, and their casual nexus, their domino effect was investigated in Indian mustard under salt stress. The synergistic action of P. fluorescens and MT under salt stress conditions was found to enhance the activity of antioxidative enzymes and proline content as well as  promote the production of secondary metabolites. This led to reduced oxidative stress following effective ROS scavenging, maintained photosynthesis, and improved growth. In mustard plants treated with MT and P. fluorescens under salt stress, eight flavonoids showed significant increase. Kaempferol and cyanidin showed the highest concentrations and are reported to act as antioxidants with protective functions under stress. Thus, we can anticipate that strategies involved in their enhancement could provide a better adaptive solution to salt toxicity in mustard plants. In conclusion, the combination of P. fluorescens and MT affected antioxidant metabolism and flavonoid profile that could be used to mitigate salt-induced stress and bolster plant resilience.

Halomonas ventosae JPT10 promotes salt tolerance in foxtail millet (Setaria italica) by affecting the levels of multiple antioxidants and phytohormones

Plant growth-promoting bacterias (PGPBs) can increase crop output under normal and abiotic conditions. However, the mechanisms underlying the plant salt tolerance-promoting role of PGPBs still remain largely unknown. In this study, we demonstrated that Halomonas ventosae JPT10 promoted the salt tolerance of both dicots and monocots. Physiological analysis revealed that JPT10 reduced reactive oxygen species accumulation by improving the antioxidant capability of foxtail millet seedlings. The metabolomic analysis of JPT10-inoculated foxtail millet seedlings led to the identification of 438 diversely accumulated metabolites, including flavonoids, phenolic acids, lignans, coumarins, sugar, alkaloids, organic acids, and lipids, under salt stress. Exogenous apigenin and chlorogenic acid increased the salt tolerance of foxtail millet seedlings. Simultaneously, JPT10 led to greater amounts of abscisic acid (ABA), indole-3-acetic acid (IAA), salicylic acid (SA), and their derivatives but lower levels of 12-oxo-phytodienoic acid (OPDA), jasmonate (JA), and JA-isoleucine (JA-Ile) under salt stress. Exogenous JA, methyl-JA, and OPDA intensified, whereas ibuprofen or phenitone, two inhibitors of JA and OPDA biosynthesis, partially reversed, the growth inhibition of foxtail millet seedlings caused by salt stress. Our results shed light on the response of foxtail millet seedlings to H. ventosae under salt stress and provide potential compounds to increase salt tolerance in foxtail millet and other crops.

Role of Arbuscular Mycorrhizal Fungi in Regulating Growth, Enhancing Productivity, and Potentially Influencing Ecosystems under Abiotic and Biotic Stresses

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with the roots of nearly all land-dwelling plants, increasing growth and productivity, especially during abiotic stress. AMF improves plant development by improving nutrient acquisition, such as phosphorus, water, and mineral uptake. AMF improves plant tolerance and resilience to abiotic stressors such as drought, salt, and heavy metal toxicity. These benefits come from the arbuscular mycorrhizal interface, which lets fungal and plant partners exchange nutrients, signalling molecules, and protective chemical compounds. Plants' antioxidant defence systems, osmotic adjustment, and hormone regulation are also affected by AMF infestation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress conditions. As a result of its positive effects on soil structure, nutrient cycling, and carbon sequestration, AMF contributes to the maintenance of resilient ecosystems. The effects of AMFs on plant growth and ecological stability are species- and environment-specific. AMF's growth-regulating, productivity-enhancing role in abiotic stress alleviation under abiotic stress is reviewed. More research is needed to understand the molecular mechanisms that drive AMF-plant interactions and their responses to abiotic stresses. AMF triggers plants' morphological, physiological, and molecular responses to abiotic stress. Water and nutrient acquisition, plant development, and abiotic stress tolerance are improved by arbuscular mycorrhizal symbiosis. In plants, AMF colonization modulates antioxidant defense mechanisms, osmotic adjustment, and hormonal regulation. These responses promote plant performance, photosynthetic efficiency, and biomass production in abiotic stress circumstances. AMF-mediated effects are also enhanced by essential oils (EOs), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), hydrogen peroxide (H2O2), malondialdehyde (MDA), and phosphorus (P). Understanding how AMF increases plant adaptation and reduces abiotic stress will help sustain agriculture, ecosystem management, and climate change mitigation. Arbuscular mycorrhizal fungi (AMF) have gained prominence in agriculture due to their multifaceted roles in promoting plant health and productivity. This review delves into how AMF influences plant growth and nutrient absorption, especially under challenging environmental conditions. We further explore the extent to which AMF bolsters plant resilience and growth during stress.

Characterization of Antagonistic Bacteria Paenibacillus polymyxa ZYPP18 and the Effects on Plant Growth

Paenibacillus polymyxa is a plant growth-promoting rhizobacteria (PGPR) that has significant biocontrol properties. Wheat sheath blight caused by Rhizoctonia cerealis is a significant soil-borne disease of wheat that causes significant losses in wheat production, and the biological control against the disease has received extensive attention. P. polymyxa ZYPP18 was identified using morphological and molecular characterization. An antagonistic activity experiment verified that ZYPP18 inhibits the growth of R. cerealis on artificial growth media. A detached leaf assay verified that ZYPP18 inhibits the expansion of wheat sheath blight on the detached leaf. ZYPP18 has been found to possess plant growth-promoting properties, as well as the ability to solubilize phosphate and generate indole-3-acetic acid. Results from hydroponic experiments showed that wheat seedlings treated with ZYPP18 grew faster. Additionally, pot experiments and field experiments demonstrated that ZYPP18 effectively controls the occurrence of wheat sheath blight. ZYPP18 reduced the incidence of wheat sheath blight in wheat seedlings by 37.37% and 37.90%, respectively. The control effect of ZYPP18 on wheat sheath blight was 56.30% and 65.57%, respectively. These findings provide evidence that P. polymyxa ZYPP18 is an effective biological factor that can control disease and promote plant growth.

Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays

A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246^T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4^T (98.4%) and Paenibacillus xanthinolyticus 11N27^T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246^T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246^T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246^T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246^T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246^T (= LMG 32093^T = CCM 9089^T = CIP 111893^T) as the type strain.