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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
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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18 pages, 2926 KB  
Article
Pseudomonas sp. UW4 Enhances Drought Resistance in Garlic by Modulating Growth and Physiological Parameters
by Yiwei Yan, Chunqian Guo, Bernard R. Glick and Jie Tian
Horticulturae 2025, 11(10), 1170; https://doi.org/10.3390/horticulturae11101170 - 1 Oct 2025
Abstract
Drought stress is one of the primary abiotic factors negatively affecting garlic growth, development, and yield formation. The application of plant growth-promoting bacteria (PGPB) could enhance plant tolerance to drought stress. The aim of this study was to explore the regulatory effect of [...] Read more.
Drought stress is one of the primary abiotic factors negatively affecting garlic growth, development, and yield formation. The application of plant growth-promoting bacteria (PGPB) could enhance plant tolerance to drought stress. The aim of this study was to explore the regulatory effect of the PGPB Pseudomonas sp. UW4 on growth and physiological indexes of garlic under drought stress. The results revealed that drought stresses significantly reduced total root length, total root surface area, root projection area and total root volume, chlorophyll content, antioxidant enzyme activity and osmolyte content (proline and soluble proteins), and increased relative electrical conductivity and malondialdehyde (MDA) content, all of which could be significantly improved by inoculating the roots with strain UW4. Under drought stress, an increase in total surface area of roots of 87.06% and an increase in root projected area of 40.71% were observed upon inoculation with strain UW4. The a, b, and total content of chlorophyll were increased significantly by 83.63%, 217.33% and 100.02%, respectively. The osmolyte content in leaves significantly increased, and decreased significantly in roots. The content of antioxidants also significantly increased. Moreover, the relative electrical conductivity in leaves and roots was decreased by 23.18% and 41.20%, respectively, upon strain UW4 inoculation. The content of malondialdehyde (MDA) was decreased by 25.23% and 54.08%, respectively, in the presence of strain UW4. The result of principal component analysis (PCA) revealed that the key factors influencing drought tolerance in garlic inoculated with Pseudomonas sp. UW4 could be summarized into two categories: photosynthetic pigments and root growth-related factors, and leaf osmotic adjustment and root antioxidant enzyme-related factors. Based on the result of the Mantel test, it can be inferred that there was a connection between the osmoregulation and antioxidant enzyme systems in the roots and leaves. Based on the D values, the comprehensive evaluation result of drought resistance was that the drought resistance of the garlic inoculated with strain UW4 under drought stress was lower than that of the garlic inoculated with UW4 under normal treatment and higher than that of the garlic under normal treatment. Therefore, Pseudomonas sp. UW4 enhanced the drought resistance of garlic seedlings by improving root phenotype and antioxidant enzyme activity, and increasing the content of shoot chlorophyll. Full article
(This article belongs to the Section Biotic and Abiotic Stress)
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19 pages, 4603 KB  
Article
Impact of Different Microbial Biostimulants and Salt Stress on the Endophytome of the Edible Part of Lettuce and Tomato Plants
by José M. Mulet, Patricia Benito, Marina Celdrán, Lynne Yenush and Rosa Porcel
Foods 2025, 14(19), 3366; https://doi.org/10.3390/foods14193366 - 29 Sep 2025
Abstract
The human gut microbiota plays a critical role in health throughout life. While fruits and vegetables are well-known sources of nutrients and prebiotics, recent studies suggest they may also contribute viable microorganisms to the gut microbiome, particularly when consumed raw. However, the impact [...] Read more.
The human gut microbiota plays a critical role in health throughout life. While fruits and vegetables are well-known sources of nutrients and prebiotics, recent studies suggest they may also contribute viable microorganisms to the gut microbiome, particularly when consumed raw. However, the impact of agricultural practices—such as the use of microbial biostimulants or exposure to salt stress—on the composition of the edible plant microbiome remains poorly understood. In this study, we performed a comprehensive metataxonomic analysis of the endophytic microbiome in the edible tissues (leaves or fruits) of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum), cultivated under standard conditions with or without microbial biostimulants and salt stress. Our results show that microbial biostimulants—Priestia megaterium (PGPB) and Rhizophagus irregularis (AMF)—as well as moderate salt stress, significantly reshape the composition and diversity of endophytes in both crops. Notably, the PGPB and NaCl treatments enhanced the abundance of bacterial genera such as Pantoea, Stenotrophomonas, and Massilia, which are associated with plant health and may have probiotic potential. Salt stress also increased alpha-diversity indices and favored the presence of Firmicutes and Bacteroidota, phyla commonly linked to a healthy human gut microbiome. Agronomic inputs used in organic and conventional farming, such as microbial biostimulants or controlled salt exposure, may represent novel strategies to enhance the microbial quality of fresh produce and promote gut microbial diversity through diet. Full article
(This article belongs to the Topic Microbes and Their Products for Sustainable Human Life)
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20 pages, 3066 KB  
Article
Enhancing Cherry Tomato Performance Under Water Deficit Through Microbial Inoculation with Bacillus subtilis and Burkholderia seminalis
by Henrique Fonseca Elias de Oliveira, Thiago Dias Silva, Jhon Lennon Bezerra da Silva, Priscila Jane Romano Gonçalves Selaria, Marcos Vinícius da Silva, Marcio Mesquita, Josef Augusto Oberdan Souza Silva and Rhuanito Soranz Ferrarezi
Horticulturae 2025, 11(10), 1157; https://doi.org/10.3390/horticulturae11101157 - 26 Sep 2025
Abstract
Crop productivity can be affected by biotic and abiotic stressors, and plant growth-promoting bacteria (PGPB) from the genera Bacillus and Burkholderia have the potential to maintain fruit yield and quality, as these bacteria can promote plant growth by solubilizing nutrients, fixing atmospheric nitrogen, [...] Read more.
Crop productivity can be affected by biotic and abiotic stressors, and plant growth-promoting bacteria (PGPB) from the genera Bacillus and Burkholderia have the potential to maintain fruit yield and quality, as these bacteria can promote plant growth by solubilizing nutrients, fixing atmospheric nitrogen, producing phytohormones, and exhibiting antagonistic activity against pathogens. This study aimed to evaluate the effects of inoculating plants with Bacillus subtilis and Burkholderia seminalis on their morphological characteristics, fruit technological attributes and yield of common cherry tomatoes (Solanum lycopersicum L.) subjected to induced water deficit. The study was arranged on a split-plot randomized block design, with four water replacement levels (40%, 60%, 80% and 100% of crop evapotranspiration, ETc) and three inoculation treatments (Bacillus subtilis ATCC 23858, Burkholderia seminalis TC3.4.2R3 and non-inoculation). Data were subjected to analysis of variance using the F-test and compared using Tukey’s test (p < 0.05) and multivariate statistics from principal component analysis. Inoculation with Burkholderia seminalis increased the plant fresh and dry shoot and root mass, as well as root volume. Inoculation with Bacillus subtilis increased carotenoid and chlorophyll b contents. Both inoculations enhanced leaf water content in plants experiencing severe water deficit (40% of ETc). The use of these strains as PGPB increased the fruit soluble solids content. Higher productivity in inoculated plants was achieved through a greater number of fruits per cluster, despite the individual fruits being lighter. Treatments with higher water replacement levels resulted in greater yield. Inoculations showed biotechnological potential in mitigating water deficit in cherry tomatoes. Full article
(This article belongs to the Special Issue Advancements in Horticultural Irrigation Water Management)
24 pages, 9056 KB  
Article
Use of Two PGPB Strains for the Valorization of Wastewater Sludge and Formulation of a Biofertilizer for the Recovery of Quercus ilex
by Vanesa M. Fernández-Pastrana, Daniel González-Reguero, Marina Robas-Mora, Diana Penalba-Iglesias, María José Pozuelo de Felipe, Agustín Probanza and Pedro Jiménez-Gómez
Life 2025, 15(9), 1490; https://doi.org/10.3390/life15091490 - 22 Sep 2025
Viewed by 163
Abstract
In response to the growing demand for agricultural production and the need for more sustainable practices, the use of biofertilizers based on the valorization of agricultural residues is presented as an alternative to traditional chemical fertilizers. This approach seeks to minimize environmental impact [...] Read more.
In response to the growing demand for agricultural production and the need for more sustainable practices, the use of biofertilizers based on the valorization of agricultural residues is presented as an alternative to traditional chemical fertilizers. This approach seeks to minimize environmental impact and improve soil health in agroforestry systems. The present work studies the effect of two plant growth-promoting bacterial strains (PGPB), Bacillus pretiosus (C1) and Pseudomonas agronomica (C2) on Quercus ilex (holm oak) seedlings. Taxonomic diversity was evaluated by massive sequencing of amplicons of the 16S rRNA gene, as well as the metabolic diversity and antibiotic resistance profile of the bacterial communities. The study also evaluated the impact of PGPB strains on the development of Quercus ilex seedlings. On the other hand, the effect of the biofertilizer on soil bacterial communities was evaluated. The results showed that the addition of biofertilizer significantly improved plant development compared to the addition of traditional irrigation (water) or the addition of fertilizer without the strains. In the same way, it was observed how the addition of the strains reduced the minimum inhibitory concentrations (MIC) in the rhizospheres of the treated individuals compared to traditional irrigation. The metagenomic analysis of the rhizospheric communities revealed the survival of the strains in the soil after their addition in any of the chemical treatments without altering the alpha and beta microbial diversity of the rhizospheric communities. Full article
(This article belongs to the Section Diversity and Ecology)
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16 pages, 3251 KB  
Article
Regulatory Mechanisms of Plant Growth-Promoting Bacteria in Alleviating Microplastic and Heavy Metal Combined Pollution: Insights from Plant Growth and Metagenomic Analysis
by Yan Chen, Han Liu, Yu-Bo Sun, Meng Wang, Yue-Liang Meng, Yong-Qi Liu, Xue-Min Ren, Bai-Lian Larry Li, Xue-Mei Han, Ling Liu and Zhao-Jin Chen
Agronomy 2025, 15(9), 2168; https://doi.org/10.3390/agronomy15092168 - 11 Sep 2025
Viewed by 258
Abstract
The co-occurrence of microplastics and heavy metals in soil can lead to synergistic interactions that may exert more pronounced toxic effects on plant growth. Previous studies have demonstrated the promising potential of plant growth-promoting bacteria (PGPB) in mitigating the combined toxicity of microplastics [...] Read more.
The co-occurrence of microplastics and heavy metals in soil can lead to synergistic interactions that may exert more pronounced toxic effects on plant growth. Previous studies have demonstrated the promising potential of plant growth-promoting bacteria (PGPB) in mitigating the combined toxicity of microplastics and heavy metals. However, the rhizosphere microbial mechanisms underlying this alleviation remain unclear. Metagenomic sequencing offers significant advantages for microbial functional analysis, yet it has been underutilized in studies involving combined microplastic and heavy metal contamination. In this study, a pot experiment was conducted to evaluate the effects of inoculating sorghum with two plant growth-promoting bacterial (PGPB) strains, Bacillus sp. SL-413 and Enterobacter sp. VY-1, on plant tolerance to co-contamination with 13 μm polyethylene (PE) microplastics (0.5%, w/w) and cadmium (Cd, 10 mg kg−1). The impact on rhizosphere microbial community structure and function was assessed using metagenomic analysis. The results showed that PE-Cd co-contamination, compared to Cd alone, caused varying degrees of reduction in sorghum height and biomass, indicating an enhanced toxic effect due to the combined pollutants. Inoculation with PGPB effectively alleviated the PE-Cd combined toxicity, resulting in increases in sorghum height by 4.81–12.50%, biomass by 0.43–38.40%, and Cd accumulation by 6.20–38.07%. Both Cd and PE-Cd treatments, as well as PGPB inoculation, significantly altered the composition of rhizosphere soil bacterial communities, particularly affecting the relative abundances of Ramlibacter, Solirubrobacter, and Streptomyces. Metagenomic analysis further revealed that PE-Cd co-contamination suppressed microbial functional potential in the rhizosphere. However, inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the functional stress induced by PE-Cd co-contamination and significantly enhanced microbial gene functions in the soil. Specifically, genes involved in nitrogen and phosphorus cycling increased by 3.35–5.32% and 2.26–7.38%, respectively, compared to the PE-Cd treatment without inoculation. This study provides fundamental data and scientific evidence for understanding the ecotoxicological effects of microplastic and heavy metal co-contamination, as well as the potential for microbial remediation using PGPB. Full article
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13 pages, 692 KB  
Article
What Bacteria Are Present in the Endosphere of Lettuce Seeds and Why?
by Polina Kuryntseva, Darya Tarasova, Nataliya Pronovich, Ilsina Gilmutdinova, Gulnaz Galieva, Liliya Biktasheva and Svetlana Selivanovskaya
Seeds 2025, 4(3), 42; https://doi.org/10.3390/seeds4030042 - 3 Sep 2025
Viewed by 312
Abstract
Increasing demand for high-quality food is driving the development of biologized farming methods, which involve the use of microorganisms, including endophytes, to stimulate plant growth. However, research on the composition of endosphere microbiomes is limited. The study presents an analysis of the bacterial [...] Read more.
Increasing demand for high-quality food is driving the development of biologized farming methods, which involve the use of microorganisms, including endophytes, to stimulate plant growth. However, research on the composition of endosphere microbiomes is limited. The study presents an analysis of the bacterial endophytic microbiome in lettuce seeds (Lactuca sativa L., cv. Ozornik) using high-throughput sequencing of 16S rRNA amplicons. It evaluates the taxonomic composition and putative functional properties of seed endophytic bacteria. The microbial community exhibited low diversity (Shannon index ranged from 1.1 to 1.84, Simpson index from 0.57 to 0.83). The bacterial endophytic community of lettuce seeds was dominated by Pseudomonadota (83%), Actinomycetota (14%), and Bacillota (3%). The genera identified within the microbiome included Pantoea (32%), Rhodococcus (13%), Candidatus Profftella (13%), Janthinobacterium (7%), Pseudomonas (9%), Enterococcus (3%), and Alcaligenes (2%), which exhibit a broad spectrum of beneficial properties: plant growth promotion (PGPB), suppression of phytopathogens, enhanced stress tolerance, participation in contaminant biodegradation, and heavy metal detoxification. The structure and functional potential of the microbiome vary between samples, potentially due to differences in source material and cultivation conditions. The obtained results expand our understanding of the composition and functions of endophytic bacteria in lettuce seeds, which is important for the development of novel biocontrol agents for plants consumed by humans in an unprocessed form. Full article
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21 pages, 1667 KB  
Article
Rhizosphere-Associated Bacteria of Saltgrass [Distichlis spicata (L.) Greene] Show Enhanced Ability to Tolerate Saline Environments and Stimulate Plant Growth
by Ángel Mena-García, Alejandro Alarcón, Fernando C. Gómez-Merino, María G. Peralta-Sánchez and Libia I. Trejo-Téllez
Microorganisms 2025, 13(9), 2046; https://doi.org/10.3390/microorganisms13092046 - 2 Sep 2025
Viewed by 601
Abstract
The use of plant growth-promoting bacteria (PGPB) tolerant to abiotic stress factors can enhance plant performance when applied under both optimal and stress conditions in crops. In this study, bacterial strains associated with the rhizosphere of the halophyte Distichlis spicata were isolated and [...] Read more.
The use of plant growth-promoting bacteria (PGPB) tolerant to abiotic stress factors can enhance plant performance when applied under both optimal and stress conditions in crops. In this study, bacterial strains associated with the rhizosphere of the halophyte Distichlis spicata were isolated and characterized for their ability to produce siderophores, solubilize phosphate, synthesize indole-3-acetic acid (IAA) and exopolysaccharides (EPS), and tolerate salinity. IAA production and antioxidant capacity were further assessed under saline stress. As expected, salinity negatively impacted bacterial growth, IAA biosynthesis, and antioxidant activity—even in strains from a salt-tolerant plant. Nevertheless, all strains except RD2 maintained growth and IAA production in LB broth supplemented with up to 1 M NaCl. Five halotolerant strains (RD2, RD4, RD17, RD26, and RD27) were selected for greenhouse inoculation assays in tomato (Solanum lycopersicum) seedlings. Inoculation with RD26 significantly enhanced seedling performance, promoting tomato growth, increasing leaf area by 22%, stem diameter by 17%, shoot dry biomass by 30%, and root biomass by 27% as compared to the uninoculated control. RD27 and RD4 also improved shoot biomass by 25 and 23%, respectively. Based on 16S rRNA gene sequencing, RD26 was identified as Pseudomonas sp. and RD27 as Zhihengliuella halotolerans. These findings demonstrate that salt stress impairs plant growth-promoting traits in rhizospheric bacteria, yet selected strains such as RD26 and RD27 can significantly promote plant growth. Their use as bioinoculants represents a promising strategy for improving crop performance in saline environments. Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)
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22 pages, 2619 KB  
Article
Biotechnological Test of Plant Growth-Promoting Bacteria Strains for Synthesis of Valorized Wastewater as Biofertilizer for Silvicultural Production of Holm Oak (Quercus ilex L.)
by Vanesa M. Fernández-Pastrana, Daniel González-Reguero, Marina Robas-Mora, Diana Penalba-Iglesias, Pablo Alonso-Torreiro, Agustín Probanza and Pedro A. Jiménez-Gómez
Plants 2025, 14(17), 2654; https://doi.org/10.3390/plants14172654 - 26 Aug 2025
Viewed by 545
Abstract
The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore [...] Read more.
The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore soil and promote plant growth, thus helping the regeneration of the ecosystem. One of these strategies is the use of plant growth-promoting bacteria (PGPB) in combination with recovered organic waste, such as that from wastewater treatment plants (WWTPs). In this paper, the effects of a biofertilizer formulated from WWTP residue (with and without sterilization), supplemented with two PGPB strains (Bacillus pretiosus and Pseudomonas agronomica), on the growth of holm oak seedlings (Quercus ilex) were evaluated under field conditions. A study was carried out on its nutritional composition, the rhizospheric cenoantibiogram, and its functional and taxonomic microbial diversity. Nine combinations of chemical and biological treatments using irrigation with water as a control were compared. The results showed that treatments with WWTP, especially combined with PGPB strains, promoted greater plant development and a lower seedling mortality rate. The cenoantibiogram exhibited a reduction in the resistance profile in soils treated with biofertilizer, without affecting soil microbial diversity, which remained unaltered across treatments, as confirmed by metagenomic and functional diversity analyses. Overall, this research reinforces the viability of the use of biofertilizers recovered from WWTP as an ecological and effective strategy for the recovery of degraded holm oak forests. Full article
(This article belongs to the Section Plant–Soil Interactions)
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28 pages, 1805 KB  
Article
Maize Crops Under Rising Temperatures: Bacterial Influence on Biochemical and Lipidomic Changes Induced by Heat
by Ricardo Pinto, Paulo Cardoso, Bruno Carneiro, Glória Pinto, Carmen Bedia and Etelvina Figueira
Plants 2025, 14(16), 2593; https://doi.org/10.3390/plants14162593 - 20 Aug 2025
Viewed by 518
Abstract
Rising global temperatures are increasingly affecting plant performance, leading to reduced growth, altered metabolism, and compromised membrane integrity. Although plant growth-promoting bacteria (PGPB) show promise in enhancing thermotolerance, the underlying mechanisms remain insufficiently explored. Therefore, this study investigated the effects of PGPB inoculation [...] Read more.
Rising global temperatures are increasingly affecting plant performance, leading to reduced growth, altered metabolism, and compromised membrane integrity. Although plant growth-promoting bacteria (PGPB) show promise in enhancing thermotolerance, the underlying mechanisms remain insufficiently explored. Therefore, this study investigated the effects of PGPB inoculation on Zea mays under control (26 °C) and heat stress (36 °C) conditions. Maize plants were inoculated with two thermotolerant bacterial strains and their effects were compared to non-inoculated plants through morphometric, biochemical, and lipidomic analyses. Heat stress negatively affected germination (−35.9%), increased oxidative stress (+46% for LPO, +57% for SOD, +68% for GPx), and altered leaf lipid composition, particularly fatty acids, glycerolipids, and sphingolipids. Inoculation with Pantoea sp. improved germination by 15% for seeds exposed to heat stress, increased growth (+28% shoot and +17% root), enhanced antioxidant defenses (+35% for CAT and +38% for APx), and reduced membrane damage by 65% compared with the control. Lipidomic profiling revealed that inoculation mitigated temperature-induced lipid alterations by reducing triacylglycerol accumulation and preserving the levels of polyunsaturated galactolipids and hexosylceramides. Notably, Pantoea sp.-inoculated plants under heat stress exhibited lipid profiles that were more similar to those of control plants, suggesting enhanced heat resilience. These results underscore the importance of specific plant–microbe interactions in mitigating heat stress and highlight PGPB inoculation as a promising strategy to enhance crop performance and resilience under projected climate warming scenarios. Full article
(This article belongs to the Special Issue Beneficial Effects of Bacteria on Plants)
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22 pages, 2112 KB  
Review
Microbial Enhancement of Plant Tolerance to Waterlogging: Mechanisms and Interplay with Biological Control of Pathogens
by Tomasz Maciag and Dorota M. Krzyżanowska
Int. J. Mol. Sci. 2025, 26(16), 8034; https://doi.org/10.3390/ijms26168034 - 20 Aug 2025
Viewed by 701
Abstract
Climate change causes major agricultural losses, driven both by the rise of plant diseases and by extreme weather events such as droughts and floods. Increased precipitation can lead to waterlogging of important crops. The roots of plants submerged in water have limited access [...] Read more.
Climate change causes major agricultural losses, driven both by the rise of plant diseases and by extreme weather events such as droughts and floods. Increased precipitation can lead to waterlogging of important crops. The roots of plants submerged in water have limited access to oxygen, which leads to hypoxia, which, in turn, reduces plant resistance to other factors, e.g., plant pathogens. On the other hand, beneficial microorganisms can help plants oppose abiotic stress, e.g., by producing plant hormones or osmoprotectants such as trehalose, to increase plant tolerance to drought. It turns out that plant-beneficial microorganisms can also increase plant resistance to waterlogging. This can be achieved by various mechanisms that involve the production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which reduces the amount of ethylene accumulated in the submerged roots. This can stimulate the production of reactive oxygen species scavengers that protect plants from the oxidative stress caused by less efficient anaerobic metabolism, produce plant hormones that help plants to better adapt to low-oxygen conditions, and shape the plant microbiome, supporting plant growth in waterlogging conditions. This review outlines plant responses to waterlogging and discusses examples of microorganisms that improve plant tolerance, focusing on their underlying mechanisms. Full article
(This article belongs to the Special Issue Plant-Microbe Interaction Studies)
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21 pages, 4239 KB  
Article
Melatonin-Producing Bacillus aerius EH2-5 Enhances Glycine max Plants Salinity Tolerance Through Physiological, Biochemical, and Molecular Modulation
by Eun-Hae Kwon, Suhaib Ahmad and In-Jung Lee
Int. J. Mol. Sci. 2025, 26(16), 7834; https://doi.org/10.3390/ijms26167834 - 13 Aug 2025
Viewed by 872
Abstract
Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, [...] Read more.
Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, the global population is projected to exceed 9 billion by 2050, demanding a 70% increase in food production (UN, 2019; FAO). Agriculture, responsible for 34% of global greenhouse gas emissions, urgently needs sustainable solutions. Microbial inoculants, known as “plant probiotics,” offer a promising eco-friendly alternative by enhancing crop resilience and reducing environmental impact. In this study, we evaluated the plant growth-promoting (PGP) traits and melatonin-producing capacity of Bacillus aerius EH2-5. To assess its efficacy under salt stress, soybean seedlings at the VC stage were inoculated with EH2-5 and subsequently subjected to salinity stress using 150 mM and 100 mM NaCl treatments. Plant growth parameters, the expression levels of salinity-related genes, and the activities of antioxidant enzymes were measured to determine the microbe’s role in promoting plant growth and mitigating salt-induced oxidative stress. Here, our study shows that the melatonin-synthesizing Bacillus aerius EH2-5 (7.48 ng/mL at 24 h after inoculation in Trp spiked LB media) significantly improved host plant (Glycine max L.) growth, biomass, and photosynthesis and reduced oxidative stress during salinity stress conditions than the non-inculcated control. Whole genome sequencing of Bacillus aerius EH2-5 identified key plant growth-promoting and salinity stress-related genes, including znuA, znuB, znuC, and zur (zinc uptake); ptsN, aspA, and nrgB (nitrogen metabolism); and phoH and pstS (phosphate transport). Genes involved in tryptophan biosynthesis and transport, such as trpA, trpB, trpP, and tspO, along with siderophore-related genes yusV, yfhA, and yfiY, were also detected. The presence of multiple stress-responsive genes, including dnaK, dps, treA, cspB, srkA, and copZ, suggests EH2-5′s genomic potential to enhance plant tolerance to salinity and other abiotic stresses. Inoculation with Bacillus aerius EH2-5 significantly enhanced soybean growth and reduced salt-induced damage, as evidenced by increased shoot biomass (29%, 41%), leaf numbers (12% and 13%), and chlorophyll content (40%, 21%) under 100 mM and 150 mM NaCl compared to non-inoculated plants. These results indicate EH2-5′s strong potential as a plant growth-promoting and salinity stress-alleviating rhizobacterium. The EH2-5 symbiosis significantly enhanced a key ABA biosynthesis enzyme-related gene NCED3, dehydration responsive transcription factors DREB2A and NAC29 salinity stresses (100 mM and 150 mM). Moreover, the reduced expression of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) by 16%, 29%, and 24%, respectively, and decreased levels of malondialdehyde (MDA) and hydroxy peroxidase (H2O2) by 12% and 23% were observed under 100 mM NaCl compared to non-inoculated plants. This study demonstrated that Bacillus aerius EH2-5, a melatonin-producing strain, not only functions effectively as a biofertilizer but also alleviates plant stress in a manner comparable to the application of exogenous melatonin. These findings highlight the potential of utilizing melatonin-producing microbes as a viable alternative to chemical treatments. Therefore, further research should focus on enhancing the melatonin biosynthetic capacity of EH2-5, improving its colonization efficiency in plants, and developing synergistic microbial consortia (SynComs) with melatonin-producing capabilities. Such efforts will contribute to the development and field application of EH2-5 as a promising plant biostimulant for sustainable agriculture. Full article
(This article belongs to the Special Issue Genetics and Novel Techniques for Soybean Pivotal Characters)
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27 pages, 1027 KB  
Review
Recent Advances and Developments in Bacterial Endophyte Identification and Application: A 20-Year Landscape Review
by Neo M. Mametja, Thanyani E. Ramadwa, Muthumuni Managa and Tracy M. Masebe
Plants 2025, 14(16), 2506; https://doi.org/10.3390/plants14162506 - 12 Aug 2025
Viewed by 1525
Abstract
Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based [...] Read more.
Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article
(This article belongs to the Special Issue Beneficial Effects of Bacteria on Plants)
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38 pages, 4443 KB  
Review
The Role of Plant Growth-Promoting Bacteria in Soil Restoration: A Strategy to Promote Agricultural Sustainability
by Mario Maciel-Rodríguez, Francisco David Moreno-Valencia and Miguel Plascencia-Espinosa
Microorganisms 2025, 13(8), 1799; https://doi.org/10.3390/microorganisms13081799 - 1 Aug 2025
Viewed by 2488
Abstract
Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant [...] Read more.
Soil degradation resulting from intensive agricultural practices, the excessive use of agrochemicals, and climate-induced stresses has significantly impaired soil fertility, disrupted microbial diversity, and reduced crop productivity. Plant growth-promoting bacteria (PGPB) represent a sustainable biological approach to restoring degraded soils by modulating plant physiology and soil function through diverse molecular mechanisms. PGPB synthesizes indole-3-acetic acid (IAA) to stimulate root development and nutrient uptake and produce ACC deaminase, which lowers ethylene accumulation under stress, mitigating growth inhibition. They also enhance nutrient availability by releasing phosphate-solubilizing enzymes and siderophores that improve iron acquisition. In parallel, PGPB activates jasmonate and salicylate pathways, priming a systemic resistance to biotic and abiotic stress. Through quorum sensing, biofilm formation, and biosynthetic gene clusters encoding antibiotics, lipopeptides, and VOCs, PGPB strengthen rhizosphere colonization and suppress pathogens. These interactions contribute to microbial community recovery, an improved soil structure, and enhanced nutrient cycling. This review synthesizes current evidence on the molecular and physiological mechanisms by which PGPB enhance soil restoration in degraded agroecosystems, highlighting their role beyond biofertilization as key agents in ecological rehabilitation. It examines advances in nutrient mobilization, stress mitigation, and signaling pathways, based on the literature retrieved from major scientific databases, focusing on studies published in the last decade. Full article
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16 pages, 2729 KB  
Article
Effect of Enterobacter bugandensis R-18 on Maize Growth Promotion Under Salt Stress
by Xingguo Tian, Qianru Liu, Jingjing Song, Xiu Zhang, Guoping Yang, Min Li, Huan Qu, Ahejiang Tastanbek and Yarong Tan
Microorganisms 2025, 13(8), 1796; https://doi.org/10.3390/microorganisms13081796 - 31 Jul 2025
Viewed by 528
Abstract
Soil salinization poses a significant constraint to agricultural productivity. However, certain plant growth-promoting bacteria (PGPB) can mitigate salinity stress and enhance crop performance. In this study, a bacterial isolate, R-18, isolated from saline-alkali soil in Ningxia, China, was identified as Enterobacter bugandensis based [...] Read more.
Soil salinization poses a significant constraint to agricultural productivity. However, certain plant growth-promoting bacteria (PGPB) can mitigate salinity stress and enhance crop performance. In this study, a bacterial isolate, R-18, isolated from saline-alkali soil in Ningxia, China, was identified as Enterobacter bugandensis based on 16S rRNA gene sequencing. The isolate was characterized for its morphological, biochemical, and plant growth-promoting traits and was evaluated for its potential to alleviate NaCl-induced stress in maize (Zea mays L.) under hydroponic conditions. Isolate R-18 exhibited halotolerance, surviving at NaCl concentrations ranging from 2.0% to 10.0%, and alkaliphilic adaptation, growing at pH 8.0–11.0. Biochemical assays confirmed it as a Gram-negative bacterium, displaying positive reactions in the Voges–Proskauer (V–P) tests, catalase activity, citrate utilization, fluorescent pigment production, starch hydrolysis, gelatin liquefaction, and ammonia production, while testing negative for the methyl red and cellulose hydrolysis. Notably, isolate R-18 demonstrated multiple plant growth-promoting attributes, including nitrogen fixation, phosphate and potassium solubilization, ACC deaminase activity, and indole-3-acetic acid (IAA) biosynthesis. Under 100 mM NaCl stress, inoculation with isolate R-18 significantly enhanced maize growth, increasing plant height, stem dry weight, root fresh weight, and root dry weight by 20.64%, 47.06%, 34.52%, and 31.25%, respectively. Furthermore, isolate R-18 improved ion homeostasis by elevating the K+/Na+ ratio in maize tissues. Physiological analyses revealed increased chlorophyll and proline content, alongside reduced malondialdehyde (MDA) levels, indicating mitigated oxidative damage. Antioxidant enzyme activity was modulated, with decreased superoxide dismutase (SOD) and peroxidase (POD) activities but increased catalase (CAT) activity. These findings demonstrated that Enterobacter bugandensis R-18 effectively alleviated NaCl-induced growth inhibition in maize by enhancing osmotic adjustment, reducing oxidative stress, and improving ion balance. Full article
(This article belongs to the Section Plant Microbe Interactions)
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