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Search Results (153)

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Keywords = siderophore-producing bacteria

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38 pages, 4443 KiB  
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 414
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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18 pages, 2018 KiB  
Article
Screening and Identification of Cadmium-Tolerant, Plant Growth-Promoting Rhizobacteria Strain KM25, and Its Effects on the Growth of Soybean and Endophytic Bacterial Community in Roots
by Jing Zhang, Enjing Yi, Yuping Jiang, Xuemei Li, Lanlan Wang, Yuzhu Dong, Fangxu Xu, Cuimei Yu and Lianju Ma
Plants 2025, 14(15), 2343; https://doi.org/10.3390/plants14152343 - 29 Jul 2025
Viewed by 297
Abstract
Cadmium (Cd) is a highly toxic heavy metal that can greatly affect crops and pose a threat to food security. Plant growth-promoting rhizobacteria (PGPR) are capable of alleviating the harm of Cd to crops. In this research, a Cd-tolerant PGPR strain was isolated [...] Read more.
Cadmium (Cd) is a highly toxic heavy metal that can greatly affect crops and pose a threat to food security. Plant growth-promoting rhizobacteria (PGPR) are capable of alleviating the harm of Cd to crops. In this research, a Cd-tolerant PGPR strain was isolated and screened from the root nodules of semi-wild soybeans. The strain was identified as Pseudomonas sp. strain KM25 by 16S rRNA. Strain KM25 has strong Cd tolerance and can produce indole-3-acetic acid (IAA) and siderophores, dissolve organic and inorganic phosphorus, and has 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Under Cd stress, all growth indicators of soybean seedlings were significantly inhibited. After inoculation with strain KM25, the heavy metal stress of soybeans was effectively alleviated. Compared with the non-inoculated group, its shoot height, shoot and root dry weight, fresh weight, and chlorophyll content were significantly increased. Strain KM25 increased the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities of soybean seedlings, reduced the malondialdehyde (MDA) content, increased the Cd content in the roots of soybeans, and decreased the Cd content in the shoot parts. In addition, inoculation treatment can affect the community structure of endophytic bacteria in the roots of soybeans under Cd stress, increasing the relative abundance of Proteobacteria, Bacteroidetes, Sphingomonas, Rhizobium, and Pseudomonas. This study demonstrates that strain KM25 is capable of significantly reducing the adverse effects of Cd on soybean plants while enhancing their growth. Full article
(This article belongs to the Section Plant Protection and Biotic Interactions)
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21 pages, 1308 KiB  
Article
Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics
by Alexander Tristancho-Baró, Ana Isabel López-Calleja, Ana Milagro, Mónica Ariza, Víctor Viñeta, Blanca Fortuño, Concepción López, Miriam Latorre-Millán, Laura Clusa, David Badenas-Alzugaray, Rosa Martínez, Carmen Torres and Antonio Rezusta
Antibiotics 2025, 14(7), 703; https://doi.org/10.3390/antibiotics14070703 - 12 Jul 2025
Viewed by 377
Abstract
Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims [...] Read more.
Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was blaNDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512. Genes associated with toxin–antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems—especially in those encoded by fec, fhu, and cir operons—play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies. Full article
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10 pages, 807 KiB  
Communication
The Siderophore Phymabactin Facilitates the Growth of the Legume Symbiont Paraburkholderia phymatum in Aluminium-Rich Martian Soil
by Daphné Golaz, Luca Bürgi, Marcel Egli, Laurent Bigler and Gabriella Pessi
Life 2025, 15(7), 1044; https://doi.org/10.3390/life15071044 - 30 Jun 2025
Viewed by 328
Abstract
Beneficial interactions between nitrogen-fixing soil bacteria and legumes offer a solution to increase crop yield on Earth and potentially in future Martian colonies. Paraburkholderia phymatum is a nitrogen-fixing beta-rhizobium, which enters symbiosis with more than 50 legumes and can survive in acidic or [...] Read more.
Beneficial interactions between nitrogen-fixing soil bacteria and legumes offer a solution to increase crop yield on Earth and potentially in future Martian colonies. Paraburkholderia phymatum is a nitrogen-fixing beta-rhizobium, which enters symbiosis with more than 50 legumes and can survive in acidic or aluminium-rich soils. In a previous RNA-sequencing study, we showed that the beta-rhizobium P. phymatum grows well in simulated microgravity and identified phymabactin as the only siderophore produced by this strain. Here, the growth of the beta-rhizobium P. phymatum was assessed in Martian simulant soil using Enhanced Mojave Mars Simulant 2 (MMS-2), which contains a high amount of iron (18.4 percent by weight) and aluminium (13.1 percent by weight). While P. phymatum wild-type’s growth was not affected by exposure to MMS-2, a mutant strain impaired in siderophore biosynthesis (ΔphmJK) grew less than P. phymatum wild-type on gradient plates in the presence of a high concentration of MMS-2 or aluminium. This result suggests that the P. phymatum siderophore phymabactin alleviates aluminium-induced heavy metal stress. Ultra-high performance liquid chromatography–mass spectrometry (UHPLC-MS) showed that phymabactin can bind to aluminium more efficiently than iron. These results not only deepen our understanding of the behaviour of rhizobia in simulated extraterrestrial environments but also provide new insights into the potential use of P. phymatum for bioremediation of aluminium-rich soils and the multiple roles of the siderophore phymabactin. Full article
(This article belongs to the Section Plant Science)
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26 pages, 2281 KiB  
Article
Soil-Gradient-Derived Bacterial Synthetic Communities Enhance Drought Tolerance in Quercus pubescens and Sorbus domestica Seedlings
by Ivan Aleksieienko, Mariana Fernandes Hertel, Jérôme Reilhan, Marie de Castro, Bertrand Légeret, Halley Caixeta Oliveira, Ilja M. Reiter and Catherine Santaella
Plants 2025, 14(11), 1659; https://doi.org/10.3390/plants14111659 - 29 May 2025
Viewed by 1008
Abstract
Climate-change-induced drought threatens forest restoration by limiting seedling establishment. To address this, we developed synthetic bacterial communities (SynComs) tailored to support drought tolerance in two Mediterranean tree species, Quercus pubescens and Sorbus domestica. Bacteria were isolated from forest soil exposed to long-term [...] Read more.
Climate-change-induced drought threatens forest restoration by limiting seedling establishment. To address this, we developed synthetic bacterial communities (SynComs) tailored to support drought tolerance in two Mediterranean tree species, Quercus pubescens and Sorbus domestica. Bacteria were isolated from forest soil exposed to long-term drought, sampling across soil depths and root-associated compartments. We selected strains with key plant-beneficial traits, including exopolysaccharide (EPS) production, hormone synthesis (auxin, ABA), siderophore release, and osmotic tolerance. SynComs were assembled based on functional complementarity and ecological origin. Biofilm assays showed that even weak individual producers could enhance community-level performance. After initial screening on Arabidopsis thaliana, the most and least effective SynComs were tested on Q. pubescens and S. domestica seedlings. Compared to controls, the best-performing SynComs reduced the proportion of drought-symptomatic seedlings by 47% in Q. pubescens and 71% in S. domestica, outperforming single-strain inoculants. Notably, EPS-rich SynCom B aligned with the conservative root traits of Q. pubescens, while hormone-rich SynCom F matched the acquisitive strategy of S. domestica. Predictive modeling identified bacterial identity and symptom timing as key predictors of drought resilience. Our results highlight the value of matching microbial traits with plant strategies and drought context for climate-smart forest restoration. Full article
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24 pages, 767 KiB  
Review
The Potential of Beneficial Microbes for Sustainable Alternative Approaches to Control Phytopathogenic Diseases
by Ramadan Bakr, Ali Abdelmoteleb, Vianey Mendez-Trujillo, Daniel Gonzalez-Mendoza and Omar Hewedy
Microbiol. Res. 2025, 16(5), 105; https://doi.org/10.3390/microbiolres16050105 - 20 May 2025
Cited by 1 | Viewed by 863
Abstract
Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the [...] Read more.
Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the environment and human health, is known as biocontrol. Microbial biological control agents (MBCAs) have proven effective against phytopathogens and are increasingly embraced in agricultural practices. MBCAs possess several beneficial traits, including antagonistic potential, rhizosphere competence, and the ability to produce lytic enzymes, antibiotics, and toxins. These biocontrol mechanisms directly target soil-borne pathogens or indirectly stimulate a plant-mediated resistance response. The effectiveness of MBCAs in managing plant diseases depends on various mechanisms, such as hyperparasitism, antibiosis, competition for nutrients or space, disruption of quorum-sensing signals, production of siderophores, generation of cell wall-degrading enzymes, and the induction and priming of plant resistance. Formulating effective biopesticides requires optimal conditions, including selecting effective strains, considering biosafety, appropriate storage methods, and ensuring a prolonged shelf life. Therefore, formulation is crucial in developing pesticide products, particularly concerning efficacy and production costs. However, several challenges must be addressed to ensure the successful application of biological control, including the shelf life of biopesticides, slower efficacy in pest management, inadequate awareness and understanding of biocontrol methods, regulatory registration for commercialization, and suitable agricultural applications. This review clarifies the principles of plant disease biocontrol, highlighting the mechanisms of action and functionality of MBCAs in biocontrol activities, the formulation of biopesticides derived from microorganisms, and the challenges and barriers associated with the development, registration, commercialization, and application of biopesticides. 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 752
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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17 pages, 2253 KiB  
Article
Unveiling the Thermotolerance and Growth-Promoting Attributes of Endophytic Bacteria Derived from Oryza sativa: Implications for Sustainable Agriculture
by Wonder Nathi Dlamini, Wei-An Lai, Wen-Ching Chen and Fo-Ting Shen
Microorganisms 2025, 13(4), 766; https://doi.org/10.3390/microorganisms13040766 - 27 Mar 2025
Cited by 1 | Viewed by 624
Abstract
High temperatures pose significant challenges to rice plants’ growth and their associated endophytic bacteria. Understanding how these bacteria respond to heat stress is vital. We assessed the potential of five endophytic bacterial strains derived from Oryza sativaBacillus tequilensis LB3, B. coagulans [...] Read more.
High temperatures pose significant challenges to rice plants’ growth and their associated endophytic bacteria. Understanding how these bacteria respond to heat stress is vital. We assessed the potential of five endophytic bacterial strains derived from Oryza sativaBacillus tequilensis LB3, B. coagulans LB6, B. paralicheniformis AS9, B. pumilus LB16, and B. paranthracis i40C—to mitigate heat stress effects on rice plants. These strains demonstrated robust abilities in producing indole-3-acetic acid (IAA) and siderophores, nitrogen fixation, and solubilization of phosphate and potassium. Under high-temperature conditions, they significantly enhanced rice plant growth, with increases in plant length of up to 78% at 40 °C. Notably, LB6 showed the highest biomass increase (195%). The strains also improved chlorophyll SPAD values, an indicator of reduced heat stress effects and improved plant health. Phytohormone profiling and biochemical analyses revealed significant increases in abscisic acid (ABA) levels, reduced lipid peroxidation (MDA), and elevated osmoprotectant proline accumulation under heat stress. Inoculated plants exhibited up to 539 ng g−1 of ABA (vs. 62 ng g−1 in uninoculated controls), a 68% reduction in MDA (indicating less oxidative damage), and enhanced proline synthesis, collectively suggesting improved stress adaptation. These changes were linked to bacterial IAA production and nutrient modulation, which alleviated heat-induced physiological decline. These findings underscore the potential of these endophytes as biofertilizers to improve rice resilience under heat stress. Among the strains, LB6 exhibited superior performance, offering the greatest promise for heat-stress mitigation in rice production. This study advances our understanding of phytohormonal, heat stress signaling, and chemical processes underlying bacterial-mediated thermotolerance, providing a foundation for sustainable agricultural strategies. Future research can explore morphological and biochemical analyses, stress-responsive gene expression (e.g., HSPs, DREBs, and APX) linked to thermotolerance, and the combined effects of selected strains with fertilizers in high-temperature rice cultivation. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture, 2nd Edition)
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13 pages, 1928 KiB  
Article
Rhizobium sp. as a Growth Inducer of Phaseolus vulgaris L., Determining the Qualitative Chemical Composition of Its Ethyl Acetate Extract Using High-Resolution Liquid Chromatography Coupled with Mass Spectrometry
by Giselle Hernández, Yoania Ríos, Trina H. García, Yusset Louis, Iraida Spengler and Yarelis Ortiz
Int. J. Plant Biol. 2025, 16(1), 37; https://doi.org/10.3390/ijpb16010037 - 20 Mar 2025
Viewed by 535
Abstract
Phaseolus vulgaris L. is one of the most important legumes for human consumption due to its contents of proteins, antioxidants, minerals, and bioactive compounds. In the last decade, there has been a growing research interest in increasing yields while reducing or replacing the [...] Read more.
Phaseolus vulgaris L. is one of the most important legumes for human consumption due to its contents of proteins, antioxidants, minerals, and bioactive compounds. In the last decade, there has been a growing research interest in increasing yields while reducing or replacing the use of chemical fertilizers. This has led to a focus on plant growth-promoting Rhizobacteria (PGPR) as biofertilizers in sustainable agricultural practices. The aim of this study was to determine the growth-promoting activity of a culture broth of the Gram-negative soil bacteria Rhizobium sp. (F7), which is conserved in the Collection of Beneficial Bacteria at the Institute of Fundamental Research in Tropical Agriculture (INIFAT), and to identify the main secondary metabolites present in the ethyl acetate crude extract using high-resolution liquid chromatography coupled with mass spectrometry (UHPLC-ESI-MS/MS). The growth-promoting activity of the culture broth on Phaseolus vulgaris L. seeds was evaluated. The ethyl acetate extract was obtained by liquid–liquid extraction with ethyl acetate from the culture broth, and UHPLC-ESI-MS/MS was used to identify secondary metabolites. The results indicated that the culture broth of Rhizobium sp. exhibited an in vitro growth-stimulating effect. Furthermore, ten secondary metabolites were identified in the ethyl acetate extract (p-coumaric acid, indole-3-lactic acid, naringenin, and siderophores B and C, among others). These findings highlight the bioactive metabolites produced by Rhizobium sp., a bacterial strain of the INIFAT collection, which have a positive effect as growth promoters in plants. They reveal the potential of Rhizobium sp. as a promising candidate for inclusion in agricultural management practices. Full article
(This article belongs to the Section Plant–Microorganisms Interactions)
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32 pages, 8118 KiB  
Article
Impact of Coal Waste Rock on Biological and Physicochemical Properties of Soils with Different Agricultural Uses
by Aleksandra Garbacz, Artur Nowak, Anna Marzec-Grządziel, Marcin Przybyś, Anna Gałązka, Jolanta Jaroszuk-Ściseł and Grzegorz Grzywaczewski
Sustainability 2025, 17(6), 2603; https://doi.org/10.3390/su17062603 - 15 Mar 2025
Viewed by 840
Abstract
During the mining process in mines, a problem arises with the formation of coal post-mining waste, which is waste rock. It is often stored by mines on various types of land to manage the resulting spoil. However, this is not without its impact [...] Read more.
During the mining process in mines, a problem arises with the formation of coal post-mining waste, which is waste rock. It is often stored by mines on various types of land to manage the resulting spoil. However, this is not without its impact on the soil. In this study, we determined the biological and physicochemical properties of rhizosphere soils of the podzolic type, subjected to waste rock reclamation and without the influence of waste rock (control), differing in the type of agricultural use and type of plant cover: field-monocotyledonous (oat cultivation), field-dicotyledonous (buckwheat cultivation), and wasteland covered with very species-poor vegetation. Research has shown that long-term cultivation (buckwheat) contributed to the elimination (leveling out) of the microbial and biochemical differences. The addition of waste rock significantly reduced the number of microorganisms synthesizing siderophore, especially on wasteland (decreased by 1.5 log10/gDW). The abundant presence of the genera Acidocella and Acidphilum, absent in wasteland without waste rock, in the unused soil under the influence of waste rock was strongly associated with the effect of lowering the pH by waste rock in soil not used for agriculture. Increased levels of 77 types of bacteria were observed in samples from buckwheat cultivation compared to wasteland. The number of microorganisms resistant to heavy metals as well as microorganisms capable of producing specific Fe-binding ligands—siderophores—decreased under the influence of waste rock. Moreover, the dehydrogenase activity in long-term cultivation both under the influence of waste rock and without its influence was at a similar level. In contrast, an almost 100-fold decrease in dehydrogenase activity was observed in soils with oat cultivation and a more than 4-fold decrease in acid phosphatase (ACP) and alkaline phosphatase (ALP) activity. These parameters provide an effective system for monitoring soil health, from inexpensive and fast methods to advanced and precise techniques. The results can be applied to solve the problems associated with coal mining wastes by developing methods for their use in soils with long-term agricultural use. Full article
(This article belongs to the Section Hazards and Sustainability)
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21 pages, 4240 KiB  
Article
Siderophore Production Capability of Nitrogen-Fixing Bacterium (NFB) GXGL-4A Regulates Cucumber Rhizosphere Soil Microecology
by Yating Zhang, Erxing Wang, Baoyun Feng, Lurong Xu, Yanwen Xue and Yunpeng Chen
Microorganisms 2025, 13(2), 346; https://doi.org/10.3390/microorganisms13020346 - 5 Feb 2025
Cited by 2 | Viewed by 1145
Abstract
Many nitrogen-fixing bacteria can produce siderophores for iron acquisition in soil, but the impact of their siderophore-producing capabilities on the rhizosphere soil microecology is not well understood. To explore the effects of root inoculation with NFB strains with different siderophore-producing capabilities on the [...] Read more.
Many nitrogen-fixing bacteria can produce siderophores for iron acquisition in soil, but the impact of their siderophore-producing capabilities on the rhizosphere soil microecology is not well understood. To explore the effects of root inoculation with NFB strains with different siderophore-producing capabilities on the rhizosphere soil microecology and deeply evaluate the application value of a high-yielding siderophore strain in promoting crop growth, the wild-type nitrogen-fixing bacterial strain Kosakonia radicincitans GXGL-4A and its Tn5 mutants M107 (high siderophore-producing ability) and M246-2 (deficient in siderophore production) were used as biofertilizers in cucumber rhizosphere soil. Iron is important for the growth of bacterial cells, and the mutant M246-2 showed the slowest growth rate compared to the other strains when incubated in an A15 nitrogen-free medium supplied with different levels of iron. The mutant M107 had the strongest chelating ability for iron, with the largest yellow halo on the CAS detection plate. There were statistically significant differences in the halo diameters among the three NFB groups. Compared with the control group, the application of NFB significantly increased the activities of soil peroxidase and dehydrogenase and altered the soil nitrogen contents. Fertilization with the mutant M107 significantly improved the cucumber biomass and reduced the abundance and diversity of bacterial communities in the rhizosphere soil compared to the other groups. The contents of soil ammonium nitrogen and total nitrogen and soil dehydrogenase showed significant correlations with the abundance of the top 50 dominant genera in the soil. The soil TN content was the essential factor affecting the abundance of Kosakonia bacteria in the cucumber rhizosphere. Full article
(This article belongs to the Special Issue Nitrogen-Fixing Microorganisms)
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26 pages, 5057 KiB  
Article
Identification of Pseudomonas protegens and Bacillus subtilis Antimicrobials for Mitigation of Fuel Biocontamination
by Amanda L. Barry Schroeder, Adam M. Reed, Osman Radwan, Loryn L. Bowen, Oscar N. Ruiz, Thusitha S. Gunasekera and Andrea Hoffmann
Biomolecules 2025, 15(2), 227; https://doi.org/10.3390/biom15020227 - 4 Feb 2025
Cited by 4 | Viewed by 1365
Abstract
Hydrocarbon fuel biofouling and biocorrosion require expensive cleanup of aviation infrastructures unless appropriate sustainment measures are applied. The identification of novel biological control agents offers promising alternatives to the current chemical biocides used in fuel sustainment. In this study, 496 microbial fuel isolates [...] Read more.
Hydrocarbon fuel biofouling and biocorrosion require expensive cleanup of aviation infrastructures unless appropriate sustainment measures are applied. The identification of novel biological control agents offers promising alternatives to the current chemical biocides used in fuel sustainment. In this study, 496 microbial fuel isolates from our in-house repository were screened to identify new endogenously produced antimicrobial compounds. Using agar plug screening, liquid culture growth testing, and Jet A fuel culture assays, the two fuel-isolate strains Pseudomonas protegens #133, and Bacillus subtilis #232 demonstrated promising biocontrol activity against bacteria, yeast, and filamentous fungi. Liquid chromatography-quadrupole time of flight tandem mass spectrometry (LC-QTOF-MS/MS) of #232 culture filtrate identified several common lipopeptide antimicrobials including gageostatin C, gageopeptin B, and miscellaneous macrolactins. In contrast, LC-QTOF-MS/MS identified the siderophore pyochelin as one of the predominant compounds in #133 culture filtrate with previously demonstrated antimicrobial effect. Jet fuel microbial consortium culture testing of #133 culture filtrate including flow-cytometry live/dead cell mechanism determination demonstrated antimicrobial action against Gram-positive bacteria. The study concludes that antimicrobial compounds secreted by #133 have bactericidal effects against Gordonia sp. and cause cell death through bacterial lysis and membrane damage with potential applications in the biocidal treatment of hydrocarbon-based aviation fuels. Full article
(This article belongs to the Section Natural and Bio-derived Molecules)
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20 pages, 5634 KiB  
Article
Association Analysis of the Genomic and Functional Characteristics of Halotolerant Glutamicibacter endophyticus J2-5-19 from the Rhizosphere of Suaeda salsa
by Longhao Sun, Shanshan Sun, Tianyang Liu, Xinmin Lei, Ruiqi Liu, Junyi Zhang, Shanshan Dai, Jing Li and Yanqin Ding
Microorganisms 2025, 13(1), 208; https://doi.org/10.3390/microorganisms13010208 - 18 Jan 2025
Cited by 2 | Viewed by 1621
Abstract
Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from [...] Read more.
Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from coastal saline-alkali soil in the Yellow River Delta was identified as Glutamicibacter endophyticus J2-5-19. The strain was capable of growing in media with up to 13% NaCl and producing proteases, siderophores, and the plant hormone IAA. Under 4‰ salt stress, inoculation with strain J2-5-19 significantly increased the wheat seed germination rate from 37.5% to 95%, enhanced the dry weight of maize seedlings by 41.92%, and notably improved the development of maize root systems. Moreover, this work presented the first whole-genome of Glutamicibacter endophyticus, revealing that G. endophyticus J2-5-19 resisted salt stress by expelling sodium ions and taking up potassium ions through Na+/H+ antiporters and potassium uptake proteins, while also accumulating compatible solutes such as betaine, proline, and trehalose. Additionally, the genome contained multiple key plant growth-promoting genes, including those involved in IAA biosynthesis, siderophore production, and GABA synthesis. The findings provide a theoretical foundation and microbial resources for the development of specialized microbial inoculants for saline-alkali soils. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture)
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22 pages, 2178 KiB  
Article
Plant Growth-Promoting and Biocontrol Characteristics of Four Bacillus Strains and Evaluation of Their Effects on Wheat (Tr. aestivum L.)
by Mariana Petkova, Marina Marcheva, Antonia-Lucia Petrova, Vanya Slavova and Stefan Shilev
Int. J. Plant Biol. 2025, 16(1), 1; https://doi.org/10.3390/ijpb16010001 - 27 Dec 2024
Cited by 4 | Viewed by 1953
Abstract
The present study investigated developing biological control agents against plant pathogens as an alternative to pesticides. The plant growth-promoting (PGP) and biocontrol potential of bacteria from the Bacillus genus is due to their ability to produce proteolytic and amylolytic enzymes, assist in the [...] Read more.
The present study investigated developing biological control agents against plant pathogens as an alternative to pesticides. The plant growth-promoting (PGP) and biocontrol potential of bacteria from the Bacillus genus is due to their ability to produce proteolytic and amylolytic enzymes, assist in the solubilization of phosphorus and zinc, and the production of siderophores. Cell culture and cell-free supernatant were used to investigate the antimicrobial activity of different Bacillus strains against the phytopathogenic fungus Fusarium graminearum in vitro. Fusarium graminearum is a fungus that causes plant disease, particularly in cereals like wheat and barley. As a result, significant suppression of the growth and development of this plant pathogen was observed. Plant growth-promoting activity manifested when the bacteria were applied alone and in combination. A single strain and combinations of two, three, and four strains of Bacillus were tested for their antimicrobial effects against Fusarium graminearum. The fluorescence spectroscopy results proved that the combination of Bacillus subtilis, Bacillus circulans, Bacillus megaterium, and Bacillus licheniformis showed the best stimulation of development, expressed as a comparative evaluation of the yield compared to the untreated control variant. The four strains showed their potential application as a biocontrol agent against Fusarium graminearum. The four Bacillus strains also can promote plant growth by affecting nutrition, root structure, and plant health, and they have the capacity to dissolve phosphates and zinc. Full article
(This article belongs to the Section Plant–Microorganisms Interactions)
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17 pages, 1151 KiB  
Review
Fungal Phytases as Useful Tools in Agricultural Practices
by Yana Gocheva, Galina Stoyancheva, Jeny Miteva-Staleva, Radoslav Abrashev, Vladislava Dishliyska, Lyudmila Yovchevska, Maria Angelova and Ekaterina Krumova
Agronomy 2024, 14(12), 3029; https://doi.org/10.3390/agronomy14123029 - 19 Dec 2024
Cited by 1 | Viewed by 1756
Abstract
In order to meet the ever-growing needs of society, modern agriculture must develop sustainable farming and livestock production. Crops need phosphorus, a macronutrient found in soils, but they are only able to utilize small quantities of it. Chemical phosphate fertilizers are ineffective and [...] Read more.
In order to meet the ever-growing needs of society, modern agriculture must develop sustainable farming and livestock production. Crops need phosphorus, a macronutrient found in soils, but they are only able to utilize small quantities of it. Chemical phosphate fertilizers are ineffective and environmentally harmful. The use of microorganisms (bacteria, yeast, filamentous fungi, and microalgae) that synthesize phytases is a promising and environmentally friendly alternative to chemical fertilizers. Phytases are also needed as feed additives in animal husbandry to overcome phosphorus deficiency for animal growth and development. Phytases are phosphatases that catalyze the release of phosphorus from phytate by stepwise hydrolysis. The broad substrate specificity, optimal pH range, higher thermal stability, and specific efficiency of fungal phytases make them interesting enzymes for agricultural applications. They improve and stimulate the growth and development of plants and animals by releasing inorganic phosphorus and producing siderophores, organic acids, hydrogen cyanide, ammonia, and phytohormones. Phytases are crucial for enhancing phosphorus use in farming and decreasing phosphorus waste’s environmental effects. This paper addresses key challenges in modern farming, such as the inefficient utilization of phosphorus from soil and the environmental harm caused by chemical fertilizers, and provides a comprehensive overview of recent advances in the research of fungal phytases. Available scientific data have been synthesized to highlight the potential of phytase use in agriculture. This review outlines key areas for future research, including the development of phytase variants with improved functionality. The potential integration of fungal phytases into sustainable agricultural practices is underlined, in contrast to previously published work focused primarily on their biochemical properties. The review offers new insight into the possible applications of micromycete phytases as a critical factor for sustainable agriculture in the future. Full article
(This article belongs to the Special Issue Role of Plant Growth-Promoting Microbes in Agriculture—2nd Edition)
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