Advanced Research on Rhizosphere Microorganisms: Plant–Microbial Interactions and Sustainable Agriculture

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant–Soil Interactions".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 7124

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Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: organic agriculture; biotechnology; seeds; medicinal plants; crops; biostimulants; horticulture; forage crops; soil science; sustainable agriculture
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Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece
Interests: organic agriculture; agrobiodiversity; vegetable crops; biostimulants; horticulture; fruit quality; wild edible species; essential oils; medicinal and aromatic plants; stress physiology; bioactve compounds
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Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: microbial and plant interaction; rhizosphere microbiome; soil microorganism; seed microorganism; organic agriculture; development and utilization of microbial resources; biotechnology; biostimulant; medicinal and aromatic plants; bioactive substances; microbial cell factory
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rhizosphere microorganisms are important organisms for biocontrol and plant growth promotion. The concept of rhizosphere was first proposed by German microbiologist Lorenz Hiltner in 1904, showing the relationship between bacteria and plants, and it was illustrated as the soil around the roots of plants influenced by root growth. Rhizosphere microorganisms are one of the main complex microbial communities on the earth with rich diversity. Important microbiomes can be divided into belowground and aboveground. The plant microbiota, its habitats, inhabitants, genomes, and surrounding environmental conditions are known as the plant microbiome. The interactions between microorganisms and plant roots have direct effects on the soil and the rhizosphere region, which is the home of diverse microorganisms. The plant microbiome includes a variety of microbes such as archaea, protists, fungi, bacteria, and viruses, which reside inside or on their host plants. The microbial population can also promote plant development and respond to a wide range of environmental conditions. Rhizosphere microorganisms refer to the diverse array of microscopic lifeforms that inhabit the rhizosphere, the narrow region of soil that is directly influenced by root secretions, and the associated soil microorganisms. The region is characterized by a high level of biological activity due to the presence of substances secreted by roots, such as organic acids, amino acids, sugars, and different secondary metabolites. These components are considered as nutrients for microorganisms, fostering a rich and dynamic microbial community around plant roots. Organisms found in the rhizosphere include fungi, bacteria, nematodes, oomycetes, algae, protozoa, archaea, viruses, and arthropods. In recent year, scholars and researchers around the world have started to intensively examine the dynamics of structure and community as well as the various functions of fungal and bacterial communities associated with plant roots. The highly diverse plant-associated microbial communities are affected by abiotic and biotic constraints changing with space and time. The diversity in the rhizosphere microbial community is also affected by various host-related parameters such as the genotype of plant, the host plant species, the interactions among microbes that span from facultative to antagonistic, the richness of plant community, the root length, and different traits of the plant-like growth rate. In terms of fungal phyla, the rhizosphere is dominated by Basidiomycota and Ascomycota, which are the most common taxonomical phyla in soil; moreover, the rhizosphere is dominated by prokaryotic phyla including Acidobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. It is also known that healthy and asymptomatic herbs and plants can maintain complex relationships with their rhizosphere microbiota and support considerable plant performance. On the other side, plants locally affect the activity and composition of their rhizosphere microbiome by changing oxygen availability, soil structure, and soil pH, and by providing an energy source via carbon-rich exudates. The Special Issue focuses on roles and functions of different types of microbes and their interactions in different agricultural and horticultural crops within the framework of sustainable crop management. It also considers both direct and indirect mechanisms, aiming to gather critical and important information regarding the positive effects of rhizosphere microorganisms on plant growth and crop yield, as well as their impacts on the quality of the final product. Furthermore, the main limitations of these practices as well as the future prospects of rhizosphere microorganisms research in sustainable agriculture will be presented. In this Special Issue, we also highlight the mechanisms of plant–microbe interactions, manipulation, modulation, and inoculation strategies, and their effects on crop growth, pathogen control, and qualitative parameter improvement. Moreover, this Special Issue aims to study the molecular mechanisms underlying the composition of root exudates under nutrient deficiency, different microbes, and their influences on alleviating nutrient scarcity effectively.

Dr. Mohamad Hesam Shahrajabian
Dr. Spyridon A. Petropoulos
Dr. Wenli Sun
Guest Editors

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Keywords

  • algae
  • arbuscular mycorrhizal fungi
  • Asteraceae
  • mineral nutrition
  • nematodes
  • nitrogen deposition
  • plant growth-promoting rhizobacteria
  • rhizobacteria
  • root exudates
  • secondary metabolites
  • signaling
  • soil bacterial community
  • soil microorganisms

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Published Papers (9 papers)

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Research

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20 pages, 2081 KiB  
Article
Application of a Synthetic Microbial Community to Enhance Pepper Resistance Against Phytophthora capsici
by Tino Flory Bashizi, Min-Ji Kim, Kyeongmo Lim, GyuDae Lee, Setu Bazie Tagele and Jae-Ho Shin
Plants 2025, 14(11), 1625; https://doi.org/10.3390/plants14111625 - 26 May 2025
Viewed by 221
Abstract
Pepper (Capsicum annuum) production faces significant challenges from soil-borne pathogens, particularly Phytophthora capsici, which induces root rot and damping-off diseases. Management of this pathogen remains challenging owing to the scarcity of resistant cultivars and the ineffectiveness of chemical control methods. [...] Read more.
Pepper (Capsicum annuum) production faces significant challenges from soil-borne pathogens, particularly Phytophthora capsici, which induces root rot and damping-off diseases. Management of this pathogen remains challenging owing to the scarcity of resistant cultivars and the ineffectiveness of chemical control methods. A single strain has been used to prevent pathogenic disease, and this approach limits the exploration of consortia comprising different genera. In this study, we isolated five bacterial strains (Bacillus sp. T3, Flavobacterium anhuiense T4, Cytobacillus firmus T8, Streptomyces roseicoloratus T14, and Pseudomonas frederiksbergensis A6) from the rhizosphere of healthy pepper plants. We then applied this 5-isolate synthetic microbial community (SynCom) to Capsicum annuum to evaluate its efficacy in improving pepper resilience against P. capsici. The SynCom members exhibited phosphate solubilization, indole-3-acetic acid production, catalase activity, siderophore synthesis, and strong antagonism against P. capsici. The SynCom reduced disease severity and enhanced the growth of pepper plants. Furthermore, the beneficial genera such as Bacillus, Fusicolla, and Trichoderma, significantly increased in the rhizosphere of pepper after the application of the SynCom. Microbial functional prediction analysis revealed that these microbial shifts were associated with nitrogen cycling and pathogen suppression. Our SynCom approach demonstrates the effectiveness of microbial consortia in promoting the growth of pathogen-infected plants by reprogramming the microbial community in the rhizosphere. Full article
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21 pages, 2070 KiB  
Article
Type III Secretion System-Mediated Induction of Systemic Resistance by Pseudomonas marginalis ORh26 Enhances Sugar Beet Defence Against Pseudomonas syringae pv. aptata
by Marija Nedeljković, Aleksandra Mesaroš, Marija Radosavljević, Nikola Đorđević, Slaviša Stanković, Jelena Lozo and Iva Atanasković
Plants 2025, 14(11), 1621; https://doi.org/10.3390/plants14111621 - 26 May 2025
Viewed by 212
Abstract
The increasing demand for sustainable agricultural practises has sparked interest in microbes that promote plant immunity. Among these, Pseudomonas species have shown the potential to enhance induced systemic resistance (ISR) in crops. While type III secretion systems (T3SSs) in pathogenic bacteria have been [...] Read more.
The increasing demand for sustainable agricultural practises has sparked interest in microbes that promote plant immunity. Among these, Pseudomonas species have shown the potential to enhance induced systemic resistance (ISR) in crops. While type III secretion systems (T3SSs) in pathogenic bacteria have been widely studied for their role in local immunosuppression, their function in beneficial Pseudomonas species and on a systemic level remains largely unexplored. We show for the first time that the T3SS of a plant-beneficial Pseudomonas strain induces ISR by root colonisation. T3SS-positive Pseudomonas isolates were applied to the roots of sugar beet (Beta vulgaris L.) and systemic effects on plant immunity were assessed in leaves exposed to the pathogen P. syringae pv. aptata P21. Our results show that P. marginalis ORh26 reduced lesion size and pathogen proliferation in sugar beet leaves. ORh26 activated peroxidase and phenylalanine ammonia-lyase and upregulated NPR1 and MYC2 defence genes. Remarkably, a T3SS-deficient mutant of ORh26 failed to induce these effects. Genomic analysis identified T3SS structural genes and effector proteins, including a pectate lyase and an effector of the HopJ family, that may mediate these responses. This study reveals a previously uncharacterised role of T3SS in the induction of ISR and improves our understanding of plant–microbe interactions. Full article
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21 pages, 2158 KiB  
Article
Smart Bioinoculants for Arachis hypogaea: Controlled Release of Bradyrhizobium and the Role of Naringin in Symbiosis Enhancement
by Adriana Belén Cesari, Natalia Soledad Paulucci and Marta Susana Dardanelli
Plants 2025, 14(11), 1601; https://doi.org/10.3390/plants14111601 - 24 May 2025
Viewed by 264
Abstract
Peanut (Arachis hypogaea L.) is one of the most important oilseeds crops worldwide. Through symbiosis with the bacterium Bradyrhizobium sp., peanuts can assimilate atmospheric nitrogen, reducing the need for chemical fertilizers. However, this nitrogen fixation process is highly sensitive to environmental factors [...] Read more.
Peanut (Arachis hypogaea L.) is one of the most important oilseeds crops worldwide. Through symbiosis with the bacterium Bradyrhizobium sp., peanuts can assimilate atmospheric nitrogen, reducing the need for chemical fertilizers. However, this nitrogen fixation process is highly sensitive to environmental factors that can inhibit the early stages of symbiotic interaction. In this study, we propose the encapsulation of Bradyrhizobium sp. SEMIA6144 and the flavonoid naringin (Nar) in alginate beads to improve flavonoid stability and promote nodulation kinetics in peanuts. Three types of beads were synthesized: A (control, SEMIA6144 only); B (SEMIA6144 induced with 10 µM Nar); and C (SEMIA6144 co-entrapped with 1 mM Nar). Although Nar increased cell mortality (2-fold compared to control) and reduced metabolic activity—particularly at 1 mM—cells in beads B and C responded by altering their membrane fatty acid profile (30% and 55.5% of 18:1, respectively) leading to a reduction in saturated fatty acids (5.8% and 13.1% for 16:0 and 18:0 in B; 11.8% and 21.2% in C). Bacterial release kinetics followed a primarily Fickian diffusion model, with minor matrix–bacteria interactions in Nar-treated beads. Notably, bacterial release in peanut root exudates was 6%, 10%, and 11% higher for beads A, B, and C, respectively, compared to release in physiological solutions. Nar-beads enhanced the formation of curved root hairs, promoted bacterial colonization in root hair zones, and stimulated the appearance of rosette-like structures associated with nodule initiation. In conclusion, encapsulating Bradyrhizobium sp. SEMIA6144 with Nar in beads represents a promising strategy to improve symbiotic nitrogen fixation in peanuts. Full article
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21 pages, 4234 KiB  
Article
Impact of Farming System on Soil Microbial Communities Associated with Common Bean in a Region of Northern Spain
by Marta Suarez-Fernandez, Juan Jose Ferreira and Ana Campa
Plants 2025, 14(9), 1359; https://doi.org/10.3390/plants14091359 - 30 Apr 2025
Viewed by 258
Abstract
Agricultural soil microbiomes play a crucial role in the modification and maintenance of soil properties such as soil fertility, nutrient availability, and organic matter decomposition. This study assessed the influence of organic and conventional farming practices on soil microbiomes associated with common bean [...] Read more.
Agricultural soil microbiomes play a crucial role in the modification and maintenance of soil properties such as soil fertility, nutrient availability, and organic matter decomposition. This study assessed the influence of organic and conventional farming practices on soil microbiomes associated with common bean (Phaseolus vulgaris L.) at the field scale in Northern Spain. Metabarcoding techniques were used to compare both microbial communities. Alpha and beta diversity analyses revealed that organic soils supported richer fungal communities with a higher species evenness, whereas conventional soils were abundant in prokaryotes. Taxonomic assignment of the observed Operational Taxonomic Units (OTUs) identified a total of 1141 prokaryotic and 622 fungal taxa. Among these, 200 prokaryotic and 113 fungal OTUs showed significant differences in response to different farming practices. This classification allowed the establishment of a core microbial community associated with the common bean crop, comprising 594 prokaryotic OTUs classified into 11 phyla, and 256 fungal OTUs classified into 11 phyla. Functional analyses indicated that organic farming promoted a broader range of prokaryotic functions related to nitrogen metabolism, stronger positive interactions between fungi and bacteria, a higher abundance of beneficial microorganisms, such as biocontrol fungi and mycorrhizae, and greater overall microbial stability. In contrast, conventional soil showed a higher prevalence of potentially phytopathogenic fungi and more complex, competitive microbial interactions. These results highlight the effect of the farming system on the diversity and microbial composition of the soils associated with bean crops in Northern Spain. While further research in different climatic regions and crop systems is essential, these findings underscore the potential of organic farming to improve soil diversity and enhance microbial network interactions. Full article
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19 pages, 5457 KiB  
Article
Genetic Diversity and Growth-Promoting Functions of Endophytic Nitrogen-Fixing Bacteria in Apple
by Hongshan Liu, Huan Cheng, Suwen Xu, Donghua Zhang, Jianrong Wu, Zongyan Li, Benzhong Fu and Li Liu
Plants 2025, 14(8), 1235; https://doi.org/10.3390/plants14081235 - 18 Apr 2025
Viewed by 493
Abstract
Understanding the dominant populations and biological functions of endophytic nitrogen-fixing bacteria in apple plants is of great significance for the healthy growth management and sustainable development of apple cultivation. In this study, we investigated the community diversity and potential plant growth-promoting abilities of [...] Read more.
Understanding the dominant populations and biological functions of endophytic nitrogen-fixing bacteria in apple plants is of great significance for the healthy growth management and sustainable development of apple cultivation. In this study, we investigated the community diversity and potential plant growth-promoting abilities of endophytic nitrogen-fixing bacteria in different tissues of apple trees by combining high-throughput sequencing of the nifH gene with traditional isolation and cultivation techniques. Sequencing results revealed that the endophytic bacteria were affiliated with 10 phyla, 14 classes, 30 orders, 42 families, and 72 genera. Rhizobium was the dominant genus in the roots and twigs, while Desulfovibrio dominated the leaf tissues. The diversity and richness of endophytic bacteria in the roots were significantly higher than those in the leaves. Using four types of nitrogen-free media, a total of 138 presumptive endophytic nitrogen-fixing bacterial strains were isolated from roots, leaves, and twigs. These isolates belonged to 32 taxonomic groups spanning 5 phyla, 8 classes, 11 orders, 13 families, and 18 genera. The nifH gene was successfully amplified from the representative strains of all 32 groups using specific primers. Nitrogenase activity among the isolates ranged from 26.86 to 982.28 nmol/(h·mL). Some strains also exhibited the ability to secrete indole-3-acetic acid (IAA), solubilize phosphate and potassium, and produce siderophores. Six individual strains and three microbial consortia were tested for their plant growth-promoting effects on apple tissue culture seedlings. All treatments showed growth-promoting effects to varying degrees, with the RD01+RC16 consortium showing the most significant results: plant height, number of leaves, and chlorophyll content were 2.4, 3.3, and 4.2 times higher than those of the control, respectively. These findings demonstrate the rich diversity of endophytic nitrogen-fixing bacteria in apple plants and their promising potential for application in promoting host plant growth. Full article
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20 pages, 4729 KiB  
Article
Aerospace Mutagenized Tea Tree Increases Rhizospheric Microorganisms, Enhances Nutrient Conversion Capacity and Promotes Growth
by Weiting Cheng, Yulin Wang, Yuhua Wang, Lei Hong, Miaoen Qiu, Yangxin Luo, Qi Zhang, Tingting Wang, Xiaoli Jia, Haibin Wang and Jianghua Ye
Plants 2025, 14(7), 981; https://doi.org/10.3390/plants14070981 - 21 Mar 2025
Viewed by 502
Abstract
The utilization of aerospace mutagenesis in plant breeding is a novel, efficient technology. This study investigates the effects of aerospace mutagenesis on tea tree growth, soil nutrient conversion, and soil microbial community structure and function. The results showed that aerospace mutagenized tea trees [...] Read more.
The utilization of aerospace mutagenesis in plant breeding is a novel, efficient technology. This study investigates the effects of aerospace mutagenesis on tea tree growth, soil nutrient conversion, and soil microbial community structure and function. The results showed that aerospace mutagenized tea trees showed increased leaf area, 100-bud weight, and yield. The rhizosphere soil of mutagenized tea tree displayed an increase in microorganisms, enhanced carbon and nitrogen cycling capacity, and significant increases in nutrient conversion and antioxidant enzyme activities. In addition, the content of available nutrients was also increased. Aerospace mutagenesis showed an increase in the abundance of soil-characteristic microorganisms (Solirubrobacterales bacterium, Capillimicrobium parvum, Mycobacterium colombiense, Mycobacterium rhizamassiliense, and Conexibacter woesei), and enhancement of the intensity of metabolic pathways, glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, carbon metabolism, fatty acid metabolism, carbon metabolism, biosynthesis of amino acids, and biosynthesis of cofactors of soil microorganisms. Interaction network and partial least squares structural equation modeling (PLS-SEM) equation analysis showed that after aerospace mutagenesis, soil-characteristic microorganisms positively affected soil microbial functions, soil microbial biomass carbon and nitrogen, respiration intensity, and soil enzyme activities; furthermore, it improved available nutrient content and tea tree growth. This study provides an important reference for the cultivation and management of aerospace mutagenized tea trees and microbial regulation of tea tree growth. Full article
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15 pages, 977 KiB  
Article
Exploring Fungal Biodiversity in Crop Rotation Systems: Impact of Soil Fertility and Winter Wheat Cropping
by Srdjan Šeremešić, Sonja Tančić Živanov, Miloš Rajković, Vladimir Aćin, Stanko Milić, Brankica Babec and Snežana Jovanović
Plants 2025, 14(1), 65; https://doi.org/10.3390/plants14010065 - 28 Dec 2024
Viewed by 1211
Abstract
This study investigated soil fungal biodiversity in wheat-based crop rotation systems on Chernozem soil within the Pannonian Basin, focusing on the effects of tillage, crop rotation, and soil properties. Over three years, soil samples from ten plots were analyzed, revealing significant fungal diversity [...] Read more.
This study investigated soil fungal biodiversity in wheat-based crop rotation systems on Chernozem soil within the Pannonian Basin, focusing on the effects of tillage, crop rotation, and soil properties. Over three years, soil samples from ten plots were analyzed, revealing significant fungal diversity with Shannon–Wiener diversity indices ranging from 1.90 in monoculture systems to 2.38 in a fertilized two-year crop rotation. Dominant fungi, including Fusarium oxysporum, Penicillium sp., and Aspergillus sp., showed distinct preferences for soil conditions such as pH and organic matter (OM). Conservation tillage significantly enhanced fungal diversity and richness, with the highest diversity observed in a three-year crop rotation system incorporating cover crops, which achieved an average winter wheat yield of 7.0 t ha−1—47% higher than unfertilized monoculture systems. Increased OM and nitrogen levels in these systems correlated with greater fungal abundance and diversity. Canonical correspondence analysis revealed strong relationships between fungal communities and soil properties, particularly pH and calcium carbonate content. These findings highlight the importance of tailored crop rotation and tillage strategies to improve soil health, enhance microbial biodiversity, and boost agricultural sustainability in temperate climates, providing valuable insights for mitigating the impacts of intensive farming and climate change. Full article
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24 pages, 2656 KiB  
Article
Microbe-Friendly Plants Enable Beneficial Interactions with Soil Rhizosphere Bacteria by Lowering Their Defense Responses
by Alexander Arkhipov, Ziyu Shao, Sean R. Muirhead, Muchineripi S. Harry, Maria Batool, Hooman Mirzaee, Lilia C. Carvalhais and Peer M. Schenk
Plants 2024, 13(21), 3065; https://doi.org/10.3390/plants13213065 - 31 Oct 2024
Viewed by 1454
Abstract
The use of plant growth-promoting rhizobacteria presents a promising addition to conventional mineral fertilizer use and an alternative strategy for sustainable agricultural crop production. However, genotypic variations in the plant host may result in variability of the beneficial effects from these plant–microbe interactions. [...] Read more.
The use of plant growth-promoting rhizobacteria presents a promising addition to conventional mineral fertilizer use and an alternative strategy for sustainable agricultural crop production. However, genotypic variations in the plant host may result in variability of the beneficial effects from these plant–microbe interactions. This study examined growth promotion effects of commercial vegetable crop cultivars of tomato, cucumber and broccoli following application with five rhizosphere bacteria. Biochemical assays revealed that the bacterial strains used possess several nutrient acquisition traits that benefit plants, including nitrogen fixation, phosphate solubilization, biofilm formation, and indole-3-acetic acid (IAA) production. However, different host cultivars displayed genotype-specific responses from the inoculations, resulting in significant (p < 0.05) plant growth promotion in some cultivars but insignificant (p > 0.05) or no growth promotion in others. Gene expression profiling in tomato cultivars revealed that these cultivar-specific phenotypes are reflected in differential expressions of defense and nutrient acquisition genes, suggesting that plants can be categorized into “microbe-friendly” cultivars (with little or no defense responses against beneficial microbes) and “microbe-hostile” cultivars (with strong defense responses). These results validate the notion that “microbe-friendly” (positive interaction with rhizosphere microbes) should be considered an important trait in breeding programs when developing new cultivars which could result in improved crop yields. Full article
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Review

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26 pages, 1498 KiB  
Review
A Study of the Different Strains of the Genus Azospirillum spp. on Increasing Productivity and Stress Resilience in Plants
by Wenli Sun, Mohamad Hesam Shahrajabian and Na Wang
Plants 2025, 14(2), 267; https://doi.org/10.3390/plants14020267 - 18 Jan 2025
Cited by 2 | Viewed by 1929
Abstract
One of the most important and essential components of sustainable agricultural production is biostimulants, which are emerging as a notable alternative of chemical-based products to mitigate soil contamination and environmental hazards. The most important modes of action of bacterial plant biostimulants on different [...] Read more.
One of the most important and essential components of sustainable agricultural production is biostimulants, which are emerging as a notable alternative of chemical-based products to mitigate soil contamination and environmental hazards. The most important modes of action of bacterial plant biostimulants on different plants are increasing disease resistance; activation of genes; production of chelating agents and organic acids; boosting quality through metabolome modulation; affecting the biosynthesis of phytochemicals; coordinating the activity of antioxidants and antioxidant enzymes; synthesis and accumulation of anthocyanins, vitamin C, and polyphenols; enhancing abiotic stress through cytokinin and abscisic acid (ABA) production; upregulation of stress-related genes; and the production of exopolysaccharides, secondary metabolites, and ACC deaminase. Azospirillum is a free-living bacterial genus which can promote the yield and growth of many species, with multiple modes of action which can vary on the basis of different climate and soil conditions. Different species of Bacillus spp. can increase the growth, yield, and biomass of plants by increasing the availability of nutrients; enhancing the solubilization and subsequent uptake of nutrients; synthesizing indole-3-acetic acid; fixing nitrogen; solubilizing phosphorus; promoting the production of phytohormones; enhancing the growth, production, and quality of fruits and crops via enhancing the production of carotenoids, flavonoids, phenols, and antioxidants; and increasing the synthesis of indoleacetic acid (IAA), gibberellins, siderophores, carotenoids, nitric oxide, and different cell surface components. The aim of this manuscript is to survey the effects of Azospirillum spp. and Bacillus spp. by presenting case studies and successful paradigms in several horticultural and agricultural plants. Full article
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