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Microorganisms
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Plant Growth-Promoting Bacteria
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Plant Growth-Promoting Bacteria

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 9587

Special Issue Editor

Prof. Dr. Mario De Andrade Lira Junior

E-Mail Website
Guest Editor
Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, s/n, Dois Irmãos, Recife 52171-900, PE, Brazil
Interests: ecosystem services; biological nitrogen fixation; plant growth-promoting bacteria
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant growth-promoting bacteria include endophytic and rhizospheric bacteria, which can increase plant growth and yield, reduce the impacts of biotic or abiotic stresses, and reduce the usage of external inputs, such as fertilizer, irrigation, or pesticides, while at least maintaining the current yield. These include bacteria isolated from different plant species. In this Special Issue, we will discuss both the diversity and taxonomical compositions of populations of these bacteria, as well as their mechanisms of action and their effects on major crops such as cereals, soybeans and pulses, oil crops, and major forage species, particularly under field conditions. We will also discuss potential strategies to evaluate them to increase the selection process' effectiveness. We are interested in biotechnological approaches that lead to their increased use in field production systems.

Prof. Dr. Mario De Andrade Lira Junior
Guest Editor

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Keywords

  • rhizobacteria
  • endophytic
  • rhizobia
  • biotic stress
  • abiotic stress
  • fertilizer
  • irrigation

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Published Papers (8 papers)

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15 pages, 1363 KB  
Article
Tackling Conifer Needle Cast and Ash Dieback with Host-Derived Microbial Antagonists Exhibiting Plant Growth-Promoting Traits
by Milana Šilanskienė, Dorotėja Vaitiekūnaitė and Vaida Sirgedaitė-Polikaitienė
Microorganisms 2025, 13(11), 2517; https://doi.org/10.3390/microorganisms13112517 - 31 Oct 2025
Viewed by 352
Abstract
Needle cast (Lophodermium seditiosum Minter, Staley & Millar) in Scots pine (Pinus sylvestris L.) and European ash (Fraxinus excelsior L.) dieback (Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz & Hosoya) are among the most destructive forest and tree plantation diseases [...] Read more.
Needle cast (Lophodermium seditiosum Minter, Staley & Millar) in Scots pine (Pinus sylvestris L.) and European ash (Fraxinus excelsior L.) dieback (Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz & Hosoya) are among the most destructive forest and tree plantation diseases in Europe, threatening not only targeted plant species but also the whole ecosystem. While considerable research effort has focused on microbial antagonists against ash dieback, comparable investigations into needle cast biocontrol remain virtually absent from the literature. Here, isolated microbial antagonists from European ash and Scots pine were evaluated for their efficacy against respective pathogens. In vitro dual-culture assays revealed bacteria with strong inhibitory effects on pathogen growth, as well as multiple plant growth-promoting traits (PGPTs). It was found that bacteria from the genera of Pantoea, Erwinia, Priestia, and Pseudomonas inhibited the growth of H. fraxineus by ≥70%. Most significantly, our investigation revealed that bacteria isolated from Scots pine, belonging to the genera Pseudomonas, Bacillus, and Priestia, inhibited the growth of L. seditiosum by 50% to 80%, representing one of the first reported bacterial antagonisms for this neglected pathogen. All isolates were positive for at least two PGPTs, primarily due to mineralization of organic phosphate and the production of siderophores. The dual functional traits of isolated bacteria highlight their potential application in integrated forest protection strategies, particularly for the previously overlooked L. seditiosum pathosystem. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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24 pages, 3179 KB  
Article
Growth-Promoting Effects and Mechanisms of Synthetic Plant Growth-Promoting Rhizobacteria on Maize Seedlings
by Shuang Yu, Minlong Mao, Hengfei Zhang, Huanyu Song and Yu Sun
Microorganisms 2025, 13(11), 2460; https://doi.org/10.3390/microorganisms13112460 - 28 Oct 2025
Viewed by 545
Abstract
With the development of microbial fertilizers, efforts have been made to enrich the strain resources of plant growth-promoting rhizobacteria (PGPR) in maize and to compare the growth-promoting effects of synthetic microbial communities (SynComs) with those of single strains. To achieve this, phenotypic measurements [...] Read more.
With the development of microbial fertilizers, efforts have been made to enrich the strain resources of plant growth-promoting rhizobacteria (PGPR) in maize and to compare the growth-promoting effects of synthetic microbial communities (SynComs) with those of single strains. To achieve this, phenotypic measurements and RNA sequencing (RNA-seq) were performed on maize roots treated with SynComs and single-strain bacterial suspensions, aiming to investigate the regulatory influence of PGPR on differential gene expression and key metabolic pathways in maize roots. In this study, 59 PGPR strains were selected, representing genera including Bacillus, Pseudomonas, Burkholderia sp., Curtobacterium pusillum, Acidovorax, Sphingobium, Mitsuaria, Bacterium, Rhodanobacter, Variovorax, Ralstonia, Brevibacillus, Terrabacter, Flavobacterium, Comamonadaceae, Achromobacter, Paraburkholderia, and Massilia. Based on the growth-promoting effects observed in pot experiments, optimal bacterial strains were selected according to the principles of functional complementarity and functional superposition to construct the SynCom. The selected strains included Burkholderia sp. A2, Pseudomonas sp. C9, Curtobacterium pusillum E2, and Bacillus velezensis F3. The results demonstrated that individual strains exerted measurable growth-promoting effects on seedlings; however, the growth-promoting capability of the SynCom was significantly stronger than that of single strains. The synthetic microbial community ALL group markedly increased root length, shoot fresh weight, shoot dry weight, number of branches, and number of root tips in maize seedlings. RNA-seq analysis of maize roots treated with the SynCom (ALL group) was conducted in comparison with CK, A2, C9, E2, and F3 treatment groups. A total of 5245 differentially expressed genes (DEGs) were identified, of which only 133 were common across treatments. GO and KEGG analyses revealed that DEGs were enriched in multiple biological processes, including cellular amide biosynthetic and metabolic processes, flavonoid biosynthetic and metabolic processes, carbohydrate metabolism, amino acid metabolism, lipid metabolism, and translation. The majority of enriched pathways were associated with primary and secondary metabolism, indicating that these bacterial strains promote plant growth by modulating a wide range of metabolic pathways in plant cells. Overall, this study provides a molecular framework for understanding the mechanisms underlying the growth-promoting effects of SynComs on maize roots and offers valuable insights for future research aimed at identifying key regulatory genes. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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13 pages, 291 KB  
Article
Agronomic Efficiency of a New Liquid Inoculant Formulated with a Mixture of Azospirillum brasilense Strains Ab-V5 and Ab-V6 in Corn (Zea mays L.)
by Ricardo Cancio Fendrich, Mayara Barbosa Silva and Ivanildo Evodio Marriel
Microorganisms 2025, 13(10), 2403; https://doi.org/10.3390/microorganisms13102403 - 21 Oct 2025
Cited by 1 | Viewed by 707
Abstract
Nitrogen fertilization is a critical factor in maize (Zea mays L.) production, as nitrogen is often the primary limiting nutrient. The use of microbial biostimulants has emerged as a promising strategy to enhance nitrogen use efficiency. This study assessed the field performance [...] Read more.
Nitrogen fertilization is a critical factor in maize (Zea mays L.) production, as nitrogen is often the primary limiting nutrient. The use of microbial biostimulants has emerged as a promising strategy to enhance nitrogen use efficiency. This study assessed the field performance of an industrially produced inoculant (Nodusoja™), formulated with Azospirillum brasilense strains Ab-V5 and Ab-V6, under contrasting soil and climatic conditions. The aim of this study is to assess the grain yield of maize cultivated in different edaphoclimatic conditions using the biostimulant, together with lower doses of topdressing fertilization. Field experiments were conducted across double cropping seasons in Sete Lagoas, Minas Gerais (19°28′ S; 44°15′ W), and Palmas, Tocantins (10°8′ S; 48°19′ W), Brazil, during the 2018, 2019, and 2021 harvests. Evaluated parameters included grain yield, shoot dry mass, and nitrogen content. The most pronounced effects were observed on productivity, with maximum grain yields of 8.76 and 9.05 t·ha−1 recorded in the 2019 season, under inoculation without topdressed N and inoculation with 50% of the recommended N dose, respectively. By contrast, uninoculated treatments with 20, 60, and 120 kg N·ha−1 yielded 6.41, 7.13, and 7.49 t·ha−1, respectively. Statistical analyses demonstrated that inoculation with strains Ab-V5 and Ab-V6 increased maize grain yield by up to 40% when combined with 50% of the recommended nitrogen fertilization. These findings highlight the potential of Azospirillum-based inoculants to improve N use efficiency and reduce dependence on synthetic fertilizers in maize cultivation. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
18 pages, 1427 KB  
Article
Plant Growth-Promoting Bacteria from Tropical Soils: In Vitro Assessment of Functional Traits
by Juliana F. Nunes, Maura S. R. A. da Silva, Natally F. R. de Oliveira, Carolina R. de Souza, Fernanda S. Arcenio, Bruno A. T. de Lima, Irene S. Coelho and Everaldo Zonta
Microorganisms 2025, 13(10), 2321; https://doi.org/10.3390/microorganisms13102321 - 7 Oct 2025
Viewed by 797
Abstract
Plant growth-promoting bacteria (PGPBs) offer a sustainable alternative for enhancing crop productivity in low-fertility tropical soils. In this study, 30 bacterial isolates were screened in vitro for multiple PGP traits, including phosphate solubilization (from aluminum phosphate—AlPO4 and thermophosphate), potassium release from phonolite [...] Read more.
Plant growth-promoting bacteria (PGPBs) offer a sustainable alternative for enhancing crop productivity in low-fertility tropical soils. In this study, 30 bacterial isolates were screened in vitro for multiple PGP traits, including phosphate solubilization (from aluminum phosphate—AlPO4 and thermophosphate), potassium release from phonolite rock, siderophore production, indole-3-acetic acid (IAA) synthesis, ACC deaminase activity, and antagonism against Fusarium spp. Statistical analysis revealed significant differences (p < 0.05) among the isolates. The most efficient isolates demonstrated a solubilization capacity ranging from 24.0 to 45.2 mg L−1 for thermophosphate and 21.7 to 23.5 mg L−1 for potassium from phonolite. Among them, Pseudomonas azotoformans K22 showed the highest AlPO4 solubilization (16.6 mg L−1). IAA production among the isolates varied widely, from 1.34 to 9.65 µg mL−1. Furthermore, 17 isolates produced carboxylate-type siderophores, and only Pseudomonas aeruginosa SS183 exhibited ACC deaminase activity, coupled with strong antifungal activity (91% inhibition). A composite performance index identified P. azotoformans K22, E. hormaechei SS150, S. sciuri SS120, and B. cereus SS18 and SS17 as the most promising isolates. This study provides a valuable foundation for characterizing plant growth-promoting traits and identifies key candidates for future validation and the development of microbial consortia. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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20 pages, 1341 KB  
Article
Endophytic Diversity in Sicilian Olive Trees: Identifying Optimal Conditions for a Functional Microbial Collection
by Dalila Crucitti, Stefano Barone, Salvadora Navarro-Torre, Paola Quatrini, Francesco Carimi, Tiziano Caruso and Davide Pacifico
Microorganisms 2025, 13(7), 1502; https://doi.org/10.3390/microorganisms13071502 - 27 Jun 2025
Viewed by 912
Abstract
This study aims to identify the optimal conditions—host, plant material, seasonality, and agricultural practices—for isolating and developing a collection of culturable endophytic microorganisms to support sustainable Olea europaea L. cultivation. Samples were collected from three Sicilian olive cultivars (‘Nocellara del Belice’, ‘Nocellara Etnea’, [...] Read more.
This study aims to identify the optimal conditions—host, plant material, seasonality, and agricultural practices—for isolating and developing a collection of culturable endophytic microorganisms to support sustainable Olea europaea L. cultivation. Samples were collected from three Sicilian olive cultivars (‘Nocellara del Belice’, ‘Nocellara Etnea’, and ‘Nocellara Messinese’) and six wild olive accessions across different phenological phases and under organic and conventional agronomic management. Endophytes were isolated from leaves and twigs using a culture-dependent approach, and their taxonomic diversity and plant-growth-promoting (PGP) traits were analyzed. A total of 133 endophytic isolates were identified, spanning bacterial (Proteobacteria, Firmicutes, and Actinobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Wild olive trees contributed more than cultivated varieties to enriching the diversity and composition of culturable endophyte collection as well as twigs instead of leaves. Winter sampling allowed to implement the taxonomic genera of olive endophyte collection. Both farming systems favored an increase in the composition of microbial collection, though organic farming systems supported greater microbial richness. Functional analysis highlighted key PGP traits in a selection of bacterial isolates, including indole-3-acetic acid and siderophore production, nitrogen fixation, and antifungal activity. Bacillus spp. dominated enzymatic activities, such as amylase, protease, and lipase production, as well as antifungal activity against the olive fungal pathogen Neofusicoccum vitifusiforme. This research highlights the significant diversity and functional potential of Mediterranean olive endophytes. Our findings emphasize the role of native microbial communities as bio-inoculants, promoting plant growth, nutrient uptake, and disease resistance. These insights lay the groundwork for developing targeted olive-microbial consortia for biocontrol and stress tolerance applications. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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14 pages, 1172 KB  
Article
Physiological Quality of Bean Seeds Cultivated with Rhizobia Reinoculation and Azospirillum Co-Inoculation at Different Growth Stages
by Nathan Mickael de Bessa Cunha, Itamar Rosa Teixeira, Gisele Carneiro da Silva Teixeira, Ednaldo Cândido Rocha, Tamires Ester Peixoto Bravo, Andressa Laís Caldeira de Souza, Eulina Fernandes Damião and Alexandre Marcos Sbroggio Filho
Microorganisms 2025, 13(4), 805; https://doi.org/10.3390/microorganisms13040805 - 1 Apr 2025
Cited by 1 | Viewed by 1035
Abstract
This study evaluates the impact of Rhizobium tropici reinoculation and Azospirillum brasilense co-inoculation at different growth stages on the physiological quality of common bean seeds. A randomized block design was used, assessing germination, vigor, electrical conductivity, seedling length, and dry mass. Treatments T7 [...] Read more.
This study evaluates the impact of Rhizobium tropici reinoculation and Azospirillum brasilense co-inoculation at different growth stages on the physiological quality of common bean seeds. A randomized block design was used, assessing germination, vigor, electrical conductivity, seedling length, and dry mass. Treatments T7 (co-inoculation R. tropici + A. brasilense at R5) showed the highest germination rates, indicating enhanced seed viability. The accelerated aging test revealed that T7 exhibited greater resistance to stress, presenting greater seedling vigor, whereas T10 and T11 were more susceptible. The electrical conductivity results remained stable across treatments, suggesting that cell membrane integrity was not significantly compromised. Seedling length and dry mass did not present significant variations, reinforcing the idea that early germination and vigor are primary indicators of seed quality. Canonical discriminant analysis and MANOVA confirmed significant treatment differences, highlighting the influence of inoculation strategies on seed physiology. Overall, co-inoculation with Rhizobium tropici and Azospirillum brasilense (particularly in T7) demonstrated potential to improve seed quality at lower cost, offering sustainable alternatives for optimizing agricultural production. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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14 pages, 5075 KB  
Article
Exploring the Potential of Bacillus subtilis IS1 and B. amyloliquificiens IS6 to Manage Salinity Stress and Fusarium Wilt Disease in Tomato Plants by Induced Physiological Responses
by Waheed Akram, Shama Sharif, Areeba Rehman, Tehmina Anjum, Basharat Ali, Zill-e-Huma Aftab, Ayesha Shafqat, Laiba Afzal, Bareera Munir, Humaira Rizwana and Guihua Li
Microorganisms 2024, 12(10), 2092; https://doi.org/10.3390/microorganisms12102092 - 19 Oct 2024
Cited by 3 | Viewed by 2669
Abstract
The intensified concerns related to agrochemicals’ ecological and health risks have encouraged the exploration of microbial agents as eco-friendly alternatives. Some members of Bacillus spp. are potential plant-growth-promoting agents and benefit numerous crop plants globally. This study aimed to explore the beneficial effects [...] Read more.
The intensified concerns related to agrochemicals’ ecological and health risks have encouraged the exploration of microbial agents as eco-friendly alternatives. Some members of Bacillus spp. are potential plant-growth-promoting agents and benefit numerous crop plants globally. This study aimed to explore the beneficial effects of two Bacillus strains (B. subtilis strain IS1 and B. amyloliquificiens strain IS6) capable of alleviating the growth of tomato plants against salinity stress and Fusarium wilt disease. These strains were able to significantly promote the growth of tomato plants and biomass accumulation in pot trials in the absence of any stress. Under salinity stress conditions (150 mM NaCl), B. subtilis strain IS1 demonstrated superior performance and significantly increased shoot length (45.74%), root length (101.39%), fresh biomass (62.17%), and dry biomass (49.69%) contents compared to control plants. Similarly, B. subtilis strain IS1 (63.7%) and B. amyloliquificiens strain IS6 (32.1%) effectively suppressed Fusarium wilt disease and significantly increased plant growth indices compared to the pathogen control. Furthermore, these strains increased the production of chlorophyll, carotenoid, and total phenolic contents. They significantly affected the activities of enzymes involved in antioxidant machinery and the phenylpropanoid pathway. Hence, this study effectively demonstrates that these Bacillus strains can effectively alleviate the growth of tomato plants under multiple stress conditions and can be used to develop bio-based formulations for use in the fields. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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10 pages, 799 KB  
Brief Report
Heterologous Expression of the Nitrogen-Fixing Gene Cluster from Paenibacillus polymyxa in Bacillus subtilis
by Xiuling Wang, Shiqing Gao, Jun Fu and Ruijuan Li
Microorganisms 2025, 13(6), 1320; https://doi.org/10.3390/microorganisms13061320 - 6 Jun 2025
Viewed by 1753
Abstract
Microbially mediated biological nitrogen fixation is pivotal to sustainable agricultural development. However, optimizing nitrogenase activity in native biological nitrogen-fixing bacteria has been hindered by the complexities of genetic manipulation. Heterologous expression has served as a foundational strategy for engineering next-generation nitrogen-fixing microbial agents. [...] Read more.
Microbially mediated biological nitrogen fixation is pivotal to sustainable agricultural development. However, optimizing nitrogenase activity in native biological nitrogen-fixing bacteria has been hindered by the complexities of genetic manipulation. Heterologous expression has served as a foundational strategy for engineering next-generation nitrogen-fixing microbial agents. In this study, genomic analysis of Paenibacillus polymyxa CR1 revealed an 11 kb nitrogen-fixing (nif) gene cluster. The nif cluster was first synthesized and then assembled using ExoCET technology and finally integrated into the genome of Bacillus subtilis 168 via double-exchange recombination. RT-PCR confirmed the transcription of the nif cluster; however, no nitrogenase activity was detected in the acetylene reduction assay. A promoter replacement strategy (replacing the native promoter with Pveg) enabled B. subtilis to produce active nitrogenase. However, stronger promoters—namely, P43 and Ptp2—did not further enhance nitrogenase activity. This demonstrates that promoter selection requires balancing transcriptional strength with systemic compatibility, particularly for metalloenzymes demanding precise cofactor assembly. This is the first report describing the heterologous expression of the nif gene cluster in B. subtilis, establishing a foundation for engineering high-efficiency nitrogen-fixing biofertilizers. Full article
(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)
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